Starting phenix.real_space_refine
on Sun Jun 15 04:46:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymw_39409/06_2025/8ymw_39409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymw_39409/06_2025/8ymw_39409.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ymw_39409/06_2025/8ymw_39409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymw_39409/06_2025/8ymw_39409.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymw_39409/06_2025/8ymw_39409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymw_39409/06_2025/8ymw_39409.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.029
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: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5526      2.51       5
     N    1446      2.21       5
     O    1584      1.98       5
     H    8466      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17079
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 356, 5693
          Classifications: {'peptide': 356}
          Link IDs: {'PTRANS': 17, 'TRANS': 338}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 12.36, per 1000 atoms: 0.72
  Number of scatterers: 17079
  At special positions: 0
  Unit cell: (95.79, 100.44, 123.69, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     O    1584      8.00
     N    1446      7.00
     C    5526      6.00
     H    8466      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 273 " - pdb=" SG  CYS A 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 106 " - pdb=" SG  CYS C 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 106 " - pdb=" SG  CYS B 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 273 " - pdb=" SG  CYS C 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 273 " - pdb=" SG  CYS B 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 282 " - pdb=" SG  CYS C 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 282 " - pdb=" SG  CYS B 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 299 " - pdb=" SG  CYS C 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 299 " - pdb=" SG  CYS B 311 " 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
  Time building additional restraints: 4.03
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      40.0% alpha, 28.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 84
    Processing helix  chain 'A' and resid 113 through 123
      removed outlier: 3.569A  pdb=" N   THR A 117 " --> pdb=" O   ASN A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
    Processing helix  chain 'A' and resid 140 through 147
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 240 through 245
    Processing helix  chain 'A' and resid 275 through 296
    Processing helix  chain 'A' and resid 313 through 335
      removed outlier: 5.470A  pdb=" N   GLU A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LYS A 333 " --> pdb=" O   GLN A 329 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLU A 334 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 398
    Processing helix  chain 'A' and resid 401 through 411
    Processing helix  chain 'B' and resid 57 through 84
    Processing helix  chain 'B' and resid 113 through 123
      removed outlier: 3.569A  pdb=" N   THR B 117 " --> pdb=" O   ASN B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 136
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 233 through 240
    Processing helix  chain 'B' and resid 240 through 245
    Processing helix  chain 'B' and resid 275 through 296
    Processing helix  chain 'B' and resid 313 through 335
      removed outlier: 5.470A  pdb=" N   GLU B 332 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LYS B 333 " --> pdb=" O   GLN B 329 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU B 334 " --> pdb=" O   ASN B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 398
    Processing helix  chain 'B' and resid 401 through 411
    Processing helix  chain 'C' and resid 57 through 84
    Processing helix  chain 'C' and resid 113 through 123
      removed outlier: 3.568A  pdb=" N   THR C 117 " --> pdb=" O   ASN C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 136
    Processing helix  chain 'C' and resid 140 through 147
    Processing helix  chain 'C' and resid 233 through 240
    Processing helix  chain 'C' and resid 240 through 245
    Processing helix  chain 'C' and resid 275 through 296
    Processing helix  chain 'C' and resid 313 through 335
      removed outlier: 5.470A  pdb=" N   GLU C 332 " --> pdb=" O   ILE C 328 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LYS C 333 " --> pdb=" O   GLN C 329 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU C 334 " --> pdb=" O   ASN C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 398
    Processing helix  chain 'C' and resid 401 through 411
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94
      removed outlier: 14.395A  pdb=" N   TYR A 371 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 10.506A  pdb=" N   ILE A 258 " --> pdb=" O   TYR A 371 " (cutoff:3.500A)
