Starting phenix.real_space_refine
on Sat Aug 23 04:23:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ave_7009/08_2025/6ave_7009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ave_7009/08_2025/6ave_7009.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ave_7009/08_2025/6ave_7009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ave_7009/08_2025/6ave_7009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ave_7009/08_2025/6ave_7009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ave_7009/08_2025/6ave_7009.cif"
  }
  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-2.0-5787/lib/python3.9/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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.29, per 1000 atoms: 0.24
  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: 0.89
  Conformation dependent library (CDL) restraints added in 389.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.39
  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: 1.47

  Time building geometry restraints manager: 1.15 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3161
        2.82 -     3.34: 8653
        3.34 -     3.86: 15709
        3.86 -     4.38: 18193
        4.38 -     4.90: 30272
  Nonbonded interactions: 75988
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 215 "
            pdb=" OD2 ASP C 408 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OG1 THR B 215 "
            pdb=" OD2 ASP B 408 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG1 THR A 215 "
            pdb=" OD2 ASP A 408 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" NE2 HIS B 111 "
            pdb=" O   LYS B 151 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NE2 HIS C 111 "
            pdb=" O   LYS C 151 "
     model   vdw
     2.308 3.120
  ... (remaining 75983 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
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:             0.590
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.300
  Find NCS groups from input model:        0.090
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.085   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  :  9.624  75.799   3540
  Min Nonbonded Distance : 2.301

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

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
  covalent geometry    : bond        0.00791 ( 9888)
  covalent geometry    : angle       0.87754 (13458)
  SS BOND              : bond        0.00706 (   21)
  SS BOND              : angle       2.05867 (   42)
  hydrogen bonds       : bond        0.12258 (  484)
  hydrogen bonds       : angle       8.77609 ( 1515)
  link_NAG-ASN         : bond        0.00781 (    6)
  link_NAG-ASN         : angle       7.75319 (   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  : 0.369 
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: 0.7706 (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: 0.6657 (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: 0.8589 (ttmm) cc_final: 0.8088 (ttmm)
REVERT: C  278 GLU cc_start: 0.8318 (tt0) cc_final: 0.7435 (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: 0.7580 (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: 0.8576 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 432
  average time/residue: 0.1236
  time to fit residues: 70.5052
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  : 0.377 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 GLN
** A 403 ASN ** 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 = 0.165058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.142391 restraints weight = 16525.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.146446 restraints weight = 9320.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.149216 restraints weight = 6241.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.151047 restraints weight = 4683.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.152150 restraints weight = 3832.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9915  Z= 0.146
  Angle     :  0.710  11.075  13518  Z= 0.361
  Chirality :  0.047   0.437   1512
  Planarity :  0.005   0.033   1749
  Dihedral  :  6.393  41.322   1500
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 14.36 %
    Favored  : 81.78 %
  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 aren not related in a simple way.
  whole: -1.53 (0.22), residues: 1266
  helix: -0.59 (0.23), residues: 441
  sheet: -1.35 (0.30), residues: 267
  loop : -1.03 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 370 
 TYR   0.012   0.001   TYR C 230 
 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
  covalent geometry    : bond        0.00299 ( 9888)
  covalent geometry    : angle       0.66746 (13458)
  SS BOND              : bond        0.00564 (   21)
