Starting phenix.real_space_refine
on Sun May 18 11:41:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymw_39409/05_2025/8ymw_39409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymw_39409/05_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_39409/05_2025/8ymw_39409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymw_39409/05_2025/8ymw_39409.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymw_39409/05_2025/8ymw_39409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymw_39409/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 12.61, per 1000 atoms: 0.74
  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: 4.51
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.52
  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: 5.89

  Time building geometry restraints manager: 5.38 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: 0.07
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 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:             1.190
  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:             0.280
  Extract box with map and model:          0.680
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     41.820
  Find NCS groups from input model:        0.240
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.140
-------------------------------------------------------------------------------
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  : 1.273 
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: 0.4298
  time to fit residues: 81.1689
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  : 1.417 
-------------------------------------------------------------------------------
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 = 39)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.139264 restraints weight = 26065.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.26
r_work: 0.3414 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
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       1.77774 (   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  : 1.530 
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: 0.7793 (t0)
REVERT: C  398 LEU cc_start: 0.8009 (mt) cc_final: 0.7617 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 142
  average time/residue: 0.3896
  time to fit residues: 81.1743
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  : 1.462 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 76 optimal weight:    2.9990
   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:    0.7980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3980 r_free = 0.3980 target = 0.176502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.140507 restraints weight = 25878.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.24
r_work: 0.3427 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8832  Z= 0.147
  Angle     :  0.504   4.385  12006  Z= 0.266
  Chirality :  0.046   0.350   1344
  Planarity :  0.004   0.036   1545
  Dihedral  :  4.408  19.939   1182
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 23.26 %
    Favored  : 75.91 %
  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: -0.40 (0.26), residues: 1062
  helix:  1.81 (0.27), residues: 390
  sheet: -1.62 (0.30), residues: 282
  loop : -1.25 (0.28), residues: 390

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        0.03212 (  457)
  hydrogen bonds       : angle       4.46657 ( 1308)
  SS BOND              : bond        0.00371 (   12)
  SS BOND              : angle       1.81845 (   24)
  covalent geometry    : bond        0.00349 ( 8820)
  covalent geometry    : angle       0.49759 (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: 8
    poor density    : 140
  time to evaluate  : 1.324 
Fit side-chains
REVERT: A  127 LYS cc_start: 0.7949 (pttt) cc_final: 0.7723 (pttp)
REVERT: A  169 SER cc_start: 0.8817 (p) cc_final: 0.8399 (t)
REVERT: A  172 ASP cc_start: 0.8169 (t0) cc_final: 0.7615 (t0)
REVERT: A  326 ASP cc_start: 0.8139 (t0) cc_final: 0.7810 (t0)
REVERT: B  172 ASP cc_start: 0.8335 (t70) cc_final: 0.7866 (t70)
REVERT: C  127 LYS cc_start: 0.8060 (pttt) cc_final: 0.7832 (pttp)
REVERT: C  169 SER cc_start: 0.8810 (p) cc_final: 0.8467 (t)
REVERT: C  398 LEU cc_start: 0.7932 (mt) cc_final: 0.7722 (mt)
  outliers start: 8
  outliers final: 5
  residues processed: 146
  average time/residue: 0.3635
  time to fit residues: 77.5618
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  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  180 LEU
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:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.3993 r_free = 0.3993 target = 0.177194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.140186 restraints weight = 26129.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.27
r_work: 0.3421 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8832  Z= 0.213
  Angle     :  0.542   4.943  12006  Z= 0.289
  Chirality :  0.047   0.350   1344
  Planarity :  0.004   0.038   1545
  Dihedral  :  4.545  19.843   1182
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.39 %
    Favored  : 75.91 %
  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: -0.47 (0.26), residues: 1062
  helix:  1.73 (0.27), residues: 387
  sheet: -1.67 (0.30), residues: 282
  loop : -1.24 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 145 
 HIS   0.004   0.001   HIS A 231 
 PHE   0.014   0.001   PHE B 205 
 TYR   0.009   0.001   TYR C 227 
 ARG   0.003   0.000   ARG A  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03290 (  457)
  hydrogen bonds       : angle       4.51430 ( 1308)
  SS BOND              : bond        0.00453 (   12)
  SS BOND              : angle       2.11959 (   24)
  covalent geometry    : bond        0.00509 ( 8820)
  covalent geometry    : angle       0.53467 (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
  174 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 1.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 LYS cc_start: 0.7990 (pttt) cc_final: 0.7790 (pttp)
REVERT: A  169 SER cc_start: 0.8813 (p) cc_final: 0.8418 (t)
REVERT: A  172 ASP cc_start: 0.8204 (t0) cc_final: 0.7641 (t0)
REVERT: A  326 ASP cc_start: 0.8419 (t0) cc_final: 0.7946 (t0)
REVERT: B  172 ASP cc_start: 0.8408 (t70) cc_final: 0.7982 (t70)
REVERT: C  127 LYS cc_start: 0.8075 (pttt) cc_final: 0.7864 (pttp)
REVERT: C  169 SER cc_start: 0.8894 (p) cc_final: 0.8562 (t)
REVERT: C  172 ASP cc_start: 0.8196 (t70) cc_final: 0.7559 (t0)
  outliers start: 26
  outliers final: 17
  residues processed: 165
  average time/residue: 0.4031
  time to fit residues: 95.5768
Evaluate side-chains
  160 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
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   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  400 ILE
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:    0.0060
   chunk 28 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.6998