      removed outlier: 9.598A  pdb=" N   GLN A 373 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   PHE A 260 " --> pdb=" O   GLN A 373 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ALA A 375 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN A 262 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   GLU A 377 " --> pdb=" O   GLN A 262 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN A 264 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU A 379 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   GLY A 162 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR A 170 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94
      removed outlier: 14.395A  pdb=" N   TYR A 371 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 10.506A  pdb=" N   ILE A 258 " --> pdb=" O   TYR A 371 " (cutoff:3.500A)
      removed outlier: 9.598A  pdb=" N   GLN A 373 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   PHE A 260 " --> pdb=" O   GLN A 373 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ALA A 375 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN A 262 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   GLU A 377 " --> pdb=" O   GLN A 262 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN A 264 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU A 379 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 183
      removed outlier: 7.193A  pdb=" N   GLN A 187 " --> pdb=" O   PRO A 107 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE A 103 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 94
      removed outlier: 14.394A  pdb=" N   TYR B 371 " --> pdb=" O   PHE B 256 " (cutoff:3.500A)
      removed outlier: 10.506A  pdb=" N   ILE B 258 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
      removed outlier: 9.598A  pdb=" N   GLN B 373 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   PHE B 260 " --> pdb=" O   GLN B 373 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   ALA B 375 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN B 262 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   GLU B 377 " --> pdb=" O   GLN B 262 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN B 264 " --> pdb=" O   GLU B 377 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU B 379 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   GLY B 162 " --> pdb=" O   TYR B 170 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR B 170 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 94
      removed outlier: 14.394A  pdb=" N   TYR B 371 " --> pdb=" O   PHE B 256 " (cutoff:3.500A)
      removed outlier: 10.506A  pdb=" N   ILE B 258 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
      removed outlier: 9.598A  pdb=" N   GLN B 373 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   PHE B 260 " --> pdb=" O   GLN B 373 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   ALA B 375 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN B 262 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   GLU B 377 " --> pdb=" O   GLN B 262 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN B 264 " --> pdb=" O   GLU B 377 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU B 379 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183
      removed outlier: 7.192A  pdb=" N   GLN B 187 " --> pdb=" O   PRO B 107 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE B 103 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 94
      removed outlier: 14.395A  pdb=" N   TYR C 371 " --> pdb=" O   PHE C 256 " (cutoff:3.500A)
      removed outlier: 10.506A  pdb=" N   ILE C 258 " --> pdb=" O   TYR C 371 " (cutoff:3.500A)
      removed outlier: 9.598A  pdb=" N   GLN C 373 " --> pdb=" O   ILE C 258 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   PHE C 260 " --> pdb=" O   GLN C 373 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   ALA C 375 " --> pdb=" O   PHE C 260 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN C 262 " --> pdb=" O   ALA C 375 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   GLU C 377 " --> pdb=" O   GLN C 262 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN C 264 " --> pdb=" O   GLU C 377 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU C 379 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   GLY C 162 " --> pdb=" O   TYR C 170 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR C 170 " --> pdb=" O   GLY C 162 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 94
      removed outlier: 14.395A  pdb=" N   TYR C 371 " --> pdb=" O   PHE C 256 " (cutoff:3.500A)
      removed outlier: 10.506A  pdb=" N   ILE C 258 " --> pdb=" O   TYR C 371 " (cutoff:3.500A)
      removed outlier: 9.598A  pdb=" N   GLN C 373 " --> pdb=" O   ILE C 258 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   PHE C 260 " --> pdb=" O   GLN C 373 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   ALA C 375 " --> pdb=" O   PHE C 260 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN C 262 " --> pdb=" O   ALA C 375 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   GLU C 377 " --> pdb=" O   GLN C 262 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN C 264 " --> pdb=" O   GLU C 377 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   LEU C 379 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98
    Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 183
      removed outlier: 7.193A  pdb=" N   GLN C 187 " --> pdb=" O   PRO C 107 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE C 103 " --> pdb=" O   ILE C 191 " (cutoff:3.500A)

    481 hydrogen bonds defined for protein.
