Starting phenix.real_space_refine
on Tue Feb 11 13:07:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qky_14057/02_2025/7qky_14057.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qky_14057/02_2025/7qky_14057.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qky_14057/02_2025/7qky_14057.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qky_14057/02_2025/7qky_14057.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qky_14057/02_2025/7qky_14057.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qky_14057/02_2025/7qky_14057.cif"
  }
  resolution = 1.86
  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=   0.003
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    1776      2.51       5
     N     504      2.21       5
     O     612      1.98       5
     H    2862      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5760
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 960
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
    Chain: "B"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 960
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
    Chain: "C"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 960
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
    Chain: "D"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 960
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
    Chain: "E"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 960
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
    Chain: "F"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 960
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
  Time building chain proxies: 4.20, per 1000 atoms: 0.73
  Number of scatterers: 5760
  At special positions: 0
  Unit cell: (111.231, 82.878, 39.258, 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     612      8.00
     N     504      7.00
     C    1776      6.00
     H    2862      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: 1.50
  Conformation dependent library (CDL) restraints added in 402.7 milliseconds
  

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 47.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 386
      removed outlier: 6.570A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU B 380 " --> pdb=" O   THR A 377 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ARG A 379 " --> pdb=" O   GLU B 380 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ALA B 382 " --> pdb=" O   ARG A 379 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASN A 381 " --> pdb=" O   ALA B 382 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ALA B 384 " --> pdb=" O   ASN A 381 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   LYS A 383 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   THR B 386 " --> pdb=" O   LYS A 383 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   LYS A 385 " --> pdb=" O   THR B 386 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   THR B 377 " --> pdb=" O   PHE E 378 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   GLU E 380 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ARG B 379 " --> pdb=" O   GLU E 380 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   ALA E 382 " --> pdb=" O   ARG B 379 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ASN B 381 " --> pdb=" O   ALA E 382 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   ALA E 384 " --> pdb=" O   ASN B 381 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LYS B 383 " --> pdb=" O   ALA E 384 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   THR E 386 " --> pdb=" O   LYS B 383 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LYS B 385 " --> pdb=" O   THR E 386 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 394
      removed outlier: 6.290A  pdb=" N   VAL A 393 " --> pdb=" O   TYR B 394 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   VAL B 393 " --> pdb=" O   TYR E 394 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 399
      removed outlier: 6.809A  pdb=" N   VAL A 398 " --> pdb=" O   VAL B 399 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   VAL B 398 " --> pdb=" O   VAL E 399 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 406 through 414
      removed outlier: 6.822A  pdb=" N   HIS A 407 " --> pdb=" O   LEU B 408 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   ASN B 410 " --> pdb=" O   HIS A 407 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   SER A 409 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   SER B 412 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL A 411 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   THR B 414 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   SER A 413 " --> pdb=" O   THR B 414 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   HIS B 407 " --> pdb=" O   LEU E 408 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   ASN E 410 " --> pdb=" O   HIS B 407 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   SER B 409 " --> pdb=" O   ASN E 410 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   SER E 412 " --> pdb=" O   SER B 409 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL B 411 " --> pdb=" O   SER E 412 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   THR E 414 " --> pdb=" O   VAL B 411 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER B 413 " --> pdb=" O   THR E 414 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 420
