Starting phenix.real_space_refine
on Fri Mar 14 07:10:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ave_7009/03_2025/6ave_7009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ave_7009/03_2025/6ave_7009.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/6ave_7009/03_2025/6ave_7009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ave_7009/03_2025/6ave_7009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ave_7009/03_2025/6ave_7009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ave_7009/03_2025/6ave_7009.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=   0.031 sd=   1.102
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      81      5.16       5
     C    6204      2.51       5
     N    1581      2.21       5
     O    1791      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9657
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3191
          Classifications: {'peptide': 424}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 403}
          Unresolved non-hydrogen bonds: 216
          Unresolved non-hydrogen angles: 269
          Unresolved non-hydrogen dihedrals: 171
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 135
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 6.33, per 1000 atoms: 0.66
  Number of scatterers: 9657
  At special positions: 0
  Unit cell: (95.68, 98.8, 128.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      81     16.00
     O    1791      8.00
     N    1581      7.00
     C    6204      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  94 " - pdb=" SG  CYS A 195 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 173 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 309 " - pdb=" SG  CYS A 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 195 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 195 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 173 " - pdb=" SG  CYS C 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 173 " - pdb=" SG  CYS B 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 309 " - pdb=" SG  CYS C 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 309 " - pdb=" SG  CYS B 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 313 " - pdb=" SG  CYS C 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 322 " - pdb=" SG  CYS C 344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 322 " - pdb=" SG  CYS B 344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 324 " - pdb=" SG  CYS C 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 324 " - pdb=" SG  CYS B 336 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 394 "
      " NAG A 602 " - " ASN A 367 "
      " NAG B 601 " - " ASN B 394 "
      " NAG B 602 " - " ASN B 367 "
      " NAG C 601 " - " ASN C 394 "
      " NAG C 602 " - " ASN C 367 "
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2382

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 12 sheets defined
      40.2% alpha, 25.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 70
    Processing helix  chain 'A' and resid 105 through 113
    Processing helix  chain 'A' and resid 132 through 143
      removed outlier: 3.712A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 162
      removed outlier: 3.733A  pdb=" N   PHE A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.522A  pdb=" N   TYR A 230 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 263
    Processing helix  chain 'A' and resid 305 through 323
      removed outlier: 3.895A  pdb=" N   ASN A 323 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 344
      removed outlier: 3.728A  pdb=" N   LYS A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 355
    Processing helix  chain 'A' and resid 356 through 360
      removed outlier: 3.814A  pdb=" N   CYS A 360 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 394
      removed outlier: 3.722A  pdb=" N   LEU A 389 " --> pdb=" O   SER A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 403
    Processing helix  chain 'A' and resid 426 through 441
    Processing helix  chain 'A' and resid 445 through 464
      removed outlier: 3.821A  pdb=" N   LYS A 461 " --> pdb=" O   TYR A 457 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   HIS A 462 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ARG A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 464 " --> pdb=" O   ILE A 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 70
    Processing helix  chain 'B' and resid 105 through 113
    Processing helix  chain 'B' and resid 132 through 143
      removed outlier: 3.712A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 162
      removed outlier: 3.734A  pdb=" N   PHE B 158 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 183
      No H-bonds generated for 'chain 'B' and resid 181 through 183'
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 3.521A  pdb=" N   TYR B 230 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 263
    Processing helix  chain 'B' and resid 305 through 323
      removed outlier: 3.895A  pdb=" N   ASN B 323 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 344
      removed outlier: 3.726A  pdb=" N   LYS B 342 " --> pdb=" O   PRO B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 355
    Processing helix  chain 'B' and resid 356 through 360
      removed outlier: 3.815A  pdb=" N   CYS B 360 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 394
      removed outlier: 3.721A  pdb=" N   LEU B 389 " --> pdb=" O   SER B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 403
