Starting phenix.real_space_refine
on Fri Feb 14 02:56:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ave_7009/02_2025/6ave_7009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ave_7009/02_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_7009/02_2025/6ave_7009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ave_7009/02_2025/6ave_7009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ave_7009/02_2025/6ave_7009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ave_7009/02_2025/6ave_7009.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.031 sd=   1.102
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      81      5.16       5
     C    6204      2.51       5
     N    1581      2.21       5
     O    1791      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9657
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3191
          Classifications: {'peptide': 424}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 403}
          Unresolved non-hydrogen bonds: 216
          Unresolved non-hydrogen angles: 269
          Unresolved non-hydrogen dihedrals: 171
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 135
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 5.87, per 1000 atoms: 0.61
  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=7, 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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 394 "
      " NAG A 602 " - " ASN A 367 "
      " NAG B 601 " - " ASN B 394 "
      " NAG B 602 " - " ASN B 367 "
      " NAG C 601 " - " ASN C 394 "
      " NAG C 602 " - " ASN C 367 "
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 12 sheets defined
      40.2% alpha, 25.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 70
    Processing helix  chain 'A' and resid 105 through 113
    Processing helix  chain 'A' and resid 132 through 143
      removed outlier: 3.712A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 162
      removed outlier: 3.733A  pdb=" N   PHE A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.522A  pdb=" N   TYR A 230 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 263
    Processing helix  chain 'A' and resid 305 through 323
      removed outlier: 3.895A  pdb=" N   ASN A 323 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 344
      removed outlier: 3.728A  pdb=" N   LYS A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 355
    Processing helix  chain 'A' and resid 356 through 360
      removed outlier: 3.814A  pdb=" N   CYS A 360 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 394
      removed outlier: 3.722A  pdb=" N   LEU A 389 " --> pdb=" O   SER A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 403
    Processing helix  chain 'A' and resid 426 through 441
    Processing helix  chain 'A' and resid 445 through 464
      removed outlier: 3.821A  pdb=" N   LYS A 461 " --> pdb=" O   TYR A 457 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   HIS A 462 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ARG A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 464 " --> pdb=" O   ILE A 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 70
    Processing helix  chain 'B' and resid 105 through 113
    Processing helix  chain 'B' and resid 132 through 143
      removed outlier: 3.712A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 162
      removed outlier: 3.734A  pdb=" N   PHE B 158 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 183
      No H-bonds generated for 'chain 'B' and resid 181 through 183'
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 3.521A  pdb=" N   TYR B 230 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 263
    Processing helix  chain 'B' and resid 305 through 323
      removed outlier: 3.895A  pdb=" N   ASN B 323 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 344
      removed outlier: 3.726A  pdb=" N   LYS B 342 " --> pdb=" O   PRO B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 355
    Processing helix  chain 'B' and resid 356 through 360
      removed outlier: 3.815A  pdb=" N   CYS B 360 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 394
      removed outlier: 3.721A  pdb=" N   LEU B 389 " --> pdb=" O   SER B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 403
    Processing helix  chain 'B' and resid 426 through 441
    Processing helix  chain 'B' and resid 445 through 464
      removed outlier: 3.822A  pdb=" N   LYS B 461 " --> pdb=" O   TYR B 457 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   HIS B 462 " --> pdb=" O   GLU B 458 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ARG B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 70
    Processing helix  chain 'C' and resid 105 through 113
    Processing helix  chain 'C' and resid 132 through 143
      removed outlier: 3.711A  pdb=" N   LEU C 139 " --> pdb=" O   GLN C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 162
      removed outlier: 3.734A  pdb=" N   PHE C 158 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 183
      No H-bonds generated for 'chain 'C' and resid 181 through 183'
    Processing helix  chain 'C' and resid 226 through 230
      removed outlier: 3.522A  pdb=" N   TYR C 230 " --> pdb=" O   GLN C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 263
    Processing helix  chain 'C' and resid 305 through 323
      removed outlier: 3.896A  pdb=" N   ASN C 323 " --> pdb=" O   VAL C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 344
      removed outlier: 3.727A  pdb=" N   LYS C 342 " --> pdb=" O   PRO C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 355
    Processing helix  chain 'C' and resid 356 through 360
      removed outlier: 3.814A  pdb=" N   CYS C 360 " --> pdb=" O   ASN C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 394
      removed outlier: 3.722A  pdb=" N   LEU C 389 " --> pdb=" O   SER C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 396 through 403
    Processing helix  chain 'C' and resid 426 through 441
    Processing helix  chain 'C' and resid 445 through 464
      removed outlier: 3.822A  pdb=" N   LYS C 461 " --> pdb=" O   TYR C 457 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   HIS C 462 " --> pdb=" O   GLU C 458 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ARG C 463 " --> pdb=" O   VAL C 459 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU C 464 " --> pdb=" O   ILE C 460 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN A 415 " --> pdb=" O   CYS A 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU A 278 " --> pdb=" O   ASN A 415 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE A 270 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER A 172 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ASP A 224 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   LEU A 170 " --> pdb=" O   ASP A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN A 415 " --> pdb=" O   CYS A 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU A 278 " --> pdb=" O   ASN A 415 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87
      removed outlier: 3.670A  pdb=" N   LEU A  86 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189
      removed outlier: 7.102A  pdb=" N   LYS A 194 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   ASN A  95 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN B 415 " --> pdb=" O   CYS B 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU B 278 " --> pdb=" O   ASN B 415 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE B 270 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER B 172 " --> pdb=" O   MET B 222 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ASP B 224 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   LEU B 170 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN B 415 " --> pdb=" O   CYS B 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU B 278 " --> pdb=" O   ASN B 415 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 87
      removed outlier: 3.670A  pdb=" N   LEU B  86 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 189
      removed outlier: 7.102A  pdb=" N   LYS B 194 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ASN B  95 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN C 415 " --> pdb=" O   CYS C 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU C 278 " --> pdb=" O   ASN C 415 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE C 270 " --> pdb=" O   ILE C 404 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER C 172 " --> pdb=" O   MET C 222 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ASP C 224 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   LEU C 170 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 82
      removed outlier: 7.397A  pdb=" N   ASN C 415 " --> pdb=" O   CYS C 276 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU C 278 " --> pdb=" O   ASN C 415 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 86 through 87
      removed outlier: 3.670A  pdb=" N   LEU C  86 " --> pdb=" O   THR C 210 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 185 through 189
      removed outlier: 7.102A  pdb=" N   LYS C 194 " --> pdb=" O   ASN C  95 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ASN C  95 " --> pdb=" O   LYS C 194 " (cutoff:3.500A)