      removed outlier: 6.310A  pdb=" N   ASP B 418 " --> pdb=" O   MET E 419 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 429
      removed outlier: 6.500A  pdb=" N   LEU A 425 " --> pdb=" O   ALA B 426 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   LEU B 428 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   THR A 427 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LEU B 425 " --> pdb=" O   ALA E 426 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   LEU E 428 " --> pdb=" O   LEU B 425 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   THR B 427 " --> pdb=" O   LEU E 428 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 432 through 433
    Processing sheet with id=AA8, first strand: chain 'A' and resid 436 through 438
    Processing sheet with id=AA9, first strand: chain 'C' and resid 377 through 386
      removed outlier: 6.548A  pdb=" N   THR C 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   GLU D 380 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ARG C 379 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   ALA D 382 " --> pdb=" O   ARG C 379 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   ASN C 381 " --> pdb=" O   ALA D 382 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   ALA D 384 " --> pdb=" O   ASN C 381 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   LYS C 383 " --> pdb=" O   ALA D 384 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   THR D 386 " --> pdb=" O   LYS C 383 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LYS C 385 " --> pdb=" O   THR D 386 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   THR D 377 " --> pdb=" O   PHE F 378 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   GLU F 380 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ARG D 379 " --> pdb=" O   GLU F 380 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ALA F 382 " --> pdb=" O   ARG D 379 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ASN D 381 " --> pdb=" O   ALA F 382 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ALA F 384 " --> pdb=" O   ASN D 381 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LYS D 383 " --> pdb=" O   ALA F 384 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   THR F 386 " --> pdb=" O   LYS D 383 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LYS D 385 " --> pdb=" O   THR F 386 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 392 through 394
      removed outlier: 6.289A  pdb=" N   VAL C 393 " --> pdb=" O   TYR D 394 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   VAL D 393 " --> pdb=" O   TYR F 394 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 398 through 399
      removed outlier: 6.831A  pdb=" N   VAL C 398 " --> pdb=" O   VAL D 399 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL D 398 " --> pdb=" O   VAL F 399 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 406 through 414
      removed outlier: 6.779A  pdb=" N   HIS C 407 " --> pdb=" O   ARG D 406 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   HIS D 407 " --> pdb=" O   ARG F 406 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 417 through 420
    Processing sheet with id=AB5, first strand: chain 'C' and resid 424 through 429
      removed outlier: 6.520A  pdb=" N   LEU C 425 " --> pdb=" O   ALA D 426 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   LEU D 428 " --> pdb=" O   LEU C 425 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   THR C 427 " --> pdb=" O   LEU D 428 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LEU D 425 " --> pdb=" O   ALA F 426 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   LEU F 428 " --> pdb=" O   LEU D 425 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   THR D 427 " --> pdb=" O   LEU F 428 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'C' and resid 432 through 433
    Processing sheet with id=AB7, first strand: chain 'C' and resid 436 through 438

    35 hydrogen bonds defined for protein.
    105 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: 1.85

  Time building geometry restraints manager: 1.79 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: 2862
        1.12 -     1.29: 516
        1.29 -     1.47: 956
        1.47 -     1.64: 1450
        1.64 -     1.81: 12
  Bond restraints: 5796
  Sorted by residual:
  bond pdb=" CE1 PHE A 378 "
       pdb=" HE1 PHE A 378 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   LYS E 383 "
       pdb=" H   LYS E 383 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CE2 TYR E 394 "
       pdb=" HE2 TYR E 394 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" NE  ARG A 379 "
       pdb=" HE  ARG A 379 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   ALA C 384 "
       pdb=" H   ALA C 384 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 5791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 7559
        1.82 -     3.64: 2072
        3.64 -     5.45: 563
        5.45 -     7.27: 289
        7.27 -     9.09: 11
  Bond angle restraints: 10494
  Sorted by residual:
  angle pdb=" CB  HIS A 407 "
        pdb=" CG  HIS A 407 "
        pdb=" CD2 HIS A 407 "
      ideal   model   delta    sigma   weight residual
     131.20  125.26    5.94 1.30e+00 5.92e-01 2.09e+01
  angle pdb=" N   ALA B 429 "
        pdb=" CA  ALA B 429 "
