Starting phenix.real_space_refine
on Sun Aug 24 03:39:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bz7_45055/08_2025/9bz7_45055.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bz7_45055/08_2025/9bz7_45055.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bz7_45055/08_2025/9bz7_45055.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bz7_45055/08_2025/9bz7_45055.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bz7_45055/08_2025/9bz7_45055.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bz7_45055/08_2025/9bz7_45055.map"
  }
  resolution = 2.9
  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=   0.000 sd=   0.002
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   11382      2.51       5
     N    2604      2.21       5
     O    2898      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16961
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2423
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 282}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 2.38, per 1000 atoms: 0.14
  Number of scatterers: 16961
  At special positions: 0
  Unit cell: (107, 107, 123.05, 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    2898      8.00
     N    2604      7.00
     C   11382      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: 1.52
  Conformation dependent library (CDL) restraints added in 747.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4074

  Finding SS restraints...
    Secondary structure from input PDB file:
      84 helices and 7 sheets defined
      71.1% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 61
      Proline residue:  A  46  - end of helix
    Processing helix  chain 'A' and resid 73 through 86
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.654A  pdb=" N   LYS A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 131
      Proline residue:  A 123  - end of helix
    Processing helix  chain 'A' and resid 131 through 158
    Processing helix  chain 'A' and resid 196 through 206
    Processing helix  chain 'A' and resid 209 through 240
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.820A  pdb=" N   LEU A 255 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 298
      Proline residue:  A 291  - end of helix
    Processing helix  chain 'A' and resid 306 through 311
      removed outlier: 3.528A  pdb=" N   VAL A 310 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 341
      removed outlier: 3.833A  pdb=" N   LEU A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 357
      removed outlier: 4.250A  pdb=" N   PHE A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS A 357 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 61
      Proline residue:  B  46  - end of helix
    Processing helix  chain 'B' and resid 73 through 86
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.653A  pdb=" N   LYS B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 131
      Proline residue:  B 123  - end of helix
    Processing helix  chain 'B' and resid 131 through 158
    Processing helix  chain 'B' and resid 196 through 206
    Processing helix  chain 'B' and resid 209 through 240
    Processing helix  chain 'B' and resid 252 through 257
      removed outlier: 3.821A  pdb=" N   LEU B 255 " --> pdb=" O   THR B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 298
      Proline residue:  B 291  - end of helix
    Processing helix  chain 'B' and resid 306 through 311
      removed outlier: 3.527A  pdb=" N   VAL B 310 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 341
      removed outlier: 3.833A  pdb=" N   LEU B 332 " --> pdb=" O   ASP B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 357
      removed outlier: 4.250A  pdb=" N   PHE B 349 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS B 357 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 61
      Proline residue:  C  46  - end of helix
    Processing helix  chain 'C' and resid 73 through 86
    Processing helix  chain 'C' and resid 103 through 108
      removed outlier: 3.654A  pdb=" N   LYS C 107 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 131
      Proline residue:  C 123  - end of helix
    Processing helix  chain 'C' and resid 131 through 158
    Processing helix  chain 'C' and resid 196 through 206
    Processing helix  chain 'C' and resid 209 through 240
    Processing helix  chain 'C' and resid 252 through 257
      removed outlier: 3.822A  pdb=" N   LEU C 255 " --> pdb=" O   THR C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 298
      Proline residue:  C 291  - end of helix
    Processing helix  chain 'C' and resid 306 through 311
      removed outlier: 3.527A  pdb=" N   VAL C 310 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 328 through 341
      removed outlier: 3.832A  pdb=" N   LEU C 332 " --> pdb=" O   ASP C 328 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 357
      removed outlier: 4.249A  pdb=" N   PHE C 349 " --> pdb=" O   LYS C 345 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS C 357 " --> pdb=" O   LEU C 353 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 61
      Proline residue:  D  46  - end of helix
    Processing helix  chain 'D' and resid 73 through 86
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 3.653A  pdb=" N   LYS D 107 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 131
      Proline residue:  D 123  - end of helix
    Processing helix  chain 'D' and resid 131 through 158
    Processing helix  chain 'D' and resid 196 through 206
    Processing helix  chain 'D' and resid 209 through 240
    Processing helix  chain 'D' and resid 252 through 257
      removed outlier: 3.820A  pdb=" N   LEU D 255 " --> pdb=" O   THR D 252 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 298
      Proline residue:  D 291  - end of helix
    Processing helix  chain 'D' and resid 306 through 311
      removed outlier: 3.528A  pdb=" N   VAL D 310 " --> pdb=" O   VAL D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 328 through 341
      removed outlier: 3.832A  pdb=" N   LEU D 332 " --> pdb=" O   ASP D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 357
      removed outlier: 4.250A  pdb=" N   PHE D 349 " --> pdb=" O   LYS D 345 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS D 357 " --> pdb=" O   LEU D 353 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 61
      Proline residue:  E  46  - end of helix
    Processing helix  chain 'E' and resid 73 through 86
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 3.653A  pdb=" N   LYS E 107 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 131
      Proline residue:  E 123  - end of helix
    Processing helix  chain 'E' and resid 131 through 158
    Processing helix  chain 'E' and resid 196 through 206
    Processing helix  chain 'E' and resid 209 through 240
    Processing helix  chain 'E' and resid 252 through 257