    1308 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.72

  Time building geometry restraints manager: 4.83 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 8457
        1.04 -     1.23: 385
        1.23 -     1.43: 3420
        1.43 -     1.63: 4943
        1.63 -     1.83: 81
  Bond restraints: 17286
  Sorted by residual:
  bond pdb=" CB  ASP A 126 "
       pdb=" CG  ASP A 126 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" CB  ASP B 126 "
       pdb=" CG  ASP B 126 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.10e+00
  bond pdb=" CB  ASP C 126 "
       pdb=" CG  ASP C 126 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.07e+00
  bond pdb=" CA  SER A 176 "
       pdb=" C   SER A 176 "
    ideal  model  delta    sigma   weight residual
    1.531  1.521  0.010 1.08e-02 8.57e+03 8.91e-01
  bond pdb=" CA  SER B 176 "
       pdb=" C   SER B 176 "
    ideal  model  delta    sigma   weight residual
    1.531  1.521  0.010 1.08e-02 8.57e+03 8.56e-01
  ... (remaining 17281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.42: 31164
        7.42 -    14.83: 0
       14.83 -    22.25: 0
       22.25 -    29.66: 0
       29.66 -    37.08: 9
  Bond angle restraints: 31173
  Sorted by residual:
  angle pdb=" N   ASP C 126 "
        pdb=" CA  ASP C 126 "
        pdb=" HA  ASP C 126 "
      ideal   model   delta    sigma   weight residual
     110.00   72.92   37.08 3.00e+00 1.11e-01 1.53e+02
  angle pdb=" N   ASP A 126 "
        pdb=" CA  ASP A 126 "
        pdb=" HA  ASP A 126 "
      ideal   model   delta    sigma   weight residual
     110.00   72.98   37.02 3.00e+00 1.11e-01 1.52e+02
  angle pdb=" N   ASP B 126 "
        pdb=" CA  ASP B 126 "
        pdb=" HA  ASP B 126 "
      ideal   model   delta    sigma   weight residual
     110.00   72.98   37.02 3.00e+00 1.11e-01 1.52e+02
  angle pdb=" C   ASP A 126 "
        pdb=" CA  ASP A 126 "
        pdb=" HA  ASP A 126 "
      ideal   model   delta    sigma   weight residual
     109.00   74.66   34.34 3.00e+00 1.11e-01 1.31e+02
  angle pdb=" C   ASP C 126 "
        pdb=" CA  ASP C 126 "
        pdb=" HA  ASP C 126 "
      ideal   model   delta    sigma   weight residual
     109.00   74.71   34.29 3.00e+00 1.11e-01 1.31e+02
  ... (remaining 31168 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 7209
       17.31 -    34.61: 739
       34.61 -    51.92: 215
       51.92 -    69.22: 63
       69.22 -    86.53: 18
  Dihedral angle restraints: 8244
    sinusoidal: 4416
      harmonic: 3828
  Sorted by residual:
  dihedral pdb=" CB  CYS C 299 "
           pdb=" SG  CYS C 299 "
           pdb=" SG  CYS C 311 "
           pdb=" CB  CYS C 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.26  -63.26     1      1.00e+01 1.00e-02 5.28e+01
  dihedral pdb=" CB  CYS B 299 "
           pdb=" SG  CYS B 299 "
           pdb=" SG  CYS B 311 "
           pdb=" CB  CYS B 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.23  -63.23     1      1.00e+01 1.00e-02 5.28e+01
  dihedral pdb=" CB  CYS A 299 "
           pdb=" SG  CYS A 299 "
           pdb=" SG  CYS A 311 "
           pdb=" CB  CYS A 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.21  -63.21     1      1.00e+01 1.00e-02 5.27e+01
  ... (remaining 8241 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1207
       0.069 -    0.139: 128
       0.139 -    0.208: 6
       0.208 -    0.278: 0
       0.278 -    0.347: 3
  Chirality restraints: 1344
  Sorted by residual:
  chirality pdb=" CA  ASP B 126 "
            pdb=" N   ASP B 126 "
            pdb=" C   ASP B 126 "
            pdb=" CB  ASP B 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  ASP A 126 "
            pdb=" N   ASP A 126 "
            pdb=" C   ASP A 126 "
            pdb=" CB  ASP A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" CA  ASP C 126 "
            pdb=" N   ASP C 126 "
            pdb=" C   ASP C 126 "
            pdb=" CB  ASP C 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.97e+00
  ... (remaining 1341 not shown)

  Planarity restraints: 2559
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 305 "   -0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO C 306 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C 306 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 306 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 305 "   -0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO B 306 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 306 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 306 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 305 "   -0.028 5.00e-02 4.00e+02   4.36e-02 3.05e+00
