Starting phenix.real_space_refine
on Fri Sep 11 13:53:24 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6ave_7009/09_2026/6ave_7009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ave_7009/09_2026/6ave_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6ave_7009/09_2026/6ave_7009.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6ave_7009/09_2026/6ave_7009.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ave_7009/09_2026/6ave_7009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ave_7009/09_2026/6ave_7009.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ave_7009/09_2026/6ave_7009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ave_7009/09_2026/6ave_7009.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.031 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 2, 'GLU:plan': 13, 'ASP:plan': 7, 'GLN:plan1': 2, 'PHE:plan': 1}
          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 chiralities: 2
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.03, per 1000 atoms: 0.21
  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 B  94 " - pdb=" SG  CYS B 195 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 195 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 173 " - pdb=" SG  CYS B 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 173 " - pdb=" SG  CYS C 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 309 " - pdb=" SG  CYS B 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 309 " - pdb=" SG  CYS C 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 313 " - pdb=" SG  CYS C 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 322 " - pdb=" SG  CYS B 344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 322 " - pdb=" SG  CYS C 344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 324 " - pdb=" SG  CYS B 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 324 " - pdb=" SG  CYS C 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: 0.76
  Conformation dependent library (CDL) restraints added in 357.7 milliseconds
  

  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: 0.22
  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: 1.27

  Time building geometry restraints manager: 1.03 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: 5570
       15.16 -    30.32: 226
       30.32 -    45.48: 45
       45.48 -    60.64: 12
       60.64 -    75.80: 6
  Dihedral angle restraints: 5859
    sinusoidal: 2142
      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 5856 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             0.470
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.720
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
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   9915  Z= 0.376
  Angle     :  0.927  13.827  13518  Z= 0.485
  Chirality :  0.068   0.945   1512
  Planarity :  0.005   0.040   1749
  Dihedral  :  9.439  75.799   3414
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.008   0.001   ARG B 325 
 TYR   0.030   0.003   TYR C 393 
 PHE   0.023   0.003   PHE B 453 
 TRP   0.009   0.002   TRP B  47 
 HIS   0.010   0.002   HIS C 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00791 /  0.38 ( 9888)
  covalent geometry    : angle       0.87754 /  0.47 (13458)
  SS BOND              : bond        0.00706 /  0.46 (   21)
  SS BOND              : angle       2.05867 /  1.56 (   42)
  hydrogen bonds       : bond        0.12258 /  8.07 (  484)
  hydrogen bonds       : angle       8.77609 /  6.10 ( 1515)
  link_NAG-ASN         : bond        0.00781 /  0.49 (    6)
  link_NAG-ASN         : angle       7.75319 /  6.39 (   18)

*********************** 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  : 0.357 
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: 0.6890 (t0)
REVERT: A  247 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8241 (ttmm)
REVERT: A  249 GLN cc_start: 0.7707 (tm-30) cc_final: 0.6781 (tm-30)
REVERT: A  278 GLU cc_start: 0.8390 (tt0) cc_final: 0.7743 (tt0)
REVERT: A  309 CYS cc_start: 0.6570 (t) cc_final: 0.6333 (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: 0.8024 (m-30)
REVERT: A  379 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7973 (tptt)
REVERT: A  420 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7476 (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: 0.7521 (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: 0.7839 (tt0)
REVERT: B  280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8115 (mtt180)
REVERT: B  309 CYS cc_start: 0.6656 (t) cc_final: 0.6456 (t)
REVERT: B  350 ASP cc_start: 0.8312 (m-30) cc_final: 0.7896 (m-30)
REVERT: B  420 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7386 (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: 0.7158 (tt0)
REVERT: C  247 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8088 (ttmm)
REVERT: C  278 GLU cc_start: 0.8318 (tt0) cc_final: 0.7436 (tt0)
REVERT: C  280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7557 (mtt180)
REVERT: C  309 CYS cc_start: 0.6709 (t) cc_final: 0.6437 (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: 0.7579 (mttt)
REVERT: C  379 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7748 (tptp)
REVERT: C  403 ASN cc_start: 0.8128 (m-40) cc_final: 0.7444 (m110)
REVERT: C  420 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7336 (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: 0.1015
  time to fit residues: 58.7066
Evaluate side-chains
  245 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.0370
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0970
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 123 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.4656

