Starting phenix.real_space_refine
on Sat Jun 14 19:38:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wzh_37952/06_2025/8wzh_37952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wzh_37952/06_2025/8wzh_37952.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wzh_37952/06_2025/8wzh_37952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wzh_37952/06_2025/8wzh_37952.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wzh_37952/06_2025/8wzh_37952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wzh_37952/06_2025/8wzh_37952.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      12      5.49       5
     S      52      5.16       5
     C   10392      2.51       5
     N    2884      2.21       5
     O    3024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 136 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16368
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "A"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "C"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "D"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "B"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 12.63, per 1000 atoms: 0.77
  Number of scatterers: 16368
  At special positions: 0
  Unit cell: (110.21, 114.49, 86.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S      52     16.00
     P      12     15.00
     O    3024      8.00
     N    2884      7.00
     C   10392      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.19
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3712

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 8 sheets defined
      40.2% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 9
    Processing helix  chain 'B' and resid 10 through 19
    Processing helix  chain 'B' and resid 54 through 65
      removed outlier: 3.685A  pdb=" N   THR B  58 " --> pdb=" O   ASP B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.564A  pdb=" N   GLU B 101 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 159
      No H-bonds generated for 'chain 'B' and resid 157 through 159'
    Processing helix  chain 'B' and resid 160 through 169
    Processing helix  chain 'B' and resid 178 through 189
      removed outlier: 3.691A  pdb=" N   VAL B 182 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 200
    Processing helix  chain 'B' and resid 201 through 205
      removed outlier: 4.020A  pdb=" N   ILE B 205 " --> pdb=" O   ASP B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 257
      removed outlier: 3.605A  pdb=" N   GLN B 255 " --> pdb=" O   ALA B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 272
    Processing helix  chain 'B' and resid 285 through 291
    Processing helix  chain 'B' and resid 324 through 329
    Processing helix  chain 'B' and resid 348 through 366
      removed outlier: 3.629A  pdb=" N   PHE B 356 " --> pdb=" O   GLN B 352 " (cutoff:3.500A)
      Proline residue:  B 359  - end of helix
    Processing helix  chain 'B' and resid 369 through 373
    Processing helix  chain 'B' and resid 415 through 419
      removed outlier: 3.930A  pdb=" N   LEU B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 451
      removed outlier: 3.855A  pdb=" N   LEU B 451 " --> pdb=" O   TYR B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 468
    Processing helix  chain 'B' and resid 471 through 486
    Processing helix  chain 'B' and resid 486 through 501
    Processing helix  chain 'A' and resid 6 through 9
    Processing helix  chain 'A' and resid 10 through 19
    Processing helix  chain 'A' and resid 54 through 65
      removed outlier: 3.683A  pdb=" N   THR A  58 " --> pdb=" O   ASP A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
      removed outlier: 3.565A  pdb=" N   GLU A 101 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 160 through 169
    Processing helix  chain 'A' and resid 178 through 189
      removed outlier: 3.692A  pdb=" N   VAL A 182 " --> pdb=" O   ASP A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 200
    Processing helix  chain 'A' and resid 201 through 205
      removed outlier: 4.020A  pdb=" N   ILE A 205 " --> pdb=" O   ASP A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.604A  pdb=" N   GLN A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 272
    Processing helix  chain 'A' and resid 285 through 291
    Processing helix  chain 'A' and resid 324 through 330
    Processing helix  chain 'A' and resid 348 through 366
      removed outlier: 3.629A  pdb=" N   PHE A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      Proline residue:  A 359  - end of helix
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 415 through 419
      removed outlier: 3.930A  pdb=" N   LEU A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.856A  pdb=" N   LEU A 451 " --> pdb=" O   TYR A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 468
    Processing helix  chain 'A' and resid 471 through 486
    Processing helix  chain 'A' and resid 486 through 501
    Processing helix  chain 'C' and resid 6 through 9
    Processing helix  chain 'C' and resid 10 through 19
    Processing helix  chain 'C' and resid 54 through 65
      removed outlier: 3.685A  pdb=" N   THR C  58 " --> pdb=" O   ASP C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
      removed outlier: 3.564A  pdb=" N   GLU C 101 " --> pdb=" O   LYS C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 159
      No H-bonds generated for 'chain 'C' and resid 157 through 159'
    Processing helix  chain 'C' and resid 160 through 169
    Processing helix  chain 'C' and resid 178 through 189
      removed outlier: 3.692A  pdb=" N   VAL C 182 " --> pdb=" O   ASP C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 200
