Starting phenix.real_space_refine
on Tue Feb 11 23:40:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q9e_18278/02_2025/8q9e_18278.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q9e_18278/02_2025/8q9e_18278.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q9e_18278/02_2025/8q9e_18278.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q9e_18278/02_2025/8q9e_18278.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q9e_18278/02_2025/8q9e_18278.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q9e_18278/02_2025/8q9e_18278.cif"
  }
  resolution = 2.97
  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    2082      2.51       5
     N     612      2.21       5
     O     612      1.98       5
     H    3456      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 6768
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1128
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "D"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1128
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "C"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1128
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "B"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1128
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "E"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1128
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "F"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1128
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
  Time building chain proxies: 4.09, per 1000 atoms: 0.60
  Number of scatterers: 6768
  At special positions: 0
  Unit cell: (95.237, 109.05, 40.712, 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     612      7.00
     C    2082      6.00
     H    3456      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: 1.54
  Conformation dependent library (CDL) restraints added in 661.8 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 52.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 309 through 310
      removed outlier: 6.687A  pdb=" N   VAL A 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.987A  pdb=" N   VAL A 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325
      removed outlier: 6.338A  pdb=" N   LYS A 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   SER F 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR A 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   CYS F 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LYS A 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   SER F 324 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   GLY A 323 " --> pdb=" O   SER F 324 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.465A  pdb=" N   ILE A 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 336 through 346
      removed outlier: 6.448A  pdb=" N   VAL A 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   LYS D 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL A 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   GLU D 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   SER A 341 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   LEU D 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   LYS A 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 10.353A  pdb=" N   PHE D 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 9.237A  pdb=" N   ASP A 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   LEU A 344 " --> pdb=" O   LYS F 343 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASP F 345 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   PHE A 346 " --> pdb=" O   ASP F 345 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.548A  pdb=" N   GLN A 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   ILE F 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LYS A 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 359 through 362
    Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 377
      removed outlier: 6.716A  pdb=" N   LYS A 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   GLU F 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE A 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   HIS F 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   THR A 373 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   LEU F 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   LYS A 375 " --> pdb=" O   LEU F 376 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 309 through 310
      removed outlier: 6.580A  pdb=" N   VAL C 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   VAL B 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.910A  pdb=" N   VAL C 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL B 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 325
      removed outlier: 6.444A  pdb=" N   LYS C 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   SER B 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   THR C 319 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   CYS B 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LYS C 321 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   SER B 324 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   GLY C 323 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.494A  pdb=" N   ILE C 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE B 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 336 through 346
      removed outlier: 6.784A  pdb=" N   LEU C 344 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ASP B 345 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   PHE C 346 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LEU B 344 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ASP E 345 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   PHE B 346 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 354
      removed outlier: 6.554A  pdb=" N   GLN C 351 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 8.058A  pdb=" N   ILE B 354 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LYS C 353 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLN B 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   ILE E 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   LYS B 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'C' and resid 359 through 362
      removed outlier: 6.410A  pdb=" N   ILE C 360 " --> pdb=" O   THR B 361 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ILE B 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 368 through 377
      removed outlier: 6.598A  pdb=" N   LYS C 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   GLU B 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ILE C 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   HIS B 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   THR C 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   LEU B 376 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LYS C 375 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LYS B 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   GLU E 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ILE B 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   HIS E 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   THR B 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 8.156A  pdb=" N   LEU E 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LYS B 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    60 hydrogen bonds defined for protein.