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.179554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.143074 restraints weight = 26382.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.25
r_work: 0.3460 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8832  Z= 0.124
  Angle     :  0.493   4.476  12006  Z= 0.259
  Chirality :  0.046   0.348   1344
  Planarity :  0.003   0.039   1545
  Dihedral  :  4.431  20.200   1182
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 22.43 %
    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: -0.32 (0.26), residues: 1062
  helix:  1.92 (0.27), residues: 387
  sheet: -1.65 (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 C 350 
 TYR   0.009   0.001   TYR A 381 
 ARG   0.002   0.000   ARG C 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02940 (  457)
  hydrogen bonds       : angle       4.33545 ( 1308)
  SS BOND              : bond        0.00451 (   12)
  SS BOND              : angle       1.93922 (   24)
  covalent geometry    : bond        0.00295 ( 8820)
  covalent geometry    : angle       0.48552 (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: 18
    poor density    : 142
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8719 (p) cc_final: 0.8347 (t)
REVERT: A  172 ASP cc_start: 0.8181 (t0) cc_final: 0.7559 (t0)
REVERT: A  326 ASP cc_start: 0.8395 (t0) cc_final: 0.7879 (t0)
REVERT: B  169 SER cc_start: 0.8723 (p) cc_final: 0.8491 (t)
REVERT: C   80 ASP cc_start: 0.7305 (m-30) cc_final: 0.6915 (t0)
REVERT: C  127 LYS cc_start: 0.8033 (pttt) cc_final: 0.7815 (pttp)
REVERT: C  169 SER cc_start: 0.8728 (p) cc_final: 0.8432 (t)
REVERT: C  344 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8314 (m)
  outliers start: 18
  outliers final: 13
  residues processed: 156
  average time/residue: 0.3745
  time to fit residues: 85.6385
Evaluate side-chains
  154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ASP
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   67 PHE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.8582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.179624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.143027 restraints weight = 26423.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.25
r_work: 0.3421 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1242

