Starting phenix.real_space_refine
on Thu Sep 18 13:02:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymw_39409/09_2025/8ymw_39409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymw_39409/09_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_39409/09_2025/8ymw_39409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymw_39409/09_2025/8ymw_39409.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymw_39409/09_2025/8ymw_39409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymw_39409/09_2025/8ymw_39409.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C
  Time building chain proxies: 4.70, per 1000 atoms: 0.28
  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 B 106 " - pdb=" SG  CYS B 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 106 " - pdb=" SG  CYS C 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 273 " - pdb=" SG  CYS B 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 273 " - pdb=" SG  CYS C 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 282 " - pdb=" SG  CYS B 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 282 " - pdb=" SG  CYS C 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 299 " - pdb=" SG  CYS B 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 299 " - pdb=" SG  CYS C 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: 1.40
  Conformation dependent library (CDL) restraints added in 453.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.48
  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: 3.66

  Time building geometry restraints manager: 2.04 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.360
  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:             0.120
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     18.110
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.980
-------------------------------------------------------------------------------
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 : 6.97
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.27), 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
 ARG   0.001   0.000   ARG A 244 
 TYR   0.007   0.001   TYR B 170 
 PHE   0.012   0.001   PHE A 350 
 TRP   0.006   0.001   TRP A 145 
 HIS   0.003   0.001   HIS A 352 

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

*********************** 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  : 0.449 
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: 0.1931
  time to fit residues: 36.6281
Evaluate side-chains
  132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.173568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.136216 restraints weight = 26093.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.31
r_work: 0.3403 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.0649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8832  Z= 0.193
  Angle     :  0.540   4.507  12006  Z= 0.288
  Chirality :  0.047   0.353   1344
  Planarity :  0.004   0.040   1545
  Dihedral  :  4.635  22.566   1188
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 22.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.26), residues: 1062
  helix:  1.55 (0.27), residues: 408
  sheet: -1.70 (0.31), residues: 267
  loop : -1.17 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 149 
 TYR   0.011   0.001   TYR A 170 
 PHE   0.013   0.001   PHE B 205 
 TRP   0.008   0.001   TRP A 145 
 HIS   0.004   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 8820)
  covalent geometry    : angle       0.53444 (11982)
  SS BOND              : bond        0.00466 (   12)
  SS BOND              : angle       1.84787 (   24)
  hydrogen bonds       : bond        0.03498 (  457)
  hydrogen bonds       : angle       4.69223 ( 1308)

*********************** 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  : 0.495 
Fit side-chains
REVERT: A  127 LYS cc_start: 0.7972 (pttt) cc_final: 0.7745 (pttp)
REVERT: A  172 ASP cc_start: 0.8199 (t0) cc_final: 0.7798 (t0)
REVERT: C  330 ASN cc_start: 0.8072 (m-40) cc_final: 0.7865 (m110)
REVERT: C  398 LEU cc_start: 0.8000 (mt) cc_final: 0.7614 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 142
  average time/residue: 0.1778
  time to fit residues: 36.7887
Evaluate side-chains
  142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
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 22 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 69 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.174040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.138026 restraints weight = 26150.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.23
r_work: 0.3396 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8832  Z= 0.198
  Angle     :  0.533   4.616  12006  Z= 0.284
  Chirality :  0.047   0.350   1344
  Planarity :  0.004   0.036   1545
  Dihedral  :  4.528  20.091   1182
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 22.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.26), residues: 1062
  helix:  1.66 (0.27), residues: 390
  sheet: -1.67 (0.30), residues: 282
  loop : -1.28 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  89 
 TYR   0.011   0.001   TYR A 381 
 PHE   0.013   0.001   PHE B 205 
 TRP   0.009   0.001   TRP A 145 
 HIS   0.004   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 8820)
  covalent geometry    : angle       0.52660 (11982)
  SS BOND              : bond        0.00466 (   12)
  SS BOND              : angle       1.97723 (   24)
  hydrogen bonds       : bond        0.03364 (  457)
  hydrogen bonds       : angle       4.54864 ( 1308)