  SS BOND              : angle       2.62317 (   42)
  hydrogen bonds       : bond        0.03781 (  484)
  hydrogen bonds       : angle       5.84510 ( 1515)
  link_NAG-ASN         : bond        0.00917 (    6)
  link_NAG-ASN         : angle       5.40079 (   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
  321 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 285
  time to evaluate  : 0.388 
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   80 GLU cc_start: 0.7343 (pm20) cc_final: 0.7095 (pm20)
REVERT: A   97 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7047 (t0)
REVERT: A  108 ASP cc_start: 0.6562 (m-30) cc_final: 0.6345 (m-30)
REVERT: A  168 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7703 (pt0)
REVERT: A  217 ASN cc_start: 0.7398 (m110) cc_final: 0.6803 (t0)
REVERT: A  249 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: A  280 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8230 (mtm180)
REVERT: A  309 CYS cc_start: 0.6534 (t) cc_final: 0.6245 (t)
REVERT: B  217 ASN cc_start: 0.7330 (m110) cc_final: 0.6708 (t0)
REVERT: B  249 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7981 (tt0)
REVERT: B  262 LEU cc_start: 0.9209 (mt) cc_final: 0.8955 (mp)
REVERT: B  278 GLU cc_start: 0.8095 (tt0) cc_final: 0.7867 (tt0)
REVERT: B  309 CYS cc_start: 0.6437 (t) cc_final: 0.6196 (t)
REVERT: C  108 ASP cc_start: 0.6597 (m-30) cc_final: 0.6381 (m-30)
REVERT: C  155 MET cc_start: 0.7942 (mmm) cc_final: 0.7671 (tpt)
REVERT: C  217 ASN cc_start: 0.7234 (m110) cc_final: 0.6204 (t0)
REVERT: C  278 GLU cc_start: 0.8143 (tt0) cc_final: 0.7908 (tt0)
REVERT: C  280 ARG cc_start: 0.8575 (mtt180) cc_final: 0.7918 (mtt180)
REVERT: C  309 CYS cc_start: 0.6472 (t) cc_final: 0.6251 (t)
REVERT: C  403 ASN cc_start: 0.8414 (m-40) cc_final: 0.7765 (m110)
  outliers start: 36
  outliers final: 13
  residues processed: 306
  average time/residue: 0.0863
  time to fit residues: 38.4660
Evaluate side-chains
  247 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 233
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ASN
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  186 LYS
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  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:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 HIS
A 227 GLN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
B 227 GLN
C 111 HIS
C 227 GLN
C 249 GLN
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.162863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.139914 restraints weight = 16600.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.143822 restraints weight = 9373.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.146246 restraints weight = 6302.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.148215 restraints weight = 4843.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.149278 restraints weight = 3964.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.3398

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= 0.151
  Angle     :  0.675  10.591  13518  Z= 0.339
  Chirality :  0.044   0.402   1512
  Planarity :  0.004   0.033   1749
  Dihedral  :  5.501  32.935   1500
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.40 %
    Favored  : 77.71 %
  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 aren not related in a simple way.
  whole: -0.90 (0.24), residues: 1266
  helix:  0.02 (0.25), residues: 462
  sheet: -1.25 (0.31), residues: 267
  loop : -0.60 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 370 
 TYR   0.021   0.002   TYR A 230 
 PHE   0.016   0.001   PHE A 270 
 TRP   0.007   0.001   TRP A  47 
 HIS   0.003   0.001   HIS C 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9888)
  covalent geometry    : angle       0.63785 (13458)
  SS BOND              : bond        0.00970 (   21)
  SS BOND              : angle       2.44100 (   42)
  hydrogen bonds       : bond        0.03459 (  484)
  hydrogen bonds       : angle       5.54819 ( 1515)
  link_NAG-ASN         : bond        0.00964 (    6)
  link_NAG-ASN         : angle       4.88457 (   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
  292 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 265
  time to evaluate  : 0.412 
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   60 LEU cc_start: 0.8647 (tp) cc_final: 0.8257 (tt)
REVERT: A  109 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7115 (tp)
REVERT: A  217 ASN cc_start: 0.7382 (m110) cc_final: 0.6797 (t0)
REVERT: A  280 ARG cc_start: 0.8524 (mtt180) cc_final: 0.8138 (mtt180)
REVERT: A  309 CYS cc_start: 0.6432 (t) cc_final: 0.6128 (t)
REVERT: A  326 MET cc_start: 0.7522 (mmm) cc_final: 0.7157 (mmm)
REVERT: A  341 TYR cc_start: 0.7264 (m-10) cc_final: 0.5866 (m-10)
REVERT: B   60 LEU cc_start: 0.8543 (tp) cc_final: 0.8206 (tt)
