Starting phenix.real_space_refine
on Thu Jul 24 08:40:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qky_14057/07_2025/7qky_14057.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qky_14057/07_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_14057/07_2025/7qky_14057.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qky_14057/07_2025/7qky_14057.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qky_14057/07_2025/7qky_14057.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qky_14057/07_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-5711/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: 4.66, per 1000 atoms: 0.81
  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: 1.26
  Conformation dependent library (CDL) restraints added in 392.5 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: 0.57
  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: 1.93

  Time building geometry restraints manager: 1.60 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: 0.01
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:             5.570
  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:             0.100
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.400
  Find NCS groups from input model:        0.140
  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:             0.010
  Load rotamer database and sin/cos tables:16.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.690
-------------------------------------------------------------------------------
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= 0.697
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09766 (   35)
  hydrogen bonds       : angle       8.57351 (  105)
  covalent geometry    : bond        0.01112 ( 2934)
  covalent geometry    : angle       1.74615 ( 3978)

*********************** 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  : 0.479 
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: 1.9686
  time to fit residues: 283.5490
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  : 0.449 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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 = 0.4934 r_free = 0.4934 target = 0.229508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.196609 restraints weight = 5518.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.4653 rms_B_bonded: 1.34
r_work: 0.4541 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.4463 rms_B_bonded: 2.26 restraints_weight: 0.2500
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3767

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= 0.114
  Angle     :  0.640   6.901   3978  Z= 0.330
  Chirality :  0.049   0.134    486
  Planarity :  0.003   0.015    516
  Dihedral  :  8.161  29.366    408
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.12 %
    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 : -2.28 (0.23), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 407 
 PHE   0.013   0.002   PHE C 378 
 TYR   0.013   0.002   TYR C 394 
 ARG   0.003   0.001   ARG B 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02904 (   35)
  hydrogen bonds       : angle       6.19701 (  105)
  covalent geometry    : bond        0.00257 ( 2934)
  covalent geometry    : angle       0.63996 ( 3978)

*********************** 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
  129 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.524 
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: A  431 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7470 (mp0)
REVERT: B  431 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7315 (mp0)
REVERT: C  431 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7521 (mp0)
REVERT: D  379 ARG cc_start: 0.7117 (mtt180) cc_final: 0.6816 (mtt180)
REVERT: D  431 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7427 (mp0)
REVERT: E  380 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7597 (tm-30)
REVERT: E  385 LYS cc_start: 0.7517 (tttm) cc_final: 0.7159 (mtpp)
REVERT: F  376 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6034 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 125
  average time/residue: 2.3501
  time to fit residues: 302.0697
Evaluate side-chains
  114 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain F residue  376 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:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0060
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.7800

-------------------------------------------------------------------------------
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 = 0.4910 r_free = 0.4910 target = 0.227314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.193759 restraints weight = 5421.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.4639 rms_B_bonded: 1.33
r_work: 0.4513 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.4434 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.4434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2934  Z= 0.091
  Angle     :  0.582   6.353   3978  Z= 0.294
  Chirality :  0.047   0.127    486
  Planarity :  0.002   0.010    516
  Dihedral  :  7.258  25.971    408
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 16.36 %
    Favored  : 83.33 %
  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   0.004   0.001   HIS D 407 
 PHE   0.008   0.002   PHE C 378 
 TYR   0.012   0.002   TYR C 394 
 ARG   0.001   0.000   ARG E 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02275 (   35)
  hydrogen bonds       : angle       5.38154 (  105)
  covalent geometry    : bond        0.00205 ( 2934)
  covalent geometry    : angle       0.58151 ( 3978)