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  97 ASN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 GLN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 GLN
B 403 ASN
C 249 GLN
C 277 GLN
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.164963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.142288 restraints weight = 16543.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.146284 restraints weight = 9342.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.149060 restraints weight = 6256.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.150748 restraints weight = 4699.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.152014 restraints weight = 3878.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9915  Z= 0.146
  Angle     :  0.715  10.998  13518  Z= 0.362
  Chirality :  0.047   0.402   1512
  Planarity :  0.005   0.034   1749
  Dihedral  :  5.648  26.285   1374
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 14.58 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.22), residues: 1266
  helix: -0.61 (0.23), residues: 441
  sheet: -1.36 (0.30), residues: 267
  loop : -1.05 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 370 
 TYR   0.013   0.001   TYR C  68 
 PHE   0.024   0.002   PHE B 270 
 TRP   0.009   0.001   TRP C  47 
 HIS   0.008   0.002   HIS C 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 9888)
  covalent geometry    : angle       0.67415 /  0.35 (13458)
  SS BOND              : bond        0.00555 /  0.40 (   21)
  SS BOND              : angle       2.62902 /  2.16 (   42)
  hydrogen bonds       : bond        0.03796 /  2.41 (  484)
  hydrogen bonds       : angle       5.86853 /  4.07 ( 1515)
  link_NAG-ASN         : bond        0.00904 /  0.55 (    6)
  link_NAG-ASN         : angle       5.28070 /  4.37 (   18)

*********************** 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
  319 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 287
  time to evaluate  : 0.267 
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: symmetry clash
REVERT: A   68 TYR cc_start: 0.8688 (t80) cc_final: 0.8303 (t80)
REVERT: A   80 GLU cc_start: 0.7354 (pm20) cc_final: 0.7089 (pm20)
REVERT: A  108 ASP cc_start: 0.6556 (m-30) cc_final: 0.6345 (m-30)
REVERT: A  168 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7690 (pt0)
REVERT: A  217 ASN cc_start: 0.7394 (m110) cc_final: 0.6804 (t0)
REVERT: A  249 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: A  278 GLU cc_start: 0.8158 (tt0) cc_final: 0.7836 (tt0)
REVERT: A  280 ARG cc_start: 0.8522 (mtt180) cc_final: 0.8010 (mtt180)
REVERT: A  309 CYS cc_start: 0.6531 (t) cc_final: 0.6250 (t)
REVERT: B  217 ASN cc_start: 0.7321 (m110) cc_final: 0.6717 (t0)
REVERT: B  242 PHE cc_start: 0.8551 (m-80) cc_final: 0.8314 (m-80)
REVERT: B  249 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7978 (tt0)
REVERT: B  262 LEU cc_start: 0.9211 (mt) cc_final: 0.8955 (mp)
REVERT: B  278 GLU cc_start: 0.8109 (tt0) cc_final: 0.7856 (tt0)
REVERT: B  309 CYS cc_start: 0.6502 (t) cc_final: 0.6273 (t)
REVERT: C  108 ASP cc_start: 0.6617 (m-30) cc_final: 0.6402 (m-30)
REVERT: C  155 MET cc_start: 0.7937 (mmm) cc_final: 0.7664 (tpt)
REVERT: C  217 ASN cc_start: 0.7231 (m110) cc_final: 0.6179 (t0)
REVERT: C  278 GLU cc_start: 0.8139 (tt0) cc_final: 0.7905 (tt0)
REVERT: C  280 ARG cc_start: 0.8573 (mtt180) cc_final: 0.7932 (mtt180)
REVERT: C  309 CYS cc_start: 0.6472 (t) cc_final: 0.6259 (t)
REVERT: C  403 ASN cc_start: 0.8417 (m-40) cc_final: 0.7768 (m110)
  outliers start: 32
  outliers final: 12
  residues processed: 308
  average time/residue: 0.0774
  time to fit residues: 35.0914
Evaluate side-chains
  248 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 236
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 THR
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  291 CYS
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
Chi-restraints excluded: chain C residue  396 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 43 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 120 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 227 GLN
C 227 GLN
C 249 GLN
C 437 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.158881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.135271 restraints weight = 16694.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.139124 restraints weight = 9473.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.141841 restraints weight = 6477.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.143431 restraints weight = 4952.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.144737 restraints weight = 4142.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9915  Z= 0.227
  Angle     :  0.699  10.204  13518  Z= 0.358
  Chirality :  0.045   0.359   1512
  Planarity :  0.004   0.035   1749
  Dihedral  :  5.126  21.815   1374
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 18.22 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.24), residues: 1266
  helix: -0.09 (0.24), residues: 462
  sheet: -1.46 (0.30), residues: 267
  loop : -0.57 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 370 
 TYR   0.018   0.002   TYR C 457 
 PHE   0.018   0.002   PHE A 270 
 TRP   0.007   0.002   TRP A  47 
 HIS   0.009   0.002   HIS B 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00486 /  0.23 ( 9888)
  covalent geometry    : angle       0.66751 /  0.35 (13458)
  SS BOND              : bond        0.00612 /  0.44 (   21)
  SS BOND              : angle       2.32200 /  1.87 (   42)
  hydrogen bonds       : bond        0.03781 /  2.45 (  484)
  hydrogen bonds       : angle       5.57509 /  3.86 ( 1515)
  link_NAG-ASN         : bond        0.00790 /  0.45 (    6)
  link_NAG-ASN         : angle       4.59974 /  3.81 (   18)