        pdb=" C   ALA B 429 "
      ideal   model   delta    sigma   weight residual
     108.99  116.02   -7.03 1.57e+00 4.06e-01 2.01e+01
  angle pdb=" CB  HIS E 407 "
        pdb=" CG  HIS E 407 "
        pdb=" CD2 HIS E 407 "
      ideal   model   delta    sigma   weight residual
     131.20  125.39    5.81 1.30e+00 5.92e-01 2.00e+01
  angle pdb=" CB  HIS C 407 "
        pdb=" CG  HIS C 407 "
        pdb=" CD2 HIS C 407 "
      ideal   model   delta    sigma   weight residual
     131.20  125.44    5.76 1.30e+00 5.92e-01 1.96e+01
  angle pdb=" CB  HIS D 407 "
        pdb=" CG  HIS D 407 "
        pdb=" CD2 HIS D 407 "
      ideal   model   delta    sigma   weight residual
     131.20  125.50    5.70 1.30e+00 5.92e-01 1.92e+01
  ... (remaining 10489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.18: 2403
       14.18 -    28.36: 238
       28.36 -    42.54: 26
       42.54 -    56.72: 43
       56.72 -    70.89: 44
  Dihedral angle restraints: 2754
    sinusoidal: 1524
      harmonic: 1230
  Sorted by residual:
  dihedral pdb=" CA  HIS C 388 "
           pdb=" C   HIS C 388 "
           pdb=" N   GLY C 389 "
           pdb=" CA  GLY C 389 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.24   28.76     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  HIS B 388 "
           pdb=" C   HIS B 388 "
           pdb=" N   GLY B 389 "
           pdb=" CA  GLY B 389 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.39   28.61     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA  HIS D 388 "
           pdb=" C   HIS D 388 "
           pdb=" N   GLY D 389 "
           pdb=" CA  GLY D 389 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.69   28.31     0      5.00e+00 4.00e-02 3.21e+01
  ... (remaining 2751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 305
       0.079 -    0.157: 151
       0.157 -    0.235: 24
       0.235 -    0.313: 1
       0.313 -    0.392: 5
  Chirality restraints: 486
  Sorted by residual:
  chirality pdb=" CA  HIS D 388 "
            pdb=" N   HIS D 388 "
            pdb=" C   HIS D 388 "
            pdb=" CB  HIS D 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.84e+00
  chirality pdb=" CA  HIS C 388 "
            pdb=" N   HIS C 388 "
            pdb=" C   HIS C 388 "
            pdb=" CB  HIS C 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CA  HIS B 388 "
            pdb=" N   HIS B 388 "
            pdb=" C   HIS B 388 "
            pdb=" CB  HIS B 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.40e+00
  ... (remaining 483 not shown)

  Planarity restraints: 888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 378 "   -0.227 2.00e-02 2.50e+03   9.08e-02 2.47e+02
        pdb=" CG  PHE C 378 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 378 "    0.075 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 378 "    0.073 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 378 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 378 "    0.045 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 378 "   -0.036 2.00e-02 2.50e+03
        pdb=" HD1 PHE C 378 "    0.113 2.00e-02 2.50e+03
        pdb=" HD2 PHE C 378 "    0.053 2.00e-02 2.50e+03
        pdb=" HE1 PHE C 378 "   -0.025 2.00e-02 2.50e+03
        pdb=" HE2 PHE C 378 "    0.024 2.00e-02 2.50e+03
        pdb=" HZ  PHE C 378 "   -0.127 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 378 "   -0.200 2.00e-02 2.50e+03   8.24e-02 2.04e+02
        pdb=" CG  PHE D 378 "    0.008 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 378 "    0.065 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 378 "    0.061 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 378 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 378 "    0.041 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 378 "   -0.042 2.00e-02 2.50e+03
        pdb=" HD1 PHE D 378 "    0.109 2.00e-02 2.50e+03
        pdb=" HD2 PHE D 378 "    0.045 2.00e-02 2.50e+03
        pdb=" HE1 PHE D 378 "   -0.014 2.00e-02 2.50e+03
        pdb=" HE2 PHE D 378 "    0.039 2.00e-02 2.50e+03
        pdb=" HZ  PHE D 378 "   -0.120 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D 388 "   -0.039 2.00e-02 2.50e+03   7.06e-02 4.99e+01
        pdb=" N   GLY D 389 "    0.122 2.00e-02 2.50e+03
        pdb=" CA  GLY D 389 "   -0.035 2.00e-02 2.50e+03
        pdb=" H   GLY D 389 "   -0.047 2.00e-02 2.50e+03
  ... (remaining 885 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.17: 551
        2.17 -     2.78: 9561
        2.78 -     3.39: 15847
        3.39 -     3.99: 21842
        3.99 -     4.60: 29797
  Nonbonded interactions: 77598
  Sorted by model distance:
  nonbonded pdb=" HG  SER F 413 "
            pdb=" OD2 ASP F 418 "
     model   vdw
     1.568 2.450
  nonbonded pdb=" HG  SER E 413 "
            pdb=" OD2 ASP E 418 "
     model   vdw
     1.574 2.450
  nonbonded pdb=" HG  SER B 413 "
            pdb=" OD2 ASP B 418 "
     model   vdw
     1.579 2.450
  nonbonded pdb=" HG  SER D 413 "
            pdb=" OD2 ASP D 418 "
     model   vdw
     1.592 2.450
  nonbonded pdb=" HG  SER A 413 "
            pdb=" OD2 ASP A 418 "
     model   vdw
     1.639 2.450
  ... (remaining 77593 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: 0.00
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:             4.000
  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:             0.110