    523 hydrogen bonds defined for protein.
    1515 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.90

  Time building geometry restraints manager: 2.80 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: 5658
       15.16 -    30.32: 226
       30.32 -    45.48: 39
       45.48 -    60.64: 14
       60.64 -    75.80: 6
  Dihedral angle restraints: 5943
    sinusoidal: 2226
      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 5940 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:
        2.01 -     2.59: 116
        2.59 -     3.17: 8052
        3.17 -     3.75: 14663
        3.75 -     4.32: 20372
        4.32 -     4.90: 32827
  Nonbonded interactions: 76030
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C  94 "
            pdb=" SG  CYS C 195 "
     model   vdw
     2.013 3.760
  nonbonded pdb=" SG  CYS B  94 "
            pdb=" SG  CYS B 195 "
     model   vdw
     2.013 3.760
  nonbonded pdb=" SG  CYS C 324 "
            pdb=" SG  CYS C 336 "
     model   vdw
     2.027 3.760
  nonbonded pdb=" SG  CYS B 324 "
            pdb=" SG  CYS B 336 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS B 313 "
            pdb=" SG  CYS B 360 "
     model   vdw
     2.028 3.760
  ... (remaining 76025 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.440
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.085   9888  Z= 0.520
  Angle     :  0.878   9.296  13458  Z= 0.474
  Chirality :  0.068   0.945   1512
  Planarity :  0.005   0.040   1749
  Dihedral  :  9.624  75.799   3540
  Min Nonbonded Distance : 2.013

