Starting phenix.real_space_refine
on Mon Apr 28 05:54:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8m_18255/04_2025/8q8m_18255.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8m_18255/04_2025/8q8m_18255.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q8m_18255/04_2025/8q8m_18255.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8m_18255/04_2025/8q8m_18255.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8m_18255/04_2025/8q8m_18255.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8m_18255/04_2025/8q8m_18255.cif"
  }
  resolution = 2.95
  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=   0.002
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       6      5.16       5
     C    2172      2.51       5
     N     642      2.21       5
     O     648      1.98       5
     H    3606      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7074
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "D"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "F"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Time building chain proxies: 5.55, per 1000 atoms: 0.78
  Number of scatterers: 7074
  At special positions: 0
  Unit cell: (117.832, 119.48, 40.376, 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       6     16.00
     O     648      8.00
     N     642      7.00
     C    2172      6.00
     H    3606      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.51
  Conformation dependent library (CDL) restraints added in 581.5 milliseconds
  

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 49.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.505A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 7.048A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 321
      removed outlier: 6.409A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 330
      removed outlier: 6.147A  pdb=" N   GLY A 326 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   HIS B 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ILE A 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ASN A 327 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 346
      removed outlier: 9.051A  pdb=" N   GLN A 336 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 10.374A  pdb=" N   VAL B 339 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 9.055A  pdb=" N   GLU A 338 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 10.061A  pdb=" N   SER B 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 9.057A  pdb=" N   LYS A 340 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 10.516A  pdb=" N   LYS B 343 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   GLU A 342 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   ASP B 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU A 344 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   VAL A 337 " --> pdb=" O   GLN C 336 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   GLU C 338 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   VAL A 339 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   SER A 341 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   GLU C 342 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LYS A 343 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 354
      removed outlier: 6.478A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 362
      removed outlier: 6.634A  pdb=" N   ASN A 359 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   HIS B 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   THR A 361 " --> pdb=" O   HIS B 362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378
      removed outlier: 6.241A  pdb=" N   LYS A 370 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   THR B 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   GLU A 372 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   LYS B 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   HIS A 374 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   THR B 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU A 376 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 306 through 310
      removed outlier: 6.517A  pdb=" N   GLN D 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   TYR F 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   VAL D 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314
      removed outlier: 7.070A  pdb=" N   VAL D 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 321
    Processing sheet with id=AB3, first strand: chain 'E' and resid 326 through 330
      removed outlier: 6.113A  pdb=" N   GLY D 326 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   HIS E 329 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ILE D 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ASN D 327 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 336 through 346
      removed outlier: 9.051A  pdb=" N   GLN D 336 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
      removed outlier: 10.416A  pdb=" N   VAL E 339 " --> pdb=" O   GLN D 336 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   GLU D 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 10.051A  pdb=" N   SER E 341 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 9.031A  pdb=" N   LYS D 340 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
      removed outlier: 10.507A  pdb=" N   LYS E 343 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   GLU D 342 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   ASP E 345 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LEU D 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   VAL D 337 " --> pdb=" O   GLN F 336 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   GLU F 338 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL D 339 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LYS F 340 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   SER D 341 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   GLU F 342 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LYS D 343 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 351 through 354
      removed outlier: 6.550A  pdb=" N   GLN D 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   ILE F 354 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LYS D 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 359 through 362
      removed outlier: 6.600A  pdb=" N   ASN D 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   HIS E 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   THR D 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 369 through 378
      removed outlier: 6.248A  pdb=" N   LYS D 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   THR E 373 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   GLU D 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   LYS E 375 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   HIS D 374 " --> pdb=" O   LYS E 375 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   THR E 377 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   LEU D 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)

    64 hydrogen bonds defined for protein.