*********************** 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
  299 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 259
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8739 (tp) cc_final: 0.8343 (tt)
REVERT: A  108 ASP cc_start: 0.6776 (m-30) cc_final: 0.6572 (m-30)
REVERT: A  109 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7374 (tp)
REVERT: A  168 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7650 (pt0)
REVERT: A  249 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7775 (tm-30)
REVERT: A  262 LEU cc_start: 0.9264 (mp) cc_final: 0.9030 (mt)
REVERT: A  278 GLU cc_start: 0.8298 (tt0) cc_final: 0.7690 (tt0)
REVERT: A  280 ARG cc_start: 0.8669 (mtt180) cc_final: 0.7869 (mtt180)
REVERT: A  309 CYS cc_start: 0.6526 (t) cc_final: 0.6219 (t)
REVERT: A  374 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7177 (mt-10)
REVERT: B   60 LEU cc_start: 0.8626 (tp) cc_final: 0.8291 (tt)
REVERT: B   68 TYR cc_start: 0.9101 (t80) cc_final: 0.8829 (t80)
REVERT: B  108 ASP cc_start: 0.6607 (m-30) cc_final: 0.6191 (m-30)
REVERT: B  109 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7477 (tp)
REVERT: B  217 ASN cc_start: 0.7507 (m110) cc_final: 0.6793 (t0)
REVERT: B  242 PHE cc_start: 0.8662 (m-80) cc_final: 0.8344 (m-80)
REVERT: B  249 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: C   60 LEU cc_start: 0.8627 (tp) cc_final: 0.8279 (tt)
REVERT: C  109 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7073 (tp)
REVERT: C  217 ASN cc_start: 0.7395 (m110) cc_final: 0.6631 (t0)
REVERT: C  242 PHE cc_start: 0.8638 (m-80) cc_final: 0.8400 (m-80)
REVERT: C  309 CYS cc_start: 0.6679 (t) cc_final: 0.6424 (t)
  outliers start: 40
  outliers final: 24
  residues processed: 278
  average time/residue: 0.0780
  time to fit residues: 31.7693
Evaluate side-chains
  249 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 222
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 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  376 SER
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  231 LEU
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  376 SER
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 73 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 101 optimal weight:    8.9990
   chunk 116 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  97 ASN
A 111 HIS
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS
C 249 GLN
** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.160808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.136982 restraints weight = 16725.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.141075 restraints weight = 9446.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.143882 restraints weight = 6342.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.145538 restraints weight = 4809.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.146801 restraints weight = 3993.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9915  Z= 0.158
  Angle     :  0.637  10.382  13518  Z= 0.322
  Chirality :  0.044   0.335   1512
  Planarity :  0.004   0.027   1749
  Dihedral  :  4.916  27.225   1374
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.90 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.24), residues: 1266
  helix:  0.43 (0.25), residues: 462
  sheet: -1.22 (0.31), residues: 270
  loop : -0.35 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 100 
 TYR   0.014   0.001   TYR C 457 
 PHE   0.022   0.001   PHE B 101 
 TRP   0.006   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.16 ( 9888)
  covalent geometry    : angle       0.60120 /  0.31 (13458)
  SS BOND              : bond        0.00445 /  0.32 (   21)
  SS BOND              : angle       2.44563 /  1.99 (   42)
  hydrogen bonds       : bond        0.03315 /  2.11 (  484)
  hydrogen bonds       : angle       5.33854 /  3.75 ( 1515)
  link_NAG-ASN         : bond        0.01045 /  0.65 (    6)
  link_NAG-ASN         : angle       4.52714 /  3.75 (   18)