        pdb=" N   PRO A 306 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 306 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 306 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 2556 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 740
        2.16 -     2.77: 33224
        2.77 -     3.38: 47905
        3.38 -     3.99: 63591
        3.99 -     4.60: 98535
  Nonbonded interactions: 243995
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 394 "
            pdb=" H   GLY A 399 "
     model   vdw
     1.551 2.450
  nonbonded pdb=" O   LEU B 394 "
            pdb=" H   GLY B 399 "
     model   vdw
     1.552 2.450
  nonbonded pdb=" O   LEU C 394 "
            pdb=" H   GLY C 399 "
     model   vdw
     1.552 2.450
  nonbonded pdb="HH21 ARG C 238 "
            pdb=" OE2 GLU C 284 "
     model   vdw
     1.645 2.450
  nonbonded pdb="HH21 ARG B 238 "
            pdb=" OE2 GLU B 284 "
     model   vdw
     1.645 2.450
  ... (remaining 243990 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: 0.06
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 individual isotropic
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:             1.340
  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:             0.330
  Extract box with map and model:          0.650
  Check model and map are aligned:         0.160
  Set scattering table:                    0.170
  Process input model:                     40.380
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
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      :  0.003   0.027   8832  Z= 0.144
  Angle     :  0.536   5.438  12006  Z= 0.287
  Chirality :  0.046   0.347   1344
  Planarity :  0.004   0.044   1545
  Dihedral  : 16.423  86.530   3237
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 23.05 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.27 (0.27), residues: 1062
  helix:  1.88 (0.27), residues: 402
  sheet: -1.72 (0.31), residues: 267
  loop : -1.14 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 145 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.012   0.001   PHE A 350 
 TYR   0.007   0.001   TYR B 170 
 ARG   0.001   0.000   ARG A 244 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11476 (  457)
  hydrogen bonds       : angle       5.57242 ( 1308)
  SS BOND              : bond        0.00345 (   12)
  SS BOND              : angle       2.21801 (   24)
  covalent geometry    : bond        0.00327 ( 8820)
  covalent geometry    : angle       0.52757 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 133
  time to evaluate  : 1.198 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7072 (mp0)
REVERT: C  330 ASN cc_start: 0.8177 (m-40) cc_final: 0.7932 (m110)
  outliers start: 3
  outliers final: 3
  residues processed: 133
  average time/residue: 0.4261
  time to fit residues: 80.3795
Evaluate side-chains
  131 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 128
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain C residue  400 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 82 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.175566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.139382 restraints weight = 26065.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.25
r_work: 0.3416 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.0654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8832  Z= 0.183
  Angle     :  0.535   4.435  12006  Z= 0.285
  Chirality :  0.047   0.351   1344
  Planarity :  0.004   0.039   1545
  Dihedral  :  4.626  22.486   1188
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 22.85 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.27), residues: 1062
  helix:  1.56 (0.27), residues: 408
  sheet: -1.70 (0.31), residues: 267
  loop : -1.16 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 145 
 HIS   0.004   0.001   HIS A 231 
 PHE   0.012   0.001   PHE B 205 
 TYR   0.011   0.001   TYR A 170 
 ARG   0.003   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  457)
  hydrogen bonds       : angle       4.66926 ( 1308)
  SS BOND              : bond        0.00438 (   12)
  SS BOND              : angle       1.77775 (   24)
  covalent geometry    : bond        0.00438 ( 8820)
  covalent geometry    : angle       0.52930 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 1.552 
Fit side-chains
REVERT: A  127 LYS cc_start: 0.7981 (pttt) cc_final: 0.7750 (pttp)
REVERT: A  172 ASP cc_start: 0.8182 (t0) cc_final: 0.7791 (t0)
REVERT: C  398 LEU cc_start: 0.8006 (mt) cc_final: 0.7616 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 142
  average time/residue: 0.4963
  time to fit residues: 101.5214
Evaluate side-chains
  140 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 133