    192 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 1.92 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 3600
        1.12 -     1.29: 576
        1.29 -     1.46: 1031
        1.46 -     1.64: 1915
        1.64 -     1.81: 6
  Bond restraints: 7128
  Sorted by residual:
  bond pdb=" NE2 GLN D 351 "
       pdb="HE22 GLN D 351 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   LEU B 315 "
       pdb=" H   LEU B 315 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" CE1 TYR C 310 "
       pdb=" HE1 TYR C 310 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" N   SER F 316 "
       pdb=" H   SER F 316 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" N   VAL F 350 "
       pdb=" H   VAL F 350 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.63e+01
  ... (remaining 7123 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 10624
        2.41 -     4.81: 1730
        4.81 -     7.22: 586
        7.22 -     9.63: 38
        9.63 -    12.03: 6
  Bond angle restraints: 12984
  Sorted by residual:
  angle pdb=" CA  ASP D 345 "
        pdb=" CB  ASP D 345 "
        pdb=" CG  ASP D 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.09   -5.49 1.00e+00 1.00e+00 3.01e+01
  angle pdb=" CA  ASP C 345 "
        pdb=" CB  ASP C 345 "
        pdb=" CG  ASP C 345 "
      ideal   model   delta    sigma   weight residual
     112.60  117.95   -5.35 1.00e+00 1.00e+00 2.86e+01
  angle pdb=" CA  GLY C 335 "
        pdb=" C   GLY C 335 "
        pdb=" N   GLN C 336 "
      ideal   model   delta    sigma   weight residual
     114.23  118.83   -4.60 8.80e-01 1.29e+00 2.74e+01
  angle pdb=" CA  ASP F 345 "
        pdb=" CB  ASP F 345 "
        pdb=" CG  ASP F 345 "
      ideal   model   delta    sigma   weight residual
     112.60  117.81   -5.21 1.00e+00 1.00e+00 2.71e+01
  angle pdb=" CA  ASP B 345 "
        pdb=" CB  ASP B 345 "
        pdb=" CG  ASP B 345 "
      ideal   model   delta    sigma   weight residual
     112.60  117.79   -5.19 1.00e+00 1.00e+00 2.70e+01
  ... (remaining 12979 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2947
       17.95 -    35.91: 152
       35.91 -    53.86: 83
       53.86 -    71.82: 94
       71.82 -    89.77: 6
  Dihedral angle restraints: 3282
    sinusoidal: 1878
      harmonic: 1404
  Sorted by residual:
  dihedral pdb=" C   ARG E 349 "
           pdb=" N   ARG E 349 "
           pdb=" CA  ARG E 349 "
           pdb=" CB  ARG E 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.11   15.51     0      2.50e+00 1.60e-01 3.85e+01
  dihedral pdb=" C   ARG F 349 "
           pdb=" N   ARG F 349 "
           pdb=" CA  ARG F 349 "
           pdb=" CB  ARG F 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.94   15.34     0      2.50e+00 1.60e-01 3.77e+01
  dihedral pdb=" C   ARG D 349 "
           pdb=" N   ARG D 349 "
           pdb=" CA  ARG D 349 "
           pdb=" CB  ARG D 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.63   15.03     0      2.50e+00 1.60e-01 3.61e+01
  ... (remaining 3279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 391
       0.112 -    0.224: 99
       0.224 -    0.336: 29
       0.336 -    0.448: 3
       0.448 -    0.560: 6
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  ARG F 349 "
            pdb=" N   ARG F 349 "
            pdb=" C   ARG F 349 "
            pdb=" CB  ARG F 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.84e+00
  chirality pdb=" CA  ARG E 349 "
            pdb=" N   ARG E 349 "
            pdb=" C   ARG E 349 "
            pdb=" CB  ARG E 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.56 2.00e-01 2.50e+01 7.70e+00
  chirality pdb=" CA  ARG C 349 "
            pdb=" N   ARG C 349 "
            pdb=" C   ARG C 349 "
            pdb=" CB  ARG C 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.55 2.00e-01 2.50e+01 7.44e+00
  ... (remaining 525 not shown)

  Planarity restraints: 1032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "   -0.162 2.00e-02 2.50e+03   6.58e-02 1.30e+02
        pdb=" CG  TYR C 310 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "    0.055 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "    0.055 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "    0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "   -0.115 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 310 "    0.009 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 310 "    0.048 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 310 "    0.018 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 310 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.125 2.00e-02 2.50e+03   5.30e-02 8.42e+01
        pdb=" CG  TYR F 310 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.098 2.00e-02 2.50e+03