      removed outlier: 3.820A  pdb=" N   LEU E 255 " --> pdb=" O   THR E 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 271 through 298
      Proline residue:  E 291  - end of helix
    Processing helix  chain 'E' and resid 306 through 311
      removed outlier: 3.528A  pdb=" N   VAL E 310 " --> pdb=" O   VAL E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 328 through 341
      removed outlier: 3.832A  pdb=" N   LEU E 332 " --> pdb=" O   ASP E 328 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 345 through 357
      removed outlier: 4.250A  pdb=" N   PHE E 349 " --> pdb=" O   LYS E 345 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS E 357 " --> pdb=" O   LEU E 353 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 32 through 61
      Proline residue:  F  46  - end of helix
    Processing helix  chain 'F' and resid 73 through 86
    Processing helix  chain 'F' and resid 103 through 108
      removed outlier: 3.653A  pdb=" N   LYS F 107 " --> pdb=" O   LEU F 103 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 108 through 131
      Proline residue:  F 123  - end of helix
    Processing helix  chain 'F' and resid 131 through 158
    Processing helix  chain 'F' and resid 196 through 206
    Processing helix  chain 'F' and resid 209 through 240
    Processing helix  chain 'F' and resid 252 through 257
      removed outlier: 3.820A  pdb=" N   LEU F 255 " --> pdb=" O   THR F 252 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 271 through 298
      Proline residue:  F 291  - end of helix
    Processing helix  chain 'F' and resid 306 through 311
      removed outlier: 3.527A  pdb=" N   VAL F 310 " --> pdb=" O   VAL F 307 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 328 through 341
      removed outlier: 3.832A  pdb=" N   LEU F 332 " --> pdb=" O   ASP F 328 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 345 through 357
      removed outlier: 4.250A  pdb=" N   PHE F 349 " --> pdb=" O   LYS F 345 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS F 357 " --> pdb=" O   LEU F 353 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 61
      Proline residue:  G  46  - end of helix
    Processing helix  chain 'G' and resid 73 through 86
    Processing helix  chain 'G' and resid 103 through 108
      removed outlier: 3.654A  pdb=" N   LYS G 107 " --> pdb=" O   LEU G 103 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 108 through 131
      Proline residue:  G 123  - end of helix
    Processing helix  chain 'G' and resid 131 through 158
    Processing helix  chain 'G' and resid 196 through 206
    Processing helix  chain 'G' and resid 209 through 240
    Processing helix  chain 'G' and resid 252 through 257
      removed outlier: 3.820A  pdb=" N   LEU G 255 " --> pdb=" O   THR G 252 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 271 through 298
      Proline residue:  G 291  - end of helix
    Processing helix  chain 'G' and resid 306 through 311
      removed outlier: 3.527A  pdb=" N   VAL G 310 " --> pdb=" O   VAL G 307 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 328 through 341
      removed outlier: 3.831A  pdb=" N   LEU G 332 " --> pdb=" O   ASP G 328 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 345 through 357
      removed outlier: 4.250A  pdb=" N   PHE G 349 " --> pdb=" O   LYS G 345 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS G 357 " --> pdb=" O   LEU G 353 " (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

    1099 hydrogen bonds defined for protein.
    3192 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: 2.73

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4956
        1.34 -     1.46: 3834
        1.46 -     1.58: 8507
        1.58 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 17395
  Sorted by residual:
  bond pdb=" CG  ARG G 256 "
       pdb=" CD  ARG G 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.48e-01
  bond pdb=" CG  ARG E 256 "
       pdb=" CD  ARG E 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.43e-01
  bond pdb=" CG  ARG C 256 "
       pdb=" CD  ARG C 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.40e-01
  bond pdb=" CG  ARG F 256 "
       pdb=" CD  ARG F 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.39e-01
  bond pdb=" CG  ARG A 256 "
       pdb=" CD  ARG A 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.24e-01
  ... (remaining 17390 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 22724
        1.15 -     2.29: 698
        2.29 -     3.44: 112
        3.44 -     4.59: 90
        4.59 -     5.73: 36
  Bond angle restraints: 23660
  Sorted by residual:
  angle pdb=" C   GLN B  56 "
        pdb=" N   GLU B  57 "
        pdb=" CA  GLU B  57 "
      ideal   model   delta    sigma   weight residual
     120.68  116.28    4.40 1.70e+00 3.46e-01 6.69e+00
  angle pdb=" C   GLN F  56 "
        pdb=" N   GLU F  57 "
        pdb=" CA  GLU F  57 "
      ideal   model   delta    sigma   weight residual
     120.68  116.32    4.36 1.70e+00 3.46e-01 6.57e+00
  angle pdb=" C   GLN G  56 "
        pdb=" N   GLU G  57 "
        pdb=" CA  GLU G  57 "
      ideal   model   delta    sigma   weight residual
     120.68  116.33    4.35 1.70e+00 3.46e-01 6.54e+00
  angle pdb=" C   GLN C  56 "
        pdb=" N   GLU C  57 "
        pdb=" CA  GLU C  57 "
      ideal   model   delta    sigma   weight residual
     120.68  116.33    4.35 1.70e+00 3.46e-01 6.54e+00
  angle pdb=" C   GLN A  56 "
        pdb=" N   GLU A  57 "
        pdb=" CA  GLU A  57 "
      ideal   model   delta    sigma   weight residual
     120.68  116.36    4.32 1.70e+00 3.46e-01 6.45e+00
  ... (remaining 23655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.02: 8729
       15.02 -    30.04: 1225
       30.04 -    45.05: 371
       45.05 -    60.07: 42
       60.07 -    75.09: 28
  Dihedral angle restraints: 10395
    sinusoidal: 4130
      harmonic: 6265
  Sorted by residual:
  dihedral pdb=" CG  LYS B 140 "
           pdb=" CD  LYS B 140 "
           pdb=" CE  LYS B 140 "
           pdb=" NZ  LYS B 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.29   59.71     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS A 140 "
           pdb=" CD  LYS A 140 "
           pdb=" CE  LYS A 140 "
           pdb=" NZ  LYS A 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.29   59.71     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS C 140 "
           pdb=" CD  LYS C 140 "
           pdb=" CE  LYS C 140 "
           pdb=" NZ  LYS C 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.31   59.69     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 10392 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1950
       0.034 -    0.067: 576
       0.067 -    0.101: 238
       0.101 -    0.134: 29
       0.134 -    0.168: 14
  Chirality restraints: 2807
  Sorted by residual:
  chirality pdb=" CB  ILE D  50 "
            pdb=" CA  ILE D  50 "
            pdb=" CG1 ILE D  50 "
            pdb=" CG2 ILE D  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CB  ILE E  50 "
            pdb=" CA  ILE E  50 "
            pdb=" CG1 ILE E  50 "
            pdb=" CG2 ILE E  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.78e-01
  chirality pdb=" CB  ILE F  50 "
            pdb=" CA  ILE F  50 "
            pdb=" CG1 ILE F  50 "
            pdb=" CG2 ILE F  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.78e-01
  ... (remaining 2804 not shown)

  Planarity restraints: 2842
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C  57 "    0.005 2.00e-02 2.50e+03   9.51e-03 9.05e-01
        pdb=" CD  GLU C  57 "   -0.016 2.00e-02 2.50e+03
        pdb=" OE1 GLU C  57 "    0.006 2.00e-02 2.50e+03
        pdb=" OE2 GLU C  57 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU E  57 "    0.004 2.00e-02 2.50e+03   8.93e-03 7.97e-01
        pdb=" CD  GLU E  57 "   -0.015 2.00e-02 2.50e+03
        pdb=" OE1 GLU E  57 "    0.006 2.00e-02 2.50e+03
        pdb=" OE2 GLU E  57 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  57 "   -0.004 2.00e-02 2.50e+03   8.92e-03 7.95e-01
        pdb=" CD  GLU A  57 "    0.015 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  57 "   -0.006 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  57 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2839 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 349
        2.71 -     3.26: 17129
        3.26 -     3.80: 27093
        3.80 -     4.35: 33413
        4.35 -     4.90: 57839
  Nonbonded interactions: 135823
  Sorted by model distance:
  nonbonded pdb=" O   GLN D  56 "
            pdb=" OG1 THR D  59 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   GLN F  56 "
            pdb=" OG1 THR F  59 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   GLN C  56 "
            pdb=" OG1 THR C  59 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   GLN E  56 "
            pdb=" OG1 THR E  59 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   GLN A  56 "
            pdb=" OG1 THR A  59 "
     model   vdw
     2.159 3.040
  ... (remaining 135818 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: 0.06
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:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     14.780
  Find NCS groups from input model:        0.160
  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:             0.010
  Load rotamer database and sin/cos tables:6.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  17409  Z= 0.111
  Angle     :  0.544   5.733  23688  Z= 0.275
  Chirality :  0.039   0.168   2807
  Planarity :  0.003   0.030   2842
  Dihedral  : 15.789  75.091   6279
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 26.52 %
    Favored  : 71.69 %
  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 aren not related in a simple way.
  whole:  1.78 (0.19), residues: 2044
  helix:  2.38 (0.14), residues: 1421
  sheet: -1.41 (0.49), residues: 84
  loop : -1.82 (0.24), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 256 
 TYR   0.005   0.001   TYR B 236 
 PHE   0.010   0.001   PHE F 109 
 TRP   0.009   0.001   TRP B  74 
 HIS   0.001   0.000   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (17395)
  covalent geometry    : angle       0.54427 (23660)
  SS BOND              : bond        0.00128 (   14)
  SS BOND              : angle       0.66479 (   28)
  hydrogen bonds       : bond        0.12106 ( 1099)
  hydrogen bonds       : angle       4.13323 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 216
  time to evaluate  : 0.763 
Fit side-chains
REVERT: B  290 MET cc_start: 0.9241 (ttm) cc_final: 0.9026 (mtp)
REVERT: C  213 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9138 (mm)
REVERT: C  306 ASN cc_start: 0.8193 (t0) cc_final: 0.7665 (t160)
REVERT: C  309 LYS cc_start: 0.8780 (tmmt) cc_final: 0.8304 (ptpp)
REVERT: D  303 LYS cc_start: 0.7329 (mttt) cc_final: 0.7023 (mtmt)
REVERT: F  338 GLU cc_start: 0.8677 (tt0) cc_final: 0.8471 (tt0)
REVERT: G  256 ARG cc_start: 0.8737 (mtm110) cc_final: 0.8496 (mtm110)
REVERT: G  303 LYS cc_start: 0.7215 (mttt) cc_final: 0.6789 (mtpt)
  outliers start: 34
  outliers final: 4
  residues processed: 249
  average time/residue: 0.7255
  time to fit residues: 198.1450
Evaluate side-chains
  168 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 163
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain C residue  213 ILE
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain E residue  254 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 200 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:   10.0000
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 282 ASN
B 266 GLN
B 282 ASN
B 355 ASN
C 266 GLN
D 266 GLN
D 282 ASN
D 355 ASN
E 266 GLN
E 282 ASN
F 266 GLN
G 266 GLN
G 282 ASN
G 306 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.107567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.075805 restraints weight = 29341.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.68
r_work: 0.2898 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  17409  Z= 0.251
  Angle     :  0.629   6.198  23688  Z= 0.311
  Chirality :  0.043   0.160   2807
  Planarity :  0.004   0.036   2842
  Dihedral  :  3.570  28.713   2263
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 22.01 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.19), residues: 2044
  helix:  2.32 (0.14), residues: 1428
  sheet: -1.42 (0.52), residues: 84
  loop : -1.89 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 152 
 TYR   0.015   0.001   TYR B  25 
 PHE   0.017   0.001   PHE C 333 
 TRP   0.009   0.001   TRP E  74 
 HIS   0.003   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 (17395)
  covalent geometry    : angle       0.62774 (23660)
  SS BOND              : bond        0.00241 (   14)
  SS BOND              : angle       1.20850 (   28)
  hydrogen bonds       : bond        0.04438 ( 1099)
  hydrogen bonds       : angle       3.78605 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 103
    poor density    : 198
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  345 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8639 (tptm)
REVERT: B  303 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6440 (mttt)
REVERT: B  345 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8696 (tptm)
REVERT: C  345 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8765 (tptm)
REVERT: D   63 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8188 (tp40)
REVERT: D  345 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8777 (tptm)
REVERT: D  355 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7910 (m-40)
REVERT: E  339 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8092 (tm-30)