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.220
  Find NCS groups from input model:        0.160
  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:12.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
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   2934  Z= 0.756
  Angle     :  1.746   7.133   3978  Z= 1.129
  Chirality :  0.092   0.392    486
  Planarity :  0.011   0.081    516
  Dihedral  : 12.756  70.894   1068
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 1.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.03 %
    Favored  : 96.36 %
  Cbeta Deviations :  0.81 %
  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: -3.08 (0.30), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.23), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 388 
 PHE   0.125   0.035   PHE C 378 
 TYR   0.027   0.009   TYR D 394 
 ARG   0.004   0.001   ARG A 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  140 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 ARG cc_start: 0.7410 (mmt90) cc_final: 0.7174 (mmt-90)
  outliers start: 2
  outliers final: 0
  residues processed: 140
  average time/residue: 1.9541
  time to fit residues: 281.5977
Evaluate side-chains
  117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.229221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.196372 restraints weight = 5516.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.4651 rms_B_bonded: 1.34
r_work: 0.4538 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.4460 rms_B_bonded: 2.25 restraints_weight: 0.2500
r_work (final): 0.4460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2934  Z= 0.167
  Angle     :  0.643   7.017   3978  Z= 0.330
  Chirality :  0.048   0.137    486
  Planarity :  0.003   0.015    516
  Dihedral  :  8.206  29.405    408
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.42 %
    Favored  : 86.36 %
  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: -3.01 (0.31), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.23), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 407 
 PHE   0.014   0.002   PHE C 378 
 TYR   0.012   0.002   TYR C 394 
 ARG   0.003   0.001   ARG B 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  128 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  431 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7310 (mp0)
REVERT: C  431 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7505 (mp0)
REVERT: D  431 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7372 (mp0)
REVERT: E  380 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7611 (tm-30)
REVERT: E  385 LYS cc_start: 0.7533 (tttm) cc_final: 0.7174 (mtpp)
  outliers start: 4
  outliers final: 1
  residues processed: 125
  average time/residue: 2.1692
  time to fit residues: 278.3753
Evaluate side-chains
  114 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  436 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 24 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.222455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.189132 restraints weight = 5416.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.4565 rms_B_bonded: 1.42
r_work: 0.4440 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.4356 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2934  Z= 0.196
  Angle     :  0.630   6.714   3978  Z= 0.320
  Chirality :  0.047   0.131    486
  Planarity :  0.002   0.014    516
  Dihedral  :  7.489  26.648    408
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 17.58 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.31), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.24), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D 407 
 PHE   0.010   0.002   PHE C 378 
 TYR   0.013   0.002   TYR C 394 
 ARG   0.001   0.000   ARG F 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: A  383 LYS cc_start: 0.7346 (mttt) cc_final: 0.6771 (mmmt)
REVERT: A  406 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7896 (mmm160)
REVERT: B  383 LYS cc_start: 0.7859 (mttm) cc_final: 0.7535 (mtmm)
REVERT: B  385 LYS cc_start: 0.7483 (tttt) cc_final: 0.7159 (mtpp)
REVERT: B  431 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7406 (mp0)
REVERT: C  385 LYS cc_start: 0.7588 (tttt) cc_final: 0.7255 (ttpp)
REVERT: C  431 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7647 (mp0)
REVERT: D  379 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6972 (mtt180)
REVERT: D  431 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7472 (mp0)
REVERT: E  380 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: F  380 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7526 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 2.3855
  time to fit residues: 283.5602
Evaluate side-chains
  106 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.219427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.186026 restraints weight = 5549.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.4525 rms_B_bonded: 1.41
r_work: 0.4405 rms_B_bonded: 1.39 restraints_weight: 0.5000
r_work: 0.4323 rms_B_bonded: 2.35 restraints_weight: 0.2500
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2934  Z= 0.251
  Angle     :  0.669   6.147   3978  Z= 0.339
  Chirality :  0.047   0.131    486
  Planarity :  0.003   0.027    516
  Dihedral  :  7.497  27.267    408