    Processing helix  chain 'C' and resid 201 through 205
      removed outlier: 4.020A  pdb=" N   ILE C 205 " --> pdb=" O   ASP C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 246 through 257
      removed outlier: 3.605A  pdb=" N   GLN C 255 " --> pdb=" O   ALA C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 272
    Processing helix  chain 'C' and resid 285 through 291
    Processing helix  chain 'C' and resid 324 through 330
    Processing helix  chain 'C' and resid 348 through 366
      removed outlier: 3.628A  pdb=" N   PHE C 356 " --> pdb=" O   GLN C 352 " (cutoff:3.500A)
      Proline residue:  C 359  - end of helix
    Processing helix  chain 'C' and resid 369 through 373
    Processing helix  chain 'C' and resid 415 through 419
      removed outlier: 3.930A  pdb=" N   LEU C 419 " --> pdb=" O   PRO C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 440 through 451
      removed outlier: 3.856A  pdb=" N   LEU C 451 " --> pdb=" O   TYR C 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 468
    Processing helix  chain 'C' and resid 471 through 486
    Processing helix  chain 'C' and resid 486 through 501
    Processing helix  chain 'D' and resid 6 through 9
    Processing helix  chain 'D' and resid 10 through 19
    Processing helix  chain 'D' and resid 54 through 65
      removed outlier: 3.683A  pdb=" N   THR D  58 " --> pdb=" O   ASP D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 101
      removed outlier: 3.564A  pdb=" N   GLU D 101 " --> pdb=" O   LYS D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 159
      No H-bonds generated for 'chain 'D' and resid 157 through 159'
    Processing helix  chain 'D' and resid 160 through 169
    Processing helix  chain 'D' and resid 178 through 189
      removed outlier: 3.692A  pdb=" N   VAL D 182 " --> pdb=" O   ASP D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 192 through 200
    Processing helix  chain 'D' and resid 201 through 205
      removed outlier: 4.020A  pdb=" N   ILE D 205 " --> pdb=" O   ASP D 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 246 through 257
      removed outlier: 3.605A  pdb=" N   GLN D 255 " --> pdb=" O   ALA D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 259 through 272
    Processing helix  chain 'D' and resid 285 through 291
    Processing helix  chain 'D' and resid 324 through 330
    Processing helix  chain 'D' and resid 348 through 366
      removed outlier: 3.628A  pdb=" N   PHE D 356 " --> pdb=" O   GLN D 352 " (cutoff:3.500A)
      Proline residue:  D 359  - end of helix
    Processing helix  chain 'D' and resid 369 through 373
    Processing helix  chain 'D' and resid 415 through 419
      removed outlier: 3.930A  pdb=" N   LEU D 419 " --> pdb=" O   PRO D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 440 through 451
      removed outlier: 3.856A  pdb=" N   LEU D 451 " --> pdb=" O   TYR D 447 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 452 through 468
    Processing helix  chain 'D' and resid 471 through 486
    Processing helix  chain 'D' and resid 486 through 501
    Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44
      removed outlier: 3.738A  pdb=" N   ARG D 430 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 344
      removed outlier: 3.678A  pdb=" N   GLY B 314 " --> pdb=" O   PHE B 279 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE B 281 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   LEU B 316 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   GLU B  86 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   LEU B 318 " --> pdb=" O   TYR B  84 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR B  84 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 429 through 431
      removed outlier: 3.532A  pdb=" N   ARG B 430 " --> pdb=" O   THR D  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44
      removed outlier: 3.507A  pdb=" N   ARG C 430 " --> pdb=" O   THR A  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344
      removed outlier: 3.678A  pdb=" N   GLY A 314 " --> pdb=" O   PHE A 279 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE A 281 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   LEU A 316 " --> pdb=" O   GLU A  86 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   GLU A  86 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   LEU A 318 " --> pdb=" O   TYR A  84 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR A  84 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431
      removed outlier: 3.627A  pdb=" N   ARG A 430 " --> pdb=" O   THR C  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 344
      removed outlier: 3.678A  pdb=" N   GLY C 314 " --> pdb=" O   PHE C 279 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE C 281 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   LEU C 316 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   GLU C  86 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   LEU C 318 " --> pdb=" O   TYR C  84 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR C  84 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 344
      removed outlier: 3.679A  pdb=" N   GLY D 314 " --> pdb=" O   PHE D 279 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE D 281 " --> pdb=" O   PRO D 312 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   LEU D 316 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   GLU D  86 " --> pdb=" O   LEU D 316 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   LEU D 318 " --> pdb=" O   TYR D  84 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR D  84 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)