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

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

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

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

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 432
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.8838 (t80) cc_final: 0.8329 (t80)
REVERT: A  198 PHE cc_start: 0.8663 (t80) cc_final: 0.8453 (t80)
REVERT: A  217 ASN cc_start: 0.7848 (m110) cc_final: 0.6891 (t0)
REVERT: A  247 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8240 (ttmm)
REVERT: A  249 GLN cc_start: 0.7706 (tm-30) cc_final: 0.6784 (tm-30)
REVERT: A  278 GLU cc_start: 0.8390 (tt0) cc_final: 0.7708 (tt0)
REVERT: A  309 CYS cc_start: 0.6570 (t) cc_final: 0.6331 (t)
REVERT: A  323 ASN cc_start: 0.8097 (m-40) cc_final: 0.7864 (m110)
REVERT: A  341 TYR cc_start: 0.7407 (m-10) cc_final: 0.7178 (m-10)
REVERT: A  350 ASP cc_start: 0.8450 (m-30) cc_final: 0.8023 (m-30)
REVERT: A  379 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7976 (tptt)
REVERT: A  420 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7478 (mt-10)
REVERT: A  454 ASP cc_start: 0.8266 (m-30) cc_final: 0.7878 (m-30)
REVERT: B  217 ASN cc_start: 0.7801 (m110) cc_final: 0.6800 (t0)
REVERT: B  249 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7520 (tt0)
REVERT: B  262 LEU cc_start: 0.9124 (mt) cc_final: 0.8839 (mp)
REVERT: B  278 GLU cc_start: 0.8303 (tt0) cc_final: 0.7838 (tt0)
REVERT: B  280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8114 (mtt180)
REVERT: B  309 CYS cc_start: 0.6657 (t) cc_final: 0.6456 (t)
REVERT: B  350 ASP cc_start: 0.8312 (m-30) cc_final: 0.7897 (m-30)
REVERT: B  420 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7388 (mt-10)
REVERT: C   61 VAL cc_start: 0.8623 (m) cc_final: 0.8221 (p)
REVERT: C  220 GLU cc_start: 0.7506 (tt0) cc_final: 0.7157 (tt0)
REVERT: C  247 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8088 (ttmm)
REVERT: C  278 GLU cc_start: 0.8318 (tt0) cc_final: 0.7666 (tt0)
REVERT: C  280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7560 (mtt180)
REVERT: C  309 CYS cc_start: 0.6709 (t) cc_final: 0.6445 (t)
REVERT: C  341 TYR cc_start: 0.7366 (m-10) cc_final: 0.7072 (m-10)
REVERT: C  350 ASP cc_start: 0.8432 (m-30) cc_final: 0.8061 (m-30)
REVERT: C  373 LYS cc_start: 0.7872 (pttm) cc_final: 0.7580 (mttt)
REVERT: C  379 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7749 (tptp)
REVERT: C  403 ASN cc_start: 0.8128 (m-40) cc_final: 0.7447 (m110)
REVERT: C  420 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7335 (mt-10)
REVERT: C  437 GLN cc_start: 0.8921 (mt0) cc_final: 0.8575 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 432
  average time/residue: 0.2579
  time to fit residues: 146.5574
Evaluate side-chains
  246 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0570
   overall best weight:    0.9504

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 GLN
A 403 ASN
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 GLN
B 403 ASN
C 249 GLN
C 277 GLN
** C 403 ASN ** 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 = 0.3895 r_free = 0.3895 target = 0.160550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.137576 restraints weight = 16761.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.141590 restraints weight = 9523.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.143994 restraints weight = 6408.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9888  Z= 0.224
  Angle     :  0.655   7.631  13458  Z= 0.345
  Chirality :  0.047   0.429   1512
  Planarity :  0.005   0.037   1749
  Dihedral  :  6.312  41.562   1500
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.47 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.22), residues: 1266
  helix: -0.65 (0.23), residues: 441
  sheet: -1.39 (0.29), residues: 267
  loop : -1.08 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  47 
 HIS   0.007   0.001   HIS C 328 
 PHE   0.023   0.002   PHE B 270 
 TYR   0.015   0.002   TYR C 230 
 ARG   0.010   0.001   ARG B 370 