REVERT: B   68 TYR cc_start: 0.8999 (t80) cc_final: 0.8707 (t80)
REVERT: B  108 ASP cc_start: 0.6249 (m-30) cc_final: 0.5841 (m-30)
REVERT: B  109 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7096 (tp)
REVERT: B  168 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7658 (pt0)
REVERT: B  217 ASN cc_start: 0.7156 (m110) cc_final: 0.6723 (t0)
REVERT: B  249 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7985 (tt0)
REVERT: B  262 LEU cc_start: 0.9240 (mt) cc_final: 0.9020 (mp)
REVERT: B  278 GLU cc_start: 0.8076 (tt0) cc_final: 0.7770 (tt0)
REVERT: B  280 ARG cc_start: 0.8716 (mtt180) cc_final: 0.7925 (mtt180)
REVERT: C   60 LEU cc_start: 0.8678 (tp) cc_final: 0.8375 (tt)
REVERT: C  108 ASP cc_start: 0.6572 (m-30) cc_final: 0.6361 (m-30)
REVERT: C  109 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6847 (tp)
REVERT: C  155 MET cc_start: 0.7901 (mmm) cc_final: 0.7630 (tpt)
REVERT: C  217 ASN cc_start: 0.7118 (m110) cc_final: 0.6548 (t0)
REVERT: C  278 GLU cc_start: 0.8165 (tt0) cc_final: 0.7894 (tt0)
REVERT: C  309 CYS cc_start: 0.6463 (t) cc_final: 0.6182 (t)
REVERT: C  420 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6633 (mt-10)
  outliers start: 27
  outliers final: 19
  residues processed: 283
  average time/residue: 0.0843
  time to fit residues: 34.5662
Evaluate side-chains
  251 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 229
  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  291 CYS
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  228 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  329 MET
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  231 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:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0980
   chunk 78 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 101 optimal weight:    0.1980
   chunk 116 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 226 GLN
C 249 GLN
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.163099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.139609 restraints weight = 16791.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.143671 restraints weight = 9474.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.146364 restraints weight = 6370.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.148065 restraints weight = 4843.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.149340 restraints weight = 4017.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.3786

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= 0.132
  Angle     :  0.613  10.912  13518  Z= 0.310
  Chirality :  0.043   0.348   1512
  Planarity :  0.004   0.027   1749
  Dihedral  :  4.996  23.153   1500
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.11 %
    Favored  : 75.78 %
  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 aren not related in a simple way.
  whole: -0.42 (0.24), residues: 1266
  helix:  0.68 (0.25), residues: 444
  sheet: -1.13 (0.32), residues: 264
  loop : -0.48 (0.28), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 370 
 TYR   0.017   0.001   TYR C  68 
 PHE   0.014   0.001   PHE B 270 
 TRP   0.005   0.001   TRP A  47 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9888)
  covalent geometry    : angle       0.57790 (13458)
  SS BOND              : bond        0.00364 (   21)
  SS BOND              : angle       2.18387 (   42)
  hydrogen bonds       : bond        0.03123 (  484)
  hydrogen bonds       : angle       5.21143 ( 1515)
  link_NAG-ASN         : bond        0.01088 (    6)
  link_NAG-ASN         : angle       4.67234 (   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
  277 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 248
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7112 (tp)
REVERT: A  309 CYS cc_start: 0.6510 (t) cc_final: 0.6180 (t)
REVERT: A  326 MET cc_start: 0.7478 (mmm) cc_final: 0.6477 (mmt)
REVERT: A  341 TYR cc_start: 0.7227 (m-10) cc_final: 0.5629 (m-10)
REVERT: A  425 TYR cc_start: 0.8553 (t80) cc_final: 0.7218 (t80)
REVERT: A  430 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8563 (tp)
REVERT: B   60 LEU cc_start: 0.8557 (tp) cc_final: 0.8274 (tt)
REVERT: B  108 ASP cc_start: 0.6352 (m-30) cc_final: 0.5906 (m-30)
REVERT: B  109 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7033 (tp)
REVERT: B  249 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7974 (tt0)
REVERT: B  262 LEU cc_start: 0.9272 (mt) cc_final: 0.8999 (mp)
REVERT: B  309 CYS cc_start: 0.6583 (t) cc_final: 0.6303 (t)
REVERT: B  314 GLU cc_start: 0.7037 (mp0) cc_final: 0.6730 (mp0)
REVERT: B  328 HIS cc_start: 0.7746 (p90) cc_final: 0.7497 (p90)
REVERT: C  109 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6840 (tp)
REVERT: C  217 ASN cc_start: 0.7344 (m110) cc_final: 0.6636 (t0)