    Processing helix  chain 'B' and resid 426 through 441
    Processing helix  chain 'B' and resid 445 through 464
      removed outlier: 3.822A  pdb=" N   LYS B 461 " --> pdb=" O   TYR B 457 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   HIS B 462 " --> pdb=" O   GLU B 458 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ARG B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 70
    Processing helix  chain 'C' and resid 105 through 113
    Processing helix  chain 'C' and resid 132 through 143
      removed outlier: 3.711A  pdb=" N   LEU C 139 " --> pdb=" O   GLN C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 162
      removed outlier: 3.734A  pdb=" N   PHE C 158 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 183
      No H-bonds generated for 'chain 'C' and resid 181 through 183'
    Processing helix  chain 'C' and resid 226 through 230
      removed outlier: 3.522A  pdb=" N   TYR C 230 " --> pdb=" O   GLN C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 263
    Processing helix  chain 'C' and resid 305 through 323
      removed outlier: 3.896A  pdb=" N   ASN C 323 " --> pdb=" O   VAL C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 344
      removed outlier: 3.727A  pdb=" N   LYS C 342 " --> pdb=" O   PRO C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 355
    Processing helix  chain 'C' and resid 356 through 360
      removed outlier: 3.814A  pdb=" N   CYS C 360 " --> pdb=" O   ASN C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 394
      removed outlier: 3.722A  pdb=" N   LEU C 389 " --> pdb=" O   SER C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 396 through 403
    Processing helix  chain 'C' and resid 426 through 441
    Processing helix  chain 'C' and resid 445 through 464
      removed outlier: 3.822A  pdb=" N   LYS C 461 " --> pdb=" O   TYR C 457 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   HIS C 462 " --> pdb=" O   GLU C 458 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ARG C 463 " --> pdb=" O   VAL C 459 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU C 464 " --> pdb=" O   ILE C 460 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN A 415 " --> pdb=" O   CYS A 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU A 278 " --> pdb=" O   ASN A 415 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE A 270 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER A 172 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ASP A 224 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   LEU A 170 " --> pdb=" O   ASP A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN A 415 " --> pdb=" O   CYS A 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU A 278 " --> pdb=" O   ASN A 415 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87
      removed outlier: 3.670A  pdb=" N   LEU A  86 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189
      removed outlier: 7.102A  pdb=" N   LYS A 194 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   ASN A  95 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN B 415 " --> pdb=" O   CYS B 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU B 278 " --> pdb=" O   ASN B 415 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE B 270 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER B 172 " --> pdb=" O   MET B 222 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ASP B 224 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   LEU B 170 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN B 415 " --> pdb=" O   CYS B 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU B 278 " --> pdb=" O   ASN B 415 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 87
      removed outlier: 3.670A  pdb=" N   LEU B  86 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 189
      removed outlier: 7.102A  pdb=" N   LYS B 194 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ASN B  95 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN C 415 " --> pdb=" O   CYS C 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU C 278 " --> pdb=" O   ASN C 415 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE C 270 " --> pdb=" O   ILE C 404 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER C 172 " --> pdb=" O   MET C 222 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ASP C 224 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   LEU C 170 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN C 415 " --> pdb=" O   CYS C 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU C 278 " --> pdb=" O   ASN C 415 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 86 through 87
      removed outlier: 3.670A  pdb=" N   LEU C  86 " --> pdb=" O   THR C 210 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 185 through 189
      removed outlier: 7.102A  pdb=" N   LYS C 194 " --> pdb=" O   ASN C  95 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ASN C  95 " --> pdb=" O   LYS C 194 " (cutoff:3.500A)

    523 hydrogen bonds defined for protein.
    1515 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.89

  Time building geometry restraints manager: 2.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3120
        1.35 -     1.47: 2594
        1.47 -     1.60: 4063
        1.60 -     1.73: 0
        1.73 -     1.85: 111
  Bond restraints: 9888
  Sorted by residual:
  bond pdb=" CG1 ILE C 259 "
       pdb=" CD1 ILE C 259 "