*********************** 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
  273 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 235
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6731 (t0)
REVERT: A  109 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7229 (tp)
REVERT: A  249 GLN cc_start: 0.8491 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: A  262 LEU cc_start: 0.9242 (mp) cc_final: 0.9018 (mt)
REVERT: A  309 CYS cc_start: 0.6422 (t) cc_final: 0.6119 (t)
REVERT: B   60 LEU cc_start: 0.8596 (tp) cc_final: 0.8246 (tt)
REVERT: B  108 ASP cc_start: 0.6204 (m-30) cc_final: 0.5758 (m-30)
REVERT: B  217 ASN cc_start: 0.7496 (m110) cc_final: 0.6747 (t0)
REVERT: B  242 PHE cc_start: 0.8663 (m-80) cc_final: 0.8241 (m-80)
REVERT: B  249 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: B  309 CYS cc_start: 0.6530 (t) cc_final: 0.6267 (t)
REVERT: B  314 GLU cc_start: 0.7031 (mp0) cc_final: 0.6727 (mp0)
REVERT: C   60 LEU cc_start: 0.8528 (tp) cc_final: 0.8196 (tt)
REVERT: C  109 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6960 (tp)
REVERT: C  217 ASN cc_start: 0.7369 (m110) cc_final: 0.6581 (t0)
REVERT: C  280 ARG cc_start: 0.8815 (mtt180) cc_final: 0.8249 (mtt180)
  outliers start: 38
  outliers final: 20
  residues processed: 259
  average time/residue: 0.0736
  time to fit residues: 28.3525
Evaluate side-chains
  246 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 223
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASN
Chi-restraints excluded: chain A residue  109 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  417 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
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  329 MET
Chi-restraints excluded: chain B residue  336 CYS
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0040
   chunk 41 optimal weight:    6.9990
   chunk 95 optimal weight:    0.0370
   chunk 97 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0030
   overall best weight:    0.3480

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
** C 277 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.163079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.138936 restraints weight = 16777.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.143020 restraints weight = 9474.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.145779 restraints weight = 6386.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.147418 restraints weight = 4860.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.148717 restraints weight = 4064.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9915  Z= 0.112
  Angle     :  0.610   9.775  13518  Z= 0.306
  Chirality :  0.042   0.346   1512
  Planarity :  0.003   0.026   1749
  Dihedral  :  4.594  25.541   1374
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.29 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.25), residues: 1266
  helix:  0.97 (0.26), residues: 444
  sheet: -1.05 (0.31), residues: 285
  loop : -0.43 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 100 
 TYR   0.015   0.001   TYR C  68 
 PHE   0.027   0.001   PHE B 101 
 TRP   0.005   0.001   TRP C  47 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 9888)
  covalent geometry    : angle       0.57728 /  0.30 (13458)
  SS BOND              : bond        0.00271 /  0.19 (   21)
  SS BOND              : angle       2.16935 /  1.59 (   42)
  hydrogen bonds       : bond        0.03080 /  1.95 (  484)
  hydrogen bonds       : angle       5.18030 /  3.62 ( 1515)
  link_NAG-ASN         : bond        0.01134 /  0.71 (    6)
  link_NAG-ASN         : angle       4.35652 /  3.61 (   18)