REVERT: C  278 GLU cc_start: 0.8170 (tt0) cc_final: 0.7880 (tt0)
REVERT: C  341 TYR cc_start: 0.7597 (m-10) cc_final: 0.6794 (m-10)
  outliers start: 29
  outliers final: 18
  residues processed: 268
  average time/residue: 0.0851
  time to fit residues: 33.4382
Evaluate side-chains
  258 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 236
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
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  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  109 LEU
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  249 GLN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0370
   chunk 20 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    2.4066

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.158514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.133866 restraints weight = 16734.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.137933 restraints weight = 9629.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.140410 restraints weight = 6554.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.142424 restraints weight = 5082.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.143498 restraints weight = 4204.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
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      :  0.005   0.043   9915  Z= 0.229
  Angle     :  0.663   9.966  13518  Z= 0.335
  Chirality :  0.045   0.345   1512
  Planarity :  0.004   0.033   1749
  Dihedral  :  5.012  18.994   1500
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 21.11 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.24), residues: 1266
  helix:  1.10 (0.26), residues: 426
  sheet: -1.07 (0.29), residues: 285
  loop : -0.58 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 370 
 TYR   0.022   0.002   TYR C  68 
 PHE   0.015   0.002   PHE B 270 
 TRP   0.008   0.002   TRP A 288 
 HIS   0.006   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 9888)
  covalent geometry    : angle       0.63404 (13458)
  SS BOND              : bond        0.00497 (   21)
  SS BOND              : angle       2.23959 (   42)
  hydrogen bonds       : bond        0.03555 (  484)
  hydrogen bonds       : angle       5.09106 ( 1515)
  link_NAG-ASN         : bond        0.00891 (    6)
  link_NAG-ASN         : angle       4.27055 (   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
  269 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 227
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7490 (tp)
REVERT: A  280 ARG cc_start: 0.8881 (mtt180) cc_final: 0.7962 (mtt180)
REVERT: B   60 LEU cc_start: 0.8621 (tp) cc_final: 0.8369 (tt)
REVERT: B  109 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7374 (tp)
REVERT: B  249 GLN cc_start: 0.8565 (tm-30) cc_final: 0.7555 (tm-30)
REVERT: B  314 GLU cc_start: 0.7166 (mp0) cc_final: 0.6953 (mp0)
REVERT: C  108 ASP cc_start: 0.6473 (m-30) cc_final: 0.5952 (m-30)
REVERT: C  278 GLU cc_start: 0.8218 (tt0) cc_final: 0.7884 (tt0)
  outliers start: 42
  outliers final: 26
  residues processed: 250
  average time/residue: 0.0755
  time to fit residues: 27.6368
Evaluate side-chains
  240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 212
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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  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  169 MET
Chi-restraints excluded: chain B residue  190 THR
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  329 MET
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   84 THR
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
Chi-restraints excluded: chain C residue  420 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 69 optimal weight:    0.8980
   chunk 82 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 112 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0770
   overall best weight:    1.1540

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.161149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.137277 restraints weight = 16684.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141281 restraints weight = 9519.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.143994 restraints weight = 6434.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.145387 restraints weight = 4912.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.146599 restraints weight = 4170.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9915  Z= 0.143
  Angle     :  0.621   9.447  13518  Z= 0.310
  Chirality :  0.043   0.333   1512
  Planarity :  0.003   0.025   1749
  Dihedral  :  4.778  18.630   1500
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 23.15 %
    Favored  : 72.99 %
  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 aren not related in a simple way.