        pdb=" HD1 TYR F 310 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR F 310 "   -0.033 2.00e-02 2.50e+03
        pdb=" HE1 TYR F 310 "   -0.012 2.00e-02 2.50e+03
        pdb=" HE2 TYR F 310 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 310 "    0.109 2.00e-02 2.50e+03   4.76e-02 6.80e+01
        pdb=" CG  TYR D 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 310 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 310 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 310 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR D 310 "    0.087 2.00e-02 2.50e+03
        pdb=" HD1 TYR D 310 "    0.011 2.00e-02 2.50e+03
        pdb=" HD2 TYR D 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" HE1 TYR D 310 "   -0.013 2.00e-02 2.50e+03
        pdb=" HE2 TYR D 310 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1029 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.16: 481
        2.16 -     2.77: 11878
        2.77 -     3.38: 19034
        3.38 -     3.99: 24896
        3.99 -     4.60: 35526
  Nonbonded interactions: 91815
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.555 2.450
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.572 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.619 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.621 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.624 2.450
  ... (remaining 91810 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             2.800
  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:             0.130
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.330
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
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      :  0.011   0.034   3522  Z= 0.689
  Angle     :  1.959   7.519   4710  Z= 1.297
  Chirality :  0.124   0.560    528
  Planarity :  0.011   0.078    600
  Dihedral  : 11.822  89.773   1350
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  1.77 %
  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: -1.64 (0.34), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.004   HIS B 330 
 PHE   0.021   0.007   PHE B 346 
 TYR   0.145   0.042   TYR C 310 
 ARG   0.003   0.001   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12334 (   64)
  hydrogen bonds       : angle       7.42996 (  192)
  covalent geometry    : bond        0.01096 ( 3522)
  covalent geometry    : angle       1.95910 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8104 (pttt) cc_final: 0.7903 (ptpt)
REVERT: A  321 LYS cc_start: 0.8151 (tttt) cc_final: 0.7899 (mttp)
REVERT: A  379 ARG cc_start: 0.6840 (ptp-170) cc_final: 0.6373 (tpt170)
REVERT: B  379 ARG cc_start: 0.6955 (ptp-170) cc_final: 0.6735 (tpt170)
REVERT: C  379 ARG cc_start: 0.6987 (ptp-170) cc_final: 0.6536 (tpt170)
REVERT: D  317 LYS cc_start: 0.8108 (pttt) cc_final: 0.7906 (ptpt)
REVERT: D  379 ARG cc_start: 0.6888 (ptp-170) cc_final: 0.6333 (tpt170)
REVERT: E  311 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7587 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 2.7101
  time to fit residues: 355.4286
Evaluate side-chains
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.160694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.146265 restraints weight = 12026.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.4335 rms_B_bonded: 1.89
r_work: 0.4242 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.4156 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.4355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3522  Z= 0.126
  Angle     :  0.682   4.392   4710  Z= 0.357
  Chirality :  0.053   0.139    528
  Planarity :  0.002   0.014    600
  Dihedral  :  6.729  20.036    468
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 13.38 %
    Favored  : 85.86 %
  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: -1.84 (0.34), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.39 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 362 
 PHE   0.006   0.001   PHE D 346 
 TYR   0.011   0.002   TYR D 310 
 ARG   0.002   0.001   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (   64)
  hydrogen bonds       : angle       5.76037 (  192)
  covalent geometry    : bond        0.00287 ( 3522)
  covalent geometry    : angle       0.68171 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.8198 (m-30) cc_final: 0.7812 (m-30)
REVERT: A  356 SER cc_start: 0.9033 (p) cc_final: 0.8551 (m)
REVERT: A  379 ARG cc_start: 0.7487 (ptp-170) cc_final: 0.6756 (tpt170)
REVERT: B  338 GLU cc_start: 0.8429 (pt0) cc_final: 0.8082 (tt0)
REVERT: B  379 ARG cc_start: 0.7739 (ptp-170) cc_final: 0.7083 (OUTLIER)
REVERT: C  345 ASP cc_start: 0.8496 (m-30) cc_final: 0.8220 (m-30)
REVERT: C  379 ARG cc_start: 0.7596 (ptp-170) cc_final: 0.6825 (tpt170)