    ideal  model  delta    sigma   weight residual
    1.513  1.428  0.085 3.90e-02 6.57e+02 4.76e+00
  bond pdb=" CG1 ILE A 259 "
       pdb=" CD1 ILE A 259 "
    ideal  model  delta    sigma   weight residual
    1.513  1.429  0.084 3.90e-02 6.57e+02 4.68e+00
  bond pdb=" CG1 ILE B 259 "
       pdb=" CD1 ILE B 259 "
    ideal  model  delta    sigma   weight residual
    1.513  1.429  0.084 3.90e-02 6.57e+02 4.66e+00
  bond pdb=" C   ASN C 367 "
       pdb=" N   VAL C 368 "
    ideal  model  delta    sigma   weight residual
    1.329  1.286  0.044 2.19e-02 2.09e+03 3.97e+00
  bond pdb=" C   ASN A 367 "
       pdb=" N   VAL A 368 "
    ideal  model  delta    sigma   weight residual
    1.329  1.287  0.043 2.19e-02 2.09e+03 3.78e+00
  ... (remaining 9883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 12845
        1.86 -     3.72: 523
        3.72 -     5.58: 72
        5.58 -     7.44: 12
        7.44 -     9.30: 6
  Bond angle restraints: 13458
  Sorted by residual:
  angle pdb=" C   ILE B 380 "
        pdb=" N   PRO B 381 "
        pdb=" CA  PRO B 381 "
      ideal   model   delta    sigma   weight residual
     127.00  135.24   -8.24 2.40e+00 1.74e-01 1.18e+01
  angle pdb=" C   ILE C 380 "
        pdb=" N   PRO C 381 "
        pdb=" CA  PRO C 381 "
      ideal   model   delta    sigma   weight residual
     127.00  135.24   -8.24 2.40e+00 1.74e-01 1.18e+01
  angle pdb=" C   ILE A 380 "
        pdb=" N   PRO A 381 "
        pdb=" CA  PRO A 381 "
      ideal   model   delta    sigma   weight residual
     127.00  135.21   -8.21 2.40e+00 1.74e-01 1.17e+01
  angle pdb=" C   ILE C 380 "
        pdb=" N   PRO C 381 "
        pdb=" CD  PRO C 381 "
      ideal   model   delta    sigma   weight residual
     120.60  113.64    6.96 2.20e+00 2.07e-01 1.00e+01
  angle pdb=" C   ILE B 380 "
        pdb=" N   PRO B 381 "
        pdb=" CD  PRO B 381 "
      ideal   model   delta    sigma   weight residual
     120.60  113.64    6.96 2.20e+00 2.07e-01 1.00e+01
  ... (remaining 13453 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.16: 5680
       15.16 -    30.32: 236
       30.32 -    45.48: 45
       45.48 -    60.64: 18
       60.64 -    75.80: 6
  Dihedral angle restraints: 5985
    sinusoidal: 2268
      harmonic: 3717
  Sorted by residual:
  dihedral pdb=" CA  THR B 337 "
           pdb=" C   THR B 337 "
           pdb=" N   PRO B 338 "
           pdb=" CA  PRO B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.40  -28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  THR C 337 "
           pdb=" C   THR C 337 "
           pdb=" N   PRO C 338 "
           pdb=" CA  PRO C 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.42  -28.58     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  THR A 337 "
           pdb=" C   THR A 337 "
           pdb=" N   PRO A 338 "
           pdb=" CA  PRO A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.44  -28.56     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 5982 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.189: 1500
       0.189 -    0.378: 9
       0.378 -    0.567: 0
       0.567 -    0.756: 0
       0.756 -    0.945: 3
  Chirality restraints: 1512
  Sorted by residual:
  chirality pdb=" C1  NAG A 602 "
            pdb=" ND2 ASN A 367 "
            pdb=" C2  NAG A 602 "
            pdb=" O5  NAG A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.45   -0.95 2.00e-01 2.50e+01 2.23e+01
  chirality pdb=" C1  NAG B 602 "
            pdb=" ND2 ASN B 367 "
            pdb=" C2  NAG B 602 "
            pdb=" O5  NAG B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.46   -0.94 2.00e-01 2.50e+01 2.20e+01
  chirality pdb=" C1  NAG C 602 "
            pdb=" ND2 ASN C 367 "
            pdb=" C2  NAG C 602 "
            pdb=" O5  NAG C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.47   -0.93 2.00e-01 2.50e+01 2.18e+01
  ... (remaining 1509 not shown)

  Planarity restraints: 1755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 107 "   -0.011 2.00e-02 2.50e+03   2.30e-02 5.27e+00
        pdb=" C   ASN C 107 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ASN C 107 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASP C 108 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 107 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.26e+00
        pdb=" C   ASN B 107 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ASN B 107 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASP B 108 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 107 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.11e+00
        pdb=" C   ASN A 107 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASN A 107 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A 108 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1752 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3161
        2.82 -     3.34: 8653
        3.34 -     3.86: 15709
        3.86 -     4.38: 18193
        4.38 -     4.90: 30272
  Nonbonded interactions: 75988
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 215 "
            pdb=" OD2 ASP C 408 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OG1 THR B 215 "
            pdb=" OD2 ASP B 408 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG1 THR A 215 "
            pdb=" OD2 ASP A 408 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" NE2 HIS B 111 "
            pdb=" O   LYS B 151 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NE2 HIS C 111 "