*********************** 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
  275 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 245
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7097 (tp)
REVERT: A  249 GLN cc_start: 0.8500 (tm-30) cc_final: 0.7928 (tm-30)
REVERT: A  278 GLU cc_start: 0.8152 (tt0) cc_final: 0.7805 (tt0)
REVERT: A  309 CYS cc_start: 0.6517 (t) cc_final: 0.6250 (t)
REVERT: A  326 MET cc_start: 0.7310 (mmm) cc_final: 0.7024 (mmm)
REVERT: A  341 TYR cc_start: 0.7380 (m-10) cc_final: 0.6759 (m-10)
REVERT: A  425 TYR cc_start: 0.8595 (t80) cc_final: 0.7293 (t80)
REVERT: A  430 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8537 (tp)
REVERT: B   60 LEU cc_start: 0.8548 (tp) cc_final: 0.8257 (tt)
REVERT: B  108 ASP cc_start: 0.6004 (m-30) cc_final: 0.5512 (m-30)
REVERT: B  217 ASN cc_start: 0.7440 (m110) cc_final: 0.6751 (t0)
REVERT: B  249 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8035 (tt0)
REVERT: B  262 LEU cc_start: 0.9275 (mt) cc_final: 0.8951 (mp)
REVERT: B  309 CYS cc_start: 0.6403 (t) cc_final: 0.6149 (t)
REVERT: B  314 GLU cc_start: 0.7171 (mp0) cc_final: 0.6948 (mp0)
REVERT: C   60 LEU cc_start: 0.8292 (tp) cc_final: 0.8085 (tt)
REVERT: C  109 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6817 (tp)
REVERT: C  217 ASN cc_start: 0.7358 (m110) cc_final: 0.6596 (t0)
REVERT: C  280 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8240 (mtt180)
REVERT: C  367 ASN cc_start: 0.6934 (p0) cc_final: 0.6534 (p0)
  outliers start: 30
  outliers final: 19
  residues processed: 264
  average time/residue: 0.0744
  time to fit residues: 29.2536
Evaluate side-chains
  252 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 230
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
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 A residue  417 GLU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  412 GLU
Chi-restraints excluded: chain B residue  434 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  329 MET
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.5984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 277 GLN ** 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 = 0.3891 r_free = 0.3891 target = 0.160844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.136245 restraints weight = 16801.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.140380 restraints weight = 9643.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.143124 restraints weight = 6556.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.144729 restraints weight = 5037.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.146050 restraints weight = 4235.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9915  Z= 0.168
  Angle     :  0.606   9.482  13518  Z= 0.305
  Chirality :  0.043   0.337   1512
  Planarity :  0.004   0.027   1749
  Dihedral  :  4.557  24.997   1374
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 23.04 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.25), residues: 1266
  helix:  1.11 (0.26), residues: 444
  sheet: -0.99 (0.31), residues: 279
  loop : -0.39 (0.28), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 100 
 TYR   0.019   0.001   TYR C  68 
 PHE   0.028   0.002   PHE B 101 
 TRP   0.005   0.001   TRP A 234 
 HIS   0.004   0.001   HIS B 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.17 ( 9888)
  covalent geometry    : angle       0.57735 /  0.30 (13458)
  SS BOND              : bond        0.00463 /  0.33 (   21)
  SS BOND              : angle       1.95003 /  1.44 (   42)
  hydrogen bonds       : bond        0.03166 /  2.01 (  484)
  hydrogen bonds       : angle       4.99821 /  3.49 ( 1515)
  link_NAG-ASN         : bond        0.00960 /  0.59 (    6)
  link_NAG-ASN         : angle       4.17223 /  3.45 (   18)