REVERT: E  354 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: F   37 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8989 (mt)
REVERT: G  256 ARG cc_start: 0.8924 (mtm110) cc_final: 0.8657 (mtm110)
REVERT: G  303 LYS cc_start: 0.7235 (mttt) cc_final: 0.6755 (mtpt)
  outliers start: 103
  outliers final: 32
  residues processed: 273
  average time/residue: 0.6737
  time to fit residues: 203.6884
Evaluate side-chains
  205 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 166
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  207 ASN
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain D residue  345 LYS
Chi-restraints excluded: chain D residue  355 ASN
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  113 LEU
Chi-restraints excluded: chain E residue  307 VAL
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  355 ASN
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  338 GLU
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain G residue  308 LEU
Chi-restraints excluded: chain G residue  341 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 195 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 148 optimal weight:    4.9990
   chunk 117 optimal weight:    9.9990
   chunk 79 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 200 optimal weight:    9.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 355 ASN
B 206 ASN
B 355 ASN
C  63 GLN
C 306 ASN
D 206 ASN
E  63 GLN
E 206 ASN
E 355 ASN
F 306 ASN
G 306 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.108554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.076840 restraints weight = 29389.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.70
r_work: 0.2914 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  17409  Z= 0.169
  Angle     :  0.565   6.994  23688  Z= 0.278
  Chirality :  0.040   0.183   2807
  Planarity :  0.003   0.037   2842
  Dihedral  :  3.314  21.138   2256
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 23.00 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.20), residues: 2044
  helix:  2.39 (0.14), residues: 1449
  sheet: -1.53 (0.52), residues: 84
  loop : -2.02 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 256 
 TYR   0.015   0.001   TYR A 111 
 PHE   0.010   0.001   PHE C 333 
 TRP   0.007   0.001   TRP E  74 
 HIS   0.002   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (17395)
  covalent geometry    : angle       0.56388 (23660)
  SS BOND              : bond        0.00184 (   14)
  SS BOND              : angle       1.08372 (   28)
  hydrogen bonds       : bond        0.03866 ( 1099)
  hydrogen bonds       : angle       3.64144 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 211
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A  345 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8626 (tptm)
REVERT: B  303 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6644 (mttt)
REVERT: B  345 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8616 (tptm)
REVERT: C  345 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8782 (tptm)
REVERT: D   63 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8220 (tp40)
REVERT: D  154 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8145 (tp)
REVERT: D  345 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8759 (tptm)
REVERT: F   37 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9012 (mt)
REVERT: F   63 GLN cc_start: 0.8412 (mm110) cc_final: 0.8115 (tp-100)
REVERT: F  124 ASN cc_start: 0.8628 (t0) cc_final: 0.8406 (m-40)
REVERT: G  206 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8252 (m-40)
REVERT: G  256 ARG cc_start: 0.8938 (mtm110) cc_final: 0.8708 (mtm110)
REVERT: G  303 LYS cc_start: 0.7123 (mttt) cc_final: 0.6628 (mppt)
  outliers start: 85
  outliers final: 38
  residues processed: 270
  average time/residue: 0.6288
  time to fit residues: 188.2369
Evaluate side-chains
  217 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 171
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  207 ASN
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  207 ASN
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain D residue  345 LYS
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  113 LEU
Chi-restraints excluded: chain E residue  307 VAL
Chi-restraints excluded: chain E residue  331 SER
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  355 ASN
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  207 ASN
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  331 SER
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue  206 ASN
Chi-restraints excluded: chain G residue  207 ASN
Chi-restraints excluded: chain G residue  308 LEU
Chi-restraints excluded: chain G residue  331 SER
Chi-restraints excluded: chain G residue  341 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 193 optimal weight:    0.9990
   chunk 43 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 143 optimal weight:    3.9990
   chunk 190 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 206 ASN
B 355 ASN
C 306 ASN
D 355 ASN
E 206 ASN
F 355 ASN
G 306 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.110090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.078278 restraints weight = 29250.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 2.73
r_work: 0.2925 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  17409  Z= 0.127
  Angle     :  0.551   6.549  23688  Z= 0.270
  Chirality :  0.039   0.166   2807
  Planarity :  0.004   0.041   2842
  Dihedral  :  3.283  21.285   2256
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 23.84 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.20), residues: 2044
  helix:  2.55 (0.14), residues: 1442
  sheet: -1.55 (0.52), residues: 84
  loop : -2.11 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 256 
 TYR   0.011   0.001   TYR B  25 
 PHE   0.008   0.001   PHE D 109 
 TRP   0.006   0.001   TRP G  74 
 HIS   0.001   0.000   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (17395)
  covalent geometry    : angle       0.55065 (23660)
  SS BOND              : bond        0.00162 (   14)
  SS BOND              : angle       1.02882 (   28)
  hydrogen bonds       : bond        0.03500 ( 1099)
  hydrogen bonds       : angle       3.52632 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 205
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A   63 GLN cc_start: 0.8426 (mm110) cc_final: 0.8222 (tp40)
REVERT: A  124 ASN cc_start: 0.8602 (t0) cc_final: 0.8397 (m-40)
REVERT: A  345 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8593 (tptm)
REVERT: B  303 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6603 (mttt)
REVERT: B  345 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8590 (tptm)
REVERT: B  354 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8418 (tm-30)
REVERT: B  355 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8158 (m-40)