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= 0.137
  Angle     :  0.496   4.923  12006  Z= 0.260
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.037   1545
  Dihedral  :  4.395  20.586   1182
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 22.43 %
    Favored  : 75.60 %
  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: -0.28 (0.26), residues: 1062
  helix:  1.97 (0.27), residues: 387
  sheet: -1.64 (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 C 231 
 PHE   0.011   0.001   PHE A 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        0.02901 (  457)
  hydrogen bonds       : angle       4.26851 ( 1308)
  SS BOND              : bond        0.00394 (   12)
  SS BOND              : angle       1.97451 (   24)
  covalent geometry    : bond        0.00327 ( 8820)
  covalent geometry    : angle       0.48846 (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
  166 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7096 (t80)
REVERT: A  169 SER cc_start: 0.8696 (p) cc_final: 0.8364 (t)
REVERT: A  172 ASP cc_start: 0.8191 (t0) cc_final: 0.7540 (t0)
REVERT: A  326 ASP cc_start: 0.8392 (t0) cc_final: 0.7866 (t0)
REVERT: B  169 SER cc_start: 0.8727 (p) cc_final: 0.8523 (t)
REVERT: C   80 ASP cc_start: 0.7417 (m-30) cc_final: 0.7052 (t0)
REVERT: C  169 SER cc_start: 0.8707 (p) cc_final: 0.8473 (t)
REVERT: C  344 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8281 (m)
  outliers start: 19
  outliers final: 13
  residues processed: 163
  average time/residue: 0.3744
  time to fit residues: 88.6945
Evaluate side-chains
  155 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
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   67 PHE
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   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:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 12 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.180692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.144146 restraints weight = 26300.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.26
r_work: 0.3469 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1306

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= 0.122
  Angle     :  0.490   5.238  12006  Z= 0.257
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.037   1545
  Dihedral  :  4.384  21.993   1182
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 22.53 %
    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: -0.25 (0.26), residues: 1062
  helix:  2.00 (0.28), residues: 387
  sheet: -1.62 (0.30), residues: 282
  loop : -1.17 (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   0.009   0.001   TYR A 381 
 ARG   0.002   0.000   ARG C 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02824 (  457)
  hydrogen bonds       : angle       4.20047 ( 1308)
  SS BOND              : bond        0.00428 (   12)
  SS BOND              : angle       2.14674 (   24)
  covalent geometry    : bond        0.00289 ( 8820)
  covalent geometry    : angle       0.48103 (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
  162 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 1.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8588 (p) cc_final: 0.8284 (t)
REVERT: A  326 ASP cc_start: 0.8384 (t0) cc_final: 0.8112 (t0)
REVERT: C   80 ASP cc_start: 0.7391 (m-30) cc_final: 0.7030 (t0)
REVERT: C  169 SER cc_start: 0.8682 (p) cc_final: 0.8461 (t)
REVERT: C  344 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8294 (m)
  outliers start: 16
  outliers final: 11
  residues processed: 160
  average time/residue: 0.3547
  time to fit residues: 83.1313
Evaluate side-chains
  152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 38 optimal weight:    0.0970
   chunk 80 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.179364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.142820 restraints weight = 26120.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.24
r_work: 0.3414 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1381

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= 0.166
  Angle     :  0.511   4.985  12006  Z= 0.269
  Chirality :  0.047   0.349   1344
  Planarity :  0.003   0.037   1545
  Dihedral  :  4.411  19.645   1182
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  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: -0.28 (0.26), residues: 1062
  helix:  1.97 (0.28), residues: 387
  sheet: -1.63 (0.30), residues: 282
  loop : -1.17 (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 231 
 PHE   0.012   0.001   PHE B 205 
 TYR   0.009   0.001   TYR A 381 
 ARG   0.002   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02912 (  457)
  hydrogen bonds       : angle       4.23688 ( 1308)
  SS BOND              : bond        0.00401 (   12)
  SS BOND              : angle       2.08647 (   24)
  covalent geometry    : bond        0.00398 ( 8820)
  covalent geometry    : angle       0.50314 (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
  156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 1.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8619 (p) cc_final: 0.8312 (t)
REVERT: A  172 ASP cc_start: 0.8202 (t0) cc_final: 0.7502 (t0)
REVERT: A  294 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7497 (mmtp)
REVERT: C  169 SER cc_start: 0.8696 (p) cc_final: 0.8480 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 153
  average time/residue: 0.3997
  time to fit residues: 88.1413
Evaluate side-chains
  147 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ASP
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 100 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0060
   chunk 55 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.181412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.144166 restraints weight = 26311.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.28
r_work: 0.3465 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1433