  whole: -0.06 (0.24), residues: 1266
  helix:  1.28 (0.26), residues: 426
  sheet: -0.93 (0.30), residues: 285
  loop : -0.48 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 207 
 TYR   0.014   0.001   TYR C  68 
 PHE   0.011   0.001   PHE A 270 
 TRP   0.006   0.001   TRP A 288 
 HIS   0.004   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9888)
  covalent geometry    : angle       0.59385 (13458)
  SS BOND              : bond        0.00382 (   21)
  SS BOND              : angle       1.86234 (   42)
  hydrogen bonds       : bond        0.03216 (  484)
  hydrogen bonds       : angle       4.96378 ( 1515)
  link_NAG-ASN         : bond        0.01036 (    6)
  link_NAG-ASN         : angle       4.22743 (   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
  260 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 224
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7239 (tp)
REVERT: A  280 ARG cc_start: 0.8872 (mtt180) cc_final: 0.7966 (mtt180)
REVERT: A  326 MET cc_start: 0.7159 (mmt) cc_final: 0.6391 (mmm)
REVERT: A  341 TYR cc_start: 0.7518 (m-10) cc_final: 0.6436 (m-10)
REVERT: A  425 TYR cc_start: 0.8581 (t80) cc_final: 0.7077 (t80)
REVERT: B   60 LEU cc_start: 0.8513 (tp) cc_final: 0.8250 (tt)
REVERT: B  108 ASP cc_start: 0.6353 (m-30) cc_final: 0.5792 (m-30)
REVERT: B  109 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7179 (tp)
REVERT: B  249 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8118 (tm-30)
REVERT: B  314 GLU cc_start: 0.7194 (mp0) cc_final: 0.6866 (mp0)
REVERT: C  108 ASP cc_start: 0.6170 (m-30) cc_final: 0.5660 (m-30)
REVERT: C  217 ASN cc_start: 0.7539 (m110) cc_final: 0.6622 (t0)
REVERT: C  278 GLU cc_start: 0.8288 (tt0) cc_final: 0.7698 (tt0)
  outliers start: 36
  outliers final: 25
  residues processed: 241
  average time/residue: 0.0806
  time to fit residues: 28.5692
Evaluate side-chains
  242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 215
  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  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  400 ILE
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  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   84 THR
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:    0.0770
   chunk 3 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.7738

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
C 111 HIS
C 226 GLN
C 437 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.161011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136884 restraints weight = 16678.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.140970 restraints weight = 9464.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.143739 restraints weight = 6373.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145433 restraints weight = 4833.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.146816 restraints weight = 4006.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9915  Z= 0.125
  Angle     :  0.606   9.326  13518  Z= 0.300
  Chirality :  0.042   0.332   1512
  Planarity :  0.003   0.029   1749
  Dihedral  :  4.603  19.303   1500
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 23.04 %
    Favored  : 73.31 %
  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 aren not related in a simple way.
  whole:  0.11 (0.25), residues: 1266
  helix:  1.30 (0.26), residues: 429
  sheet: -0.78 (0.31), residues: 285
  loop : -0.32 (0.29), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 207 
 TYR   0.011   0.001   TYR C  68 
 PHE   0.010   0.001   PHE A 300 
 TRP   0.005   0.001   TRP A 288 
 HIS   0.006   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9888)
  covalent geometry    : angle       0.57912 (13458)
  SS BOND              : bond        0.00296 (   21)
  SS BOND              : angle       1.82060 (   42)
  hydrogen bonds       : bond        0.03055 (  484)
  hydrogen bonds       : angle       4.88189 ( 1515)
  link_NAG-ASN         : bond        0.01042 (    6)
  link_NAG-ASN         : angle       4.17341 (   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
  257 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 223
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.8935 (t80) cc_final: 0.8591 (t80)
REVERT: A  109 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7061 (tp)
REVERT: A  280 ARG cc_start: 0.8855 (mtt180) cc_final: 0.8020 (mtt180)
REVERT: A  326 MET cc_start: 0.7074 (mmt) cc_final: 0.6850 (mmm)
REVERT: A  341 TYR cc_start: 0.7399 (m-10) cc_final: 0.7043 (m-10)
REVERT: A  425 TYR cc_start: 0.8473 (t80) cc_final: 0.6864 (t80)
REVERT: B   60 LEU cc_start: 0.8320 (tp) cc_final: 0.8041 (tt)
REVERT: B  108 ASP cc_start: 0.6203 (m-30) cc_final: 0.5679 (m-30)
REVERT: B  109 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7134 (tp)
REVERT: B  249 GLN cc_start: 0.8633 (tm-30) cc_final: 0.7489 (tm-30)
REVERT: B  309 CYS cc_start: 0.6363 (t) cc_final: 0.6068 (t)
REVERT: B  314 GLU cc_start: 0.7067 (mp0) cc_final: 0.6825 (mp0)
REVERT: C   60 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8286 (mm)
REVERT: C  108 ASP cc_start: 0.5824 (m-30) cc_final: 0.5266 (m-30)
REVERT: C  217 ASN cc_start: 0.7489 (m110) cc_final: 0.6620 (t0)
  outliers start: 34
  outliers final: 25
  residues processed: 241
  average time/residue: 0.0835