*********************** 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
  159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 LYS cc_start: 0.7988 (pttt) cc_final: 0.7775 (pttp)
REVERT: A  169 SER cc_start: 0.8827 (p) cc_final: 0.8397 (t)
REVERT: A  172 ASP cc_start: 0.8188 (t0) cc_final: 0.7668 (t0)
REVERT: A  294 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7372 (ttmt)
REVERT: B  172 ASP cc_start: 0.8357 (t70) cc_final: 0.7961 (t70)
REVERT: B  294 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7163 (mttm)
REVERT: C  127 LYS cc_start: 0.8063 (pttt) cc_final: 0.7841 (pttp)
REVERT: C  169 SER cc_start: 0.8855 (p) cc_final: 0.8497 (t)
REVERT: C  330 ASN cc_start: 0.8099 (m-40) cc_final: 0.7898 (m-40)
REVERT: C  398 LEU cc_start: 0.7942 (mt) cc_final: 0.7734 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 151
  average time/residue: 0.1964
  time to fit residues: 42.5552
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  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  166 ILE
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  133 LEU
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 80 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.179552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.143198 restraints weight = 26232.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.23
r_work: 0.3455 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1012

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= 0.135
  Angle     :  0.499   4.412  12006  Z= 0.263
  Chirality :  0.046   0.349   1344
  Planarity :  0.004   0.039   1545
  Dihedral  :  4.459  19.944   1182
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.26), residues: 1062
  helix:  1.86 (0.28), residues: 387
  sheet: -1.66 (0.30), residues: 282
  loop : -1.23 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 149 
 TYR   0.009   0.001   TYR A 381 
 PHE   0.010   0.001   PHE B 205 
 TRP   0.007   0.001   TRP A 145 
 HIS   0.003   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8820)
  covalent geometry    : angle       0.49213 (11982)
  SS BOND              : bond        0.00383 (   12)
  SS BOND              : angle       1.90660 (   24)
  hydrogen bonds       : bond        0.03027 (  457)
  hydrogen bonds       : angle       4.38126 ( 1308)

*********************** 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
  164 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 LYS cc_start: 0.7987 (pttt) cc_final: 0.7780 (pttp)
REVERT: A  169 SER cc_start: 0.8788 (p) cc_final: 0.8396 (t)
REVERT: A  172 ASP cc_start: 0.8181 (t0) cc_final: 0.7590 (t0)
REVERT: A  326 ASP cc_start: 0.8416 (t0) cc_final: 0.8050 (t0)
REVERT: C   80 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7244 (t0)
REVERT: C  127 LYS cc_start: 0.8089 (pttt) cc_final: 0.7879 (pttp)
REVERT: C  169 SER cc_start: 0.8802 (p) cc_final: 0.8475 (t)
  outliers start: 19
  outliers final: 14
  residues processed: 158
  average time/residue: 0.1687
  time to fit residues: 39.1622
Evaluate side-chains
  157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
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   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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0970
   chunk 14 optimal weight:    0.0980
   chunk 2 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.180447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.143888 restraints weight = 26082.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.25
r_work: 0.3466 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8832  Z= 0.117
  Angle     :  0.484   4.359  12006  Z= 0.254
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.037   1545
  Dihedral  :  4.348  19.742   1182
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 22.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.26), residues: 1062
  helix:  1.98 (0.27), residues: 387
  sheet: -1.63 (0.30), residues: 282
  loop : -1.19 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.009   0.001   TYR A 381 
 PHE   0.012   0.001   PHE C 350 
 TRP   0.006   0.001   TRP B 145 
 HIS   0.003   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8820)
  covalent geometry    : angle       0.47899 (11982)
  SS BOND              : bond        0.00352 (   12)
  SS BOND              : angle       1.69089 (   24)
  hydrogen bonds       : bond        0.02859 (  457)
  hydrogen bonds       : angle       4.26427 ( 1308)

*********************** 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
  164 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8759 (p) cc_final: 0.8393 (t)
REVERT: A  172 ASP cc_start: 0.8173 (t0) cc_final: 0.7551 (t0)
REVERT: A  326 ASP cc_start: 0.8340 (t0) cc_final: 0.7994 (t0)
REVERT: B  169 SER cc_start: 0.8690 (p) cc_final: 0.8474 (t)
REVERT: C   80 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7199 (t0)
REVERT: C  127 LYS cc_start: 0.8054 (pttt) cc_final: 0.7835 (pttp)
REVERT: C  169 SER cc_start: 0.8718 (p) cc_final: 0.8447 (t)
REVERT: C  326 ASP cc_start: 0.8211 (t0) cc_final: 0.7899 (t0)
REVERT: C  344 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8286 (m)
  outliers start: 21
  outliers final: 13
  residues processed: 160
  average time/residue: 0.1677
  time to fit residues: 39.8206
Evaluate side-chains
  153 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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  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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9980
   chunk 2 optimal weight:    0.2980
   chunk 93 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   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 = 0.4028 r_free = 0.4028 target = 0.180256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.144085 restraints weight = 26032.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.20
r_work: 0.3450 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8832  Z= 0.147
  Angle     :  0.500   4.632  12006  Z= 0.262
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.037   1545
  Dihedral  :  4.383  20.782   1182
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.91 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.26), residues: 1062
  helix:  1.97 (0.27), residues: 387
  sheet: -1.61 (0.30), residues: 282
  loop : -1.16 (0.28), residues: 393