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.18 %
    Favored  : 80.00 %
  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: -3.03 (0.32), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.24), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D 407 
 PHE   0.011   0.003   PHE C 378 
 TYR   0.010   0.002   TYR C 394 
 ARG   0.002   0.000   ARG B 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: A  383 LYS cc_start: 0.7407 (mttt) cc_final: 0.6796 (mmmt)
REVERT: B  380 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7671 (tm-30)
REVERT: B  383 LYS cc_start: 0.7837 (mttm) cc_final: 0.7561 (mtpm)
REVERT: B  431 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7381 (mp0)
REVERT: C  380 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: C  383 LYS cc_start: 0.7711 (ptpp) cc_final: 0.7124 (mmmt)
REVERT: C  385 LYS cc_start: 0.7621 (tttt) cc_final: 0.7263 (ttpp)
REVERT: C  431 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7628 (mp0)
REVERT: D  379 ARG cc_start: 0.7270 (mtt180) cc_final: 0.7014 (mtt180)
REVERT: D  431 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7527 (mp0)
REVERT: E  380 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7721 (tm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 114
  average time/residue: 2.4052
  time to fit residues: 281.0827
Evaluate side-chains
  112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain D residue  386 THR
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain E residue  414 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 9 optimal weight:    0.2980
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.221077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.188015 restraints weight = 5523.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.4553 rms_B_bonded: 1.38
r_work: 0.4428 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.4348 rms_B_bonded: 2.38 restraints_weight: 0.2500
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.4578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2934  Z= 0.192
  Angle     :  0.621   5.972   3978  Z= 0.314
  Chirality :  0.047   0.129    486
  Planarity :  0.002   0.018    516
  Dihedral  :  7.155  25.624    408
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.79 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.32), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.25), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS D 407 
 PHE   0.008   0.002   PHE C 378 
 TYR   0.013   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  118 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7760 (tm-30)
REVERT: A  383 LYS cc_start: 0.7384 (mttt) cc_final: 0.6785 (mmmt)
REVERT: A  385 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7448 (ttpt)
REVERT: A  406 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8056 (mmm160)
REVERT: B  380 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7686 (tm-30)
REVERT: B  383 LYS cc_start: 0.7877 (mttm) cc_final: 0.7604 (mtpm)
REVERT: B  431 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7480 (mp0)
REVERT: C  383 LYS cc_start: 0.7745 (ptpp) cc_final: 0.7122 (mmmt)
REVERT: C  385 LYS cc_start: 0.7592 (tttt) cc_final: 0.7329 (mtpp)
REVERT: C  431 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7603 (mp0)
REVERT: D  379 ARG cc_start: 0.7285 (mtt180) cc_final: 0.7032 (mtt180)
REVERT: D  431 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7495 (mp0)
REVERT: E  380 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7740 (tm-30)
  outliers start: 5
  outliers final: 3
  residues processed: 113
  average time/residue: 2.3649
  time to fit residues: 273.7202
Evaluate side-chains
  112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain E residue  414 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.9986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.218665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.185187 restraints weight = 5452.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.4543 rms_B_bonded: 1.34
r_work: 0.4419 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.4339 rms_B_bonded: 2.36 restraints_weight: 0.2500
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2934  Z= 0.208
  Angle     :  0.634   5.544   3978  Z= 0.320
  Chirality :  0.047   0.128    486
  Planarity :  0.002   0.019    516
  Dihedral  :  7.104  25.398    408
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.48 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.32), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.25), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D 407 
 PHE   0.009   0.003   PHE C 378 
 TYR   0.013   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: A  385 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7443 (ttpt)
REVERT: A  406 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8059 (mmm160)
REVERT: B  380 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: B  431 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7472 (mp0)
REVERT: C  383 LYS cc_start: 0.7775 (ptpp) cc_final: 0.7148 (mmmt)
REVERT: C  385 LYS cc_start: 0.7606 (tttt) cc_final: 0.7351 (mtpp)
REVERT: C  431 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7618 (mp0)
REVERT: D  379 ARG cc_start: 0.7280 (mtt180) cc_final: 0.7047 (mtt180)
REVERT: D  431 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7501 (mp0)