    647 hydrogen bonds defined for protein.
    1833 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.91

  Time building geometry restraints manager: 5.00 seconds

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

  Histogram of bond lengths:
        1.21 -     1.39: 6843
        1.39 -     1.57: 9921
        1.57 -     1.75: 20
        1.75 -     1.93: 92
        1.93 -     2.11: 12
  Bond restraints: 16888
  Sorted by residual:
  bond pdb=" O2B NDP D3002 "
       pdb=" P2B NDP D3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.616  0.217 3.80e-02 6.93e+02 3.26e+01
  bond pdb=" O2B NDP B3002 "
       pdb=" P2B NDP B3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.616  0.217 3.80e-02 6.93e+02 3.25e+01
  bond pdb=" O2B NDP A3002 "
       pdb=" P2B NDP A3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.617  0.216 3.80e-02 6.93e+02 3.23e+01
  bond pdb=" O2B NDP C3002 "
       pdb=" P2B NDP C3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.617  0.216 3.80e-02 6.93e+02 3.23e+01
  bond pdb=" O5D NDP A3002 "
       pdb=" PN  NDP A3002 "
    ideal  model  delta    sigma   weight residual
    1.757  1.589  0.168 3.50e-02 8.16e+02 2.30e+01
  ... (remaining 16883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 19711
        2.03 -     4.06: 3203
        4.06 -     6.09: 94
        6.09 -     8.12: 20
        8.12 -    10.15: 12
  Bond angle restraints: 23040
  Sorted by residual:
  angle pdb=" O1X NDP A3002 "
        pdb=" P2B NDP A3002 "
        pdb=" O3X NDP A3002 "
      ideal   model   delta    sigma   weight residual
     117.46  111.91    5.55 1.17e+00 7.36e-01 2.26e+01
  angle pdb=" O1X NDP D3002 "
        pdb=" P2B NDP D3002 "
        pdb=" O3X NDP D3002 "
      ideal   model   delta    sigma   weight residual
     117.46  111.96    5.50 1.17e+00 7.36e-01 2.23e+01
  angle pdb=" O1X NDP B3002 "
        pdb=" P2B NDP B3002 "
        pdb=" O3X NDP B3002 "
      ideal   model   delta    sigma   weight residual
     117.46  111.97    5.49 1.17e+00 7.36e-01 2.22e+01
  angle pdb=" O1X NDP C3002 "
        pdb=" P2B NDP C3002 "
        pdb=" O3X NDP C3002 "
      ideal   model   delta    sigma   weight residual
     117.46  112.02    5.44 1.17e+00 7.36e-01 2.18e+01
  angle pdb=" O2B NDP B3002 "
        pdb=" P2B NDP B3002 "
        pdb=" O3X NDP B3002 "
      ideal   model   delta    sigma   weight residual
      97.70  107.85  -10.15 2.45e+00 1.67e-01 1.72e+01
  ... (remaining 23035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 8836
       17.89 -    35.78: 776
       35.78 -    53.67: 148
       53.67 -    71.56: 76
       71.56 -    89.45: 24
  Dihedral angle restraints: 9860
    sinusoidal: 4080
      harmonic: 5780
  Sorted by residual:
  dihedral pdb=" CA  ASN D 439 "
           pdb=" C   ASN D 439 "
           pdb=" N   VAL D 440 "
           pdb=" CA  VAL D 440 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.46  -18.54     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASN A 439 "
           pdb=" C   ASN A 439 "
           pdb=" N   VAL A 440 "
           pdb=" CA  VAL A 440 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.46  -18.54     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASN B 439 "
           pdb=" C   ASN B 439 "
           pdb=" N   VAL B 440 "
           pdb=" CA  VAL B 440 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.48  -18.52     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 9857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 960
       0.040 -    0.079: 701
       0.079 -    0.119: 480
       0.119 -    0.159: 167
       0.159 -    0.198: 20
  Chirality restraints: 2328
  Sorted by residual:
  chirality pdb=" C4D NDP D3002 "
            pdb=" C3D NDP D3002 "
            pdb=" C5D NDP D3002 "
            pdb=" O4D NDP D3002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.52   -0.20 2.00e-01 2.50e+01 9.84e-01
  chirality pdb=" C4D NDP C3002 "
            pdb=" C3D NDP C3002 "
            pdb=" C5D NDP C3002 "
            pdb=" O4D NDP C3002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.52   -0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" C4D NDP A3002 "
            pdb=" C3D NDP A3002 "
            pdb=" C5D NDP A3002 "
            pdb=" O4D NDP A3002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.52   -0.20 2.00e-01 2.50e+01 9.72e-01
  ... (remaining 2325 not shown)

  Planarity restraints: 3052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  HEM B3001 "   -0.011 2.00e-02 2.50e+03   1.34e-02 4.02e+00
        pdb=" C1B HEM B3001 "    0.004 2.00e-02 2.50e+03
        pdb=" C2B HEM B3001 "   -0.001 2.00e-02 2.50e+03
        pdb=" C3B HEM B3001 "    0.003 2.00e-02 2.50e+03
        pdb=" C4B HEM B3001 "   -0.014 2.00e-02 2.50e+03
        pdb=" CAB HEM B3001 "    0.020 2.00e-02 2.50e+03
        pdb=" CHB HEM B3001 "    0.021 2.00e-02 2.50e+03
        pdb=" CHC HEM B3001 "    0.000 2.00e-02 2.50e+03
        pdb=" CMB HEM B3001 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  HEM A3001 "   -0.011 2.00e-02 2.50e+03   1.34e-02 4.02e+00
        pdb=" C1B HEM A3001 "    0.003 2.00e-02 2.50e+03
        pdb=" C2B HEM A3001 "   -0.001 2.00e-02 2.50e+03
        pdb=" C3B HEM A3001 "    0.003 2.00e-02 2.50e+03
        pdb=" C4B HEM A3001 "   -0.014 2.00e-02 2.50e+03
        pdb=" CAB HEM A3001 "    0.020 2.00e-02 2.50e+03
        pdb=" CHB HEM A3001 "    0.021 2.00e-02 2.50e+03
        pdb=" CHC HEM A3001 "   -0.000 2.00e-02 2.50e+03
        pdb=" CMB HEM A3001 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  HEM C3001 "    0.012 2.00e-02 2.50e+03   1.31e-02 3.88e+00
        pdb=" C1B HEM C3001 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2B HEM C3001 "    0.001 2.00e-02 2.50e+03
        pdb=" C3B HEM C3001 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4B HEM C3001 "    0.013 2.00e-02 2.50e+03
        pdb=" CAB HEM C3001 "   -0.019 2.00e-02 2.50e+03
        pdb=" CHB HEM C3001 "   -0.021 2.00e-02 2.50e+03
        pdb=" CHC HEM C3001 "    0.000 2.00e-02 2.50e+03
        pdb=" CMB HEM C3001 "    0.021 2.00e-02 2.50e+03
  ... (remaining 3049 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3826
        2.83 -     3.35: 16437
        3.35 -     3.86: 26663
        3.86 -     4.38: 32562
        4.38 -     4.90: 54551
  Nonbonded interactions: 134039
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 137 "
            pdb=" O   VAL A 375 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR C 137 "
            pdb=" O   VAL C 375 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR D 137 "
            pdb=" O   VAL D 375 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OH  TYR B 137 "
            pdb=" O   VAL B 375 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   LEU A 451 "
            pdb=" NH2 ARG A 456 "
     model   vdw
     2.318 3.120
  ... (remaining 134034 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: 0.15
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.630
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     41.750
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.110
  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:             0.020
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
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      :  0.013   0.217  16892  Z= 0.890
  Angle     :  1.375  10.147  23040  Z= 0.981
  Chirality :  0.070   0.198   2328
  Planarity :  0.004   0.018   3052
  Dihedral  : 15.634  89.449   6148
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  3.74 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.16), residues: 1980
  helix: -1.14 (0.17), residues: 676
  sheet: -1.12 (0.28), residues: 220
  loop : -2.43 (0.16), residues: 1084