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

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 277
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.8735 (t80) cc_final: 0.8319 (t80)
REVERT: A  108 ASP cc_start: 0.6665 (m-30) cc_final: 0.6415 (m-30)
REVERT: A  217 ASN cc_start: 0.7530 (m110) cc_final: 0.6860 (t0)
REVERT: A  249 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: A  280 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8241 (mtt180)
REVERT: A  309 CYS cc_start: 0.6644 (t) cc_final: 0.6354 (t)
REVERT: A  430 LEU cc_start: 0.9114 (tp) cc_final: 0.8813 (tt)
REVERT: B  217 ASN cc_start: 0.7370 (m110) cc_final: 0.6786 (t0)
REVERT: B  242 PHE cc_start: 0.8616 (m-80) cc_final: 0.8385 (m-80)
REVERT: B  249 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8006 (tt0)
REVERT: B  262 LEU cc_start: 0.9223 (mt) cc_final: 0.8972 (mp)
REVERT: B  278 GLU cc_start: 0.8158 (tt0) cc_final: 0.7920 (tt0)
REVERT: B  309 CYS cc_start: 0.8697 (t) cc_final: 0.7929 (t)
REVERT: B  362 CYS cc_start: 0.5833 (m) cc_final: 0.5335 (m)
REVERT: C  108 ASP cc_start: 0.6789 (m-30) cc_final: 0.6537 (m-30)
REVERT: C  155 MET cc_start: 0.7919 (mmm) cc_final: 0.7663 (tpt)
REVERT: C  217 ASN cc_start: 0.7336 (m110) cc_final: 0.6354 (t0)
REVERT: C  280 ARG cc_start: 0.8615 (mtt180) cc_final: 0.7940 (mtt180)
REVERT: C  309 CYS cc_start: 0.8751 (t) cc_final: 0.7768 (t)
REVERT: C  362 CYS cc_start: 0.5461 (m) cc_final: 0.5245 (m)
REVERT: C  403 ASN cc_start: 0.8454 (m-40) cc_final: 0.7853 (m110)
  outliers start: 34
  outliers final: 13
  residues processed: 297
  average time/residue: 0.1991
  time to fit residues: 84.7990
Evaluate side-chains
  246 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 233
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  291 CYS
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  360 CYS
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  396 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 50 optimal weight:   30.0000
   chunk 53 optimal weight:    0.9990
   chunk 116 optimal weight:   10.0000
   chunk 99 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
B 227 GLN
C 227 GLN
** C 403 ASN ** 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 = 0.3848 r_free = 0.3848 target = 0.157054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.133273 restraints weight = 17045.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.137088 restraints weight = 9743.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.139681 restraints weight = 6658.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9888  Z= 0.305
  Angle     :  0.630   6.972  13458  Z= 0.332
  Chirality :  0.046   0.365   1512
  Planarity :  0.004   0.034   1749
  Dihedral  :  5.583  31.226   1500
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.68 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.23), residues: 1266
  helix: -0.09 (0.24), residues: 462
  sheet: -1.46 (0.29), residues: 270
  loop : -0.70 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A  47 
 HIS   0.008   0.002   HIS B 111 
 PHE   0.020   0.002   PHE A 270 
 TYR   0.017   0.002   TYR C 457 
 ARG   0.009   0.001   ARG C 370 

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

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 260
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8708 (tp) cc_final: 0.8341 (tt)
REVERT: A  108 ASP cc_start: 0.6794 (m-30) cc_final: 0.6577 (m-30)
REVERT: A  109 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7394 (tp)
REVERT: A  169 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8304 (ttt)
REVERT: A  249 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: A  262 LEU cc_start: 0.9267 (mp) cc_final: 0.9042 (mt)
REVERT: A  278 GLU cc_start: 0.8321 (tt0) cc_final: 0.7674 (tt0)
REVERT: A  280 ARG cc_start: 0.8699 (mtt180) cc_final: 0.7946 (mtt180)
REVERT: A  309 CYS cc_start: 0.6621 (t) cc_final: 0.6321 (t)
REVERT: A  374 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7177 (mt-10)
REVERT: B   60 LEU cc_start: 0.8651 (tp) cc_final: 0.8323 (tt)
REVERT: B   68 TYR cc_start: 0.9106 (t80) cc_final: 0.8831 (t80)
REVERT: B  108 ASP cc_start: 0.6806 (m-30) cc_final: 0.6318 (m-30)
REVERT: B  109 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7416 (tp)
REVERT: B  242 PHE cc_start: 0.8682 (m-80) cc_final: 0.8344 (m-80)
REVERT: B  249 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8053 (tm-30)
REVERT: B  309 CYS cc_start: 0.8795 (t) cc_final: 0.8377 (t)
REVERT: B  328 HIS cc_start: 0.7931 (p90) cc_final: 0.7690 (p90)
REVERT: C   60 LEU cc_start: 0.8765 (tp) cc_final: 0.8422 (tt)
REVERT: C  109 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7074 (tp)
REVERT: C  224 ASP cc_start: 0.8755 (t0) cc_final: 0.8554 (t0)
REVERT: C  242 PHE cc_start: 0.8676 (m-80) cc_final: 0.8424 (m-80)
REVERT: C  280 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8417 (mtt180)
REVERT: C  309 CYS cc_start: 0.8799 (t) cc_final: 0.8276 (t)
  outliers start: 42
  outliers final: 27
  residues processed: 283
  average time/residue: 0.1997
  time to fit residues: 80.9278
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  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain 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  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  360 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  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  291 CYS
Chi-restraints excluded: chain C residue  313 CYS
Chi-restraints excluded: chain C residue  366 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0030
   chunk 48 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9980
   chunk 118 optimal weight:    5.9990
   chunk 125 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
A 111 HIS
B 111 HIS
C 111 HIS
C 227 GLN
** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.159991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.136034 restraints weight = 16953.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.139984 restraints weight = 9651.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.142675 restraints weight = 6573.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9888  Z= 0.177
  Angle     :  0.566   7.368  13458  Z= 0.296
  Chirality :  0.043   0.349   1512
  Planarity :  0.004   0.025   1749
  Dihedral  :  5.122  25.740   1500
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.90 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.24), residues: 1266
  helix:  0.72 (0.25), residues: 444
  sheet: -1.20 (0.31), residues: 270
  loop : -0.50 (0.28), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  47 
 HIS   0.003   0.001   HIS A 251 
 PHE   0.015   0.001   PHE A 270 
 TYR   0.015   0.001   TYR C  68 
 ARG   0.005   0.001   ARG C 100 