REVERT: D  356 SER cc_start: 0.9024 (p) cc_final: 0.8627 (m)
REVERT: D  379 ARG cc_start: 0.7411 (ptp-170) cc_final: 0.6684 (tpt170)
REVERT: E  311 LYS cc_start: 0.8666 (mtpt) cc_final: 0.7648 (tptt)
REVERT: E  321 LYS cc_start: 0.8525 (mttm) cc_final: 0.7561 (tmtp)
REVERT: E  338 GLU cc_start: 0.8495 (pt0) cc_final: 0.8145 (tt0)
REVERT: E  340 LYS cc_start: 0.8377 (tttt) cc_final: 0.8163 (mtpm)
REVERT: E  358 ASP cc_start: 0.8512 (m-30) cc_final: 0.8258 (m-30)
  outliers start: 3
  outliers final: 2
  residues processed: 98
  average time/residue: 2.0740
  time to fit residues: 209.9772
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  317 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0670
   chunk 39 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.3122

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
C 359 ASN
C 368 ASN
D 368 ASN
E 368 ASN
F 368 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.160166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.146042 restraints weight = 12078.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.4330 rms_B_bonded: 1.84
r_work: 0.4226 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.4138 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.4981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3522  Z= 0.101
  Angle     :  0.599   3.815   4710  Z= 0.316
  Chirality :  0.053   0.139    528
  Planarity :  0.002   0.016    600
  Dihedral  :  5.988  19.016    468
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.40 %
    Favored  : 83.08 %
  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: -1.69 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.003   0.001   PHE C 378 
 TYR   0.012   0.003   TYR F 310 
 ARG   0.002   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02886 (   64)
  hydrogen bonds       : angle       5.02007 (  192)
  covalent geometry    : bond        0.00233 ( 3522)
  covalent geometry    : angle       0.59941 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 ARG cc_start: 0.7476 (ptp-170) cc_final: 0.6752 (tpt170)
REVERT: B  338 GLU cc_start: 0.8519 (pt0) cc_final: 0.8124 (tt0)
REVERT: B  379 ARG cc_start: 0.7655 (ptp-170) cc_final: 0.6968 (OUTLIER)
REVERT: C  379 ARG cc_start: 0.7545 (ptp-170) cc_final: 0.6797 (tpt170)
REVERT: D  356 SER cc_start: 0.8894 (p) cc_final: 0.8678 (m)
REVERT: D  379 ARG cc_start: 0.7319 (ptp-170) cc_final: 0.6602 (tpt170)
REVERT: E  321 LYS cc_start: 0.8572 (mttm) cc_final: 0.7577 (tmtp)
REVERT: E  338 GLU cc_start: 0.8623 (pt0) cc_final: 0.8256 (tt0)
REVERT: F  359 ASN cc_start: 0.8929 (m-40) cc_final: 0.8699 (m110)
  outliers start: 6
  outliers final: 1
  residues processed: 88
  average time/residue: 2.0735
  time to fit residues: 188.5650
Evaluate side-chains
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    0.0970
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 21 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
D 368 ASN
E 368 ASN
F 368 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.152701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.138578 restraints weight = 12197.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.4210 rms_B_bonded: 1.83
r_work: 0.4107 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.4020 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.5224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3522  Z= 0.151
  Angle     :  0.620   3.617   4710  Z= 0.331
  Chirality :  0.054   0.146    528
  Planarity :  0.003   0.016    600
  Dihedral  :  5.889  18.581    468
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.91 %
    Favored  : 81.06 %
  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: -1.73 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 362 
 PHE   0.005   0.001   PHE D 378 
 TYR   0.016   0.004   TYR D 310 
 ARG   0.002   0.000   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02632 (   64)
  hydrogen bonds       : angle       4.75664 (  192)
  covalent geometry    : bond        0.00353 ( 3522)
  covalent geometry    : angle       0.61969 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.645 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.7003 (ptm160) cc_final: 0.6778 (ptp90)
REVERT: A  356 SER cc_start: 0.9031 (p) cc_final: 0.8612 (m)
REVERT: A  379 ARG cc_start: 0.7562 (ptp-170) cc_final: 0.6795 (tpt170)
REVERT: B  338 GLU cc_start: 0.8519 (pt0) cc_final: 0.8301 (tt0)
REVERT: B  379 ARG cc_start: 0.7678 (ptp-170) cc_final: 0.6946 (OUTLIER)
REVERT: C  379 ARG cc_start: 0.7575 (ptp-170) cc_final: 0.6741 (tpt170)
REVERT: D  379 ARG cc_start: 0.7396 (ptp-170) cc_final: 0.6662 (tpt170)
REVERT: E  338 GLU cc_start: 0.8753 (pt0) cc_final: 0.8502 (tt0)
REVERT: F  359 ASN cc_start: 0.8982 (m-40) cc_final: 0.8745 (m110)
  outliers start: 12