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  299 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
C 330 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.175583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.139344 restraints weight = 25964.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.26
r_work: 0.3413 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.0824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8832  Z= 0.161
  Angle     :  0.513   4.372  12006  Z= 0.271
  Chirality :  0.047   0.350   1344
  Planarity :  0.004   0.036   1545
  Dihedral  :  4.433  19.908   1182
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 23.26 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.42 (0.26), residues: 1062
  helix:  1.78 (0.27), residues: 390
  sheet: -1.63 (0.30), residues: 282
  loop : -1.26 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 145 
 HIS   0.004   0.001   HIS A 231 
 PHE   0.011   0.001   PHE B 205 
 TYR   0.009   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03274 (  457)
  hydrogen bonds       : angle       4.50594 ( 1308)
  SS BOND              : bond        0.00389 (   12)
  SS BOND              : angle       1.93056 (   24)
  covalent geometry    : bond        0.00384 ( 8820)
  covalent geometry    : angle       0.50624 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 139
  time to evaluate  : 1.254 
Fit side-chains
REVERT: A  127 LYS cc_start: 0.7956 (pttt) cc_final: 0.7727 (pttp)
REVERT: A  169 SER cc_start: 0.8828 (p) cc_final: 0.8399 (t)
REVERT: A  172 ASP cc_start: 0.8169 (t0) cc_final: 0.7638 (t0)
REVERT: A  326 ASP cc_start: 0.8151 (t0) cc_final: 0.7847 (t0)
REVERT: B  172 ASP cc_start: 0.8338 (t70) cc_final: 0.7867 (t70)
REVERT: C  127 LYS cc_start: 0.8069 (pttt) cc_final: 0.7835 (pttp)
REVERT: C  169 SER cc_start: 0.8824 (p) cc_final: 0.8470 (t)
REVERT: C  398 LEU cc_start: 0.7928 (mt) cc_final: 0.7718 (mt)
  outliers start: 9
  outliers final: 5
  residues processed: 144
  average time/residue: 0.3650
  time to fit residues: 77.1449
Evaluate side-chains
  141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain C residue  299 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.176605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.139452 restraints weight = 25904.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.30
r_work: 0.3413 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.0966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8832  Z= 0.149
  Angle     :  0.504   4.395  12006  Z= 0.266
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.038   1545
  Dihedral  :  4.408  19.852   1182
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 22.22 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.26), residues: 1062
  helix:  1.86 (0.27), residues: 387
  sheet: -1.62 (0.30), residues: 282
  loop : -1.21 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 145 
 HIS   0.003   0.001   HIS A 231 
 PHE   0.011   0.001   PHE B 205 
 TYR   0.009   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03066 (  457)
  hydrogen bonds       : angle       4.39113 ( 1308)
  SS BOND              : bond        0.00375 (   12)
  SS BOND              : angle       1.87230 (   24)
  covalent geometry    : bond        0.00355 ( 8820)
  covalent geometry    : angle       0.49721 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A  127 LYS cc_start: 0.8005 (pttt) cc_final: 0.7801 (pttp)
REVERT: A  169 SER cc_start: 0.8828 (p) cc_final: 0.8422 (t)
REVERT: A  172 ASP cc_start: 0.8199 (t0) cc_final: 0.7578 (t0)
REVERT: A  326 ASP cc_start: 0.8364 (t0) cc_final: 0.7877 (t0)
REVERT: B  127 LYS cc_start: 0.8044 (pttt) cc_final: 0.7841 (pttp)
REVERT: B  172 ASP cc_start: 0.8376 (t70) cc_final: 0.7883 (t70)
REVERT: C   80 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7241 (t0)
REVERT: C  127 LYS cc_start: 0.8101 (pttt) cc_final: 0.7871 (pttp)
REVERT: C  169 SER cc_start: 0.8773 (p) cc_final: 0.8428 (t)
  outliers start: 20
  outliers final: 12
  residues processed: 158
  average time/residue: 0.3622
  time to fit residues: 83.7573
Evaluate side-chains
  153 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  282 CYS
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  282 CYS
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  299 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0870
   chunk 28 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 70 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.0362

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.178988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.142267 restraints weight = 26401.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.26