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8820)
  covalent geometry    : angle       0.49221 (11982)
  SS BOND              : bond        0.00386 (   12)
  SS BOND              : angle       1.97362 (   24)
  hydrogen bonds       : bond        0.02916 (  457)
  hydrogen bonds       : angle       4.25124 ( 1308)

*********************** 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
  167 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8663 (p) cc_final: 0.8318 (t)
REVERT: A  172 ASP cc_start: 0.8202 (t0) cc_final: 0.7553 (t0)
REVERT: A  326 ASP cc_start: 0.8316 (t0) cc_final: 0.7936 (t0)
REVERT: B  172 ASP cc_start: 0.8085 (t70) cc_final: 0.7786 (t70)
REVERT: C   80 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7227 (t0)
REVERT: C  127 LYS cc_start: 0.8063 (pttt) cc_final: 0.7842 (pttp)
REVERT: C  169 SER cc_start: 0.8687 (p) cc_final: 0.8459 (t)
REVERT: C  344 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8310 (m)
  outliers start: 20
  outliers final: 14
  residues processed: 163
  average time/residue: 0.1705
  time to fit residues: 40.8821
Evaluate side-chains
  156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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   67 PHE
Chi-restraints excluded: chain B residue   95 GLN
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  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 82 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0070
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0870
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.4776

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.182704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.146194 restraints weight = 26074.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.23
r_work: 0.3481 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8832  Z= 0.104
  Angle     :  0.476   4.429  12006  Z= 0.249
  Chirality :  0.046   0.349   1344
  Planarity :  0.003   0.037   1545
  Dihedral  :  4.296  20.559   1182
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.26), residues: 1062
  helix:  2.06 (0.27), residues: 387
  sheet: -1.60 (0.31), residues: 276
  loop : -1.02 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.007   0.001   TYR A 381 
 PHE   0.009   0.001   PHE C 350 
 TRP   0.006   0.001   TRP C 145 
 HIS   0.002   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8820)
  covalent geometry    : angle       0.47028 (11982)
  SS BOND              : bond        0.00334 (   12)
  SS BOND              : angle       1.77271 (   24)
  hydrogen bonds       : bond        0.02737 (  457)
  hydrogen bonds       : angle       4.13272 ( 1308)

*********************** 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: 17
    poor density    : 145
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A   67 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7090 (t80)
REVERT: A  169 SER cc_start: 0.8579 (p) cc_final: 0.8300 (t)
REVERT: B  172 ASP cc_start: 0.8046 (t70) cc_final: 0.7794 (t70)
REVERT: C   80 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7147 (t0)
REVERT: C  344 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8281 (m)
  outliers start: 17
  outliers final: 11
  residues processed: 160
  average time/residue: 0.1796
  time to fit residues: 42.3987
Evaluate side-chains
  150 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4042 r_free = 0.4042 target = 0.182145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.144694 restraints weight = 26150.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.30
r_work: 0.3475 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1387

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= 0.124
  Angle     :  0.488   4.621  12006  Z= 0.256
  Chirality :  0.046   0.356   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.265  19.403   1182
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 22.01 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.26), residues: 1062
  helix:  2.06 (0.27), residues: 387
  sheet: -1.58 (0.31), residues: 276
  loop : -1.01 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.007   0.001   TYR A 381 
 PHE   0.010   0.001   PHE B 205 
 TRP   0.006   0.001   TRP B 145 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8820)
  covalent geometry    : angle       0.48279 (11982)
  SS BOND              : bond        0.00330 (   12)
  SS BOND              : angle       1.72511 (   24)
  hydrogen bonds       : bond        0.02732 (  457)
  hydrogen bonds       : angle       4.10231 ( 1308)

