Starting phenix.real_space_refine
on Tue Mar 11 23:30:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q9g_18280/03_2025/8q9g_18280.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q9g_18280/03_2025/8q9g_18280.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q9g_18280/03_2025/8q9g_18280.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q9g_18280/03_2025/8q9g_18280.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q9g_18280/03_2025/8q9g_18280.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q9g_18280/03_2025/8q9g_18280.cif"
  }
  resolution = 2.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2106      2.51       5
     N     606      2.21       5
     O     624      1.98       5
     H    3480      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6822
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "C"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "E"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "B"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "D"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "F"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Time building chain proxies: 4.97, per 1000 atoms: 0.73
  Number of scatterers: 6822
  At special positions: 0
  Unit cell: (150.489, 92.329, 42.166, 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     624      8.00
     N     606      7.00
     C    2106      6.00
     H    3480      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: 1.69
  Conformation dependent library (CDL) restraints added in 615.2 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 50.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310
      removed outlier: 6.518A  pdb=" N   GLN A 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   TYR E 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL A 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.556A  pdb=" N   VAL A 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.339A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   LYS C 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   SER A 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330
      removed outlier: 5.949A  pdb=" N   GLY A 326 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)
      removed outlier: 8.548A  pdb=" N   HIS C 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY E 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ASN A 327 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342
      removed outlier: 6.755A  pdb=" N   GLU A 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   SER E 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   LYS A 340 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.611A  pdb=" N   ASP A 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357
      removed outlier: 6.508A  pdb=" N   GLN A 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ILE E 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS A 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   SER E 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   GLY A 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.417A  pdb=" N   THR A 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377
    Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 310
      removed outlier: 6.801A  pdb=" N   ILE B 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.658A  pdb=" N   VAL B 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 322
      removed outlier: 6.250A  pdb=" N   VAL B 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   LYS D 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   SER B 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330
      removed outlier: 5.981A  pdb=" N   GLY B 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   HIS D 329 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   GLY F 326 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ASN B 327 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342
    Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.676A  pdb=" N   ASP B 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 357
      removed outlier: 6.546A  pdb=" N   GLN B 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   ILE F 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LYS B 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   SER F 356 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY B 355 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 360 through 362
      removed outlier: 6.350A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 377