r_work: 0.3452 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8832  Z= 0.153
  Angle     :  0.504   4.563  12006  Z= 0.266
  Chirality :  0.046   0.350   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.413  20.095   1182
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 22.12 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.31 (0.26), residues: 1062
  helix:  1.90 (0.27), residues: 387
  sheet: -1.63 (0.30), residues: 282
  loop : -1.18 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 145 
 HIS   0.003   0.001   HIS A 231 
 PHE   0.011   0.001   PHE B 205 
 TYR   0.009   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03012 (  457)
  hydrogen bonds       : angle       4.35309 ( 1308)
  SS BOND              : bond        0.00377 (   12)
  SS BOND              : angle       1.90982 (   24)
  covalent geometry    : bond        0.00365 ( 8820)
  covalent geometry    : angle       0.49676 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 1.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 LYS cc_start: 0.7966 (pttt) cc_final: 0.7760 (pttp)
REVERT: A  169 SER cc_start: 0.8785 (p) cc_final: 0.8418 (t)
REVERT: A  172 ASP cc_start: 0.8202 (t0) cc_final: 0.7571 (t0)
REVERT: A  326 ASP cc_start: 0.8405 (t0) cc_final: 0.7914 (t0)
REVERT: B  169 SER cc_start: 0.8727 (p) cc_final: 0.8492 (t)
REVERT: C   80 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7210 (t0)
REVERT: C  127 LYS cc_start: 0.8041 (pttt) cc_final: 0.7836 (pttp)
REVERT: C  169 SER cc_start: 0.8772 (p) cc_final: 0.8467 (t)
REVERT: C  344 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8314 (m)
  outliers start: 20
  outliers final: 17
  residues processed: 155
  average time/residue: 0.4656
  time to fit residues: 106.9962
Evaluate side-chains
  157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 1.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  282 CYS
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain B residue   95 GLN
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  282 CYS
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain C residue   95 GLN
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  299 CYS
Chi-restraints excluded: chain C residue  344 THR
Chi-restraints excluded: chain C residue  400 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0020
   chunk 95 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.181207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.145075 restraints weight = 26322.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.22
r_work: 0.3466 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8832  Z= 0.119
  Angle     :  0.484   4.416  12006  Z= 0.254
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.336  20.194   1182
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 22.33 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.23 (0.26), residues: 1062
  helix:  1.99 (0.27), residues: 387
  sheet: -1.59 (0.30), residues: 282
  loop : -1.14 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 145 
 HIS   0.003   0.001   HIS A 231 
 PHE   0.013   0.001   PHE C 350 
 TYR   0.009   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02851 (  457)
  hydrogen bonds       : angle       4.24446 ( 1308)
  SS BOND              : bond        0.00343 (   12)
  SS BOND              : angle       1.74237 (   24)
  covalent geometry    : bond        0.00282 ( 8820)
  covalent geometry    : angle       0.47816 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 LYS cc_start: 0.7973 (pttt) cc_final: 0.7752 (pttp)
REVERT: A  169 SER cc_start: 0.8715 (p) cc_final: 0.8379 (t)
REVERT: A  172 ASP cc_start: 0.8190 (t0) cc_final: 0.7541 (t0)
REVERT: A  326 ASP cc_start: 0.8386 (t0) cc_final: 0.7825 (t0)
REVERT: C   80 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7220 (t0)
REVERT: C  169 SER cc_start: 0.8675 (p) cc_final: 0.8449 (t)
REVERT: C  344 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8279 (m)
  outliers start: 18
  outliers final: 13
  residues processed: 163
  average time/residue: 0.3651
  time to fit residues: 87.4087
Evaluate side-chains
  154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  282 CYS
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  282 CYS
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain C residue   95 GLN
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  299 CYS
Chi-restraints excluded: chain C residue  344 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 12 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.181486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.144868 restraints weight = 26230.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.24
r_work: 0.3467 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8832  Z= 0.128