  outliers final: 4
  residues processed: 80
  average time/residue: 2.4998
  time to fit residues: 205.7524
Evaluate side-chains
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain D residue  331 LYS
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0570
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.2104

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
D 368 ASN
E 368 ASN
F 368 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.157138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.143285 restraints weight = 12118.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.4308 rms_B_bonded: 1.84
r_work: 0.4211 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.4125 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3522  Z= 0.096
  Angle     :  0.548   5.093   4710  Z= 0.286
  Chirality :  0.052   0.132    528
  Planarity :  0.002   0.015    600
  Dihedral  :  5.480  17.981    468
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.68 %
    Favored  : 80.30 %
  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: -1.67 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.003   0.001   PHE C 378 
 TYR   0.009   0.002   TYR D 310 
 ARG   0.003   0.000   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02305 (   64)
  hydrogen bonds       : angle       4.54638 (  192)
  covalent geometry    : bond        0.00220 ( 3522)
  covalent geometry    : angle       0.54790 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 ARG cc_start: 0.7521 (ptp-170) cc_final: 0.6758 (tpt170)
REVERT: B  379 ARG cc_start: 0.7544 (ptp-170) cc_final: 0.6893 (OUTLIER)
REVERT: C  356 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8540 (m)
REVERT: C  379 ARG cc_start: 0.7509 (ptp-170) cc_final: 0.6703 (tpt170)
REVERT: D  379 ARG cc_start: 0.7582 (ptp-170) cc_final: 0.6743 (tpt170)
REVERT: F  315 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8848 (mt)
REVERT: F  359 ASN cc_start: 0.8943 (m-40) cc_final: 0.8714 (m110)
REVERT: F  379 ARG cc_start: 0.7883 (mmt180) cc_final: 0.6522 (tmt170)
  outliers start: 8
  outliers final: 5
  residues processed: 74
  average time/residue: 1.9721
  time to fit residues: 151.2582
Evaluate side-chains
  71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0980
   chunk 20 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
C 368 ASN
D 368 ASN
E 368 ASN
F 368 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.155153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.141229 restraints weight = 12251.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.4282 rms_B_bonded: 1.84
r_work: 0.4190 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.4103 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.5602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3522  Z= 0.104
  Angle     :  0.533   4.099   4710  Z= 0.281
  Chirality :  0.052   0.134    528
  Planarity :  0.002   0.014    600
  Dihedral  :  5.361  17.585    468
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.43 %
    Favored  : 79.80 %
  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: -1.66 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 362 
 PHE   0.004   0.001   PHE C 378 
 TYR   0.012   0.003   TYR D 310 
 ARG   0.001   0.000   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02130 (   64)
  hydrogen bonds       : angle       4.40871 (  192)
  covalent geometry    : bond        0.00241 ( 3522)
  covalent geometry    : angle       0.53280 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.7019 (ptm160) cc_final: 0.6774 (ptp90)
REVERT: A  379 ARG cc_start: 0.7505 (ptp-170) cc_final: 0.6730 (tpt170)
REVERT: B  379 ARG cc_start: 0.7527 (ptp-170) cc_final: 0.6860 (OUTLIER)
REVERT: C  356 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8594 (m)
REVERT: C  379 ARG cc_start: 0.7487 (ptp-170) cc_final: 0.6696 (tpt170)
REVERT: D  379 ARG cc_start: 0.7550 (ptp-170) cc_final: 0.6735 (tpt170)
REVERT: E  345 ASP cc_start: 0.8341 (m-30) cc_final: 0.8066 (m-30)
REVERT: F  315 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8854 (mp)
REVERT: F  359 ASN cc_start: 0.8949 (m-40) cc_final: 0.8714 (m110)
REVERT: F  379 ARG cc_start: 0.7858 (mmt180) cc_final: 0.6517 (tmt170)
  outliers start: 7
  outliers final: 4
  residues processed: 70
  average time/residue: 2.2878
  time to fit residues: 165.2192
Evaluate side-chains
  71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  315 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
C 368 ASN
D 368 ASN
E 368 ASN
F 368 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.153058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.139111 restraints weight = 12197.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 1.84