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

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 234
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.6713 (m-30) cc_final: 0.6504 (m-30)
REVERT: A  109 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7150 (tp)
REVERT: A  249 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7884 (tm-30)
REVERT: A  280 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8124 (mtt180)
REVERT: A  425 TYR cc_start: 0.8557 (t80) cc_final: 0.7192 (t80)
REVERT: A  430 LEU cc_start: 0.9152 (tp) cc_final: 0.8865 (tp)
REVERT: A  441 PHE cc_start: 0.8109 (m-80) cc_final: 0.7905 (m-80)
REVERT: B   60 LEU cc_start: 0.8602 (tp) cc_final: 0.8246 (tt)
REVERT: B   68 TYR cc_start: 0.9060 (t80) cc_final: 0.8801 (t80)
REVERT: B  109 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7282 (tp)
REVERT: B  217 ASN cc_start: 0.7607 (m110) cc_final: 0.6467 (t0)
REVERT: B  249 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8000 (tt0)
REVERT: B  262 LEU cc_start: 0.9318 (mp) cc_final: 0.8950 (mt)
REVERT: B  309 CYS cc_start: 0.8790 (t) cc_final: 0.8265 (t)
REVERT: C   60 LEU cc_start: 0.8456 (tp) cc_final: 0.8121 (tt)
REVERT: C  109 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6865 (tp)
REVERT: C  217 ASN cc_start: 0.7517 (m110) cc_final: 0.6662 (t0)
REVERT: C  309 CYS cc_start: 0.8768 (t) cc_final: 0.8184 (t)
  outliers start: 31
  outliers final: 19
  residues processed: 257
  average time/residue: 0.1792
  time to fit residues: 66.6990
Evaluate side-chains
  239 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 217
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 ASN
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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**
C 227 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.158532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.134401 restraints weight = 16838.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138366 restraints weight = 9705.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.141004 restraints weight = 6634.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9888  Z= 0.236
  Angle     :  0.575   7.281  13458  Z= 0.297
  Chirality :  0.043   0.336   1512
  Planarity :  0.004   0.027   1749
  Dihedral  :  4.817  24.527   1500
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.65 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.24), residues: 1266
  helix:  1.04 (0.25), residues: 441
  sheet: -1.07 (0.32), residues: 258
  loop : -0.56 (0.28), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 234 
 HIS   0.004   0.001   HIS B 328 
 PHE   0.014   0.002   PHE B  93 
 TYR   0.014   0.001   TYR B 399 
 ARG   0.004   0.001   ARG C 310 

*********************** 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
  259 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 227
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7277 (tp)
REVERT: A  224 ASP cc_start: 0.8645 (t0) cc_final: 0.8378 (t0)
REVERT: A  249 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7891 (tm-30)
REVERT: A  262 LEU cc_start: 0.9263 (mp) cc_final: 0.9025 (mt)
REVERT: A  278 GLU cc_start: 0.8209 (tt0) cc_final: 0.7743 (tt0)
REVERT: A  280 ARG cc_start: 0.8681 (mtt180) cc_final: 0.8023 (mtt180)
REVERT: B   60 LEU cc_start: 0.8633 (tp) cc_final: 0.8363 (tt)
REVERT: B  108 ASP cc_start: 0.6549 (m-30) cc_final: 0.5990 (m-30)
REVERT: B  217 ASN cc_start: 0.7656 (m110) cc_final: 0.6666 (t0)
REVERT: B  249 GLN cc_start: 0.8624 (tm-30) cc_final: 0.7430 (tm-30)
REVERT: B  309 CYS cc_start: 0.8872 (t) cc_final: 0.8414 (t)
REVERT: B  314 GLU cc_start: 0.7123 (mp0) cc_final: 0.6855 (mp0)
REVERT: C  109 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7060 (tp)
REVERT: C  280 ARG cc_start: 0.8935 (mtt180) cc_final: 0.8480 (mtt180)
REVERT: C  309 CYS cc_start: 0.8739 (t) cc_final: 0.8182 (t)
  outliers start: 32
  outliers final: 22
  residues processed: 246
  average time/residue: 0.1842
  time to fit residues: 65.1893
Evaluate side-chains
  238 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 214
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
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  380 ILE
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  313 CYS
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0470
   chunk 101 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.0084