  Angle     :  0.491   5.315  12006  Z= 0.257
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.037   1545
  Dihedral  :  4.352  21.752   1182
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 22.33 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.20 (0.26), residues: 1062
  helix:  2.02 (0.28), residues: 387
  sheet: -1.57 (0.30), residues: 282
  loop : -1.13 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 145 
 HIS   0.003   0.001   HIS C 231 
 PHE   0.011   0.001   PHE A 350 
 TYR   0.008   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02848 (  457)
  hydrogen bonds       : angle       4.19746 ( 1308)
  SS BOND              : bond        0.00359 (   12)
  SS BOND              : angle       2.10287 (   24)
  covalent geometry    : bond        0.00305 ( 8820)
  covalent geometry    : angle       0.48191 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 1.288 
Fit side-chains
REVERT: A   67 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7092 (t80)
REVERT: A  127 LYS cc_start: 0.7914 (pttt) cc_final: 0.7714 (pttp)
REVERT: A  169 SER cc_start: 0.8617 (p) cc_final: 0.8304 (t)
REVERT: A  172 ASP cc_start: 0.8198 (t0) cc_final: 0.7552 (t0)
REVERT: A  326 ASP cc_start: 0.8353 (t0) cc_final: 0.8080 (t0)
REVERT: B  172 ASP cc_start: 0.8071 (t70) cc_final: 0.7780 (t70)
REVERT: C   80 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7235 (t0)
REVERT: C  169 SER cc_start: 0.8647 (p) cc_final: 0.8441 (t)
  outliers start: 18
  outliers final: 12
  residues processed: 162
  average time/residue: 0.3667
  time to fit residues: 87.1547
Evaluate side-chains
  156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  282 CYS
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  282 CYS
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  299 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.180503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.143199 restraints weight = 26168.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.28
r_work: 0.3455 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8832  Z= 0.149
  Angle     :  0.502   4.632  12006  Z= 0.264
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.348  19.555   1182
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 22.33 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.23 (0.26), residues: 1062
  helix:  2.01 (0.28), residues: 387
  sheet: -1.60 (0.30), residues: 282
  loop : -1.16 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 145 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.011   0.001   PHE B 205 
 TYR   0.009   0.001   TYR B 366 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02866 (  457)
  hydrogen bonds       : angle       4.21586 ( 1308)
  SS BOND              : bond        0.00363 (   12)
  SS BOND              : angle       1.94921 (   24)
  covalent geometry    : bond        0.00356 ( 8820)
  covalent geometry    : angle       0.49442 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 LYS cc_start: 0.7943 (pttt) cc_final: 0.7736 (pttp)
REVERT: A  169 SER cc_start: 0.8610 (p) cc_final: 0.8302 (t)
REVERT: A  172 ASP cc_start: 0.8205 (t0) cc_final: 0.7545 (t0)
REVERT: A  294 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7510 (mmtp)
REVERT: B  172 ASP cc_start: 0.8085 (t70) cc_final: 0.7586 (t70)
REVERT: C   80 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7226 (t0)
REVERT: C  344 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8309 (m)
  outliers start: 15
  outliers final: 11
  residues processed: 157
  average time/residue: 0.4381
  time to fit residues: 99.5950
Evaluate side-chains
  148 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  282 CYS
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  282 CYS
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  299 CYS
Chi-restraints excluded: chain C residue  344 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.180907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.143416 restraints weight = 26403.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.29
r_work: 0.3456 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8832  Z= 0.137
  Angle     :  0.498   5.677  12006  Z= 0.261
  Chirality :  0.046   0.350   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.365  21.833   1182
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 22.43 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.16 (0.26), residues: 1062
  helix:  2.03 (0.28), residues: 387
  sheet: -1.62 (0.30), residues: 276
  loop : -1.03 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 145 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.013   0.001   PHE A 350 
 TYR   0.008   0.001   TYR A 381 