REVERT: C  345 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8771 (tptm)
REVERT: D   63 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8307 (tp40)
REVERT: D  151 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8430 (m-40)
REVERT: D  154 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8100 (tp)
REVERT: D  345 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8703 (tptm)
REVERT: D  354 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: D  355 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7887 (m-40)
REVERT: E  339 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: F   63 GLN cc_start: 0.8472 (mm110) cc_final: 0.8244 (tp-100)
REVERT: F  124 ASN cc_start: 0.8629 (t0) cc_final: 0.8425 (m-40)
REVERT: F  339 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: G  256 ARG cc_start: 0.8933 (mtm110) cc_final: 0.8692 (mtm110)
REVERT: G  303 LYS cc_start: 0.7151 (mttt) cc_final: 0.6647 (mtpt)
  outliers start: 79
  outliers final: 33
  residues processed: 254
  average time/residue: 0.6400
  time to fit residues: 179.6387
Evaluate side-chains
  231 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 189
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  355 ASN
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  151 ASN
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain D residue  345 LYS
Chi-restraints excluded: chain D residue  355 ASN
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue  113 LEU
Chi-restraints excluded: chain E residue  254 ILE
Chi-restraints excluded: chain E residue  331 SER
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain F residue  207 ASN
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  331 SER
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain G residue  207 ASN
Chi-restraints excluded: chain G residue  307 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 158 optimal weight:   10.0000
   chunk 148 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 181 optimal weight:    5.9990
   chunk 151 optimal weight:    6.9990
   chunk 174 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 146 optimal weight:    0.6980
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B  56 GLN
B 206 ASN
B 355 ASN
C 306 ASN
D 355 ASN
E 206 ASN
F  56 GLN
G 206 ASN
G 306 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.109583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.078144 restraints weight = 29196.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.70
r_work: 0.2921 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  17409  Z= 0.138
  Angle     :  0.560   6.521  23688  Z= 0.275
  Chirality :  0.039   0.182   2807
  Planarity :  0.004   0.037   2842
  Dihedral  :  3.260  21.156   2256
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 24.32 %
    Favored  : 71.32 %
  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 aren not related in a simple way.
  whole:  1.95 (0.20), residues: 2044
  helix:  2.56 (0.14), residues: 1442
  sheet: -1.53 (0.52), residues: 84
  loop : -2.10 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 152 
 TYR   0.011   0.001   TYR B  25 
 PHE   0.009   0.001   PHE C 333 
 TRP   0.005   0.001   TRP E  74 
 HIS   0.001   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (17395)
  covalent geometry    : angle       0.55903 (23660)
  SS BOND              : bond        0.00174 (   14)
  SS BOND              : angle       1.01336 (   28)
  hydrogen bonds       : bond        0.03510 ( 1099)
  hydrogen bonds       : angle       3.49844 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 205
  time to evaluate  : 0.595 
Fit side-chains
REVERT: A  124 ASN cc_start: 0.8640 (t0) cc_final: 0.8384 (m-40)
REVERT: A  151 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8396 (m-40)
REVERT: A  345 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8619 (tptm)
REVERT: B  303 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6528 (mttt)
REVERT: B  345 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8518 (tptm)
REVERT: C  345 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8766 (tptm)
REVERT: D  154 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8088 (tp)
REVERT: D  345 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8723 (tptm)
REVERT: E  354 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8489 (tm-30)
REVERT: F   37 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8962 (mt)
REVERT: F   56 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7694 (pp30)
REVERT: F   63 GLN cc_start: 0.8491 (mm110) cc_final: 0.8264 (tp-100)
REVERT: F  124 ASN cc_start: 0.8637 (t0) cc_final: 0.8410 (m-40)
REVERT: F  339 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: G  256 ARG cc_start: 0.8936 (mtm110) cc_final: 0.8698 (mtm110)
REVERT: G  303 LYS cc_start: 0.7143 (mttt) cc_final: 0.6641 (mtpt)
  outliers start: 83
  outliers final: 36
  residues processed: 263
  average time/residue: 0.6227
  time to fit residues: 180.7010
Evaluate side-chains
  222 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 177
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  151 ASN
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue  145 GLU
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain D residue  345 LYS
Chi-restraints excluded: chain E residue  254 ILE
Chi-restraints excluded: chain E residue  307 VAL
Chi-restraints excluded: chain E residue  331 SER
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  207 ASN
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  331 SER
Chi-restraints excluded: chain F residue  338 GLU
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain G residue  207 ASN
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain G residue  331 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 124 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 146 optimal weight:    0.0870
   chunk 37 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:   20.0000
   chunk 122 optimal weight:   10.0000
   chunk 28 optimal weight:    0.4980
   chunk 141 optimal weight:    8.9990
   overall best weight:    1.8562

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B  56 GLN
B 206 ASN
B 355 ASN
C  63 GLN
C 306 ASN
E  63 GLN
E 206 ASN
G 306 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.109616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.077982 restraints weight = 29131.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.71
r_work: 0.2922 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  17409  Z= 0.145
  Angle     :  0.576   6.835  23688  Z= 0.283
  Chirality :  0.040   0.182   2807
  Planarity :  0.004   0.043   2842
  Dihedral  :  3.281  20.793   2256
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.37 %
    Favored  : 70.12 %
  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 aren not related in a simple way.