    180 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.19

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 3450
        1.12 -     1.29: 546
        1.29 -     1.47: 1122
        1.47 -     1.64: 1698
        1.64 -     1.82: 6
  Bond restraints: 6822
  Sorted by residual:
  bond pdb=" CE1 TYR D 310 "
       pdb=" HE1 TYR D 310 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   ASP D 358 "
       pdb=" H   ASP D 358 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" ND2 ASN E 359 "
       pdb="HD21 ASN E 359 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   VAL C 309 "
       pdb=" H   VAL C 309 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   ILE A 354 "
       pdb=" H   ILE A 354 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 6817 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 10451
        2.55 -     5.10: 1530
        5.10 -     7.65: 432
        7.65 -    10.20: 18
       10.20 -    12.75: 7
  Bond angle restraints: 12438
  Sorted by residual:
  angle pdb=" C   ASP E 348 "
        pdb=" N   ARG E 349 "
        pdb=" CA  ARG E 349 "
      ideal   model   delta    sigma   weight residual
     120.90  129.73   -8.83 1.41e+00 5.03e-01 3.92e+01
  angle pdb=" C   ASP D 348 "
        pdb=" N   ARG D 349 "
        pdb=" CA  ARG D 349 "
      ideal   model   delta    sigma   weight residual
     121.05  129.38   -8.33 1.43e+00 4.89e-01 3.40e+01
  angle pdb=" C   ASP B 348 "
        pdb=" N   ARG B 349 "
        pdb=" CA  ARG B 349 "
      ideal   model   delta    sigma   weight residual
     120.90  128.94   -8.04 1.41e+00 5.03e-01 3.25e+01
  angle pdb=" C   ASP A 348 "
        pdb=" N   ARG A 349 "
        pdb=" CA  ARG A 349 "
      ideal   model   delta    sigma   weight residual
     120.90  128.56   -7.66 1.41e+00 5.03e-01 2.95e+01
  angle pdb=" C   ASP C 348 "
        pdb=" N   ARG C 349 "
        pdb=" CA  ARG C 349 "
      ideal   model   delta    sigma   weight residual
     121.05  128.64   -7.59 1.43e+00 4.89e-01 2.82e+01
  ... (remaining 12433 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.53: 2655
       13.53 -    27.07: 283
       27.07 -    40.60: 84
       40.60 -    54.13: 48
       54.13 -    67.66: 68
  Dihedral angle restraints: 3138
    sinusoidal: 1794
      harmonic: 1344
  Sorted by residual:
  dihedral pdb=" C   LYS F 370 "
           pdb=" N   LYS F 370 "
           pdb=" CA  LYS F 370 "
           pdb=" CB  LYS F 370 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.46   14.86     0      2.50e+00 1.60e-01 3.53e+01
  dihedral pdb=" N   LYS F 370 "
           pdb=" C   LYS F 370 "
           pdb=" CA  LYS F 370 "
           pdb=" CB  LYS F 370 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.27  -14.47     0      2.50e+00 1.60e-01 3.35e+01
  dihedral pdb=" CA  THR F 377 "
           pdb=" C   THR F 377 "
           pdb=" N   PHE F 378 "
           pdb=" CA  PHE F 378 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.14   28.86     0      5.00e+00 4.00e-02 3.33e+01
  ... (remaining 3135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 406
       0.124 -    0.249: 81
       0.249 -    0.373: 13
       0.373 -    0.497: 3
       0.497 -    0.621: 1
  Chirality restraints: 504
  Sorted by residual:
  chirality pdb=" CA  LYS F 370 "
            pdb=" N   LYS F 370 "
            pdb=" C   LYS F 370 "
            pdb=" CB  LYS F 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.89    0.62 2.00e-01 2.50e+01 9.64e+00
  chirality pdb=" CA  LYS E 370 "
            pdb=" N   LYS E 370 "
            pdb=" C   LYS E 370 "
            pdb=" CB  LYS E 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.86e+00
  chirality pdb=" CA  PRO A 332 "
            pdb=" N   PRO A 332 "
            pdb=" C   PRO A 332 "
            pdb=" CB  PRO A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.29    0.43 2.00e-01 2.50e+01 4.63e+00
  ... (remaining 501 not shown)

  Planarity restraints: 978
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 378 "    0.107 2.00e-02 2.50e+03   4.21e-02 5.33e+01