-------------------------------------------------------------------------------
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**
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.160036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.136253 restraints weight = 16817.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.140270 restraints weight = 9631.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.142968 restraints weight = 6541.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9888  Z= 0.186
  Angle     :  0.560   8.018  13458  Z= 0.287
  Chirality :  0.042   0.329   1512
  Planarity :  0.003   0.024   1749
  Dihedral  :  4.586  23.166   1500
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 22.51 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.25), residues: 1266
  helix:  1.22 (0.25), residues: 441
  sheet: -0.91 (0.32), residues: 258
  loop : -0.46 (0.28), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  47 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.012   0.001   PHE B 242 
 TYR   0.015   0.001   TYR C  68 
 ARG   0.004   0.000   ARG C 310 

*********************** 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
  257 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 223
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8394 (tp) cc_final: 0.8142 (tt)
REVERT: A  109 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7139 (tp)
REVERT: A  224 ASP cc_start: 0.8646 (t0) cc_final: 0.8418 (t0)
REVERT: A  249 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: A  278 GLU cc_start: 0.8203 (tt0) cc_final: 0.7896 (tt0)
REVERT: A  280 ARG cc_start: 0.8680 (mtt180) cc_final: 0.8103 (mtt180)
REVERT: A  341 TYR cc_start: 0.7495 (m-10) cc_final: 0.6977 (m-10)
REVERT: A  425 TYR cc_start: 0.8606 (t80) cc_final: 0.7202 (t80)
REVERT: B   60 LEU cc_start: 0.8498 (tp) cc_final: 0.8212 (tt)
REVERT: B  249 GLN cc_start: 0.8631 (tm-30) cc_final: 0.7359 (tm-30)
REVERT: B  309 CYS cc_start: 0.8838 (t) cc_final: 0.8369 (t)
REVERT: B  314 GLU cc_start: 0.7227 (mp0) cc_final: 0.6997 (mp0)
REVERT: C  109 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6930 (tp)
REVERT: C  280 ARG cc_start: 0.8945 (mtt180) cc_final: 0.8527 (mtt180)
REVERT: C  309 CYS cc_start: 0.8724 (t) cc_final: 0.8122 (t)
  outliers start: 34
  outliers final: 24
  residues processed: 242
  average time/residue: 0.1912
  time to fit residues: 67.9603
Evaluate side-chains
  242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 216
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
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  380 ILE
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  249 GLN
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  313 CYS
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:    0.1980
   chunk 42 optimal weight:    6.9990
   chunk 121 optimal weight:    6.9990
   chunk 89 optimal weight:    0.1980
   chunk 44 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 93 optimal weight:   20.0000
   chunk 101 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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**
C 437 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.159285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.135600 restraints weight = 17052.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.139592 restraints weight = 9694.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.142279 restraints weight = 6554.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9888  Z= 0.187
  Angle     :  0.561   8.096  13458  Z= 0.285
  Chirality :  0.042   0.325   1512
  Planarity :  0.004   0.032   1749
  Dihedral  :  4.480  22.024   1500
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 21.97 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.25), residues: 1266
  helix:  1.30 (0.26), residues: 441
  sheet: -0.83 (0.33), residues: 258
  loop : -0.38 (0.28), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  47 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.012   0.001   PHE B  93 
 TYR   0.016   0.001   TYR B  68 
 ARG   0.004   0.000   ARG C 310 