      removed outlier: 6.233A  pdb=" N   LYS B 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   THR D 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   GLU B 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   LYS D 375 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   HIS B 374 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   THR D 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LEU B 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)

    83 hydrogen bonds defined for protein.
    249 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: 2.24

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        0.94 -     1.11: 3474
        1.11 -     1.29: 558
        1.29 -     1.46: 916
        1.46 -     1.63: 1922
        1.63 -     1.81: 6
  Bond restraints: 6876
  Sorted by residual:
  bond pdb=" N   SER F 324 "
       pdb=" H   SER F 324 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" CD1 TYR B 310 "
       pdb=" HD1 TYR B 310 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   TYR A 310 "
       pdb=" H   TYR A 310 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" NE2 GLN E 336 "
       pdb="HE21 GLN E 336 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" NE2 HIS B 362 "
       pdb=" HE2 HIS B 362 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.63e+01
  ... (remaining 6871 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 10268
        2.38 -     4.75: 1697
        4.75 -     7.12: 536
        7.12 -     9.50: 39
        9.50 -    11.87: 6
  Bond angle restraints: 12546
  Sorted by residual:
  angle pdb=" N   SER B 316 "
        pdb=" CA  SER B 316 "
        pdb=" C   SER B 316 "
      ideal   model   delta    sigma   weight residual
     110.53  117.64   -7.11 1.32e+00 5.74e-01 2.90e+01
  angle pdb=" N   GLY B 326 "
        pdb=" CA  GLY B 326 "
        pdb=" C   GLY B 326 "
      ideal   model   delta    sigma   weight residual
     110.69  117.25   -6.56 1.33e+00 5.65e-01 2.43e+01
  angle pdb=" N   GLU F 372 "
        pdb=" CA  GLU F 372 "
        pdb=" CB  GLU F 372 "
      ideal   model   delta    sigma   weight residual
     111.13  102.34    8.79 1.79e+00 3.12e-01 2.41e+01
  angle pdb=" CB  HIS E 374 "
        pdb=" CG  HIS E 374 "
        pdb=" CD2 HIS E 374 "
      ideal   model   delta    sigma   weight residual
     131.20  124.85    6.35 1.30e+00 5.92e-01 2.38e+01
  angle pdb=" CB  HIS D 329 "
        pdb=" CG  HIS D 329 "
        pdb=" CD2 HIS D 329 "
      ideal   model   delta    sigma   weight residual
     131.20  124.85    6.35 1.30e+00 5.92e-01 2.38e+01
  ... (remaining 12541 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.63: 2843
       14.63 -    29.25: 115
       29.25 -    43.87: 81
       43.87 -    58.50: 80
       58.50 -    73.12: 49
  Dihedral angle restraints: 3168
    sinusoidal: 1806
      harmonic: 1362
  Sorted by residual:
  dihedral pdb=" C   LYS C 343 "
           pdb=" N   LYS C 343 "
           pdb=" CA  LYS C 343 "
           pdb=" CB  LYS C 343 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.81   10.21     0      2.50e+00 1.60e-01 1.67e+01
  dihedral pdb=" CA  ILE A 360 "
           pdb=" C   ILE A 360 "
           pdb=" N   THR A 361 "
           pdb=" CA  THR A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.38   18.62     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  LYS A 369 "
           pdb=" C   LYS A 369 "
           pdb=" N   LYS A 370 "
           pdb=" CA  LYS A 370 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.77   18.23     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 3165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 303
       0.066 -    0.132: 152
       0.132 -    0.198: 46
       0.198 -    0.264: 13
       0.264 -    0.329: 2
  Chirality restraints: 516
  Sorted by residual:
  chirality pdb=" CA  LYS C 343 "
            pdb=" N   LYS C 343 "
            pdb=" C   LYS C 343 "
            pdb=" CB  LYS C 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" CA  ASP D 358 "
            pdb=" N   ASP D 358 "
            pdb=" C   ASP D 358 "
            pdb=" CB  ASP D 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  LYS B 317 "
            pdb=" N   LYS B 317 "
            pdb=" C   LYS B 317 "
            pdb=" CB  LYS B 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 513 not shown)

  Planarity restraints: 990
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 362 "   -0.075 2.00e-02 2.50e+03   4.52e-02 4.59e+01