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= 0.114
  Angle     :  0.485   5.790  12006  Z= 0.254
  Chirality :  0.046   0.351   1344
  Planarity :  0.003   0.038   1545
  Dihedral  :  4.364  22.157   1182
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.63
  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: -0.16 (0.26), residues: 1062
  helix:  2.03 (0.28), residues: 387
  sheet: -1.63 (0.31), residues: 276
  loop : -1.03 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 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        0.02765 (  457)
  hydrogen bonds       : angle       4.14680 ( 1308)
  SS BOND              : bond        0.00402 (   12)
  SS BOND              : angle       2.10447 (   24)
  covalent geometry    : bond        0.00269 ( 8820)
  covalent geometry    : angle       0.47665 (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
  154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 1.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8541 (p) cc_final: 0.8263 (t)
REVERT: B  172 ASP cc_start: 0.7863 (t70) cc_final: 0.7504 (t70)
REVERT: C   80 ASP cc_start: 0.7388 (m-30) cc_final: 0.7035 (t0)
REVERT: C  169 SER cc_start: 0.8635 (p) cc_final: 0.8435 (t)
REVERT: C  344 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8251 (m)
  outliers start: 15
  outliers final: 11
  residues processed: 151
  average time/residue: 0.4005
  time to fit residues: 87.4401
Evaluate side-chains
  147 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 88 optimal weight:    0.2980
   chunk 38 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.181987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.144731 restraints weight = 26225.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.28
r_work: 0.3469 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1473

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= 0.114
  Angle     :  0.487   5.335  12006  Z= 0.255
  Chirality :  0.046   0.348   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.314  21.365   1182
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 22.64 %
    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: -0.11 (0.26), residues: 1062
  helix:  2.09 (0.28), residues: 387
  sheet: -1.60 (0.31), residues: 276
  loop : -1.01 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 145 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.012   0.001   PHE A 350 
 TYR   0.007   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02709 (  457)
  hydrogen bonds       : angle       4.07922 ( 1308)
  SS BOND              : bond        0.00371 (   12)
  SS BOND              : angle       2.18037 (   24)
  covalent geometry    : bond        0.00271 ( 8820)
  covalent geometry    : angle       0.47756 (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
  151 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 1.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8443 (p) cc_final: 0.8185 (t)
REVERT: A  294 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7441 (mmtp)
REVERT: B  172 ASP cc_start: 0.7856 (t70) cc_final: 0.7536 (t70)
REVERT: C   80 ASP cc_start: 0.7436 (m-30) cc_final: 0.7089 (t0)
  outliers start: 11
  outliers final: 11
  residues processed: 150
  average time/residue: 0.4142
  time to fit residues: 89.4074
Evaluate side-chains
  146 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
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  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=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:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 64 optimal weight:    0.1980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.181688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.144558 restraints weight = 26375.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.27
r_work: 0.3464 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1504

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     :  0.497   5.065  12006  Z= 0.260
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.333  20.890   1182
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 22.85 %
    Favored  : 75.91 %
  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: -0.12 (0.26), residues: 1062
  helix:  2.07 (0.27), residues: 387
  sheet: -1.60 (0.30), residues: 276
  loop : -1.02 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 145 
 HIS   0.005   0.001   HIS B 352 
 PHE   0.015   0.001   PHE B 350 
 TYR   0.008   0.001   TYR B 366 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02767 (  457)
  hydrogen bonds       : angle       4.10639 ( 1308)
  SS BOND              : bond        0.00363 (   12)
  SS BOND              : angle       2.12827 (   24)
  covalent geometry    : bond        0.00326 ( 8820)
  covalent geometry    : angle       0.48797 (11982)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9168.24 seconds
wall clock time: 157 minutes 34.49 seconds (9454.49 seconds total)