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B 183 
 HIS   0.008   0.003   HIS C 166 
 PHE   0.020   0.003   PHE C 356 
 TYR   0.022   0.003   TYR C 489 
 ARG   0.005   0.001   ARG D 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15783 (  647)
  hydrogen bonds       : angle       7.44833 ( 1833)
  covalent geometry    : bond        0.01342 (16888)
  covalent geometry    : angle       1.37502 (23040)
  Misc. bond           : bond        0.08834 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 205
  time to evaluate  : 1.861 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 ASP cc_start: 0.7180 (m-30) cc_final: 0.6839 (m-30)
REVERT: B  119 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7272 (mp0)
REVERT: B  259 ASP cc_start: 0.8290 (p0) cc_final: 0.7653 (p0)
REVERT: B  260 TYR cc_start: 0.7497 (t80) cc_final: 0.7095 (t80)
REVERT: B  321 ASN cc_start: 0.8352 (m-40) cc_final: 0.8136 (m-40)
REVERT: B  330 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7934 (mm-30)
REVERT: A  119 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7075 (mp0)
REVERT: A  259 ASP cc_start: 0.8077 (p0) cc_final: 0.7397 (p0)
REVERT: A  330 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: A  339 MET cc_start: 0.8073 (mtm) cc_final: 0.7856 (mtm)
REVERT: C   59 ASP cc_start: 0.7099 (m-30) cc_final: 0.6725 (m-30)
REVERT: C  119 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7326 (mp0)
REVERT: C  259 ASP cc_start: 0.8260 (p0) cc_final: 0.7599 (p0)
REVERT: C  260 TYR cc_start: 0.7509 (t80) cc_final: 0.7108 (t80)
REVERT: C  321 ASN cc_start: 0.8343 (m-40) cc_final: 0.8129 (m-40)
REVERT: C  330 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7927 (mm-30)
REVERT: C  339 MET cc_start: 0.8066 (mtm) cc_final: 0.7860 (mtm)
REVERT: D  119 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7134 (mp0)
REVERT: D  259 ASP cc_start: 0.8179 (p0) cc_final: 0.7496 (p0)
REVERT: D  330 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7869 (mm-30)
  outliers start: 16
  outliers final: 4
  residues processed: 217
  average time/residue: 0.2917
  time to fit residues: 94.5385
Evaluate side-chains
  154 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 1.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain D residue  119 GLU
Chi-restraints excluded: chain D residue  440 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    0.9990
   chunk 148 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 50 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 153 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 114 optimal weight:    0.7980
   chunk 177 optimal weight:    3.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B  89 HIS
B 148 ASN
B 282 GLN
B 331 GLN
** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  89 HIS
A 282 GLN
A 331 GLN
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 HIS
C 282 GLN
** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  89 HIS
D 282 GLN
D 331 GLN
** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.111941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.087108 restraints weight = 25587.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.089718 restraints weight = 16074.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.091482 restraints weight = 12052.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  16892  Z= 0.134
  Angle     :  0.547   4.775  23040  Z= 0.280
  Chirality :  0.043   0.134   2328
  Planarity :  0.004   0.039   3052
  Dihedral  :  8.498  93.722   2268
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  :  8.00 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.18), residues: 1980
  helix:  0.73 (0.20), residues: 684
  sheet: -0.13 (0.28), residues: 272
  loop : -1.52 (0.17), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 183 
 HIS   0.004   0.001   HIS C 364 
 PHE   0.020   0.002   PHE A 132 
 TYR   0.017   0.001   TYR A 489 
 ARG   0.003   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  647)
  hydrogen bonds       : angle       5.38335 ( 1833)
  covalent geometry    : bond        0.00338 (16888)
  covalent geometry    : angle       0.54709 (23040)
  Misc. bond           : bond        0.02152 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 170
  time to evaluate  : 1.800 
Fit side-chains
REVERT: B   60 GLU cc_start: 0.7790 (tp30) cc_final: 0.7584 (tp30)
REVERT: B  259 ASP cc_start: 0.7310 (p0) cc_final: 0.6887 (p0)
REVERT: B  321 ASN cc_start: 0.8814 (m-40) cc_final: 0.8571 (m-40)
REVERT: B  394 MET cc_start: 0.6588 (tmm) cc_final: 0.5975 (ttt)
REVERT: A  259 ASP cc_start: 0.7260 (p0) cc_final: 0.6848 (p0)
REVERT: C   26 VAL cc_start: 0.7519 (OUTLIER) cc_final: 0.7301 (p)
REVERT: C   60 GLU cc_start: 0.7858 (tp30) cc_final: 0.7653 (tp30)
REVERT: C  259 ASP cc_start: 0.7276 (p0) cc_final: 0.6794 (p0)
REVERT: C  321 ASN cc_start: 0.8835 (m-40) cc_final: 0.8616 (m-40)
REVERT: D  259 ASP cc_start: 0.7323 (p0) cc_final: 0.6860 (p0)
  outliers start: 44
  outliers final: 25
  residues processed: 189
  average time/residue: 0.2719
  time to fit residues: 82.4374
Evaluate side-chains
  163 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 1.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain C residue   26 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0370
   chunk 50 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 42 optimal weight:    0.4980
   chunk 147 optimal weight:    0.9990
   chunk 182 optimal weight:    2.9990
   chunk 163 optimal weight:    5.9990
   chunk 117 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 179 optimal weight:    4.9990
   overall best weight:    1.5064