            pdb=" O   LYS C 151 "
     model   vdw
     2.308 3.120
  ... (remaining 75983 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.570
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.085   9888  Z= 0.518
  Angle     :  0.878   9.296  13458  Z= 0.474
  Chirality :  0.068   0.945   1512
  Planarity :  0.005   0.040   1749
  Dihedral  :  9.624  75.799   3540
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.23 (0.20), residues: 1266
  helix: -2.76 (0.17), residues: 432
  sheet: -1.68 (0.28), residues: 279
  loop : -1.67 (0.24), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  47 
 HIS   0.010   0.002   HIS C 251 
 PHE   0.023   0.003   PHE B 453 
 TYR   0.030   0.003   TYR C 393 
 ARG   0.008   0.001   ARG B 325 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 432
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.8838 (t80) cc_final: 0.8329 (t80)
REVERT: A  198 PHE cc_start: 0.8663 (t80) cc_final: 0.8453 (t80)
REVERT: A  217 ASN cc_start: 0.7848 (m110) cc_final: 0.6891 (t0)
REVERT: A  247 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8240 (ttmm)
REVERT: A  249 GLN cc_start: 0.7706 (tm-30) cc_final: 0.6784 (tm-30)
REVERT: A  278 GLU cc_start: 0.8390 (tt0) cc_final: 0.7708 (tt0)
REVERT: A  309 CYS cc_start: 0.6570 (t) cc_final: 0.6331 (t)
REVERT: A  323 ASN cc_start: 0.8097 (m-40) cc_final: 0.7864 (m110)
REVERT: A  341 TYR cc_start: 0.7407 (m-10) cc_final: 0.7178 (m-10)
REVERT: A  350 ASP cc_start: 0.8450 (m-30) cc_final: 0.8023 (m-30)
REVERT: A  379 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7976 (tptt)
REVERT: A  420 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7478 (mt-10)
REVERT: A  454 ASP cc_start: 0.8266 (m-30) cc_final: 0.7878 (m-30)
REVERT: B  217 ASN cc_start: 0.7801 (m110) cc_final: 0.6800 (t0)
REVERT: B  249 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7520 (tt0)
REVERT: B  262 LEU cc_start: 0.9124 (mt) cc_final: 0.8839 (mp)
REVERT: B  278 GLU cc_start: 0.8303 (tt0) cc_final: 0.7838 (tt0)
REVERT: B  280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8114 (mtt180)
REVERT: B  309 CYS cc_start: 0.6657 (t) cc_final: 0.6456 (t)
REVERT: B  350 ASP cc_start: 0.8312 (m-30) cc_final: 0.7897 (m-30)
REVERT: B  420 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7388 (mt-10)
REVERT: C   61 VAL cc_start: 0.8623 (m) cc_final: 0.8221 (p)
REVERT: C  220 GLU cc_start: 0.7506 (tt0) cc_final: 0.7157 (tt0)
REVERT: C  247 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8088 (ttmm)
REVERT: C  278 GLU cc_start: 0.8318 (tt0) cc_final: 0.7666 (tt0)
REVERT: C  280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7560 (mtt180)
REVERT: C  309 CYS cc_start: 0.6709 (t) cc_final: 0.6445 (t)
REVERT: C  341 TYR cc_start: 0.7366 (m-10) cc_final: 0.7072 (m-10)
REVERT: C  350 ASP cc_start: 0.8432 (m-30) cc_final: 0.8061 (m-30)
REVERT: C  373 LYS cc_start: 0.7872 (pttm) cc_final: 0.7580 (mttt)
REVERT: C  379 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7749 (tptp)
REVERT: C  403 ASN cc_start: 0.8128 (m-40) cc_final: 0.7447 (m110)
REVERT: C  420 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7335 (mt-10)
REVERT: C  437 GLN cc_start: 0.8921 (mt0) cc_final: 0.8575 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 432
  average time/residue: 0.2660
  time to fit residues: 151.1683
Evaluate side-chains
  246 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 98 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 114 optimal weight:    0.5980
   overall best weight:    0.8762

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 GLN
A 403 ASN
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 GLN
B 403 ASN
C 249 GLN
C 277 GLN
C 403 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.161675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.138850 restraints weight = 16373.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.142937 restraints weight = 9297.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.145602 restraints weight = 6223.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9888  Z= 0.224
  Angle     :  0.682   8.054  13458  Z= 0.356
  Chirality :  0.048   0.451   1512
  Planarity :  0.005   0.036   1749
  Dihedral  :  6.507  42.107   1500
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 14.79 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.23), residues: 1266
  helix: -0.66 (0.23), residues: 441
  sheet: -1.40 (0.29), residues: 291
  loop : -1.00 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  47 
 HIS   0.008   0.001   HIS C 328 
 PHE   0.022   0.002   PHE B 270 
 TYR   0.015   0.002   TYR C 230 
 ARG   0.009   0.001   ARG B 370 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 282
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.8726 (t80) cc_final: 0.8303 (t80)
REVERT: A  108 ASP cc_start: 0.6686 (m-30) cc_final: 0.6453 (m-30)
REVERT: A  217 ASN cc_start: 0.7506 (m110) cc_final: 0.6874 (t0)
REVERT: A  249 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7749 (tm-30)
REVERT: A  280 ARG cc_start: 0.8537 (mtt180) cc_final: 0.8251 (mtt180)
REVERT: A  309 CYS cc_start: 0.6620 (t) cc_final: 0.6327 (t)
REVERT: A  430 LEU cc_start: 0.9120 (tp) cc_final: 0.8821 (tt)
REVERT: B  217 ASN cc_start: 0.7335 (m110) cc_final: 0.6779 (t0)
REVERT: B  242 PHE cc_start: 0.8609 (m-80) cc_final: 0.8387 (m-80)
REVERT: B  249 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8065 (tm-30)
REVERT: B  278 GLU cc_start: 0.8121 (tt0) cc_final: 0.7921 (tt0)