REVERT: E  380 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7743 (tm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 111
  average time/residue: 2.4340
  time to fit residues: 276.6698
Evaluate side-chains
  110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain E residue  414 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4900 r_free = 0.4900 target = 0.225252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.192304 restraints weight = 5559.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.4611 rms_B_bonded: 1.35
r_work: 0.4489 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.4409 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.4894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2934  Z= 0.151
  Angle     :  0.591   5.483   3978  Z= 0.294
  Chirality :  0.047   0.129    486
  Planarity :  0.002   0.014    516
  Dihedral  :  6.683  22.875    408
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 20.00 %
    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: -2.99 (0.33), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.25), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 407 
 PHE   0.006   0.002   PHE E 378 
 TYR   0.013   0.001   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7693 (tm-30)
REVERT: A  383 LYS cc_start: 0.7756 (ptpt) cc_final: 0.7103 (mmmt)
REVERT: A  406 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8020 (mmm160)
REVERT: B  383 LYS cc_start: 0.7774 (mtpm) cc_final: 0.7399 (mttp)
REVERT: B  385 LYS cc_start: 0.7459 (tttt) cc_final: 0.7195 (mtpp)
REVERT: B  431 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7430 (mp0)
REVERT: C  383 LYS cc_start: 0.7765 (ptpp) cc_final: 0.7083 (mmmt)
REVERT: C  385 LYS cc_start: 0.7575 (tttt) cc_final: 0.7311 (mtpp)
REVERT: C  406 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.7663 (mmm160)
REVERT: C  431 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7595 (mp0)
REVERT: D  379 ARG cc_start: 0.7244 (mtt180) cc_final: 0.7007 (mtt180)
REVERT: D  431 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7449 (mp0)
REVERT: E  380 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7708 (tm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 114
  average time/residue: 2.3780
  time to fit residues: 277.7670
Evaluate side-chains
  110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain E residue  414 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    2.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.218016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.184232 restraints weight = 5380.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.4540 rms_B_bonded: 1.37
r_work: 0.4415 rms_B_bonded: 1.37 restraints_weight: 0.5000
r_work: 0.4332 rms_B_bonded: 2.30 restraints_weight: 0.2500
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.4914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2934  Z= 0.249
  Angle     :  0.666   5.518   3978  Z= 0.336
  Chirality :  0.047   0.127    486
  Planarity :  0.003   0.015    516
  Dihedral  :  7.018  23.985    408
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 19.70 %
    Favored  : 79.09 %
  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: -3.02 (0.33), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.25), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D 407 
 PHE   0.010   0.003   PHE C 378 
 TYR   0.015   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 379 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: A  383 LYS cc_start: 0.7728 (ptpt) cc_final: 0.7141 (mmmt)
REVERT: A  385 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7298 (ttpp)
REVERT: A  406 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8039 (mmm160)
REVERT: B  383 LYS cc_start: 0.7728 (mtpm) cc_final: 0.7350 (mttp)
REVERT: B  385 LYS cc_start: 0.7459 (tttt) cc_final: 0.7219 (mtpp)
REVERT: B  431 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7340 (mp0)
REVERT: C  383 LYS cc_start: 0.7780 (ptpp) cc_final: 0.7099 (mmmt)
REVERT: C  385 LYS cc_start: 0.7603 (tttt) cc_final: 0.7329 (mtpp)
REVERT: C  406 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.7660 (mmm160)
REVERT: C  431 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7595 (mp0)
REVERT: D  379 ARG cc_start: 0.7320 (mtt180) cc_final: 0.7081 (mtt180)
REVERT: D  431 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7525 (mp0)
REVERT: E  380 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7724 (tm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 110
  average time/residue: 2.4541
  time to fit residues: 276.2302
Evaluate side-chains
  111 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain F residue  386 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 424 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.228247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.194163 restraints weight = 5498.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.4632 rms_B_bonded: 1.37
r_work: 0.4508 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.4431 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.5078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2934  Z= 0.142
  Angle     :  0.575   5.301   3978  Z= 0.287
  Chirality :  0.047   0.129    486
  Planarity :  0.002   0.013    516
  Dihedral  :  6.559  22.471    408
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 19.09 %