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

Flipped N/Q/H residues before XYZ refinement:
B 407 ASN
A 407 ASN
C 331 GLN
C 407 ASN
D 407 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.086870 restraints weight = 25584.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.089539 restraints weight = 15899.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.091284 restraints weight = 11809.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  16892  Z= 0.129
  Angle     :  0.531   4.865  23040  Z= 0.269
  Chirality :  0.043   0.139   2328
  Planarity :  0.004   0.043   3052
  Dihedral  :  7.788  91.109   2256
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  :  9.17 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.18), residues: 1980
  helix:  1.17 (0.20), residues: 684
  sheet:  0.18 (0.29), residues: 272
  loop : -1.28 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 183 
 HIS   0.004   0.001   HIS B 235 
 PHE   0.023   0.002   PHE B 100 
 TYR   0.015   0.001   TYR A 489 
 ARG   0.002   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03719 (  647)
  hydrogen bonds       : angle       5.06074 ( 1833)
  covalent geometry    : bond        0.00331 (16888)
  covalent geometry    : angle       0.53107 (23040)
  Misc. bond           : bond        0.02218 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 153
  time to evaluate  : 2.897 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7298 (p0) cc_final: 0.6907 (p0)
REVERT: B  321 ASN cc_start: 0.8834 (m-40) cc_final: 0.8566 (m-40)
REVERT: A  259 ASP cc_start: 0.7221 (p0) cc_final: 0.6699 (p0)
REVERT: A  260 TYR cc_start: 0.7381 (t80) cc_final: 0.7159 (t80)
REVERT: C  236 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8713 (p90)
REVERT: C  259 ASP cc_start: 0.7311 (p0) cc_final: 0.6888 (p0)
REVERT: C  321 ASN cc_start: 0.8878 (m-40) cc_final: 0.8635 (m-40)
REVERT: C  392 MET cc_start: 0.8761 (tpt) cc_final: 0.8551 (tpt)
REVERT: C  394 MET cc_start: 0.7764 (mmt) cc_final: 0.7414 (mmt)
REVERT: D  259 ASP cc_start: 0.7314 (p0) cc_final: 0.6851 (p0)
REVERT: D  494 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7694 (tp-100)
  outliers start: 43
  outliers final: 29
  residues processed: 176
  average time/residue: 0.2490
  time to fit residues: 70.8251
Evaluate side-chains
  165 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 1.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  497 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 149 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 161 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0270
   chunk 135 optimal weight:    0.0470
   chunk 189 optimal weight:    8.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    2.4140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.110872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.086498 restraints weight = 25754.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.089130 restraints weight = 16070.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.090891 restraints weight = 11991.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  16892  Z= 0.179
  Angle     :  0.554   4.808  23040  Z= 0.283
  Chirality :  0.044   0.137   2328
  Planarity :  0.004   0.048   3052
  Dihedral  :  7.807  88.791   2253
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  :  9.75 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.18), residues: 1980
  helix:  1.24 (0.20), residues: 684
  sheet:  0.24 (0.29), residues: 272
  loop : -1.22 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 183 
 HIS   0.004   0.001   HIS C 362 
 PHE   0.029   0.002   PHE B 100 
 TYR   0.016   0.001   TYR D 489 
 ARG   0.003   0.000   ARG D 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03998 (  647)
  hydrogen bonds       : angle       5.11122 ( 1833)
  covalent geometry    : bond        0.00459 (16888)
  covalent geometry    : angle       0.55423 (23040)
  Misc. bond           : bond        0.04906 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 149
  time to evaluate  : 1.740 
Fit side-chains
   revert: symmetry clash
REVERT: B  259 ASP cc_start: 0.7254 (p0) cc_final: 0.6846 (p0)
REVERT: B  321 ASN cc_start: 0.8852 (m-40) cc_final: 0.8584 (m-40)
REVERT: B  500 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6653 (m-80)
REVERT: A  259 ASP cc_start: 0.7244 (p0) cc_final: 0.6740 (p0)
REVERT: A  494 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7705 (tp-100)
REVERT: A  500 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6682 (m-80)
REVERT: C  236 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8734 (p90)
REVERT: C  259 ASP cc_start: 0.7267 (p0) cc_final: 0.6857 (p0)
REVERT: C  321 ASN cc_start: 0.8866 (m-40) cc_final: 0.8598 (m-40)
REVERT: C  394 MET cc_start: 0.7806 (mmt) cc_final: 0.7337 (mmt)
REVERT: D  259 ASP cc_start: 0.7273 (p0) cc_final: 0.6824 (p0)
REVERT: D  321 ASN cc_start: 0.8863 (m-40) cc_final: 0.8586 (m-40)
  outliers start: 52
  outliers final: 28
  residues processed: 181
  average time/residue: 0.2510
  time to fit residues: 72.0328
Evaluate side-chains
  172 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 1.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 159 optimal weight:    9.9990
   chunk 186 optimal weight:    0.0270
   chunk 101 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 127 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 148 optimal weight:    5.9990
   chunk 181 optimal weight:    0.8980
   overall best weight:    2.1442