  whole:  1.98 (0.20), residues: 2044
  helix:  2.59 (0.14), residues: 1442
  sheet: -1.52 (0.52), residues: 84
  loop : -2.09 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G 152 
 TYR   0.011   0.001   TYR A  25 
 PHE   0.009   0.001   PHE C 333 
 TRP   0.005   0.001   TRP F  74 
 HIS   0.001   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (17395)
  covalent geometry    : angle       0.57530 (23660)
  SS BOND              : bond        0.00184 (   14)
  SS BOND              : angle       1.02907 (   28)
  hydrogen bonds       : bond        0.03537 ( 1099)
  hydrogen bonds       : angle       3.50502 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 200
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A  124 ASN cc_start: 0.8666 (t0) cc_final: 0.8427 (m-40)
REVERT: A  345 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8638 (tptm)
REVERT: B  303 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6536 (mttt)
REVERT: B  345 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8535 (tptm)
REVERT: B  354 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8427 (tm-30)
REVERT: B  355 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8029 (m-40)
REVERT: C  345 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8781 (tptm)
REVERT: D  154 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8111 (tp)
REVERT: E  339 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: E  354 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8515 (tm-30)
REVERT: F   37 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8986 (mt)
REVERT: F  124 ASN cc_start: 0.8632 (t0) cc_final: 0.8425 (m-40)
REVERT: F  339 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: G  144 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8800 (mm-30)
REVERT: G  256 ARG cc_start: 0.8935 (mtm110) cc_final: 0.8697 (mtm110)
REVERT: G  303 LYS cc_start: 0.7049 (mttt) cc_final: 0.6524 (mtpt)
  outliers start: 86
  outliers final: 37
  residues processed: 259
  average time/residue: 0.5920
  time to fit residues: 169.4719
Evaluate side-chains
  233 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 189
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  355 ASN
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  207 ASN
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  113 LEU
Chi-restraints excluded: chain E residue  254 ILE
Chi-restraints excluded: chain E residue  307 VAL
Chi-restraints excluded: chain E residue  331 SER
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  207 ASN
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  331 SER
Chi-restraints excluded: chain F residue  338 GLU
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain G residue  207 ASN
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain G residue  308 LEU
Chi-restraints excluded: chain G residue  331 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 169 optimal weight:    0.4980
   chunk 72 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   chunk 161 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 142 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   chunk 135 optimal weight:    7.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  56 GLN
B 206 ASN
B 355 ASN
C  63 GLN
C 266 GLN
C 306 ASN
D 355 ASN
E  56 GLN
E 355 ASN
G 306 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.110905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.079042 restraints weight = 28380.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.67
r_work: 0.2954 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  17409  Z= 0.127
  Angle     :  0.580   7.041  23688  Z= 0.286
  Chirality :  0.040   0.196   2807
  Planarity :  0.004   0.052   2842
  Dihedral  :  3.270  20.725   2256
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 25.89 %
    Favored  : 69.80 %
  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 aren not related in a simple way.
  whole:  2.02 (0.20), residues: 2044
  helix:  2.62 (0.14), residues: 1442
  sheet: -1.49 (0.52), residues: 84
  loop : -2.08 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 152 
 TYR   0.010   0.001   TYR A  25 
 PHE   0.008   0.001   PHE F 333 
 TRP   0.006   0.001   TRP G  74 
 HIS   0.001   0.000   HIS F 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (17395)
  covalent geometry    : angle       0.57932 (23660)
  SS BOND              : bond        0.00160 (   14)
  SS BOND              : angle       0.97035 (   28)
  hydrogen bonds       : bond        0.03369 ( 1099)
  hydrogen bonds       : angle       3.44986 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 199
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  124 ASN cc_start: 0.8643 (t0) cc_final: 0.8421 (m-40)
REVERT: A  152 ARG cc_start: 0.7399 (mtm110) cc_final: 0.7128 (mtm110)
REVERT: A  345 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8650 (tptm)
REVERT: B  303 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6549 (mttt)
REVERT: B  345 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8571 (tptm)
REVERT: C  345 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8813 (tptm)
REVERT: D  151 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8488 (m-40)
REVERT: D  154 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8112 (tp)
REVERT: D  204 THR cc_start: 0.9264 (p) cc_final: 0.8994 (p)
REVERT: E  152 ARG cc_start: 0.7624 (mtm110) cc_final: 0.7408 (mtm110)
REVERT: E  339 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: E  354 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8574 (tm-30)
REVERT: F   37 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8989 (mt)
REVERT: F  339 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: F  350 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8831 (mm)
REVERT: G  144 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8836 (mm-30)
REVERT: G  152 ARG cc_start: 0.7439 (mtm110) cc_final: 0.7216 (mtm110)
REVERT: G  256 ARG cc_start: 0.8979 (mtm110) cc_final: 0.8730 (mtm110)
REVERT: G  303 LYS cc_start: 0.7080 (mttt) cc_final: 0.6549 (mtpt)
  outliers start: 82
  outliers final: 34
  residues processed: 259
  average time/residue: 0.6449
  time to fit residues: 185.1273
Evaluate side-chains
  226 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 184
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  151 ASN
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  113 LEU
Chi-restraints excluded: chain E residue  254 ILE
Chi-restraints excluded: chain E residue  307 VAL
Chi-restraints excluded: chain E residue  331 SER
Chi-restraints excluded: chain E residue  355 ASN
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue  207 ASN
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  331 SER
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  350 LEU
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain G residue  207 ASN
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain G residue  331 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 163 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 175 optimal weight:   10.0000
   chunk 150 optimal weight:    5.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B  56 GLN
B 206 ASN
C  63 GLN
C 266 GLN
C 306 ASN
C 355 ASN
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  63 GLN
E 206 ASN
G  56 GLN
G 266 GLN
G 306 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.109182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.077087 restraints weight = 28867.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.69
r_work: 0.2916 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  17409  Z= 0.180
  Angle     :  0.637  12.015  23688  Z= 0.312
  Chirality :  0.041   0.194   2807
  Planarity :  0.004   0.058   2842
  Dihedral  :  3.354  20.689   2256
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 26.21 %
    Favored  : 69.28 %
  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 aren not related in a simple way.