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

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 213
  time to evaluate  : 1.077 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8394 (tp) cc_final: 0.8126 (tt)
REVERT: A  109 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7231 (tp)
REVERT: A  224 ASP cc_start: 0.8653 (t0) cc_final: 0.8407 (t0)
REVERT: A  249 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: A  278 GLU cc_start: 0.8229 (tt0) cc_final: 0.7939 (tt0)
REVERT: A  280 ARG cc_start: 0.8671 (mtt180) cc_final: 0.8007 (mtt180)
REVERT: A  341 TYR cc_start: 0.7496 (m-10) cc_final: 0.6973 (m-10)
REVERT: A  425 TYR cc_start: 0.8557 (t80) cc_final: 0.7136 (t80)
REVERT: B   60 LEU cc_start: 0.8429 (tp) cc_final: 0.8137 (tt)
REVERT: B  108 ASP cc_start: 0.6428 (m-30) cc_final: 0.5882 (m-30)
REVERT: B  249 GLN cc_start: 0.8659 (tm-30) cc_final: 0.7427 (tm-30)
REVERT: B  309 CYS cc_start: 0.8777 (t) cc_final: 0.8339 (t)
REVERT: C  109 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6929 (tp)
REVERT: C  280 ARG cc_start: 0.8944 (mtt180) cc_final: 0.8546 (mtt180)
REVERT: C  309 CYS cc_start: 0.8718 (t) cc_final: 0.8236 (t)
  outliers start: 38
  outliers final: 26
  residues processed: 236
  average time/residue: 0.1807
  time to fit residues: 62.3931
Evaluate side-chains
  236 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 208
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
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  380 ILE
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  313 CYS
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0000
   chunk 14 optimal weight:    0.8980
   chunk 94 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 101 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 103 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
** B  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.159158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.135132 restraints weight = 17003.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.139162 restraints weight = 9660.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.141837 restraints weight = 6556.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9888  Z= 0.197
  Angle     :  0.579   7.639  13458  Z= 0.294
  Chirality :  0.043   0.321   1512
  Planarity :  0.004   0.031   1749
  Dihedral  :  4.411  21.317   1500
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 21.86 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.25), residues: 1266
  helix:  1.30 (0.26), residues: 444
  sheet: -0.82 (0.32), residues: 270
  loop : -0.24 (0.29), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  47 
 HIS   0.003   0.001   HIS A 251 
 PHE   0.016   0.001   PHE B  93 
 TYR   0.012   0.001   TYR C  68 
 ARG   0.004   0.000   ARG C 310 

*********************** 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
  254 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 215
  time to evaluate  : 1.037 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8404 (tp) cc_final: 0.8132 (tt)
REVERT: A  109 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7212 (tp)
REVERT: A  224 ASP cc_start: 0.8665 (t0) cc_final: 0.8422 (t0)
REVERT: A  249 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7886 (tm-30)
REVERT: A  280 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8107 (mtt180)
REVERT: A  326 MET cc_start: 0.7358 (mmm) cc_final: 0.7104 (mmm)
REVERT: A  341 TYR cc_start: 0.7377 (m-10) cc_final: 0.7071 (m-10)
REVERT: A  425 TYR cc_start: 0.8570 (t80) cc_final: 0.7164 (t80)
REVERT: B   60 LEU cc_start: 0.8431 (tp) cc_final: 0.8117 (tt)
REVERT: B  249 GLN cc_start: 0.8657 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: B  309 CYS cc_start: 0.8844 (t) cc_final: 0.8429 (t)
REVERT: C  109 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6949 (tp)
REVERT: C  280 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8506 (mtt180)
REVERT: C  309 CYS cc_start: 0.8731 (t) cc_final: 0.8240 (t)
REVERT: C  437 GLN cc_start: 0.8732 (mt0) cc_final: 0.8508 (mt0)
  outliers start: 39
  outliers final: 31
  residues processed: 238
  average time/residue: 0.1848
  time to fit residues: 64.5403
Evaluate side-chains
  243 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 210
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  169 MET
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 B residue   84 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  314 GLU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  380 ILE
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  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  313 CYS
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  412 GLU
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0170
   chunk 98 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
** B  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.161627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.137710 restraints weight = 16902.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141741 restraints weight = 9633.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.144426 restraints weight = 6529.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   9888  Z= 0.156
  Angle     :  0.570   9.149  13458  Z= 0.288
  Chirality :  0.042   0.318   1512
  Planarity :  0.004   0.040   1749
  Dihedral  :  4.239  19.870   1500
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.94 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.25), residues: 1266
  helix:  1.47 (0.26), residues: 441
  sheet: -0.57 (0.33), residues: 258
  loop : -0.25 (0.28), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  47 
 HIS   0.003   0.001   HIS A 251 
 PHE   0.013   0.001   PHE B 300 
 TYR   0.010   0.001   TYR B 457 
 ARG   0.005   0.000   ARG B 310 