REVERT: B  309 CYS cc_start: 0.6583 (t) cc_final: 0.6343 (t)
REVERT: B  398 GLN cc_start: 0.8348 (pp30) cc_final: 0.8129 (pp30)
REVERT: C  108 ASP cc_start: 0.6756 (m-30) cc_final: 0.6509 (m-30)
REVERT: C  155 MET cc_start: 0.7979 (mmm) cc_final: 0.7726 (tpt)
REVERT: C  217 ASN cc_start: 0.7330 (m110) cc_final: 0.6227 (t0)
REVERT: C  278 GLU cc_start: 0.8175 (tt0) cc_final: 0.7844 (tt0)
REVERT: C  280 ARG cc_start: 0.8606 (mtt180) cc_final: 0.7918 (mtt180)
REVERT: C  309 CYS cc_start: 0.6705 (t) cc_final: 0.6467 (t)
REVERT: C  403 ASN cc_start: 0.8530 (m110) cc_final: 0.7879 (m110)
  outliers start: 31
  outliers final: 12
  residues processed: 301
  average time/residue: 0.1823
  time to fit residues: 78.7897
Evaluate side-chains
  245 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 233
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  186 LYS
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  329 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 50 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 116 optimal weight:    6.9990
   chunk 99 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
C 227 GLN
C 249 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.153701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.129443 restraints weight = 16644.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.133457 restraints weight = 9418.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136245 restraints weight = 6406.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   9888  Z= 0.464
  Angle     :  0.752   8.520  13458  Z= 0.396
  Chirality :  0.049   0.396   1512
  Planarity :  0.005   0.051   1749
  Dihedral  :  5.956  31.153   1500
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 18.86 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.23), residues: 1266
  helix: -0.29 (0.24), residues: 459
  sheet: -1.64 (0.29), residues: 267
  loop : -0.76 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 234 
 HIS   0.010   0.003   HIS B 111 
 PHE   0.019   0.003   PHE A 270 
 TYR   0.024   0.003   TYR A 110 
 ARG   0.010   0.001   ARG C 370 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 252
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8656 (tp) cc_final: 0.8306 (tt)
REVERT: A  108 ASP cc_start: 0.6862 (m-30) cc_final: 0.6536 (m-30)
REVERT: A  249 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: A  262 LEU cc_start: 0.9265 (mp) cc_final: 0.9033 (mt)
REVERT: A  309 CYS cc_start: 0.6554 (t) cc_final: 0.6253 (t)
REVERT: B   68 TYR cc_start: 0.9181 (t80) cc_final: 0.8876 (t80)
REVERT: B  108 ASP cc_start: 0.6933 (m-30) cc_final: 0.6422 (m-30)
REVERT: B  242 PHE cc_start: 0.8766 (m-80) cc_final: 0.8463 (m-80)
REVERT: B  275 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8408 (p)
REVERT: C   60 LEU cc_start: 0.8724 (tp) cc_final: 0.8399 (tt)
REVERT: C  109 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7409 (tp)
REVERT: C  275 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8345 (p)
REVERT: C  309 CYS cc_start: 0.6800 (t) cc_final: 0.6552 (t)
REVERT: C  420 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6889 (mt-10)
REVERT: C  422 LYS cc_start: 0.9375 (mmtt) cc_final: 0.9138 (mmtt)
  outliers start: 42
  outliers final: 22
  residues processed: 271
  average time/residue: 0.2071
  time to fit residues: 79.0543
Evaluate side-chains
  230 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  448 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0570
   chunk 48 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 118 optimal weight:    1.9990
   chunk 125 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.7502

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 HIS
B 111 HIS
C 111 HIS
C 227 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.158686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.134743 restraints weight = 16536.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138887 restraints weight = 9281.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.141706 restraints weight = 6222.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9888  Z= 0.218
  Angle     :  0.604   8.076  13458  Z= 0.315
  Chirality :  0.044   0.339   1512
  Planarity :  0.004   0.024   1749
  Dihedral  :  5.357  26.568   1500
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.33 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.24), residues: 1266
  helix:  0.33 (0.25), residues: 462
  sheet: -1.37 (0.31), residues: 270
  loop : -0.41 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 111 
 PHE   0.015   0.001   PHE A 270 
 TYR   0.014   0.001   TYR C 457 
 ARG   0.010   0.001   ARG B 370 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 237
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLU cc_start: 0.7046 (pm20) cc_final: 0.6826 (pm20)
REVERT: A  169 MET cc_start: 0.8594 (mtt) cc_final: 0.8249 (ttt)
REVERT: A  249 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8123 (tm-30)
REVERT: A  280 ARG cc_start: 0.8732 (mtt180) cc_final: 0.7931 (mtt180)
REVERT: B   60 LEU cc_start: 0.8573 (tp) cc_final: 0.8312 (tt)
REVERT: B  217 ASN cc_start: 0.7686 (m110) cc_final: 0.6555 (t0)
REVERT: B  249 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8074 (tm-30)
REVERT: B  275 SER cc_start: 0.9047 (m) cc_final: 0.8244 (p)
REVERT: B  309 CYS cc_start: 0.6557 (t) cc_final: 0.6285 (t)
REVERT: B  314 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7093 (mp0)