*********************** 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
  114 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7676 (tm-30)
REVERT: A  383 LYS cc_start: 0.7126 (mttt) cc_final: 0.6621 (mmmt)
REVERT: A  406 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7873 (mmm160)
REVERT: B  385 LYS cc_start: 0.7444 (tttt) cc_final: 0.7133 (mtpp)
REVERT: B  431 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7369 (mp0)
REVERT: C  383 LYS cc_start: 0.7281 (mttt) cc_final: 0.6731 (mmmt)
REVERT: C  431 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7596 (mp0)
REVERT: D  379 ARG cc_start: 0.7216 (mtt180) cc_final: 0.6948 (mtt180)
REVERT: D  431 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7471 (mp0)
REVERT: E  380 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7739 (tm-30)
REVERT: E  385 LYS cc_start: 0.7488 (tttm) cc_final: 0.7133 (mtpp)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 2.5704
  time to fit residues: 298.1480
Evaluate side-chains
  108 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.4815 r_free = 0.4815 target = 0.218069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.184943 restraints weight = 5556.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.4516 rms_B_bonded: 1.41
r_work: 0.4389 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.4308 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.4308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.4347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2934  Z= 0.192
  Angle     :  0.683   6.293   3978  Z= 0.346
  Chirality :  0.047   0.132    486
  Planarity :  0.003   0.030    516
  Dihedral  :  7.538  27.209    408
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.06 %
    Favored  : 82.73 %
  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 (0.32), 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   0.008   0.002   HIS D 407 
 PHE   0.011   0.003   PHE C 378 
 TYR   0.011   0.002   TYR F 394 
 ARG   0.002   0.000   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03526 (   35)
  hydrogen bonds       : angle       5.52746 (  105)
  covalent geometry    : bond        0.00398 ( 2934)
  covalent geometry    : angle       0.68254 ( 3978)

*********************** 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
  115 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: A  383 LYS cc_start: 0.7397 (mttt) cc_final: 0.6835 (mmmt)
REVERT: A  406 ARG cc_start: 0.8474 (mmt90) cc_final: 0.7954 (mmm160)
REVERT: B  385 LYS cc_start: 0.7507 (tttt) cc_final: 0.7200 (mtpp)
REVERT: B  431 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7379 (mp0)
REVERT: C  380 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7765 (tm-30)
REVERT: C  385 LYS cc_start: 0.7690 (tttt) cc_final: 0.7349 (ttpp)
REVERT: C  431 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7680 (mp0)
REVERT: D  379 ARG cc_start: 0.7290 (mtt180) cc_final: 0.7034 (mtt180)
REVERT: D  431 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7551 (mp0)
REVERT: E  380 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7754 (tm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 111
  average time/residue: 2.5836
  time to fit residues: 293.6139
Evaluate side-chains
  109 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain D residue  386 THR
Chi-restraints excluded: chain E residue  386 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 11 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.4851 r_free = 0.4851 target = 0.221543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.188371 restraints weight = 5544.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.4560 rms_B_bonded: 1.40
r_work: 0.4435 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.4355 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.4623

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= 0.135
  Angle     :  0.616   6.200   3978  Z= 0.311
  Chirality :  0.047   0.130    486
  Planarity :  0.002   0.018    516
  Dihedral  :  7.148  25.624    408
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 18.79 %
    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: -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   0.005   0.002   HIS C 407 
 PHE   0.008   0.002   PHE C 378 
 TYR   0.013   0.002   TYR C 394 
 ARG   0.001   0.000   ARG B 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02879 (   35)
  hydrogen bonds       : angle       5.23957 (  105)
  covalent geometry    : bond        0.00285 ( 2934)
  covalent geometry    : angle       0.61609 ( 3978)

*********************** 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
  115 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: A  383 LYS cc_start: 0.7359 (mttt) cc_final: 0.6812 (mmmt)
REVERT: A  406 ARG cc_start: 0.8493 (mmt90) cc_final: 0.7981 (mmm160)
REVERT: B  380 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: B  383 LYS cc_start: 0.7880 (mttm) cc_final: 0.7606 (mtpm)
REVERT: B  431 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7453 (mp0)
REVERT: C  383 LYS cc_start: 0.7674 (ptpp) cc_final: 0.7167 (mmmt)
REVERT: C  385 LYS cc_start: 0.7621 (tttt) cc_final: 0.7272 (ttpp)
REVERT: C  431 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7679 (mp0)
REVERT: D  379 ARG cc_start: 0.7297 (mtt180) cc_final: 0.7043 (mtt180)
REVERT: D  431 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7512 (mp0)
REVERT: E  380 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7762 (tm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 112
  average time/residue: 2.2888
  time to fit residues: 262.8238
Evaluate side-chains
  110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:   10.0000
   chunk 35 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.4825 r_free = 0.4825 target = 0.219121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.186318 restraints weight = 5472.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.4526 rms_B_bonded: 1.31
r_work: 0.4399 rms_B_bonded: 1.38 restraints_weight: 0.5000
r_work: 0.4320 rms_B_bonded: 2.29 restraints_weight: 0.2500
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2934  Z= 0.198
  Angle     :  0.675   6.005   3978  Z= 0.344
  Chirality :  0.047   0.130    486
  Planarity :  0.003   0.019    516
  Dihedral  :  7.343  26.252    408
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 18.79 %
    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: -3.06 (0.32), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (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   0.013   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03542 (   35)
  hydrogen bonds       : angle       5.22980 (  105)
  covalent geometry    : bond        0.00407 ( 2934)
  covalent geometry    : angle       0.67503 ( 3978)