*********************** 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
  157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8543 (p) cc_final: 0.8266 (t)
REVERT: B  172 ASP cc_start: 0.8069 (t70) cc_final: 0.7774 (t70)
REVERT: C   80 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7235 (t0)
REVERT: C  344 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8278 (m)
  outliers start: 15
  outliers final: 11
  residues processed: 155
  average time/residue: 0.1829
  time to fit residues: 41.3738
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  : 0.466 
-------------------------------------------------------------------------------
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 94 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.0988

-------------------------------------------------------------------------------
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 = 0.180669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.143654 restraints weight = 26238.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.26
r_work: 0.3456 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8832  Z= 0.157
  Angle     :  0.509   6.356  12006  Z= 0.267
  Chirality :  0.047   0.354   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.346  21.619   1182
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 22.22 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.26), residues: 1062
  helix:  2.01 (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
 ARG   0.002   0.000   ARG B 149 
 TYR   0.008   0.001   TYR A 381 
 PHE   0.011   0.001   PHE B 205 
 TRP   0.007   0.001   TRP B 145 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8820)
  covalent geometry    : angle       0.50015 (11982)
  SS BOND              : bond        0.00380 (   12)
  SS BOND              : angle       2.18033 (   24)
  hydrogen bonds       : bond        0.02848 (  457)
  hydrogen bonds       : angle       4.15812 ( 1308)

*********************** 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
  155 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8632 (p) cc_final: 0.8359 (t)
REVERT: A  172 ASP cc_start: 0.8200 (t0) cc_final: 0.7498 (t0)
REVERT: B   91 ASP cc_start: 0.7827 (m-30) cc_final: 0.7615 (t0)
REVERT: B  172 ASP cc_start: 0.8122 (t70) cc_final: 0.7751 (t70)
REVERT: C   80 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7255 (t0)
REVERT: C  344 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8316 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 154
  average time/residue: 0.1945
  time to fit residues: 43.2232
Evaluate side-chains
  152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
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 39 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 64 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0870
   chunk 90 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6762

-------------------------------------------------------------------------------
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 = 0.182052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.145196 restraints weight = 26030.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.25
r_work: 0.3474 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1484

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= 0.120
  Angle     :  0.489   4.945  12006  Z= 0.256
  Chirality :  0.046   0.355   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.293  20.598   1182
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 4.74
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.26), residues: 1062
  helix:  2.07 (0.27), residues: 387
  sheet: -1.60 (0.31), residues: 276
  loop : -1.00 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 149 
 TYR   0.007   0.001   TYR A 381 
 PHE   0.010   0.001   PHE B 205 
 TRP   0.007   0.001   TRP B 145 
 HIS   0.003   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8820)
  covalent geometry    : angle       0.48177 (11982)
  SS BOND              : bond        0.00350 (   12)
  SS BOND              : angle       1.89685 (   24)
  hydrogen bonds       : bond        0.02740 (  457)
  hydrogen bonds       : angle       4.08973 ( 1308)

********************** 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: 13
    poor density    : 138
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 SER cc_start: 0.8582 (p) cc_final: 0.8318 (t)
REVERT: A  326 ASP cc_start: 0.8309 (t0) cc_final: 0.8030 (t0)
REVERT: B  172 ASP cc_start: 0.8093 (t70) cc_final: 0.7759 (t70)
REVERT: C   80 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7258 (t0)
REVERT: C  344 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8279 (m)
  outliers start: 13
  outliers final: 11
  residues processed: 150
  average time/residue: 0.1910
  time to fit residues: 41.6068
Evaluate side-chains
  149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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 43 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0170
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.182629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.145498 restraints weight = 26214.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.28
r_work: 0.3479 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.1532

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= 0.108
  Angle     :  0.479   4.519  12006  Z= 0.250
  Chirality :  0.046   0.355   1344
  Planarity :  0.003   0.036   1545
  Dihedral  :  4.229  20.323   1182
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 22.33 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.26), residues: 1062
  helix:  2.13 (0.27), residues: 387
  sheet: -1.56 (0.31), residues: 276
  loop : -0.97 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.007   0.001   TYR A 381 
 PHE   0.011   0.001   PHE B 350 
 TRP   0.006   0.001   TRP B 145 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8820)
  covalent geometry    : angle       0.47275 (11982)
  SS BOND              : bond        0.00312 (   12)
  SS BOND              : angle       1.72657 (   24)
  hydrogen bonds       : bond        0.02645 (  457)
  hydrogen bonds       : angle       4.00742 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4828.04 seconds
wall clock time: 82 minutes 29.92 seconds (4949.92 seconds total)