REVERT: C   60 LEU cc_start: 0.8456 (tp) cc_final: 0.8105 (tt)
REVERT: C  109 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6913 (tp)
REVERT: C  278 GLU cc_start: 0.8295 (tt0) cc_final: 0.7671 (tt0)
REVERT: C  280 ARG cc_start: 0.8826 (mtt180) cc_final: 0.7939 (mtt180)
  outliers start: 28
  outliers final: 15
  residues processed: 255
  average time/residue: 0.1906
  time to fit residues: 70.0747
Evaluate side-chains
  238 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 222
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 63 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 403 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.160736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.136632 restraints weight = 16486.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.140713 restraints weight = 9381.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.143219 restraints weight = 6347.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9888  Z= 0.211
  Angle     :  0.588   8.900  13458  Z= 0.302
  Chirality :  0.043   0.342   1512
  Planarity :  0.004   0.026   1749
  Dihedral  :  4.973  26.396   1500
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.44 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.24), residues: 1266
  helix:  0.88 (0.25), residues: 447
  sheet: -1.10 (0.31), residues: 264
  loop : -0.40 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 234 
 HIS   0.008   0.001   HIS B 328 
 PHE   0.015   0.001   PHE B 270 
 TYR   0.013   0.001   TYR C 457 
 ARG   0.005   0.001   ARG B 370 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 223
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8444 (tp) cc_final: 0.8218 (tt)
REVERT: A   80 GLU cc_start: 0.6948 (pm20) cc_final: 0.6651 (pm20)
REVERT: A  108 ASP cc_start: 0.6500 (m-30) cc_final: 0.6241 (m-30)
REVERT: A  249 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: A  280 ARG cc_start: 0.8727 (mtt180) cc_final: 0.7875 (mtt180)
REVERT: A  341 TYR cc_start: 0.7355 (m-10) cc_final: 0.6907 (m-10)
REVERT: B   68 TYR cc_start: 0.9049 (t80) cc_final: 0.8800 (t80)
REVERT: B  108 ASP cc_start: 0.6461 (m-30) cc_final: 0.5864 (m-30)
REVERT: B  249 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: B  275 SER cc_start: 0.9068 (m) cc_final: 0.8278 (p)
REVERT: B  309 CYS cc_start: 0.6574 (t) cc_final: 0.6275 (t)
REVERT: B  314 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7140 (mp0)
REVERT: B  441 PHE cc_start: 0.8348 (m-80) cc_final: 0.8145 (m-80)
REVERT: C  109 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7017 (tp)
REVERT: C  280 ARG cc_start: 0.8846 (mtt180) cc_final: 0.8207 (mtt180)
REVERT: C  437 GLN cc_start: 0.8750 (mt0) cc_final: 0.8390 (mt0)
  outliers start: 29
  outliers final: 21
  residues processed: 243
  average time/residue: 0.1931
  time to fit residues: 67.4478
Evaluate side-chains
  234 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0970
   chunk 101 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN
B  74 HIS
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.161559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137944 restraints weight = 16482.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.142074 restraints weight = 9217.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.144836 restraints weight = 6165.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9888  Z= 0.174
  Angle     :  0.556   7.831  13458  Z= 0.285
  Chirality :  0.042   0.332   1512
  Planarity :  0.003   0.025   1749
  Dihedral  :  4.682  24.341   1500
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.62 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.25), residues: 1266
  helix:  0.99 (0.25), residues: 459
  sheet: -0.99 (0.32), residues: 270
  loop : -0.19 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  47 
 HIS   0.006   0.001   HIS C 328 
 PHE   0.013   0.001   PHE B 242 
 TYR   0.011   0.001   TYR C 457 
 ARG   0.004   0.000   ARG B 370 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 226
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.6366 (m-30) cc_final: 0.6050 (m-30)
REVERT: A  249 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: A  280 ARG cc_start: 0.8779 (mtt180) cc_final: 0.8005 (mtt180)
REVERT: A  341 TYR cc_start: 0.7373 (m-10) cc_final: 0.6823 (m-10)
REVERT: B  249 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7443 (tm-30)
REVERT: B  275 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8298 (p)
REVERT: B  309 CYS cc_start: 0.6402 (t) cc_final: 0.6104 (t)
REVERT: B  314 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7095 (mp0)
REVERT: C  109 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6906 (tp)
REVERT: C  230 TYR cc_start: 0.8490 (m-80) cc_final: 0.8237 (m-10)
  outliers start: 32
  outliers final: 21
  residues processed: 244
  average time/residue: 0.1835
  time to fit residues: 65.1668
Evaluate side-chains
  247 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 224
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:   20.0000
   chunk 42 optimal weight:    7.9990
   chunk 121 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 51 optimal weight:   20.0000
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 101 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
C 111 HIS
** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.153130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.128213 restraints weight = 16752.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.132242 restraints weight = 9718.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.135014 restraints weight = 6655.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.065   9888  Z= 0.587
  Angle     :  0.785   8.186  13458  Z= 0.407
  Chirality :  0.050   0.321   1512
  Planarity :  0.005   0.056   1749
  Dihedral  :  5.392  27.180   1500
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 21.33 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.24), residues: 1266
  helix:  0.44 (0.25), residues: 459
  sheet: -1.19 (0.32), residues: 264
  loop : -0.50 (0.28), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP A 234 
 HIS   0.013   0.003   HIS C 111 
 PHE   0.023   0.003   PHE B 175 
 TYR   0.022   0.003   TYR C 110 
 ARG   0.004   0.000   ARG B 310 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 204
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.9077 (t80) cc_final: 0.8852 (t80)
REVERT: A  108 ASP cc_start: 0.6932 (m-30) cc_final: 0.6578 (m-30)
REVERT: A  169 MET cc_start: 0.8780 (ttp) cc_final: 0.8515 (ttm)
REVERT: A  249 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8054 (tm-30)
REVERT: B  275 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8419 (p)
REVERT: B  408 ASP cc_start: 0.8493 (t0) cc_final: 0.8263 (t0)
REVERT: C   60 LEU cc_start: 0.8566 (tp) cc_final: 0.8353 (tt)
REVERT: C  109 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7512 (tp)
REVERT: C  275 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8605 (p)
REVERT: C  437 GLN cc_start: 0.8762 (mt0) cc_final: 0.8488 (mt0)
  outliers start: 42
  outliers final: 28
  residues processed: 225
  average time/residue: 0.1822
  time to fit residues: 60.3631
Evaluate side-chains
  227 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 196
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  373 LYS
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  412 GLU
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  400 ILE
Chi-restraints excluded: chain C residue  448 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 101 optimal weight:    0.0870
   chunk 71 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0870
   chunk 43 optimal weight:    7.9990
   chunk 124 optimal weight:    5.9990
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 437 GLN
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.160751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.136906 restraints weight = 16589.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.141081 restraints weight = 9300.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143899 restraints weight = 6203.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.4643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9888  Z= 0.187
  Angle     :  0.609   9.074  13458  Z= 0.310
  Chirality :  0.043   0.317   1512
  Planarity :  0.004   0.036   1749
  Dihedral  :  4.828  21.972   1500
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.15 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.25), residues: 1266
  helix:  0.85 (0.25), residues: 462
  sheet: -0.93 (0.33), residues: 264
  loop : -0.22 (0.29), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  47 
 HIS   0.004   0.001   HIS A 251 
 PHE   0.014   0.001   PHE B 300 
 TYR   0.012   0.001   TYR B 341 
 ARG   0.005   0.001   ARG B  65 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 214
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.6306 (m-30) cc_final: 0.6037 (m-30)
REVERT: A  249 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: A  280 ARG cc_start: 0.8724 (mtt180) cc_final: 0.7946 (mtt180)
REVERT: A  311 ILE cc_start: 0.9073 (tt) cc_final: 0.8766 (mt)
REVERT: A  341 TYR cc_start: 0.7389 (m-10) cc_final: 0.6654 (m-80)
REVERT: B  249 GLN cc_start: 0.8613 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: B  275 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8338 (p)
REVERT: B  280 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8205 (mtt180)
REVERT: C  109 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6937 (tp)
REVERT: C  234 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.7712 (p-90)
REVERT: C  249 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7922 (tt0)
REVERT: C  275 SER cc_start: 0.9059 (m) cc_final: 0.8500 (p)
REVERT: C  278 GLU cc_start: 0.8351 (tt0) cc_final: 0.8086 (tt0)
REVERT: C  437 GLN cc_start: 0.8688 (mt0) cc_final: 0.8465 (mt0)
  outliers start: 28
  outliers final: 18
  residues processed: 228
  average time/residue: 0.1890
  time to fit residues: 62.1432
Evaluate side-chains
  229 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  249 GLN
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 106 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.159884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.135902 restraints weight = 16569.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.140082 restraints weight = 9367.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.142907 restraints weight = 6292.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.4734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9888  Z= 0.226
  Angle     :  0.617   8.835  13458  Z= 0.313
  Chirality :  0.043   0.319   1512
  Planarity :  0.004   0.049   1749
  Dihedral  :  4.704  22.807   1500
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.37 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.25), residues: 1266