*********************** 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
  112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7782 (tm-30)
REVERT: A  383 LYS cc_start: 0.7412 (mttt) cc_final: 0.6818 (mmmt)
REVERT: A  385 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7362 (ttpp)
REVERT: A  406 ARG cc_start: 0.8474 (mmt180) cc_final: 0.7925 (mmm160)
REVERT: B  380 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7689 (tm-30)
REVERT: B  383 LYS cc_start: 0.7857 (mttm) cc_final: 0.7568 (mtpm)
REVERT: B  385 LYS cc_start: 0.7444 (tttt) cc_final: 0.7076 (ttpp)
REVERT: B  431 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7411 (mp0)
REVERT: C  383 LYS cc_start: 0.7747 (ptpp) cc_final: 0.7223 (mmmt)
REVERT: C  385 LYS cc_start: 0.7615 (tttt) cc_final: 0.7357 (mtpp)
REVERT: C  431 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7647 (mp0)
REVERT: D  379 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7095 (mtt180)
REVERT: D  431 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7544 (mp0)
REVERT: E  380 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7733 (tm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 109
  average time/residue: 2.2628
  time to fit residues: 252.7057
Evaluate side-chains
  108 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.4853 r_free = 0.4853 target = 0.221954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.188412 restraints weight = 5544.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.4551 rms_B_bonded: 1.45
r_work: 0.4430 rms_B_bonded: 1.39 restraints_weight: 0.5000
r_work: 0.4348 rms_B_bonded: 2.36 restraints_weight: 0.2500
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.4697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2934  Z= 0.144
  Angle     :  0.630   6.001   3978  Z= 0.318
  Chirality :  0.046   0.127    486
  Planarity :  0.002   0.014    516
  Dihedral  :  7.085  24.558    408
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.48 %
    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: -3.04 (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   0.001   HIS D 407 
 PHE   0.008   0.003   PHE C 378 
 TYR   0.014   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02937 (   35)
  hydrogen bonds       : angle       4.82441 (  105)
  covalent geometry    : bond        0.00300 ( 2934)
  covalent geometry    : angle       0.62976 ( 3978)

*********************** 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
  118 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: A  383 LYS cc_start: 0.7412 (mttt) cc_final: 0.6826 (mmmt)
REVERT: A  385 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7276 (tttm)
REVERT: A  406 ARG cc_start: 0.8491 (mmt180) cc_final: 0.7959 (mmm160)
REVERT: B  380 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7667 (tm-30)
REVERT: B  383 LYS cc_start: 0.7875 (mttm) cc_final: 0.7594 (mtpm)
REVERT: B  385 LYS cc_start: 0.7454 (tttt) cc_final: 0.7105 (ttpp)
REVERT: B  431 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7474 (mp0)
REVERT: C  383 LYS cc_start: 0.7736 (ptpp) cc_final: 0.7156 (mmmt)
REVERT: C  385 LYS cc_start: 0.7627 (tttt) cc_final: 0.7360 (mtpp)
REVERT: C  406 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7676 (mmm160)
REVERT: C  431 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7623 (mp0)
REVERT: D  379 ARG cc_start: 0.7276 (mtt180) cc_final: 0.7035 (mtt180)
REVERT: D  431 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7491 (mp0)
REVERT: E  380 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7736 (tm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 114
  average time/residue: 2.4490
  time to fit residues: 285.9591
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  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  438 LYS
Chi-restraints excluded: chain C residue  406 ARG
Chi-restraints excluded: chain E residue  386 THR
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:    0.9990
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.4831 r_free = 0.4831 target = 0.219233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.185875 restraints weight = 5470.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.4529 rms_B_bonded: 1.42
r_work: 0.4404 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.4321 rms_B_bonded: 2.34 restraints_weight: 0.2500
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2934  Z= 0.188
  Angle     :  0.677   5.763   3978  Z= 0.343
  Chirality :  0.047   0.129    486
  Planarity :  0.003   0.017    516
  Dihedral  :  7.218  25.434    408
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.18 %
    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: -3.07 (0.32), residues: 384
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (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   0.016   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (   35)
  hydrogen bonds       : angle       4.96791 (  105)
  covalent geometry    : bond        0.00386 ( 2934)
  covalent geometry    : angle       0.67727 ( 3978)