        pdb=" CG  PHE B 378 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 378 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 378 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 378 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 378 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 378 "    0.023 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 378 "   -0.027 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 378 "   -0.029 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 378 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 378 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 378 "    0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 327 "   -0.038 2.00e-02 2.50e+03   5.20e-02 4.05e+01
        pdb=" CG  ASN A 327 "   -0.001 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 327 "    0.056 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 327 "   -0.053 2.00e-02 2.50e+03
        pdb="HD21 ASN A 327 "   -0.045 2.00e-02 2.50e+03
        pdb="HD22 ASN A 327 "    0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 358 "   -0.034 2.00e-02 2.50e+03   6.09e-02 3.71e+01
        pdb=" N   ASN B 359 "    0.105 2.00e-02 2.50e+03
        pdb=" CA  ASN B 359 "   -0.030 2.00e-02 2.50e+03
        pdb=" H   ASN B 359 "   -0.041 2.00e-02 2.50e+03
  ... (remaining 975 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 542
        2.18 -     2.78: 11409
        2.78 -     3.39: 17221
        3.39 -     3.99: 23083
        3.99 -     4.60: 31947
  Nonbonded interactions: 84202
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.569 2.450
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.571 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.578 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.580 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.601 2.450
  ... (remaining 84197 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.340
  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:                     18.320
  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:13.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
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   0.035   3366  Z= 0.748
  Angle     :  1.893   8.827   4500  Z= 1.248
  Chirality :  0.109   0.621    504
  Planarity :  0.010   0.044    570
  Dihedral  : 11.771  57.284   1296
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 0.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  1.85 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.53 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.35), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.11 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS E 362 
 PHE   0.066   0.019   PHE B 378 
 TYR   0.034   0.009   TYR E 310 
 ARG   0.008   0.001   ARG E 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 171
  time to evaluate  : 0.649 
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: A  316 SER cc_start: 0.8954 (p) cc_final: 0.8580 (p)
REVERT: A  317 LYS cc_start: 0.7485 (mttt) cc_final: 0.7016 (tttt)
REVERT: A  342 GLU cc_start: 0.7325 (tt0) cc_final: 0.6999 (tt0)
REVERT: A  375 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7533 (ptmt)
REVERT: D  317 LYS cc_start: 0.7539 (mttt) cc_final: 0.6944 (tttt)
REVERT: D  336 GLN cc_start: 0.6989 (tt0) cc_final: 0.6618 (mp10)
REVERT: D  342 GLU cc_start: 0.7203 (tt0) cc_final: 0.6970 (tt0)
REVERT: D  375 LYS cc_start: 0.7989 (ptpt) cc_final: 0.7647 (ptmt)
REVERT: C  317 LYS cc_start: 0.8137 (mttt) cc_final: 0.7386 (tttt)
REVERT: C  318 VAL cc_start: 0.8930 (t) cc_final: 0.8714 (p)
REVERT: C  321 LYS cc_start: 0.7684 (ptpt) cc_final: 0.7225 (pttt)
REVERT: C  336 GLN cc_start: 0.7296 (tt0) cc_final: 0.6224 (mp10)
REVERT: C  340 LYS cc_start: 0.7393 (mttt) cc_final: 0.6863 (mmtm)
REVERT: B  311 LYS cc_start: 0.7617 (tttt) cc_final: 0.7332 (ptpt)
REVERT: B  317 LYS cc_start: 0.8208 (mttt) cc_final: 0.7446 (tttt)
REVERT: B  342 GLU cc_start: 0.7555 (tt0) cc_final: 0.7202 (tt0)
REVERT: B  349 ARG cc_start: 0.7162 (ttm170) cc_final: 0.6845 (mtm180)
REVERT: B  373 THR cc_start: 0.8221 (m) cc_final: 0.7942 (p)
REVERT: B  375 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7737 (ptpt)
REVERT: E  311 LYS cc_start: 0.7799 (tttt) cc_final: 0.7563 (ptpt)
REVERT: E  317 LYS cc_start: 0.8525 (mttt) cc_final: 0.7966 (tttt)
REVERT: E  321 LYS cc_start: 0.7417 (ptpt) cc_final: 0.6283 (pptt)
REVERT: E  342 GLU cc_start: 0.7566 (tt0) cc_final: 0.7253 (tt0)
REVERT: E  349 ARG cc_start: 0.6942 (ttm170) cc_final: 0.5361 (pmt-80)
REVERT: E  368 ASN cc_start: 0.6046 (m110) cc_final: 0.5768 (m110)
REVERT: E  369 LYS cc_start: 0.8195 (pttm) cc_final: 0.7975 (ptpt)
REVERT: E  370 LYS cc_start: 0.5995 (mmtp) cc_final: 0.5375 (ptmt)