  time to fit residues: 29.9497
Evaluate side-chains
  237 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 209
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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  336 CYS
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
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  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   60 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   87 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 103 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 118 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 GLN
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 HIS
C 226 GLN
** C 437 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 = 0.3908 r_free = 0.3908 target = 0.162527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.138526 restraints weight = 16587.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.142541 restraints weight = 9482.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145348 restraints weight = 6415.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.146983 restraints weight = 4870.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148379 restraints weight = 4056.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.4519

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= 0.123
  Angle     :  0.593   9.196  13518  Z= 0.293
  Chirality :  0.042   0.327   1512
  Planarity :  0.003   0.027   1749
  Dihedral  :  4.427  19.639   1500
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 23.15 %
    Favored  : 73.53 %
  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 aren not related in a simple way.
  whole:  0.29 (0.25), residues: 1266
  helix:  1.46 (0.26), residues: 426
  sheet: -0.67 (0.31), residues: 285
  loop : -0.20 (0.29), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.011   0.001   TYR C  68 
 PHE   0.011   0.001   PHE A 300 
 TRP   0.004   0.001   TRP B 234 
 HIS   0.003   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9888)
  covalent geometry    : angle       0.56942 (13458)
  SS BOND              : bond        0.00292 (   21)
  SS BOND              : angle       1.54547 (   42)
  hydrogen bonds       : bond        0.02952 (  484)
  hydrogen bonds       : angle       4.76043 ( 1515)
  link_NAG-ASN         : bond        0.01023 (    6)
  link_NAG-ASN         : angle       4.06653 (   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
  257 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 226
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7042 (tp)
REVERT: A  280 ARG cc_start: 0.8821 (mtt180) cc_final: 0.7845 (mtt180)
REVERT: A  326 MET cc_start: 0.6984 (mmt) cc_final: 0.6560 (mmm)
REVERT: A  341 TYR cc_start: 0.7329 (m-10) cc_final: 0.7103 (m-10)
REVERT: A  425 TYR cc_start: 0.8444 (t80) cc_final: 0.6977 (t80)
REVERT: A  430 LEU cc_start: 0.9124 (tp) cc_final: 0.8871 (tp)
REVERT: B   60 LEU cc_start: 0.8424 (tp) cc_final: 0.8139 (tt)
REVERT: B  108 ASP cc_start: 0.6304 (m-30) cc_final: 0.5749 (m-30)
REVERT: B  109 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7161 (tp)
REVERT: B  249 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8043 (tt0)
REVERT: B  262 LEU cc_start: 0.9332 (mt) cc_final: 0.9009 (mp)
REVERT: B  309 CYS cc_start: 0.6415 (t) cc_final: 0.6102 (t)
REVERT: B  314 GLU cc_start: 0.7195 (mp0) cc_final: 0.6954 (mp0)
REVERT: B  437 GLN cc_start: 0.8887 (mt0) cc_final: 0.8595 (mt0)
REVERT: C   60 LEU cc_start: 0.8588 (tt) cc_final: 0.8177 (mm)
REVERT: C  108 ASP cc_start: 0.5850 (m-30) cc_final: 0.5303 (m-30)
REVERT: C  254 ASP cc_start: 0.7691 (t0) cc_final: 0.7468 (t0)
  outliers start: 31
  outliers final: 25
  residues processed: 240
  average time/residue: 0.0731
  time to fit residues: 26.1202
Evaluate side-chains
  241 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 214
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
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  336 CYS
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  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue   84 THR
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  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:    7.9990
   chunk 86 optimal weight:    0.7980
   chunk 119 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 121 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 226 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.161215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.137075 restraints weight = 16536.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141102 restraints weight = 9483.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.143837 restraints weight = 6449.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145683 restraints weight = 4909.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.146589 restraints weight = 4044.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9915  Z= 0.163
  Angle     :  0.620   9.052  13518  Z= 0.308
  Chirality :  0.043   0.323   1512
  Planarity :  0.004   0.027   1749
  Dihedral  :  4.454  19.140   1500
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.90 %
    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 aren not related in a simple way.