 ARG   0.002   0.000   ARG C 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02821 (  457)
  hydrogen bonds       : angle       4.17684 ( 1308)
  SS BOND              : bond        0.00354 (   12)
  SS BOND              : angle       2.10049 (   24)
  covalent geometry    : bond        0.00326 ( 8820)
  covalent geometry    : angle       0.48932 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 LYS cc_start: 0.7909 (pttt) cc_final: 0.7707 (pttp)
REVERT: A  169 SER cc_start: 0.8561 (p) cc_final: 0.8289 (t)
REVERT: A  172 ASP cc_start: 0.8218 (t0) cc_final: 0.7510 (t0)
REVERT: B  172 ASP cc_start: 0.8104 (t70) cc_final: 0.7564 (t70)
REVERT: C   80 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7245 (t0)
REVERT: C  344 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8306 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 148
  average time/residue: 0.4061
  time to fit residues: 86.5064
Evaluate side-chains
  147 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  282 CYS
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  282 CYS
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  299 CYS
Chi-restraints excluded: chain C residue  344 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    0.2980
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0770
   chunk 62 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.183021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.145701 restraints weight = 26255.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.30
r_work: 0.3485 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8832  Z= 0.104
  Angle     :  0.478   4.496  12006  Z= 0.250
  Chirality :  0.046   0.348   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.257  19.842   1182
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 22.43 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1062
  helix:  2.10 (0.28), residues: 387
  sheet: -1.58 (0.31), residues: 276
  loop : -1.00 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 145 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.010   0.001   PHE C 350 
 TYR   0.007   0.001   TYR B 366 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02657 (  457)
  hydrogen bonds       : angle       4.05865 ( 1308)
  SS BOND              : bond        0.00332 (   12)
  SS BOND              : angle       1.83555 (   24)
  covalent geometry    : bond        0.00245 ( 8820)
  covalent geometry    : angle       0.47098 (11982)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 2.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 LYS cc_start: 0.7974 (pttt) cc_final: 0.7759 (pttp)
REVERT: A  169 SER cc_start: 0.8499 (p) cc_final: 0.8249 (t)
REVERT: B  172 ASP cc_start: 0.8068 (t70) cc_final: 0.7805 (t70)
REVERT: C  344 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8264 (m)
  outliers start: 13
  outliers final: 12
  residues processed: 145
  average time/residue: 0.5471
  time to fit residues: 118.6591
Evaluate side-chains
  145 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 3.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  282 CYS
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  282 CYS
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  299 CYS
Chi-restraints excluded: chain C residue  344 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 97 optimal weight:    0.4980
   chunk 93 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.182193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.144845 restraints weight = 26410.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.29
r_work: 0.3469 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8832  Z= 0.123
  Angle     :  0.485   4.369  12006  Z= 0.254
  Chirality :  0.046   0.350   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.264  20.299   1182
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 22.22 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.07 (0.26), residues: 1062
  helix:  2.09 (0.27), residues: 387
  sheet: -1.54 (0.31), residues: 276
  loop : -0.99 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 145 
 HIS   0.004   0.001   HIS B 352 
 PHE   0.013   0.001   PHE B 350 
 TYR   0.007   0.001   TYR B 366 
 ARG   0.002   0.000   ARG C 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02705 (  457)
  hydrogen bonds       : angle       4.05459 ( 1308)
  SS BOND              : bond        0.00336 (   12)
  SS BOND              : angle       1.81461 (   24)
  covalent geometry    : bond        0.00294 ( 8820)
  covalent geometry    : angle       0.47834 (11982)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10526.96 seconds
wall clock time: 187 minutes 18.42 seconds (11238.42 seconds total)