*********************** 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
  270 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 235
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.6431 (m-30) cc_final: 0.5948 (m-30)
REVERT: A  109 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7236 (tp)
REVERT: A  224 ASP cc_start: 0.8684 (t0) cc_final: 0.8472 (t0)
REVERT: A  249 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: A  262 LEU cc_start: 0.9240 (mp) cc_final: 0.9004 (mt)
REVERT: A  278 GLU cc_start: 0.8194 (tt0) cc_final: 0.7742 (tt0)
REVERT: A  280 ARG cc_start: 0.8672 (mtt180) cc_final: 0.8072 (mtt180)
REVERT: A  425 TYR cc_start: 0.8664 (t80) cc_final: 0.7333 (t80)
REVERT: A  430 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8491 (tp)
REVERT: B   60 LEU cc_start: 0.8537 (tp) cc_final: 0.8313 (tt)
REVERT: B  249 GLN cc_start: 0.8606 (tm-30) cc_final: 0.7425 (tm-30)
REVERT: B  309 CYS cc_start: 0.6457 (t) cc_final: 0.6154 (t)
REVERT: B  314 GLU cc_start: 0.7200 (mp0) cc_final: 0.6918 (mp0)
REVERT: C   60 LEU cc_start: 0.8401 (tp) cc_final: 0.8195 (tt)
REVERT: C  109 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7048 (tp)
  outliers start: 35
  outliers final: 24
  residues processed: 251
  average time/residue: 0.0768
  time to fit residues: 28.8300
Evaluate side-chains
  240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 213
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 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  417 GLU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
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  329 MET
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  434 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  329 MET
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 61 optimal weight:    0.4980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  97 ASN
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.161122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.136807 restraints weight = 16730.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.140922 restraints weight = 9500.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.143740 restraints weight = 6411.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.145381 restraints weight = 4868.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.146234 restraints weight = 4059.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9915  Z= 0.145
  Angle     :  0.607   9.284  13518  Z= 0.304
  Chirality :  0.043   0.331   1512
  Planarity :  0.004   0.027   1749
  Dihedral  :  4.512  23.567   1374
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 23.04 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.25), residues: 1266
  helix:  1.13 (0.26), residues: 444
  sheet: -0.79 (0.33), residues: 258
  loop : -0.37 (0.28), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.016   0.001   TYR B  68 
 PHE   0.029   0.001   PHE B 101 
 TRP   0.004   0.001   TRP A 288 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 9888)
  covalent geometry    : angle       0.57982 /  0.30 (13458)
  SS BOND              : bond        0.00421 /  0.28 (   21)
  SS BOND              : angle       1.90408 /  1.45 (   42)
  hydrogen bonds       : bond        0.03129 /  1.99 (  484)
  hydrogen bonds       : angle       4.91838 /  3.44 ( 1515)
  link_NAG-ASN         : bond        0.01005 /  0.62 (    6)
  link_NAG-ASN         : angle       4.11209 /  3.39 (   18)

*********************** 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
  265 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 223
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ASN cc_start: 0.6650 (OUTLIER) cc_final: 0.6350 (t0)
REVERT: A  109 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7215 (tp)
REVERT: A  224 ASP cc_start: 0.8693 (t0) cc_final: 0.8482 (t0)
REVERT: A  249 GLN cc_start: 0.8500 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: A  341 TYR cc_start: 0.7511 (m-10) cc_final: 0.6616 (m-10)
REVERT: A  425 TYR cc_start: 0.8639 (t80) cc_final: 0.7321 (t80)
REVERT: A  430 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8513 (tp)
REVERT: B   60 LEU cc_start: 0.8448 (tp) cc_final: 0.8154 (tt)
REVERT: B  249 GLN cc_start: 0.8614 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: B  309 CYS cc_start: 0.6435 (t) cc_final: 0.6143 (t)
REVERT: B  314 GLU cc_start: 0.7252 (mp0) cc_final: 0.6986 (mp0)
REVERT: B  326 MET cc_start: 0.7177 (mmt) cc_final: 0.6868 (mmm)
REVERT: C  109 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6957 (tp)
REVERT: C  230 TYR cc_start: 0.8569 (m-80) cc_final: 0.8325 (m-10)
  outliers start: 42
  outliers final: 28
  residues processed: 246
  average time/residue: 0.0701
  time to fit residues: 25.9910
Evaluate side-chains
  245 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 213
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASN
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  102 SER
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  329 MET
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  434 ILE
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  318 LEU
Chi-restraints excluded: chain C residue  329 MET
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 118 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0570
   chunk 78 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.7298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 437 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.162694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.138326 restraints weight = 16656.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.142481 restraints weight = 9477.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.144992 restraints weight = 6409.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.147007 restraints weight = 4952.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.148127 restraints weight = 4067.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9915  Z= 0.119
  Angle     :  0.584   9.201  13518  Z= 0.293
  Chirality :  0.042   0.329   1512
  Planarity :  0.003   0.028   1749
  Dihedral  :  4.399  22.669   1374
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 23.69 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.25), residues: 1266
  helix:  1.15 (0.26), residues: 447
  sheet: -0.80 (0.32), residues: 279
  loop : -0.24 (0.29), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.010   0.001   TYR B  68 
 PHE   0.026   0.001   PHE B 101 
 TRP   0.004   0.001   TRP B 234 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 ( 9888)
  covalent geometry    : angle       0.55950 /  0.29 (13458)
  SS BOND              : bond        0.00319 /  0.23 (   21)
  SS BOND              : angle       1.57037 /  1.18 (   42)
  hydrogen bonds       : bond        0.03014 /  1.92 (  484)
  hydrogen bonds       : angle       4.87243 /  3.39 ( 1515)
  link_NAG-ASN         : bond        0.01049 /  0.64 (    6)
  link_NAG-ASN         : angle       4.04822 /  3.33 (   18)