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

Flipped N/Q/H residues before XYZ refinement:
C 471 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.088711 restraints weight = 25974.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.091403 restraints weight = 16108.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.093162 restraints weight = 11972.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  16892  Z= 0.162
  Angle     :  0.560  11.979  23040  Z= 0.281
  Chirality :  0.044   0.134   2328
  Planarity :  0.004   0.050   3052
  Dihedral  :  7.715  87.523   2252
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 10.92 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.18), residues: 1980
  helix:  1.30 (0.20), residues: 684
  sheet:  0.31 (0.29), residues: 272
  loop : -1.17 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 183 
 HIS   0.004   0.001   HIS B 235 
 PHE   0.022   0.002   PHE C 100 
 TYR   0.014   0.001   TYR A 489 
 ARG   0.002   0.000   ARG A 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  647)
  hydrogen bonds       : angle       5.08510 ( 1833)
  covalent geometry    : bond        0.00416 (16888)
  covalent geometry    : angle       0.56016 (23040)
  Misc. bond           : bond        0.03703 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 156
  time to evaluate  : 1.686 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7188 (p0) cc_final: 0.6809 (p0)
REVERT: B  321 ASN cc_start: 0.8846 (m-40) cc_final: 0.8577 (m-40)
REVERT: B  500 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6661 (m-80)
REVERT: A  259 ASP cc_start: 0.7189 (p0) cc_final: 0.6841 (p0)
REVERT: A  394 MET cc_start: 0.7900 (mmm) cc_final: 0.7529 (mmm)
REVERT: C  259 ASP cc_start: 0.7245 (p0) cc_final: 0.6826 (p0)
REVERT: C  321 ASN cc_start: 0.8870 (m-40) cc_final: 0.8602 (m-40)
REVERT: C  394 MET cc_start: 0.7603 (mmt) cc_final: 0.7122 (mmt)
REVERT: C  500 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6715 (m-80)
REVERT: D  259 ASP cc_start: 0.7228 (p0) cc_final: 0.6811 (p0)
REVERT: D  394 MET cc_start: 0.6756 (ttt) cc_final: 0.6548 (ttp)
REVERT: D  494 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7622 (tp-100)
REVERT: D  500 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6781 (m-80)
  outliers start: 47
  outliers final: 32
  residues processed: 183
  average time/residue: 0.2691
  time to fit residues: 77.6235
Evaluate side-chains
  182 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 147
  time to evaluate  : 1.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  497 LEU
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 138 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 123 optimal weight:    9.9990
   chunk 134 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 144 optimal weight:   10.0000
   chunk 194 optimal weight:    5.9990
   chunk 145 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  33 ASN
A 211 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
C 471 GLN
D  33 ASN
** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.085855 restraints weight = 25906.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.088394 restraints weight = 16050.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.090141 restraints weight = 12023.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  16892  Z= 0.179
  Angle     :  0.569  10.155  23040  Z= 0.286
  Chirality :  0.044   0.134   2328
  Planarity :  0.004   0.051   3052
  Dihedral  :  7.724  86.111   2252
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 11.68 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.19), residues: 1980
  helix:  1.36 (0.20), residues: 684
  sheet:  0.38 (0.30), residues: 272
  loop : -1.17 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 183 
 HIS   0.004   0.001   HIS C 362 
 PHE   0.021   0.002   PHE B 100 
 TYR   0.014   0.001   TYR D 489 
 ARG   0.003   0.000   ARG A 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03921 (  647)
  hydrogen bonds       : angle       5.10368 ( 1833)
  covalent geometry    : bond        0.00456 (16888)
  covalent geometry    : angle       0.56882 (23040)
  Misc. bond           : bond        0.04630 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 160
  time to evaluate  : 1.709 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7233 (p0) cc_final: 0.6822 (p0)
REVERT: B  321 ASN cc_start: 0.8850 (m-40) cc_final: 0.8596 (m-40)
REVERT: A  259 ASP cc_start: 0.7187 (p0) cc_final: 0.6827 (p0)
REVERT: A  500 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.6649 (m-80)
REVERT: C  259 ASP cc_start: 0.7281 (p0) cc_final: 0.6846 (p0)
REVERT: C  321 ASN cc_start: 0.8868 (m-40) cc_final: 0.8595 (m-40)
REVERT: C  394 MET cc_start: 0.7641 (mmt) cc_final: 0.6860 (mmm)
REVERT: C  500 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6724 (m-80)
REVERT: D  259 ASP cc_start: 0.7270 (p0) cc_final: 0.6840 (p0)
REVERT: D  500 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6704 (m-80)
  outliers start: 46
  outliers final: 35
  residues processed: 186
  average time/residue: 0.2549
  time to fit residues: 73.7193
Evaluate side-chains
  185 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 147
  time to evaluate  : 1.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 163 optimal weight:    0.8980
   chunk 195 optimal weight:    2.9990
   chunk 145 optimal weight:    5.9990
   chunk 148 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 152 optimal weight:    0.9990
   chunk 100 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0970
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B  33 ASN
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  33 ASN
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
D  33 ASN
** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.087611 restraints weight = 25796.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.090304 restraints weight = 15915.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.092068 restraints weight = 11803.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16892  Z= 0.115
  Angle     :  0.540   9.305  23040  Z= 0.271
  Chirality :  0.042   0.135   2328
  Planarity :  0.004   0.049   3052
  Dihedral  :  7.524  84.805   2252
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.09 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.19), residues: 1980
  helix:  1.39 (0.20), residues: 684
  sheet:  0.52 (0.30), residues: 272
  loop : -1.10 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 183 
 HIS   0.004   0.001   HIS A 235 
 PHE   0.022   0.001   PHE C 132 
 TYR   0.012   0.001   TYR A 489 
 ARG   0.002   0.000   ARG A 458 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  647)
  hydrogen bonds       : angle       4.97501 ( 1833)
  covalent geometry    : bond        0.00294 (16888)
  covalent geometry    : angle       0.54023 (23040)
  Misc. bond           : bond        0.00384 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 154
  time to evaluate  : 1.711 
Fit side-chains