REVERT: F  317 LYS cc_start: 0.7969 (mttt) cc_final: 0.7729 (tttt)
REVERT: F  342 GLU cc_start: 0.7552 (tt0) cc_final: 0.7274 (tt0)
REVERT: F  375 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7824 (ptmt)
  outliers start: 5
  outliers final: 0
  residues processed: 173
  average time/residue: 2.4404
  time to fit residues: 433.4101
Evaluate side-chains
  138 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
A 368 ASN
D 351 GLN
D 368 ASN
C 351 GLN
C 368 ASN
B 327 ASN
B 351 GLN
E 327 ASN
F 351 GLN
F 359 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.177641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.166163 restraints weight = 12276.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 1.72
r_work: 0.3995 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3919 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3366  Z= 0.276
  Angle     :  0.750   7.713   4500  Z= 0.389
  Chirality :  0.054   0.143    504
  Planarity :  0.004   0.035    570
  Dihedral  :  7.574  23.746    444
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 13.49 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.35), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.17 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 330 
 PHE   0.009   0.002   PHE B 378 
 TYR   0.010   0.001   TYR A 310 
 ARG   0.006   0.001   ARG D 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  349 ARG cc_start: 0.7931 (ttm170) cc_final: 0.6475 (tpt90)
REVERT: C  317 LYS cc_start: 0.8527 (mttt) cc_final: 0.8165 (tttt)
REVERT: C  318 VAL cc_start: 0.9033 (t) cc_final: 0.8789 (p)
REVERT: C  321 LYS cc_start: 0.8164 (ptpt) cc_final: 0.7689 (pttt)
REVERT: C  336 GLN cc_start: 0.7500 (tt0) cc_final: 0.6959 (mt0)
REVERT: C  342 GLU cc_start: 0.8035 (tt0) cc_final: 0.7782 (tt0)
REVERT: C  351 GLN cc_start: 0.8363 (mt0) cc_final: 0.8149 (mt0)
REVERT: C  358 ASP cc_start: 0.7896 (m-30) cc_final: 0.7659 (m-30)
REVERT: B  317 LYS cc_start: 0.8620 (mttt) cc_final: 0.8172 (tttt)
REVERT: B  321 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7820 (pttt)
REVERT: B  336 GLN cc_start: 0.7862 (tt0) cc_final: 0.7057 (mp10)
REVERT: B  379 ARG cc_start: 0.6916 (mtt180) cc_final: 0.6391 (mtm110)
REVERT: E  314 ASP cc_start: 0.8762 (t0) cc_final: 0.8517 (t70)
REVERT: E  321 LYS cc_start: 0.7841 (ptpt) cc_final: 0.6942 (pmtt)
REVERT: E  349 ARG cc_start: 0.7690 (ttm170) cc_final: 0.6232 (pmt170)
REVERT: E  351 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (mt0)
REVERT: F  342 GLU cc_start: 0.7907 (tt0) cc_final: 0.7694 (tt0)
REVERT: F  370 LYS cc_start: 0.5695 (mmtp) cc_final: 0.4796 (pttt)
  outliers start: 13
  outliers final: 3
  residues processed: 142
  average time/residue: 2.7642
  time to fit residues: 401.6021
Evaluate side-chains
  134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain F residue  309 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 GLN
F 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.175263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.163420 restraints weight = 12537.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 1.73
r_work: 0.3968 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3891 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.5133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3366  Z= 0.215
  Angle     :  0.662   6.552   4500  Z= 0.336
  Chirality :  0.054   0.143    504
  Planarity :  0.004   0.044    570
  Dihedral  :  6.406  18.900    444
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.96 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.34), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 330 
 PHE   0.011   0.002   PHE B 378 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.004   0.001   ARG A 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7787 (mtm-85)
REVERT: D  349 ARG cc_start: 0.7958 (ttm170) cc_final: 0.6442 (tpt90)
REVERT: C  317 LYS cc_start: 0.8602 (mttt) cc_final: 0.8314 (tttt)
REVERT: C  321 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7902 (pttt)
REVERT: C  349 ARG cc_start: 0.8002 (ttm170) cc_final: 0.6921 (mmp-170)
REVERT: B  314 ASP cc_start: 0.8691 (t0) cc_final: 0.8438 (t70)
REVERT: B  317 LYS cc_start: 0.8543 (mttt) cc_final: 0.8209 (tttt)
REVERT: B  321 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7769 (pttt)
REVERT: B  379 ARG cc_start: 0.6855 (mtt180) cc_final: 0.6353 (mtm110)
REVERT: E  321 LYS cc_start: 0.7915 (ptpt) cc_final: 0.7034 (pmtt)