  helix:  0.91 (0.26), residues: 465
  sheet: -0.88 (0.33), residues: 264
  loop : -0.12 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 234 
 HIS   0.004   0.001   HIS B 111 
 PHE   0.014   0.001   PHE B 300 
 TYR   0.019   0.001   TYR A 230 
 ARG   0.016   0.001   ARG A 370 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 207
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.6513 (m-30) cc_final: 0.6179 (m-30)
REVERT: A  249 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7934 (tm-30)
REVERT: B  249 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7488 (tm-30)
REVERT: B  275 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8336 (p)
REVERT: B  314 GLU cc_start: 0.7117 (mp0) cc_final: 0.6879 (mp0)
REVERT: C  109 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7038 (tp)
REVERT: C  234 TRP cc_start: 0.8026 (OUTLIER) cc_final: 0.7734 (p-90)
REVERT: C  249 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7955 (tt0)
REVERT: C  275 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8505 (p)
REVERT: C  278 GLU cc_start: 0.8347 (tt0) cc_final: 0.8072 (tt0)
REVERT: C  437 GLN cc_start: 0.8716 (mt0) cc_final: 0.8427 (mt0)
  outliers start: 27
  outliers final: 18
  residues processed: 221
  average time/residue: 0.1784
  time to fit residues: 57.7193
Evaluate side-chains
  226 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  249 GLN
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  422 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 101 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 118 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.156885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.132890 restraints weight = 16800.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.137011 restraints weight = 9485.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.139650 restraints weight = 6361.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.4820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9888  Z= 0.279
  Angle     :  0.639  10.585  13458  Z= 0.323
  Chirality :  0.044   0.316   1512
  Planarity :  0.004   0.060   1749
  Dihedral  :  4.757  22.509   1500
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 22.94 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1266
  helix:  0.91 (0.25), residues: 465
  sheet: -0.95 (0.33), residues: 264
  loop : -0.11 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 234 
 HIS   0.005   0.001   HIS B 111 
 PHE   0.015   0.001   PHE B 300 
 TYR   0.019   0.002   TYR A 230 
 ARG   0.014   0.001   ARG A 370 

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 209
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.6554 (m-30) cc_final: 0.6302 (m-30)
REVERT: A  249 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: A  341 TYR cc_start: 0.7272 (m-10) cc_final: 0.6885 (m-10)
REVERT: B  220 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6992 (mt-10)
REVERT: B  249 GLN cc_start: 0.8627 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: B  275 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8347 (p)
REVERT: B  314 GLU cc_start: 0.7183 (mp0) cc_final: 0.6870 (mp0)
REVERT: C  109 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7104 (tp)
REVERT: C  234 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7753 (p-90)
REVERT: C  249 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7957 (tt0)
REVERT: C  275 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8564 (p)
REVERT: C  278 GLU cc_start: 0.8374 (tt0) cc_final: 0.8090 (tt0)
REVERT: C  326 MET cc_start: 0.7077 (mmt) cc_final: 0.6807 (mmm)
  outliers start: 31
  outliers final: 20
  residues processed: 226
  average time/residue: 0.1805
  time to fit residues: 60.0955
Evaluate side-chains
  235 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 210
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  249 GLN
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  412 GLU
Chi-restraints excluded: chain C residue  422 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 119 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 109 optimal weight:    0.6980
   chunk 94 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 101 optimal weight:   10.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS
** C 403 ASN ** 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 = 0.3885 r_free = 0.3885 target = 0.160880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.137564 restraints weight = 16681.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.141543 restraints weight = 9324.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.144271 restraints weight = 6264.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.4901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9888  Z= 0.186
  Angle     :  0.611  10.442  13458  Z= 0.308
  Chirality :  0.043   0.314   1512
  Planarity :  0.004   0.050   1749
  Dihedral  :  4.553  21.050   1500
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 22.94 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1266
  helix:  1.00 (0.25), residues: 465
  sheet: -0.82 (0.33), residues: 264
  loop : -0.01 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 234 
 HIS   0.003   0.001   HIS A 251 
 PHE   0.016   0.001   PHE B 300 
 TYR   0.010   0.001   TYR A 230 
 ARG   0.014   0.001   ARG A 370 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3038.84 seconds
wall clock time: 53 minutes 58.03 seconds (3238.03 seconds total)