  whole:  1.94 (0.20), residues: 2044
  helix:  2.52 (0.14), residues: 1442
  sheet: -1.83 (0.41), residues: 126
  loop : -1.86 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 152 
 TYR   0.013   0.001   TYR G  25 
 PHE   0.012   0.001   PHE C 333 
 TRP   0.007   0.001   TRP E  85 
 HIS   0.002   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (17395)
  covalent geometry    : angle       0.63583 (23660)
  SS BOND              : bond        0.00223 (   14)
  SS BOND              : angle       1.10253 (   28)
  hydrogen bonds       : bond        0.03809 ( 1099)
  hydrogen bonds       : angle       3.58716 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 205
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A  345 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8697 (tptm)
REVERT: A  355 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8184 (m-40)
REVERT: B  303 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6601 (mttt)
REVERT: B  345 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8604 (tptm)
REVERT: B  354 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8444 (tm-30)
REVERT: C  345 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8837 (tptm)
REVERT: D  151 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8490 (m-40)
REVERT: D  154 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8076 (tp)
REVERT: E  339 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8171 (tm-30)
REVERT: E  354 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8474 (tm-30)
REVERT: F   37 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8991 (mt)
REVERT: F  339 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8141 (tm-30)
REVERT: G   56 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7801 (pp30)
REVERT: G  144 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8857 (mm-30)
REVERT: G  205 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8924 (tppp)
  outliers start: 86
  outliers final: 41
  residues processed: 269
  average time/residue: 0.7289
  time to fit residues: 215.7933
Evaluate side-chains
  236 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 185
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain A residue  355 ASN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  207 ASN
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  355 ASN
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  355 ASN
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  151 ASN
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  207 ASN
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  113 LEU
Chi-restraints excluded: chain E residue  307 VAL
Chi-restraints excluded: chain E residue  331 SER
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue  207 ASN
Chi-restraints excluded: chain F residue  307 VAL
Chi-restraints excluded: chain F residue  331 SER
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain G residue  205 LYS
Chi-restraints excluded: chain G residue  207 ASN
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain G residue  331 SER
Chi-restraints excluded: chain G residue  338 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 102 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 190 optimal weight:    0.9990
   chunk 112 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 164 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 157 optimal weight:    0.9990
   chunk 191 optimal weight:    4.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  56 GLN
B 206 ASN
C  63 GLN
C 306 ASN
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 266 GLN
D 282 ASN
D 355 ASN
E  56 GLN
E 266 GLN
E 355 ASN
F 355 ASN
G  56 GLN
G 306 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.109869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.077856 restraints weight = 28632.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 2.69
r_work: 0.2929 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  17409  Z= 0.152
  Angle     :  0.645   9.252  23688  Z= 0.318
  Chirality :  0.041   0.201   2807
  Planarity :  0.005   0.060   2842
  Dihedral  :  3.376  20.441   2256
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 27.68 %
    Favored  : 68.70 %
  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 aren not related in a simple way.