REVERT: E  349 ARG cc_start: 0.7743 (ttm170) cc_final: 0.6366 (pmt-80)
REVERT: F  370 LYS cc_start: 0.5701 (mmtp) cc_final: 0.4909 (pttt)
  outliers start: 10
  outliers final: 3
  residues processed: 138
  average time/residue: 2.6401
  time to fit residues: 373.1865
Evaluate side-chains
  131 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain F residue  309 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 2 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
D 327 ASN
C 359 ASN
B 327 ASN
B 351 GLN
E 327 ASN
E 351 GLN
E 359 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.174228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.162559 restraints weight = 12772.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 1.77
r_work: 0.3972 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3893 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.5556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3366  Z= 0.174
  Angle     :  0.603   5.946   4500  Z= 0.300
  Chirality :  0.052   0.130    504
  Planarity :  0.004   0.045    570
  Dihedral  :  5.791  16.253    444
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 26.46 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.34), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 374 
 PHE   0.009   0.002   PHE B 378 
 TYR   0.008   0.001   TYR A 310 
 ARG   0.006   0.001   ARG F 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7835 (tt0) cc_final: 0.7624 (mp0)
REVERT: A  348 ASP cc_start: 0.8097 (t0) cc_final: 0.7891 (t0)
REVERT: D  340 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7833 (mmmt)
REVERT: D  349 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7653 (mtt90)
REVERT: C  317 LYS cc_start: 0.8629 (mttt) cc_final: 0.8357 (tttt)
REVERT: C  321 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7869 (pttt)
REVERT: C  349 ARG cc_start: 0.7839 (ttm170) cc_final: 0.6901 (mmp-170)
REVERT: B  311 LYS cc_start: 0.8525 (pttt) cc_final: 0.8000 (mttt)
REVERT: B  314 ASP cc_start: 0.8683 (t0) cc_final: 0.8372 (t0)
REVERT: B  317 LYS cc_start: 0.8577 (mttt) cc_final: 0.8193 (tttt)
REVERT: B  318 VAL cc_start: 0.9153 (t) cc_final: 0.8886 (p)
REVERT: B  321 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7762 (pttt)
REVERT: B  379 ARG cc_start: 0.6694 (mtt180) cc_final: 0.6274 (mtm110)
REVERT: E  314 ASP cc_start: 0.8322 (t70) cc_final: 0.7972 (t0)
REVERT: E  321 LYS cc_start: 0.7924 (ptpt) cc_final: 0.7060 (pmtt)
REVERT: E  349 ARG cc_start: 0.7722 (ttm170) cc_final: 0.6203 (pmt-80)
REVERT: E  369 LYS cc_start: 0.8710 (ptpt) cc_final: 0.8066 (pptt)
REVERT: F  370 LYS cc_start: 0.5684 (mmtp) cc_final: 0.4923 (pttt)
  outliers start: 7
  outliers final: 2
  residues processed: 131
  average time/residue: 2.7393
  time to fit residues: 367.8363
Evaluate side-chains
  129 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 126
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  344 LEU
Chi-restraints excluded: chain B residue  321 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
E 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.168392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.156728 restraints weight = 12599.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 1.73
r_work: 0.3842 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.5644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3366  Z= 0.276
  Angle     :  0.633   5.785   4500  Z= 0.318
  Chirality :  0.052   0.151    504
  Planarity :  0.005   0.064    570
  Dihedral  :  5.797  15.787    444
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 25.40 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 330 
 PHE   0.009   0.002   PHE B 378 
 TYR   0.014   0.002   TYR A 310 
 ARG   0.005   0.001   ARG F 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  340 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7755 (mmmt)
REVERT: D  349 ARG cc_start: 0.7887 (ttm170) cc_final: 0.6312 (tpt90)
REVERT: C  317 LYS cc_start: 0.8640 (mttt) cc_final: 0.8270 (tttt)
REVERT: C  321 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7821 (pttt)
REVERT: C  342 GLU cc_start: 0.8016 (tt0) cc_final: 0.7786 (tt0)
REVERT: C  349 ARG cc_start: 0.8006 (ttm170) cc_final: 0.6880 (mmp-170)
REVERT: B  311 LYS cc_start: 0.8570 (pttt) cc_final: 0.7908 (mttt)
REVERT: B  317 LYS cc_start: 0.8585 (mttt) cc_final: 0.8115 (tttt)
REVERT: B  321 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7631 (pttt)