  whole:  0.33 (0.25), residues: 1266
  helix:  1.43 (0.26), residues: 429
  sheet: -0.67 (0.31), residues: 285
  loop : -0.12 (0.29), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  65 
 TYR   0.021   0.001   TYR A  68 
 PHE   0.011   0.001   PHE B  93 
 TRP   0.005   0.001   TRP A 288 
 HIS   0.003   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9888)
  covalent geometry    : angle       0.59522 (13458)
  SS BOND              : bond        0.00379 (   21)
  SS BOND              : angle       1.86799 (   42)
  hydrogen bonds       : bond        0.03066 (  484)
  hydrogen bonds       : angle       4.74655 ( 1515)
  link_NAG-ASN         : bond        0.00949 (    6)
  link_NAG-ASN         : angle       4.00951 (   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
  251 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 221
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7280 (tp)
REVERT: A  280 ARG cc_start: 0.8827 (mtt180) cc_final: 0.7856 (mtt180)
REVERT: A  425 TYR cc_start: 0.8530 (t80) cc_final: 0.7127 (t80)
REVERT: A  430 LEU cc_start: 0.9178 (tp) cc_final: 0.8910 (tp)
REVERT: B   60 LEU cc_start: 0.8517 (tp) cc_final: 0.8227 (tt)
REVERT: B  108 ASP cc_start: 0.6394 (m-30) cc_final: 0.5828 (m-30)
REVERT: B  109 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7219 (tp)
REVERT: B  242 PHE cc_start: 0.8220 (m-80) cc_final: 0.7998 (m-80)
REVERT: B  249 GLN cc_start: 0.8598 (tm-30) cc_final: 0.7421 (tm-30)
REVERT: B  309 CYS cc_start: 0.6470 (t) cc_final: 0.6152 (t)
REVERT: B  314 GLU cc_start: 0.7241 (mp0) cc_final: 0.6975 (mp0)
REVERT: B  437 GLN cc_start: 0.8788 (mt0) cc_final: 0.8516 (mt0)
REVERT: C   60 LEU cc_start: 0.8627 (tt) cc_final: 0.8195 (mm)
REVERT: C  108 ASP cc_start: 0.6228 (m-30) cc_final: 0.5666 (m-30)
REVERT: C  254 ASP cc_start: 0.7710 (t0) cc_final: 0.7484 (t0)
  outliers start: 30
  outliers final: 24
  residues processed: 234
  average time/residue: 0.0632
  time to fit residues: 22.3108
Evaluate side-chains
  245 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 219
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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  336 CYS
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  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue   84 THR
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 45 optimal weight:    0.0670
   chunk 22 optimal weight:    0.0060
   chunk 123 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 63 optimal weight:    0.0020
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5744

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

Flipped N/Q/H residues before XYZ refinement:
** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 226 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.162533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.138876 restraints weight = 16510.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.142940 restraints weight = 9318.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145677 restraints weight = 6262.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.147294 restraints weight = 4741.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.148630 restraints weight = 3941.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9915  Z= 0.118
  Angle     :  0.624  10.253  13518  Z= 0.307
  Chirality :  0.042   0.323   1512
  Planarity :  0.004   0.025   1749
  Dihedral  :  4.309  18.271   1500
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.26 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.25), residues: 1266
  helix:  1.56 (0.26), residues: 426
  sheet: -0.53 (0.32), residues: 285
  loop : -0.04 (0.29), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  65 
 TYR   0.011   0.001   TYR A 230 
 PHE   0.014   0.001   PHE A 300 
 TRP   0.005   0.001   TRP B 234 
 HIS   0.003   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9888)
  covalent geometry    : angle       0.59891 (13458)