  whole:  1.96 (0.19), residues: 2044
  helix:  2.53 (0.14), residues: 1442
  sheet: -1.78 (0.41), residues: 126
  loop : -1.86 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 152 
 TYR   0.011   0.001   TYR B  25 
 PHE   0.009   0.001   PHE C 333 
 TRP   0.006   0.001   TRP G  74 
 HIS   0.001   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (17395)
  covalent geometry    : angle       0.64475 (23660)
  SS BOND              : bond        0.00191 (   14)
  SS BOND              : angle       1.03183 (   28)
  hydrogen bonds       : bond        0.03591 ( 1099)
  hydrogen bonds       : angle       3.52614 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 199
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  345 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8672 (tptm)
REVERT: B  303 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6578 (mttt)
REVERT: B  345 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8640 (tptm)
REVERT: C  345 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8837 (tptm)
REVERT: D  151 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8493 (m-40)
REVERT: D  154 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8036 (tp)
REVERT: D  204 THR cc_start: 0.9314 (p) cc_final: 0.9105 (p)
REVERT: E  354 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8528 (tm-30)
REVERT: E  355 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8467 (t0)
REVERT: F   37 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8992 (mt)
REVERT: F  339 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: G   56 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8021 (pp30)
REVERT: G  144 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8870 (mm-30)
REVERT: G  152 ARG cc_start: 0.7430 (mtm110) cc_final: 0.7220 (mtm110)
  outliers start: 69
  outliers final: 35
  residues processed: 244
  average time/residue: 0.7321
  time to fit residues: 196.1930
Evaluate side-chains
  229 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 185
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   56 GLN
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue   56 GLN
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   56 GLN
Chi-restraints excluded: chain D residue  151 ASN
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue  113 LEU
Chi-restraints excluded: chain E residue  307 VAL
Chi-restraints excluded: chain E residue  331 SER
Chi-restraints excluded: chain E residue  355 ASN
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue  207 ASN
Chi-restraints excluded: chain F residue  331 SER
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain G residue  207 ASN
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain G residue  331 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 169 optimal weight:    0.3980
   chunk 80 optimal weight:    5.9990
   chunk 147 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:   10.0000
   chunk 126 optimal weight:    0.8980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
** B  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 206 ASN
C  63 GLN
C 306 ASN
C 355 ASN
D 282 ASN
D 355 ASN
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  63 GLN
E 266 GLN
E 355 ASN
F 306 ASN
G  56 GLN
G 306 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.111109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.079413 restraints weight = 28251.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.66
r_work: 0.2957 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17409  Z= 0.130
  Angle     :  0.646   9.447  23688  Z= 0.319
  Chirality :  0.040   0.219   2807
  Planarity :  0.005   0.063   2842
  Dihedral  :  3.342  20.258   2256
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 28.68 %
    Favored  : 68.64 %
  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 aren not related in a simple way.
  whole:  2.02 (0.20), residues: 2044
  helix:  2.57 (0.14), residues: 1442
  sheet: -1.79 (0.41), residues: 126
  loop : -1.81 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 152 
 TYR   0.010   0.001   TYR A  25 
 PHE   0.009   0.001   PHE F 109 
 TRP   0.007   0.001   TRP G  74 
 HIS   0.001   0.000   HIS G 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (17395)
  covalent geometry    : angle       0.64537 (23660)
  SS BOND              : bond        0.00146 (   14)
  SS BOND              : angle       0.94167 (   28)
  hydrogen bonds       : bond        0.03321 ( 1099)
  hydrogen bonds       : angle       3.45678 ( 3192)

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

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

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4088 Ramachandran restraints generated.
    2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 202
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A   63 GLN cc_start: 0.8428 (mm110) cc_final: 0.8165 (tp40)
REVERT: A  345 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8625 (tptm)
REVERT: B   56 GLN cc_start: 0.8121 (pp30) cc_final: 0.7838 (pp30)
REVERT: B  303 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6556 (mttt)
REVERT: B  339 GLU cc_start: 0.8758 (tp30) cc_final: 0.8481 (tm-30)
REVERT: B  345 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8566 (tptm)
REVERT: C  345 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8819 (tptm)
REVERT: D  151 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8473 (m-40)
REVERT: D  154 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8011 (tp)
REVERT: E  256 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.7927 (mtm-85)
REVERT: E  339 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8172 (tm-30)
REVERT: F   37 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8982 (mt)
REVERT: F  339 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: G   56 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7963 (pp30)
  outliers start: 51
  outliers final: 24
  residues processed: 233
  average time/residue: 0.7465
  time to fit residues: 191.1928
Evaluate side-chains
  213 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 181
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   56 GLN
Chi-restraints excluded: chain D residue  151 ASN
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  307 VAL
Chi-restraints excluded: chain E residue  331 SER
Chi-restraints excluded: chain E residue  355 ASN
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue  207 ASN
Chi-restraints excluded: chain F residue  331 SER
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  307 VAL
Chi-restraints excluded: chain G residue  331 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 119 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0070
   chunk 99 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 143 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0070
   chunk 169 optimal weight:   20.0000
   chunk 81 optimal weight:    0.9990
   chunk 195 optimal weight:    0.9990
   overall best weight:    0.6020

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B  56 GLN
B 206 ASN
C  63 GLN
C 306 ASN
C 355 ASN
D 355 ASN
E  56 GLN
E  63 GLN
G  56 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.111920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.080278 restraints weight = 28220.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.66
r_work: 0.2978 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  17409  Z= 0.129
  Angle     :  0.654   9.961  23688  Z= 0.320
  Chirality :  0.040   0.223   2807
  Planarity :  0.005   0.063   2842
  Dihedral  :  3.287  20.149   2256
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 28.68 %
    Favored  : 68.80 %
  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 aren not related in a simple way.
  whole:  2.08 (0.20), residues: 2044
  helix:  2.57 (0.14), residues: 1449
  sheet: -1.72 (0.41), residues: 126
  loop : -1.69 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG G 152 
 TYR   0.020   0.001   TYR C 111 
 PHE   0.009   0.001   PHE E 109 
 TRP   0.007   0.001   TRP G  74 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (17395)
  covalent geometry    : angle       0.65358 (23660)
  SS BOND              : bond        0.00126 (   14)
  SS BOND              : angle       0.88683 (   28)
  hydrogen bonds       : bond        0.03177 ( 1099)
  hydrogen bonds       : angle       3.40516 ( 3192)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4803.99 seconds
wall clock time: 83 minutes 5.74 seconds (4985.74 seconds total)