REVERT: B  379 ARG cc_start: 0.6655 (mtt180) cc_final: 0.6089 (mtm110)
REVERT: E  314 ASP cc_start: 0.8421 (t70) cc_final: 0.7945 (t0)
REVERT: E  317 LYS cc_start: 0.8598 (tttt) cc_final: 0.8323 (tmtp)
REVERT: E  321 LYS cc_start: 0.7960 (ptpt) cc_final: 0.6974 (pmtt)
REVERT: E  369 LYS cc_start: 0.8736 (ptpt) cc_final: 0.8029 (pmtt)
REVERT: F  348 ASP cc_start: 0.8146 (t0) cc_final: 0.7538 (p0)
REVERT: F  370 LYS cc_start: 0.5739 (mmtp) cc_final: 0.4749 (pttt)
  outliers start: 9
  outliers final: 2
  residues processed: 134
  average time/residue: 2.7512
  time to fit residues: 377.3265
Evaluate side-chains
  128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  344 LEU
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain E residue  316 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 9 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 24 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0030
   chunk 36 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.2794

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
E 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.172510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.160776 restraints weight = 12489.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 1.74
r_work: 0.3952 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3875 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.5967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3366  Z= 0.168
  Angle     :  0.575   5.957   4500  Z= 0.282
  Chirality :  0.052   0.130    504
  Planarity :  0.005   0.054    570
  Dihedral  :  5.239  14.791    444
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 27.51 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.18 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 374 
 PHE   0.008   0.002   PHE C 346 
 TYR   0.008   0.001   TYR A 310 
 ARG   0.006   0.001   ARG D 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  311 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7953 (mtpt)
REVERT: D  340 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7805 (mmmt)
REVERT: D  349 ARG cc_start: 0.7862 (ttm170) cc_final: 0.6388 (tpt90)
REVERT: C  317 LYS cc_start: 0.8653 (mttt) cc_final: 0.8409 (tttt)
REVERT: C  321 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7759 (pttt)
REVERT: C  342 GLU cc_start: 0.8013 (tt0) cc_final: 0.7808 (tt0)
REVERT: C  349 ARG cc_start: 0.7946 (ttm170) cc_final: 0.6957 (mmp-170)
REVERT: B  311 LYS cc_start: 0.8551 (pttt) cc_final: 0.8001 (mttt)
REVERT: B  317 LYS cc_start: 0.8536 (mttt) cc_final: 0.8241 (tttt)
REVERT: B  379 ARG cc_start: 0.6567 (mtt180) cc_final: 0.6030 (mtm110)
REVERT: E  314 ASP cc_start: 0.8312 (t70) cc_final: 0.7943 (t0)
REVERT: E  317 LYS cc_start: 0.8595 (tttt) cc_final: 0.8326 (tmtp)
REVERT: E  321 LYS cc_start: 0.7980 (ptpt) cc_final: 0.7073 (pmtt)
REVERT: E  369 LYS cc_start: 0.8691 (ptpt) cc_final: 0.8063 (pptt)
REVERT: F  340 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8355 (tptt)
REVERT: F  348 ASP cc_start: 0.8072 (t0) cc_final: 0.7612 (p0)
  outliers start: 4
  outliers final: 1
  residues processed: 125
  average time/residue: 2.6877
  time to fit residues: 344.1135
Evaluate side-chains
  126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  344 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
E 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.171043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.159002 restraints weight = 12511.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 1.75
r_work: 0.3932 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3852 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.6084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3366  Z= 0.188
  Angle     :  0.563   5.940   4500  Z= 0.276
  Chirality :  0.051   0.133    504
  Planarity :  0.006   0.104    570
  Dihedral  :  5.116  14.949    444
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 27.78 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.17 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 374 
 PHE   0.006   0.001   PHE C 346 
 TYR   0.010   0.002   TYR A 310 
 ARG   0.010   0.001   ARG F 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  340 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7867 (mmmt)
REVERT: D  349 ARG cc_start: 0.7864 (ttm170) cc_final: 0.6408 (tpt90)
REVERT: C  317 LYS cc_start: 0.8655 (mttt) cc_final: 0.8431 (tttt)