  SS BOND              : bond        0.00277 (   21)
  SS BOND              : angle       1.87840 (   42)
  hydrogen bonds       : bond        0.02935 (  484)
  hydrogen bonds       : angle       4.72645 ( 1515)
  link_NAG-ASN         : bond        0.01063 (    6)
  link_NAG-ASN         : angle       3.99795 (   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
  256 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 228
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7002 (tp)
REVERT: A  280 ARG cc_start: 0.8823 (mtt180) cc_final: 0.7964 (mtt180)
REVERT: A  341 TYR cc_start: 0.7388 (m-10) cc_final: 0.5721 (m-10)
REVERT: A  425 TYR cc_start: 0.8423 (t80) cc_final: 0.7000 (t80)
REVERT: A  430 LEU cc_start: 0.9192 (tp) cc_final: 0.8932 (tp)
REVERT: B   60 LEU cc_start: 0.8436 (tp) cc_final: 0.8102 (tt)
REVERT: B  108 ASP cc_start: 0.6146 (m-30) cc_final: 0.5641 (m-30)
REVERT: B  249 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8095 (tt0)
REVERT: B  262 LEU cc_start: 0.9323 (mt) cc_final: 0.9026 (mp)
REVERT: B  309 CYS cc_start: 0.6391 (t) cc_final: 0.6130 (t)
REVERT: B  314 GLU cc_start: 0.7097 (mp0) cc_final: 0.6862 (mp0)
REVERT: B  341 TYR cc_start: 0.6944 (m-10) cc_final: 0.5785 (m-10)
REVERT: C   60 LEU cc_start: 0.8519 (tt) cc_final: 0.8086 (mm)
REVERT: C  108 ASP cc_start: 0.5802 (m-30) cc_final: 0.5285 (m-30)
REVERT: C  278 GLU cc_start: 0.8270 (tt0) cc_final: 0.8053 (tt0)
REVERT: C  437 GLN cc_start: 0.8666 (tt0) cc_final: 0.8457 (tt0)
  outliers start: 28
  outliers final: 23
  residues processed: 240
  average time/residue: 0.0636
  time to fit residues: 22.8674
Evaluate side-chains
  240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 216
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
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  336 CYS
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  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  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  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
Chi-restraints excluded: chain C residue  438 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0170
   chunk 51 optimal weight:    0.3980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 164 HIS
C 226 GLN
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.162652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139308 restraints weight = 16730.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.143238 restraints weight = 9525.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145993 restraints weight = 6463.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.147626 restraints weight = 4881.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148970 restraints weight = 4041.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9915  Z= 0.114
  Angle     :  0.618  10.065  13518  Z= 0.303
  Chirality :  0.042   0.323   1512
  Planarity :  0.003   0.025   1749
  Dihedral  :  4.190  17.920   1500
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.79 %
    Favored  : 73.53 %
  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 aren not related in a simple way.
  whole:  0.60 (0.25), residues: 1266
  helix:  1.66 (0.26), residues: 423
  sheet: -0.46 (0.32), residues: 285
  loop :  0.01 (0.30), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  65 
 TYR   0.039   0.001   TYR A  68 
 PHE   0.018   0.001   PHE A 300 
 TRP   0.005   0.001   TRP B 234 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9888)
  covalent geometry    : angle       0.59331 (13458)
  SS BOND              : bond        0.00266 (   21)
  SS BOND              : angle       1.82163 (   42)
  hydrogen bonds       : bond        0.02894 (  484)
  hydrogen bonds       : angle       4.67771 ( 1515)
  link_NAG-ASN         : bond        0.01031 (    6)
  link_NAG-ASN         : angle       3.96241 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1580.47 seconds
wall clock time: 28 minutes 2.00 seconds (1682.00 seconds total)