*********************** 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
  256 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 220
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7212 (tp)
REVERT: A  224 ASP cc_start: 0.8657 (t0) cc_final: 0.8441 (t0)
REVERT: A  249 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7824 (tm-30)
REVERT: A  341 TYR cc_start: 0.7366 (m-10) cc_final: 0.6974 (m-10)
REVERT: A  425 TYR cc_start: 0.8605 (t80) cc_final: 0.7289 (t80)
REVERT: A  430 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8468 (tp)
REVERT: B   60 LEU cc_start: 0.8320 (tp) cc_final: 0.8033 (tt)
REVERT: B  249 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7368 (tm-30)
REVERT: B  309 CYS cc_start: 0.6412 (t) cc_final: 0.6099 (t)
REVERT: B  314 GLU cc_start: 0.7319 (mp0) cc_final: 0.7052 (mp0)
REVERT: B  326 MET cc_start: 0.7189 (mmt) cc_final: 0.6860 (mmm)
REVERT: C  109 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6873 (tp)
REVERT: C  230 TYR cc_start: 0.8485 (m-80) cc_final: 0.8244 (m-10)
  outliers start: 36
  outliers final: 26
  residues processed: 238
  average time/residue: 0.0744
  time to fit residues: 26.7754
Evaluate side-chains
  238 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 209
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  430 LEU
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  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  336 CYS
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 B residue  434 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  318 LEU
Chi-restraints excluded: chain C residue  329 MET
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 1 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0970
   chunk 119 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 95 optimal weight:    0.0060
   chunk 46 optimal weight:    2.9990
   chunk 121 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 96 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0170
   chunk 73 optimal weight:   10.0000
   overall best weight:    0.7434

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 GLN
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
** B 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 = 0.3915 r_free = 0.3915 target = 0.163190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139040 restraints weight = 16602.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.143135 restraints weight = 9392.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.145902 restraints weight = 6347.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.147732 restraints weight = 4819.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.148930 restraints weight = 3990.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9915  Z= 0.119
  Angle     :  0.594   9.100  13518  Z= 0.296
  Chirality :  0.042   0.327   1512
  Planarity :  0.003   0.029   1749
  Dihedral  :  4.330  21.654   1374
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 23.69 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.25), residues: 1266
  helix:  1.18 (0.26), residues: 447
  sheet: -0.71 (0.32), residues: 279
  loop : -0.15 (0.29), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.010   0.001   TYR B 457 
 PHE   0.028   0.001   PHE B 101 
 TRP   0.004   0.001   TRP B 234 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 9888)
  covalent geometry    : angle       0.56784 /  0.29 (13458)
  SS BOND              : bond        0.00275 /  0.19 (   21)
  SS BOND              : angle       1.88990 /  1.38 (   42)
  hydrogen bonds       : bond        0.02923 /  1.87 (  484)
  hydrogen bonds       : angle       4.78195 /  3.33 ( 1515)
  link_NAG-ASN         : bond        0.01022 /  0.63 (    6)
  link_NAG-ASN         : angle       3.99630 /  3.29 (   18)