REVERT: C  321 LYS cc_start: 0.8181 (ptpt) cc_final: 0.7806 (pttt)
REVERT: C  342 GLU cc_start: 0.8012 (tt0) cc_final: 0.7751 (tt0)
REVERT: C  349 ARG cc_start: 0.7933 (ttm170) cc_final: 0.6963 (mmp-170)
REVERT: B  311 LYS cc_start: 0.8555 (pttt) cc_final: 0.7986 (mttt)
REVERT: B  317 LYS cc_start: 0.8594 (mttt) cc_final: 0.8253 (tttt)
REVERT: B  379 ARG cc_start: 0.6545 (mtt180) cc_final: 0.5964 (mtm110)
REVERT: E  317 LYS cc_start: 0.8588 (tttt) cc_final: 0.8310 (tmtp)
REVERT: E  321 LYS cc_start: 0.7967 (ptpt) cc_final: 0.7064 (pmtt)
REVERT: E  369 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8058 (pptt)
REVERT: F  348 ASP cc_start: 0.8120 (t0) cc_final: 0.7644 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 121
  average time/residue: 2.6897
  time to fit residues: 333.5418
Evaluate side-chains
  119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  344 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 13 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0370
   chunk 11 optimal weight:    0.0670
   chunk 41 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.9000

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
E 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.174894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.162974 restraints weight = 12555.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 1.73
r_work: 0.3948 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3872 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.6278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3366  Z= 0.158
  Angle     :  0.552   5.611   4500  Z= 0.269
  Chirality :  0.052   0.149    504
  Planarity :  0.005   0.071    570
  Dihedral  :  4.754  15.191    444
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 27.78 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.10 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 374 
 PHE   0.007   0.001   PHE C 346 
 TYR   0.008   0.001   TYR A 310 
 ARG   0.011   0.001   ARG F 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  340 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7766 (mmmt)
REVERT: D  349 ARG cc_start: 0.7714 (ttm170) cc_final: 0.6233 (tpt90)
REVERT: C  317 LYS cc_start: 0.8653 (mttt) cc_final: 0.8327 (tttt)
REVERT: C  321 LYS cc_start: 0.8147 (ptpt) cc_final: 0.7765 (pttt)
REVERT: C  336 GLN cc_start: 0.7501 (tt0) cc_final: 0.6737 (mp10)
REVERT: C  342 GLU cc_start: 0.7997 (tt0) cc_final: 0.7711 (tt0)
REVERT: C  349 ARG cc_start: 0.7808 (ttm170) cc_final: 0.6814 (mmp-170)
REVERT: B  311 LYS cc_start: 0.8556 (pttt) cc_final: 0.7892 (mttt)
REVERT: B  317 LYS cc_start: 0.8591 (mttt) cc_final: 0.8158 (tttt)
REVERT: B  379 ARG cc_start: 0.6542 (mtt180) cc_final: 0.5865 (mtm110)
REVERT: E  314 ASP cc_start: 0.8611 (t0) cc_final: 0.8300 (t0)
REVERT: E  317 LYS cc_start: 0.8512 (tttt) cc_final: 0.8251 (tmtp)
REVERT: E  321 LYS cc_start: 0.7910 (ptpt) cc_final: 0.6962 (pmtt)
REVERT: E  369 LYS cc_start: 0.8701 (ptpt) cc_final: 0.7980 (pptt)
REVERT: F  311 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7976 (mttt)
REVERT: F  349 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7695 (mtp85)
  outliers start: 3
  outliers final: 2
  residues processed: 125
  average time/residue: 2.7070
  time to fit residues: 346.8450
Evaluate side-chains
  118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  344 LEU
Chi-restraints excluded: chain C residue  318 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
E 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.170965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.158895 restraints weight = 12605.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 1.76
r_work: 0.3917 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3842 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.6308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3366  Z= 0.229
  Angle     :  0.587   6.129   4500  Z= 0.289
  Chirality :  0.051   0.144    504
  Planarity :  0.005   0.086    570
  Dihedral  :  4.988  15.149    444
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 27.78 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.11 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 330 
 PHE   0.007   0.001   PHE B 378 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.010   0.001   ARG F 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 117