        pdb=" CG  HIS B 362 "    0.054 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 362 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 362 "    0.050 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 362 "    0.021 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 362 "    0.039 2.00e-02 2.50e+03
        pdb=" HD2 HIS B 362 "   -0.008 2.00e-02 2.50e+03
        pdb=" HE1 HIS B 362 "   -0.035 2.00e-02 2.50e+03
        pdb=" HE2 HIS B 362 "   -0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 310 "   -0.088 2.00e-02 2.50e+03   3.90e-02 4.56e+01
        pdb=" CG  TYR D 310 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 310 "    0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 310 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 310 "    0.026 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 310 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 310 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR D 310 "   -0.083 2.00e-02 2.50e+03
        pdb=" HD1 TYR D 310 "    0.010 2.00e-02 2.50e+03
        pdb=" HD2 TYR D 310 "    0.012 2.00e-02 2.50e+03
        pdb=" HE1 TYR D 310 "    0.009 2.00e-02 2.50e+03
        pdb=" HE2 TYR D 310 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "    0.079 2.00e-02 2.50e+03   3.54e-02 3.76e+01
        pdb=" CG  TYR C 310 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "    0.076 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 310 "   -0.012 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 310 "   -0.008 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 310 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 987 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 616
        2.20 -     2.80: 12494
        2.80 -     3.40: 17578
        3.40 -     4.00: 24431
        4.00 -     4.60: 33683
  Nonbonded interactions: 88802
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.627 2.450
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.644 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.653 2.450
  ... (remaining 88797 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:             5.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.660
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  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:13.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6455
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   0.038   3396  Z= 0.756
  Angle     :  1.947   8.792   4548  Z= 1.280
  Chirality :  0.085   0.329    516
  Planarity :  0.009   0.055    576
  Dihedral  : 10.250  57.110   1296
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  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: -1.98 (0.33), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.50 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.017   0.005   HIS A 330 
 PHE   0.043   0.014   PHE C 346 
 TYR   0.082   0.024   TYR D 310 
 ARG   0.006   0.001   ARG C 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6748 (mttm)
REVERT: A  351 GLN cc_start: 0.7879 (mt0) cc_final: 0.7615 (mt0)
REVERT: A  358 ASP cc_start: 0.8773 (m-30) cc_final: 0.8567 (m-30)
REVERT: C  311 LYS cc_start: 0.5407 (ttpt) cc_final: 0.5090 (mmtm)
REVERT: C  321 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6624 (mttt)
REVERT: C  345 ASP cc_start: 0.7808 (t0) cc_final: 0.7314 (t70)
REVERT: C  349 ARG cc_start: 0.7392 (mtt180) cc_final: 0.5388 (mmp-170)
REVERT: C  369 LYS cc_start: 0.6597 (mttt) cc_final: 0.6299 (mttp)
REVERT: C  372 GLU cc_start: 0.7657 (tt0) cc_final: 0.7193 (tp30)
REVERT: E  321 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7620 (mttp)
REVERT: E  345 ASP cc_start: 0.8028 (t0) cc_final: 0.7684 (t0)
REVERT: E  347 LYS cc_start: 0.7772 (mttt) cc_final: 0.6817 (pttm)
REVERT: B  314 ASP cc_start: 0.5622 (t0) cc_final: 0.5104 (t0)
REVERT: B  320 SER cc_start: 0.7792 (t) cc_final: 0.6924 (p)
REVERT: B  321 LYS cc_start: 0.7391 (mtpt) cc_final: 0.6989 (mttt)
REVERT: B  345 ASP cc_start: 0.6889 (t0) cc_final: 0.6689 (m-30)
REVERT: B  369 LYS cc_start: 0.6550 (mttt) cc_final: 0.6131 (mtpp)
REVERT: B  375 LYS cc_start: 0.4806 (tttt) cc_final: 0.4483 (ttmm)
REVERT: D  320 SER cc_start: 0.8259 (t) cc_final: 0.7998 (p)
REVERT: D  321 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7146 (mtmm)
REVERT: D  345 ASP cc_start: 0.6786 (t0) cc_final: 0.6586 (p0)
REVERT: D  349 ARG cc_start: 0.7661 (mtt180) cc_final: 0.6544 (mmp-170)
REVERT: D  375 LYS cc_start: 0.4901 (tttt) cc_final: 0.4679 (tttm)
REVERT: F  314 ASP cc_start: 0.5583 (t0) cc_final: 0.5371 (t0)
REVERT: F  316 SER cc_start: 0.6735 (m) cc_final: 0.6453 (p)
REVERT: F  320 SER cc_start: 0.7944 (t) cc_final: 0.7290 (p)