   revert: symmetry clash
REVERT: B  259 ASP cc_start: 0.7207 (p0) cc_final: 0.6785 (p0)
REVERT: B  321 ASN cc_start: 0.8827 (m-40) cc_final: 0.8542 (m-40)
REVERT: B  500 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6610 (m-80)
REVERT: A  259 ASP cc_start: 0.7162 (p0) cc_final: 0.6683 (p0)
REVERT: A  500 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6680 (m-80)
REVERT: C  259 ASP cc_start: 0.7266 (p0) cc_final: 0.6832 (p0)
REVERT: C  321 ASN cc_start: 0.8844 (m-40) cc_final: 0.8563 (m-40)
REVERT: C  494 GLN cc_start: 0.8129 (tp40) cc_final: 0.7835 (tp-100)
REVERT: C  500 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6701 (m-80)
REVERT: D   33 ASN cc_start: 0.8169 (m-40) cc_final: 0.7951 (m110)
REVERT: D  259 ASP cc_start: 0.7100 (p0) cc_final: 0.6694 (p0)
REVERT: D  494 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7669 (tp-100)
REVERT: D  500 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6601 (m-80)
  outliers start: 48
  outliers final: 34
  residues processed: 183
  average time/residue: 0.3189
  time to fit residues: 91.5865
Evaluate side-chains
  184 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 2.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  497 LEU
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   chunk 148 optimal weight:    0.2980
   chunk 25 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 147 optimal weight:    6.9990
   chunk 183 optimal weight:    2.9990
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  33 ASN
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.085962 restraints weight = 25802.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.088600 restraints weight = 16018.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.090277 restraints weight = 11957.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  16892  Z= 0.171
  Angle     :  0.566   8.904  23040  Z= 0.286
  Chirality :  0.044   0.136   2328
  Planarity :  0.004   0.052   3052
  Dihedral  :  7.624  83.531   2252
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.68 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.19), residues: 1980
  helix:  1.35 (0.20), residues: 692
  sheet:  0.53 (0.30), residues: 272
  loop : -1.09 (0.18), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 183 
 HIS   0.004   0.001   HIS B 362 
 PHE   0.021   0.002   PHE A 132 
 TYR   0.013   0.001   TYR A 236 
 ARG   0.002   0.000   ARG A 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03801 (  647)
  hydrogen bonds       : angle       5.03987 ( 1833)
  covalent geometry    : bond        0.00437 (16888)
  covalent geometry    : angle       0.56555 (23040)
  Misc. bond           : bond        0.04384 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 155
  time to evaluate  : 3.230 
Fit side-chains
   revert: symmetry clash
REVERT: B  259 ASP cc_start: 0.7220 (p0) cc_final: 0.6803 (p0)
REVERT: B  321 ASN cc_start: 0.8836 (m-40) cc_final: 0.8559 (m-40)
REVERT: B  500 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6672 (m-80)
REVERT: A  259 ASP cc_start: 0.7169 (p0) cc_final: 0.6832 (p0)
REVERT: A  500 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6674 (m-80)
REVERT: C   33 ASN cc_start: 0.8322 (m-40) cc_final: 0.8109 (m110)
REVERT: C  259 ASP cc_start: 0.7260 (p0) cc_final: 0.6837 (p0)
REVERT: C  321 ASN cc_start: 0.8887 (m-40) cc_final: 0.8619 (m-40)
REVERT: C  500 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6654 (m-80)
REVERT: D  259 ASP cc_start: 0.7101 (p0) cc_final: 0.6686 (p0)
REVERT: D  500 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6753 (m-80)
  outliers start: 46
  outliers final: 37
  residues processed: 184
  average time/residue: 0.3037
  time to fit residues: 89.2263
Evaluate side-chains
  194 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 153
  time to evaluate  : 1.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  440 VAL
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  497 LEU
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 179 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 137 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 79 optimal weight:    0.3980
   chunk 148 optimal weight:    4.9990
   chunk 159 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 107 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  33 ASN
** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.112448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.087924 restraints weight = 25763.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.090563 restraints weight = 15968.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.092309 restraints weight = 11917.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  16892  Z= 0.118
  Angle     :  0.546   8.575  23040  Z= 0.275
  Chirality :  0.042   0.136   2328
  Planarity :  0.004   0.049   3052
  Dihedral  :  7.438  81.906   2252
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.55 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.19), residues: 1980
  helix:  1.42 (0.20), residues: 692
  sheet:  0.57 (0.30), residues: 272
  loop : -0.99 (0.19), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 183 
 HIS   0.004   0.001   HIS D 235 
 PHE   0.019   0.001   PHE D 100 
 TYR   0.011   0.001   TYR A 489 
 ARG   0.002   0.000   ARG C 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  647)
  hydrogen bonds       : angle       4.95195 ( 1833)
  covalent geometry    : bond        0.00301 (16888)
  covalent geometry    : angle       0.54579 (23040)
  Misc. bond           : bond        0.00660 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 156
  time to evaluate  : 2.036 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7052 (p0) cc_final: 0.6637 (p0)
REVERT: B  321 ASN cc_start: 0.8827 (m-40) cc_final: 0.8539 (m-40)
REVERT: B  500 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6640 (m-80)
REVERT: A  259 ASP cc_start: 0.7155 (p0) cc_final: 0.6662 (p0)
REVERT: A  500 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.6673 (m-80)
REVERT: C  259 ASP cc_start: 0.7085 (p0) cc_final: 0.6660 (p0)
REVERT: C  321 ASN cc_start: 0.8846 (m-40) cc_final: 0.8572 (m-40)
REVERT: C  500 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6672 (m-80)
REVERT: D  259 ASP cc_start: 0.7048 (p0) cc_final: 0.6629 (p0)
REVERT: D  500 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6671 (m-80)
  outliers start: 40
  outliers final: 34
  residues processed: 181
  average time/residue: 0.3399
  time to fit residues: 95.8942
Evaluate side-chains
  182 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 144
  time to evaluate  : 3.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 171 optimal weight:    0.4980
   chunk 101 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 172 optimal weight:    1.9990
   chunk 168 optimal weight:    7.9990
   chunk 9 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 103 optimal weight:    0.0670
   chunk 178 optimal weight:    7.9990
   overall best weight:    2.3124