*********************** 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
  248 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 216
  time to evaluate  : 1.753 
Fit side-chains
REVERT: A  109 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7200 (tp)
REVERT: A  249 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: A  280 ARG cc_start: 0.8659 (mtt180) cc_final: 0.7982 (mtt180)
REVERT: A  326 MET cc_start: 0.7407 (mmm) cc_final: 0.7143 (mmm)
REVERT: A  341 TYR cc_start: 0.7144 (m-10) cc_final: 0.6714 (m-10)
REVERT: A  425 TYR cc_start: 0.8512 (t80) cc_final: 0.7186 (t80)
REVERT: B  108 ASP cc_start: 0.6456 (m-30) cc_final: 0.5877 (m-30)
REVERT: B  249 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8046 (tt0)
REVERT: B  262 LEU cc_start: 0.9323 (mt) cc_final: 0.9062 (mp)
REVERT: B  309 CYS cc_start: 0.8746 (t) cc_final: 0.8288 (t)
REVERT: C  109 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6934 (tp)
REVERT: C  280 ARG cc_start: 0.8884 (mtt180) cc_final: 0.8519 (mtt180)
REVERT: C  309 CYS cc_start: 0.8693 (t) cc_final: 0.8205 (t)
  outliers start: 32
  outliers final: 24
  residues processed: 231
  average time/residue: 0.1858
  time to fit residues: 63.4469
Evaluate side-chains
  235 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 209
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
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 B residue   84 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  314 GLU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  313 CYS
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  417 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 118 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** B  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.159034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.134090 restraints weight = 17143.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.138108 restraints weight = 9730.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.140706 restraints weight = 6620.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.4636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9888  Z= 0.226
  Angle     :  0.593   9.443  13458  Z= 0.300
  Chirality :  0.043   0.307   1512
  Planarity :  0.004   0.041   1749
  Dihedral  :  4.321  18.310   1500
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.25), residues: 1266
  helix:  1.39 (0.26), residues: 441
  sheet: -0.70 (0.32), residues: 270
  loop : -0.08 (0.29), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 234 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.017   0.001   PHE B  93 
 TYR   0.014   0.001   TYR C 110 
 ARG   0.004   0.000   ARG B 310 

********************** 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
  245 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 217
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A  109 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7251 (tp)
REVERT: A  224 ASP cc_start: 0.8695 (t0) cc_final: 0.8451 (t0)
REVERT: A  249 GLN cc_start: 0.8480 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: A  326 MET cc_start: 0.7432 (mmm) cc_final: 0.6495 (mmm)
REVERT: A  341 TYR cc_start: 0.7435 (m-10) cc_final: 0.6452 (m-10)
REVERT: B   61 VAL cc_start: 0.8734 (p) cc_final: 0.8509 (p)
REVERT: B  230 TYR cc_start: 0.9318 (m-80) cc_final: 0.9063 (m-80)
REVERT: B  249 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8054 (tt0)
REVERT: B  309 CYS cc_start: 0.8752 (t) cc_final: 0.8271 (t)
REVERT: B  329 MET cc_start: 0.7561 (ptp) cc_final: 0.7274 (ptp)
REVERT: C  109 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7062 (tp)
REVERT: C  280 ARG cc_start: 0.8900 (mtt180) cc_final: 0.8564 (mtt180)
REVERT: C  309 CYS cc_start: 0.8680 (t) cc_final: 0.8192 (t)
REVERT: C  437 GLN cc_start: 0.8783 (mt0) cc_final: 0.8521 (mt0)
  outliers start: 28
  outliers final: 23
  residues processed: 230
  average time/residue: 0.1801
  time to fit residues: 60.6725
Evaluate side-chains
  237 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 212
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
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 B residue   84 THR
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  366 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  109 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  313 CYS
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 95 optimal weight:    0.1980
   chunk 80 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0060
   chunk 18 optimal weight:    6.9990
   chunk 119 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    0.8200

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.159466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.134649 restraints weight = 16987.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.138635 restraints weight = 9575.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.141251 restraints weight = 6496.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9888  Z= 0.170
  Angle     :  0.575   9.115  13458  Z= 0.291
  Chirality :  0.042   0.310   1512
  Planarity :  0.004   0.039   1749
  Dihedral  :  4.235  17.609   1500
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.79 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.25), residues: 1266
  helix:  1.44 (0.26), residues: 441
  sheet: -0.58 (0.33), residues: 270
  loop :  0.00 (0.29), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 234 
 HIS   0.003   0.001   HIS A 251 
 PHE   0.013   0.001   PHE B  93 
 TYR   0.010   0.001   TYR B 457 
 ARG   0.004   0.001   ARG C 310 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2982.79 seconds
wall clock time: 54 minutes 17.60 seconds (3257.60 seconds total)