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  340 LYS cc_start: 0.8429 (mtpt) cc_final: 0.7950 (mmmt)
REVERT: D  349 ARG cc_start: 0.7887 (ttm170) cc_final: 0.6418 (tpt90)
REVERT: C  317 LYS cc_start: 0.8645 (mttt) cc_final: 0.8424 (tttt)
REVERT: C  321 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7833 (pttt)
REVERT: C  336 GLN cc_start: 0.7552 (tt0) cc_final: 0.6876 (mp10)
REVERT: C  342 GLU cc_start: 0.7997 (tt0) cc_final: 0.7772 (tt0)
REVERT: C  349 ARG cc_start: 0.7943 (ttm170) cc_final: 0.6958 (mmp-170)
REVERT: B  311 LYS cc_start: 0.8574 (pttt) cc_final: 0.8010 (mttt)
REVERT: B  317 LYS cc_start: 0.8627 (mttt) cc_final: 0.8299 (tttt)
REVERT: B  379 ARG cc_start: 0.6547 (mtt180) cc_final: 0.5960 (mtm110)
REVERT: E  317 LYS cc_start: 0.8534 (tttt) cc_final: 0.8232 (tmtp)
REVERT: E  321 LYS cc_start: 0.7968 (ptpt) cc_final: 0.7077 (pmtt)
REVERT: E  369 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8119 (pptt)
REVERT: F  311 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8041 (mttt)
  outliers start: 3
  outliers final: 1
  residues processed: 117
  average time/residue: 2.8291
  time to fit residues: 339.0139
Evaluate side-chains
  116 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.4155 r_free = 0.4155 target = 0.173141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.161139 restraints weight = 12638.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 1.74
r_work: 0.3939 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3864 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.6388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3366  Z= 0.168
  Angle     :  0.573   6.145   4500  Z= 0.277
  Chirality :  0.052   0.130    504
  Planarity :  0.005   0.080    570
  Dihedral  :  4.752  15.575    444
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 28.31 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.34), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.09 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 374 
 PHE   0.007   0.001   PHE C 346 
 TYR   0.008   0.001   TYR A 310 
 ARG   0.010   0.001   ARG F 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: D  340 LYS cc_start: 0.8378 (mtpt) cc_final: 0.7922 (mmmt)
REVERT: D  349 ARG cc_start: 0.7763 (ttm170) cc_final: 0.6289 (tpt90)
REVERT: C  311 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7405 (mmpt)
REVERT: C  317 LYS cc_start: 0.8658 (mttt) cc_final: 0.8356 (tttt)
REVERT: C  321 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7782 (pttt)
REVERT: C  336 GLN cc_start: 0.7558 (tt0) cc_final: 0.6800 (mp10)
REVERT: C  342 GLU cc_start: 0.7984 (tt0) cc_final: 0.7696 (tt0)
REVERT: C  349 ARG cc_start: 0.7859 (ttm170) cc_final: 0.6860 (mmp-170)
REVERT: B  311 LYS cc_start: 0.8576 (pttt) cc_final: 0.7925 (mttt)
REVERT: B  317 LYS cc_start: 0.8630 (mttt) cc_final: 0.8207 (tttt)
REVERT: B  379 ARG cc_start: 0.6561 (mtt180) cc_final: 0.5852 (mtm110)
REVERT: E  321 LYS cc_start: 0.7910 (ptpt) cc_final: 0.6966 (pmtt)
REVERT: E  369 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8049 (pptt)
REVERT: F  311 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7992 (mttt)
REVERT: F  349 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7737 (mtp85)
  outliers start: 2
  outliers final: 1
  residues processed: 117
  average time/residue: 2.7944
  time to fit residues: 334.8137
Evaluate side-chains
  114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.174218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.162119 restraints weight = 12611.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.4026 rms_B_bonded: 1.71
r_work: 0.3958 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3886 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.6445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3366  Z= 0.160
  Angle     :  0.558   6.004   4500  Z= 0.271
  Chirality :  0.052   0.127    504
  Planarity :  0.005   0.078    570
  Dihedral  :  4.612  15.871    444
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 28.31 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.34), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.06 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 374 
 PHE   0.006   0.001   PHE D 346 
 TYR   0.009   0.001   TYR A 310 
 ARG   0.010   0.001   ARG F 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7658.79 seconds
wall clock time: 134 minutes 45.89 seconds (8085.89 seconds total)