*********************** 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
  114 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: A  383 LYS cc_start: 0.7454 (mttt) cc_final: 0.6825 (mmmt)
REVERT: A  385 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7265 (tttm)
REVERT: A  406 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7924 (mmm160)
REVERT: B  380 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7651 (tm-30)
REVERT: B  383 LYS cc_start: 0.7861 (mttm) cc_final: 0.7569 (mtpm)
REVERT: B  385 LYS cc_start: 0.7453 (tttt) cc_final: 0.7113 (ttpp)
REVERT: B  431 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7340 (mp0)
REVERT: C  383 LYS cc_start: 0.7764 (ptpp) cc_final: 0.7161 (mmmt)
REVERT: C  385 LYS cc_start: 0.7588 (tttt) cc_final: 0.7327 (mtpp)
REVERT: C  406 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7678 (mmm160)
REVERT: C  431 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7638 (mp0)
REVERT: D  379 ARG cc_start: 0.7324 (mtt180) cc_final: 0.7088 (mtt180)
REVERT: D  431 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7535 (mp0)
REVERT: E  380 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7697 (tm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 107
  average time/residue: 3.0318
  time to fit residues: 332.5726
Evaluate side-chains
  111 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  438 LYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 34 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 26 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.4863 r_free = 0.4863 target = 0.223360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.189297 restraints weight = 5486.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.4580 rms_B_bonded: 1.45
r_work: 0.4462 rms_B_bonded: 1.36 restraints_weight: 0.5000
r_work: 0.4380 rms_B_bonded: 2.32 restraints_weight: 0.2500
r_work (final): 0.4380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.4860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2934  Z= 0.115
  Angle     :  0.601   5.648   3978  Z= 0.302
  Chirality :  0.047   0.128    486
  Planarity :  0.002   0.014    516
  Dihedral  :  6.848  23.752    408
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 19.39 %
    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: -3.02 (0.33), 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   0.004   0.001   HIS D 407 
 PHE   0.007   0.002   PHE E 378 
 TYR   0.015   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02520 (   35)
  hydrogen bonds       : angle       4.52644 (  105)
  covalent geometry    : bond        0.00250 ( 2934)
  covalent geometry    : angle       0.60089 ( 3978)