r_work: 0.4154 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.4065 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.5711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3522  Z= 0.127
  Angle     :  0.549   4.344   4710  Z= 0.291
  Chirality :  0.053   0.134    528
  Planarity :  0.002   0.017    600
  Dihedral  :  5.420  17.759    468
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.93 %
    Favored  : 79.80 %
  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: -1.73 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.004   0.001   PHE C 378 
 TYR   0.014   0.003   TYR D 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02163 (   64)
  hydrogen bonds       : angle       4.39498 (  192)
  covalent geometry    : bond        0.00294 ( 3522)
  covalent geometry    : angle       0.54923 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.7048 (ptm160) cc_final: 0.6696 (ttp-110)
REVERT: A  379 ARG cc_start: 0.7530 (ptp-170) cc_final: 0.6761 (tpt170)
REVERT: B  379 ARG cc_start: 0.7506 (ptp-170) cc_final: 0.6869 (OUTLIER)
REVERT: C  356 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8574 (m)
REVERT: C  379 ARG cc_start: 0.7517 (ptp-170) cc_final: 0.6719 (tpt170)
REVERT: D  379 ARG cc_start: 0.7536 (ptp-170) cc_final: 0.6749 (tpt170)
REVERT: F  359 ASN cc_start: 0.8982 (m-40) cc_final: 0.8744 (m110)
REVERT: F  379 ARG cc_start: 0.7875 (mmt180) cc_final: 0.6519 (tmt170)
  outliers start: 9
  outliers final: 6
  residues processed: 69
  average time/residue: 2.2770
  time to fit residues: 162.1405
Evaluate side-chains
  71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.0040
   chunk 33 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0030
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.9806

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
D 368 ASN
E 368 ASN
F 368 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.158027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.144165 restraints weight = 12077.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.4316 rms_B_bonded: 1.85
r_work: 0.4214 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.4125 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.5793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3522  Z= 0.083
  Angle     :  0.502   3.642   4710  Z= 0.261
  Chirality :  0.051   0.128    528
  Planarity :  0.002   0.014    600
  Dihedral  :  5.183  17.257    468
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 19.19 %
    Favored  : 80.05 %
  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: -1.74 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 362 
 PHE   0.002   0.001   PHE F 378 
 TYR   0.009   0.002   TYR D 310 
 ARG   0.002   0.000   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01955 (   64)
  hydrogen bonds       : angle       4.28208 (  192)
  covalent geometry    : bond        0.00191 ( 3522)
  covalent geometry    : angle       0.50200 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.7003 (ptm160) cc_final: 0.6753 (ptp90)
REVERT: A  379 ARG cc_start: 0.7474 (ptp-170) cc_final: 0.6728 (tpt170)
REVERT: B  379 ARG cc_start: 0.7456 (ptp-170) cc_final: 0.6833 (OUTLIER)
REVERT: C  356 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8454 (m)
REVERT: C  379 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.6698 (tpt170)
REVERT: D  379 ARG cc_start: 0.7501 (ptp-170) cc_final: 0.6770 (tpt170)
REVERT: E  345 ASP cc_start: 0.8341 (m-30) cc_final: 0.8055 (m-30)
REVERT: F  356 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8521 (m)
REVERT: F  359 ASN cc_start: 0.8959 (m-40) cc_final: 0.8719 (m110)
REVERT: F  379 ARG cc_start: 0.7853 (mmt180) cc_final: 0.6494 (tmt170)
  outliers start: 3
  outliers final: 2
  residues processed: 68
  average time/residue: 2.2400
  time to fit residues: 157.2777
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
D 368 ASN
E 368 ASN
F 368 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.153722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.139591 restraints weight = 12371.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.4251 rms_B_bonded: 1.87
r_work: 0.4159 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.4070 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.5814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3522  Z= 0.129
  Angle     :  0.537   3.683   4710  Z= 0.284
  Chirality :  0.052   0.135    528
  Planarity :  0.002   0.016    600
  Dihedral  :  5.304  17.401    468
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 18.94 %
    Favored  : 79.80 %
  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: -1.76 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.004   0.001   PHE C 378 
 TYR   0.014   0.003   TYR D 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02049 (   64)