*********************** 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
  252 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 220
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7178 (tp)
REVERT: A  249 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7918 (tm-30)
REVERT: A  341 TYR cc_start: 0.7375 (m-10) cc_final: 0.5926 (m-10)
REVERT: A  425 TYR cc_start: 0.8605 (t80) cc_final: 0.7329 (t80)
REVERT: A  430 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8257 (tp)
REVERT: B  249 GLN cc_start: 0.8627 (tm-30) cc_final: 0.7384 (tm-30)
REVERT: B  309 CYS cc_start: 0.6354 (t) cc_final: 0.6049 (t)
REVERT: B  314 GLU cc_start: 0.7285 (mp0) cc_final: 0.6977 (mp0)
REVERT: C  109 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6855 (tp)
REVERT: C  326 MET cc_start: 0.7311 (mmt) cc_final: 0.7026 (mmm)
  outliers start: 32
  outliers final: 24
  residues processed: 235
  average time/residue: 0.0743
  time to fit residues: 26.6170
Evaluate side-chains
  240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 213
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  430 LEU
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  231 LEU
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  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  318 LEU
Chi-restraints excluded: chain C residue  329 MET
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 124 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   chunk 58 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  74 HIS
A  97 ASN
A 437 GLN
** B  97 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 = 0.3912 r_free = 0.3912 target = 0.162892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138738 restraints weight = 16568.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.142778 restraints weight = 9401.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.145450 restraints weight = 6362.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147287 restraints weight = 4872.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148291 restraints weight = 4034.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9915  Z= 0.133
  Angle     :  0.612   9.037  13518  Z= 0.304
  Chirality :  0.043   0.326   1512
  Planarity :  0.004   0.029   1749
  Dihedral  :  4.313  21.513   1374
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 24.44 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.25), residues: 1266
  helix:  1.16 (0.26), residues: 447
  sheet: -0.54 (0.34), residues: 258
  loop : -0.05 (0.28), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 325 
 TYR   0.010   0.001   TYR A 399 
 PHE   0.024   0.001   PHE B 101 
 TRP   0.004   0.001   TRP B 234 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 9888)
  covalent geometry    : angle       0.58839 /  0.30 (13458)
  SS BOND              : bond        0.00347 /  0.25 (   21)
  SS BOND              : angle       1.68282 /  1.23 (   42)
  hydrogen bonds       : bond        0.02950 /  1.91 (  484)
  hydrogen bonds       : angle       4.72069 /  3.28 ( 1515)
  link_NAG-ASN         : bond        0.00988 /  0.60 (    6)
  link_NAG-ASN         : angle       3.95726 /  3.25 (   18)

********************** 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
  247 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 217
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7229 (tp)
REVERT: A  249 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7904 (tm-30)
REVERT: A  341 TYR cc_start: 0.7342 (m-10) cc_final: 0.5964 (m-10)
REVERT: A  425 TYR cc_start: 0.8651 (t80) cc_final: 0.7380 (t80)
REVERT: A  430 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8322 (tp)
REVERT: B  249 GLN cc_start: 0.8635 (tm-30) cc_final: 0.7383 (tm-30)
REVERT: B  309 CYS cc_start: 0.6390 (t) cc_final: 0.6087 (t)
REVERT: B  314 GLU cc_start: 0.7232 (mp0) cc_final: 0.6964 (mp0)
REVERT: B  341 TYR cc_start: 0.7083 (m-10) cc_final: 0.5966 (m-10)
REVERT: C  109 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6950 (tp)
REVERT: C  278 GLU cc_start: 0.8302 (tt0) cc_final: 0.8019 (tt0)
REVERT: C  326 MET cc_start: 0.7166 (mmt) cc_final: 0.6845 (mmm)
  outliers start: 30
  outliers final: 23
  residues processed: 231
  average time/residue: 0.0712
  time to fit residues: 24.9525
Evaluate side-chains
  242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 216
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  430 LEU
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  231 LEU
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  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  329 MET
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  97 ASN ** 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 = 0.3896 r_free = 0.3896 target = 0.161713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.138146 restraints weight = 16636.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.142193 restraints weight = 9504.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.144855 restraints weight = 6401.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.146534 restraints weight = 4878.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.147890 restraints weight = 4053.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9915  Z= 0.134
  Angle     :  0.617   9.575  13518  Z= 0.305
  Chirality :  0.042   0.326   1512
  Planarity :  0.004   0.030   1749
  Dihedral  :  4.291  21.153   1374
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 23.79 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.25), residues: 1266
  helix:  1.23 (0.26), residues: 447
  sheet: -0.49 (0.34), residues: 258
  loop :  0.04 (0.29), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  65 
 TYR   0.010   0.001   TYR A 399 
 PHE   0.024   0.001   PHE B 101 
 TRP   0.004   0.001   TRP B 234 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 9888)
  covalent geometry    : angle       0.59221 /  0.30 (13458)
  SS BOND              : bond        0.00332 /  0.24 (   21)
  SS BOND              : angle       1.86348 /  1.40 (   42)
  hydrogen bonds       : bond        0.02929 /  1.87 (  484)
  hydrogen bonds       : angle       4.68125 /  3.26 ( 1515)
  link_NAG-ASN         : bond        0.00992 /  0.61 (    6)
  link_NAG-ASN         : angle       3.92712 /  3.23 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1518.12 seconds
wall clock time: 26 minutes 55.96 seconds (1615.96 seconds total)