*********************** 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: 3
    poor density    : 113
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: A  383 LYS cc_start: 0.7391 (mttt) cc_final: 0.6802 (mmmt)
REVERT: A  385 LYS cc_start: 0.7753 (ttpt) cc_final: 0.7327 (ttpp)
REVERT: A  406 ARG cc_start: 0.8484 (mmt180) cc_final: 0.7959 (mmm160)
REVERT: B  383 LYS cc_start: 0.7864 (mttm) cc_final: 0.7586 (mtpm)
REVERT: B  385 LYS cc_start: 0.7420 (tttt) cc_final: 0.7103 (ttpp)
REVERT: B  431 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7421 (mp0)
REVERT: C  383 LYS cc_start: 0.7732 (ptpp) cc_final: 0.7127 (mmmt)
REVERT: C  385 LYS cc_start: 0.7578 (tttt) cc_final: 0.7309 (mtpp)
REVERT: C  406 ARG cc_start: 0.8297 (mmt-90) cc_final: 0.7658 (mmm160)
REVERT: C  431 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7611 (mp0)
REVERT: D  379 ARG cc_start: 0.7278 (mtt180) cc_final: 0.7041 (mtt180)
REVERT: D  431 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7475 (mp0)
REVERT: E  380 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: F  376 LEU cc_start: 0.6651 (mt) cc_final: 0.6437 (mp)
  outliers start: 3
  outliers final: 3
  residues processed: 114
  average time/residue: 2.3615
  time to fit residues: 276.3903
Evaluate side-chains
  113 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  385 LYS
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain E residue  414 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    0.2980
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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 = 0.4842 r_free = 0.4842 target = 0.220757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.187032 restraints weight = 5472.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.4559 rms_B_bonded: 1.40
r_work: 0.4435 rms_B_bonded: 1.39 restraints_weight: 0.5000
r_work: 0.4355 rms_B_bonded: 2.32 restraints_weight: 0.2500
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2934  Z= 0.142
  Angle     :  0.629   5.418   3978  Z= 0.317
  Chirality :  0.047   0.126    486
  Planarity :  0.002   0.016    516
  Dihedral  :  6.896  23.560    408
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 20.61 %
    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: -3.02 (0.33), 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   0.001   HIS D 407 
 PHE   0.008   0.002   PHE E 378 
 TYR   0.016   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02806 (   35)
  hydrogen bonds       : angle       4.55235 (  105)
  covalent geometry    : bond        0.00299 ( 2934)
  covalent geometry    : angle       0.62914 ( 3978)

********************** 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: 2
    poor density    : 110
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: A  383 LYS cc_start: 0.7412 (mttt) cc_final: 0.6836 (mmmt)
REVERT: A  385 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7324 (ttpp)
REVERT: A  406 ARG cc_start: 0.8482 (mmt180) cc_final: 0.7945 (mmm160)
REVERT: B  383 LYS cc_start: 0.7855 (mttm) cc_final: 0.7569 (mtpm)
REVERT: B  385 LYS cc_start: 0.7399 (tttt) cc_final: 0.7084 (ttpp)
REVERT: B  431 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7450 (mp0)
REVERT: C  383 LYS cc_start: 0.7765 (ptpp) cc_final: 0.7131 (mmmt)
REVERT: C  385 LYS cc_start: 0.7576 (tttt) cc_final: 0.7310 (mtpp)
REVERT: C  406 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.7659 (mmm160)
REVERT: C  431 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7592 (mp0)
REVERT: D  379 ARG cc_start: 0.7289 (mtt180) cc_final: 0.7050 (mtt180)
REVERT: D  431 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7520 (mp0)
REVERT: E  380 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7735 (tm-30)
REVERT: F  376 LEU cc_start: 0.6650 (mt) cc_final: 0.6443 (mp)
  outliers start: 2
  outliers final: 2
  residues processed: 110
  average time/residue: 2.3258
  time to fit residues: 262.0892
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  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain E residue  414 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:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 23 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.1560

-------------------------------------------------------------------------------
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 = 0.4875 r_free = 0.4875 target = 0.224157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.190141 restraints weight = 5550.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.4593 rms_B_bonded: 1.42
r_work: 0.4472 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.4392 rms_B_bonded: 2.37 restraints_weight: 0.2500
r_work (final): 0.4392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.4957

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= 0.107
  Angle     :  0.595   5.390   3978  Z= 0.298
  Chirality :  0.047   0.130    486
  Planarity :  0.002   0.015    516
  Dihedral  :  6.666  22.871    408
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 20.30 %
    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: -3.00 (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   0.004   0.001   HIS D 407 
 PHE   0.007   0.002   PHE E 378 
 TYR   0.015   0.002   TYR C 394 
 ARG   0.001   0.000   ARG C 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02274 (   35)
  hydrogen bonds       : angle       4.29531 (  105)
  covalent geometry    : bond        0.00238 ( 2934)
  covalent geometry    : angle       0.59494 ( 3978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9985.40 seconds
wall clock time: 174 minutes 37.37 seconds (10477.37 seconds total)