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

Flipped N/Q/H residues before XYZ refinement:
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.086003 restraints weight = 25965.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.088615 restraints weight = 16065.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.090369 restraints weight = 11995.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  16892  Z= 0.176
  Angle     :  0.581   8.598  23040  Z= 0.295
  Chirality :  0.044   0.143   2328
  Planarity :  0.004   0.051   3052
  Dihedral  :  7.575  80.289   2252
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.96 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.19), residues: 1980
  helix:  1.39 (0.20), residues: 692
  sheet:  0.47 (0.30), residues: 272
  loop : -1.05 (0.19), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 183 
 HIS   0.004   0.001   HIS B 362 
 PHE   0.019   0.002   PHE C 100 
 TYR   0.017   0.002   TYR B 447 
 ARG   0.003   0.000   ARG D 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03797 (  647)
  hydrogen bonds       : angle       5.07811 ( 1833)
  covalent geometry    : bond        0.00450 (16888)
  covalent geometry    : angle       0.58123 (23040)
  Misc. bond           : bond        0.04727 (    4)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 152
  time to evaluate  : 1.889 
Fit side-chains
REVERT: B  259 ASP cc_start: 0.7131 (p0) cc_final: 0.6711 (p0)
REVERT: B  321 ASN cc_start: 0.8838 (m-40) cc_final: 0.8558 (m-40)
REVERT: B  500 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6616 (m-80)
REVERT: A  259 ASP cc_start: 0.7189 (p0) cc_final: 0.6714 (p0)
REVERT: A  500 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6711 (m-80)
REVERT: C  259 ASP cc_start: 0.7165 (p0) cc_final: 0.6742 (p0)
REVERT: C  321 ASN cc_start: 0.8868 (m-40) cc_final: 0.8599 (m-40)
REVERT: C  500 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6702 (m-80)
REVERT: D  259 ASP cc_start: 0.7130 (p0) cc_final: 0.6702 (p0)
REVERT: D  500 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6791 (m-80)
  outliers start: 39
  outliers final: 35
  residues processed: 176
  average time/residue: 0.2581
  time to fit residues: 70.9041
Evaluate side-chains
  190 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 151
  time to evaluate  : 1.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  202 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  500 TYR
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  198 PHE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain C residue  500 TYR
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  198 PHE
Chi-restraints excluded: chain D residue  202 ASP
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  383 VAL
Chi-restraints excluded: chain D residue  423 ILE
Chi-restraints excluded: chain D residue  440 VAL
Chi-restraints excluded: chain D residue  450 VAL
Chi-restraints excluded: chain D residue  497 LEU
Chi-restraints excluded: chain D residue  500 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 118 optimal weight:    8.9990
   chunk 28 optimal weight:    0.4980
   chunk 70 optimal weight:    9.9990
   chunk 181 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 86 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   chunk 113 optimal weight:    0.8980
   chunk 177 optimal weight:    0.0770
   chunk 9 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.2540

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

Flipped N/Q/H residues before XYZ refinement:
** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 398 GLN
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.112705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.087903 restraints weight = 25775.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.090623 restraints weight = 15857.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.092386 restraints weight = 11800.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  16892  Z= 0.120
  Angle     :  0.548   8.384  23040  Z= 0.275
  Chirality :  0.042   0.149   2328
  Planarity :  0.004   0.050   3052
  Dihedral  :  7.378  78.734   2252
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.02 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.19), residues: 1980
  helix:  1.47 (0.20), residues: 692
  sheet:  0.50 (0.30), residues: 272
  loop : -0.96 (0.19), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 183 
 HIS   0.004   0.001   HIS D 364 
 PHE   0.018   0.001   PHE C 100 
 TYR   0.018   0.001   TYR D 447 
 ARG   0.003   0.000   ARG D 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03348 (  647)
  hydrogen bonds       : angle       4.96444 ( 1833)
  covalent geometry    : bond        0.00308 (16888)
  covalent geometry    : angle       0.54780 (23040)
  Misc. bond           : bond        0.00644 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4899.60 seconds
wall clock time: 88 minutes 56.93 seconds (5336.93 seconds total)