  hydrogen bonds       : angle       4.27101 (  192)
  covalent geometry    : bond        0.00300 ( 3522)
  covalent geometry    : angle       0.53747 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.7065 (ptm160) cc_final: 0.6709 (ttp-110)
REVERT: A  379 ARG cc_start: 0.7517 (ptp-170) cc_final: 0.6738 (tpt170)
REVERT: B  379 ARG cc_start: 0.7336 (ptp-170) cc_final: 0.6835 (OUTLIER)
REVERT: C  356 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8563 (m)
REVERT: C  379 ARG cc_start: 0.7519 (ptp-170) cc_final: 0.6731 (tpt170)
REVERT: D  379 ARG cc_start: 0.7503 (ptp-170) cc_final: 0.6745 (tpt170)
REVERT: E  345 ASP cc_start: 0.8353 (m-30) cc_final: 0.8081 (m-30)
REVERT: F  356 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8614 (m)
REVERT: F  359 ASN cc_start: 0.8988 (m-40) cc_final: 0.8763 (m110)
REVERT: F  379 ARG cc_start: 0.7892 (mmt180) cc_final: 0.6457 (tmt170)
  outliers start: 5
  outliers final: 3
  residues processed: 68
  average time/residue: 2.5072
  time to fit residues: 176.3513
Evaluate side-chains
  71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0770
   chunk 5 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0370
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.4416

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
D 368 ASN
E 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.161529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.147631 restraints weight = 12270.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.4373 rms_B_bonded: 1.89
r_work: 0.4278 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.4190 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.4190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.5977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3522  Z= 0.072
  Angle     :  0.479   3.408   4710  Z= 0.247
  Chirality :  0.051   0.132    528
  Planarity :  0.002   0.014    600
  Dihedral  :  4.979  16.993    468
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 19.44 %
    Favored  : 80.05 %
  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: -1.75 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 330 
 PHE   0.002   0.000   PHE F 378 
 TYR   0.007   0.001   TYR A 310 
 ARG   0.001   0.000   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01819 (   64)
  hydrogen bonds       : angle       4.11444 (  192)
  covalent geometry    : bond        0.00170 ( 3522)
  covalent geometry    : angle       0.47928 ( 4710)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 ARG cc_start: 0.7486 (ptp-170) cc_final: 0.6753 (tpt170)
REVERT: B  379 ARG cc_start: 0.7347 (ptp-170) cc_final: 0.6842 (OUTLIER)
REVERT: C  356 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8400 (m)
REVERT: C  379 ARG cc_start: 0.7499 (ptp-170) cc_final: 0.6733 (tpt170)
REVERT: D  379 ARG cc_start: 0.7501 (ptp-170) cc_final: 0.6788 (tpt170)
REVERT: E  345 ASP cc_start: 0.8318 (m-30) cc_final: 0.8056 (m-30)
REVERT: F  315 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8827 (mp)
REVERT: F  356 SER cc_start: 0.8970 (p) cc_final: 0.8520 (m)
REVERT: F  379 ARG cc_start: 0.7860 (mmt180) cc_final: 0.6406 (tmt170)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 2.2681
  time to fit residues: 174.4329
Evaluate side-chains
  70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain F residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0570
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.1702

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
B 368 ASN
C 359 ASN
D 368 ASN
E 368 ASN
F 359 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.158402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.144404 restraints weight = 12145.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.4312 rms_B_bonded: 1.85
r_work: 0.4217 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.4124 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.6018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3522  Z= 0.091
  Angle     :  0.514   6.068   4710  Z= 0.264
  Chirality :  0.051   0.130    528
  Planarity :  0.002   0.014    600
  Dihedral  :  4.967  16.600    468
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 20.45 %
    Favored  : 78.79 %
  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: -1.69 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.003   0.001   PHE C 378 
 TYR   0.011   0.002   TYR D 310 
 ARG   0.001   0.000   ARG D 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01924 (   64)
  hydrogen bonds       : angle       4.05967 (  192)
  covalent geometry    : bond        0.00214 ( 3522)
  covalent geometry    : angle       0.51398 ( 4710)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6561.34 seconds
wall clock time: 113 minutes 22.84 seconds (6802.84 seconds total)