    Favored  : 79.39 %
  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: -3.00 (0.33), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.25), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 407 
 PHE   0.006   0.002   PHE E 378 
 TYR   0.014   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: A  383 LYS cc_start: 0.7759 (ptpt) cc_final: 0.7111 (mmmt)
REVERT: A  406 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7997 (mmm160)
REVERT: B  383 LYS cc_start: 0.7785 (mtpm) cc_final: 0.7412 (mttt)
REVERT: B  385 LYS cc_start: 0.7464 (tttt) cc_final: 0.7243 (mtpp)
REVERT: B  431 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7415 (mp0)
REVERT: C  383 LYS cc_start: 0.7762 (ptpp) cc_final: 0.7061 (mmmt)
REVERT: C  385 LYS cc_start: 0.7576 (tttt) cc_final: 0.7302 (mtpp)
REVERT: C  406 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7655 (mmm160)
REVERT: C  431 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7547 (mp0)
REVERT: D  379 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6995 (mtt180)
REVERT: D  431 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7475 (mp0)
REVERT: E  380 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: E  385 LYS cc_start: 0.7582 (tttm) cc_final: 0.7238 (mtpp)
  outliers start: 5
  outliers final: 3
  residues processed: 111
  average time/residue: 2.4673
  time to fit residues: 280.4816
Evaluate side-chains
  113 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain C residue  406 ARG
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain E residue  414 THR
Chi-restraints excluded: chain F residue  386 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.2582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.223290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.189116 restraints weight = 5467.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4586 rms_B_bonded: 1.39
r_work: 0.4464 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.4382 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.4382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.5031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2934  Z= 0.169
  Angle     :  0.603   5.110   3978  Z= 0.301
  Chirality :  0.047   0.126    486
  Planarity :  0.002   0.014    516
  Dihedral  :  6.592  22.096    408
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 19.70 %
    Favored  : 79.09 %
  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: -2.95 (0.33), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.25), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 407 
 PHE   0.007   0.002   PHE C 378 
 TYR   0.015   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Residue ALA  382 is missing expected H atoms. Skipping.
Evaluate side-chains
  112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7778 (tm-30)
REVERT: A  383 LYS cc_start: 0.7769 (ptpt) cc_final: 0.7103 (mmmt)
REVERT: A  406 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8040 (mmm160)
REVERT: B  383 LYS cc_start: 0.7778 (mtpm) cc_final: 0.7406 (mttt)
REVERT: B  385 LYS cc_start: 0.7446 (tttt) cc_final: 0.7213 (mtpp)
REVERT: B  431 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7425 (mp0)
REVERT: C  383 LYS cc_start: 0.7777 (ptpp) cc_final: 0.7100 (mmmt)
REVERT: C  385 LYS cc_start: 0.7582 (tttt) cc_final: 0.7314 (mtpp)
REVERT: C  406 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7491 (mmt180)
REVERT: C  431 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7572 (mp0)
REVERT: D  379 ARG cc_start: 0.7281 (mtt180) cc_final: 0.7034 (mtt180)
REVERT: D  431 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7461 (mp0)
REVERT: E  380 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: E  385 LYS cc_start: 0.7602 (tttm) cc_final: 0.7260 (mtpp)
REVERT: F  376 LEU cc_start: 0.6617 (mt) cc_final: 0.6403 (mp)
  outliers start: 4
  outliers final: 2
  residues processed: 108
  average time/residue: 2.5108
  time to fit residues: 277.6817
Evaluate side-chains
  112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain C residue  406 ARG
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain F residue  386 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    0.0870
   chunk 7 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 22 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    1.5162

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4865 r_free = 0.4865 target = 0.222830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.188665 restraints weight = 5504.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.4578 rms_B_bonded: 1.43
r_work: 0.4454 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.4372 rms_B_bonded: 2.38 restraints_weight: 0.2500
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2934  Z= 0.181
  Angle     :  0.612   5.248   3978  Z= 0.307
  Chirality :  0.046   0.128    486
  Planarity :  0.002   0.014    516
  Dihedral  :  6.647  22.311    408
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 20.00 %
    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: -2.96 (0.33), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.25), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 407 
 PHE   0.007   0.002   PHE D 378 
 TYR   0.016   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8526.27 seconds
wall clock time: 149 minutes 53.81 seconds (8993.81 seconds total)