REVERT: F  349 ARG cc_start: 0.6698 (mtt180) cc_final: 0.6472 (ptt-90)
REVERT: F  375 LYS cc_start: 0.6681 (tttt) cc_final: 0.6255 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 3.0104
  time to fit residues: 409.2097
Evaluate side-chains
  94 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
E 307 GLN
E 336 GLN
E 362 HIS
B 362 HIS
F 362 HIS
F 368 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.154028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.123162 restraints weight = 10448.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 1.55
r_work: 0.3749 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3396  Z= 0.256
  Angle     :  0.605   4.840   4548  Z= 0.319
  Chirality :  0.051   0.135    516
  Planarity :  0.003   0.034    576
  Dihedral  :  5.533  16.503    444
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 0.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.46 %
    Favored  : 86.46 %
  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: -1.92 (0.33), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.45 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 362 
 PHE   0.009   0.002   PHE C 346 
 TYR   0.008   0.002   TYR B 310 
 ARG   0.004   0.001   ARG E 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
REVERT: C  345 ASP cc_start: 0.7615 (t0) cc_final: 0.7256 (t70)
REVERT: C  349 ARG cc_start: 0.7471 (mtt180) cc_final: 0.5578 (mmp-170)
REVERT: E  347 LYS cc_start: 0.7583 (mttt) cc_final: 0.6827 (pttm)
REVERT: E  349 ARG cc_start: 0.7166 (mtm180) cc_final: 0.6950 (mtt180)
REVERT: B  320 SER cc_start: 0.8367 (t) cc_final: 0.7982 (p)
REVERT: B  321 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7926 (mttt)
REVERT: B  342 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6122 (tt0)
REVERT: B  345 ASP cc_start: 0.6637 (t0) cc_final: 0.6048 (m-30)
REVERT: B  349 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6728 (mtp85)
REVERT: B  375 LYS cc_start: 0.8124 (tttt) cc_final: 0.7800 (ttmm)
REVERT: D  321 LYS cc_start: 0.8290 (mtpt) cc_final: 0.8080 (mttm)
REVERT: D  345 ASP cc_start: 0.6631 (t0) cc_final: 0.6150 (p0)
REVERT: D  349 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6175 (mmp-170)
REVERT: F  320 SER cc_start: 0.8423 (t) cc_final: 0.8109 (p)
REVERT: F  375 LYS cc_start: 0.8410 (tttt) cc_final: 0.8140 (mtpp)
  outliers start: 8
  outliers final: 3
  residues processed: 96
  average time/residue: 3.0024
  time to fit residues: 294.9964
Evaluate side-chains
  86 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain F residue  342 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0970
   overall best weight:    3.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
E 336 GLN
E 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.151082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.120553 restraints weight = 11408.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 1.63
r_work: 0.3755 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3686 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3396  Z= 0.317
  Angle     :  0.617   4.771   4548  Z= 0.327
  Chirality :  0.051   0.144    516
  Planarity :  0.003   0.023    576
  Dihedral  :  5.256  16.569    444
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.10 %
    Favored  : 81.77 %
  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: -2.10 (0.33), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 374 
 PHE   0.010   0.002   PHE C 346 
 TYR   0.012   0.003   TYR C 310 
 ARG   0.003   0.001   ARG C 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7961 (mttm)
REVERT: A  347 LYS cc_start: 0.7844 (mttt) cc_final: 0.7501 (mmmm)
REVERT: C  321 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8387 (mttp)
REVERT: C  345 ASP cc_start: 0.7577 (t0) cc_final: 0.7345 (t70)
REVERT: C  347 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7311 (mmmm)
REVERT: C  349 ARG cc_start: 0.7533 (mtt180) cc_final: 0.5714 (mmp-170)
REVERT: E  338 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6827 (tt0)
REVERT: E  347 LYS cc_start: 0.7779 (mttt) cc_final: 0.6973 (pttm)
REVERT: B  320 SER cc_start: 0.8492 (t) cc_final: 0.8164 (p)
REVERT: B  321 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7943 (mttt)
REVERT: B  342 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6293 (tt0)
REVERT: B  375 LYS cc_start: 0.8169 (tttt) cc_final: 0.7930 (mtpp)
REVERT: D  349 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6150 (mmp-170)
REVERT: D  369 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8132 (ttmt)
REVERT: F  320 SER cc_start: 0.8378 (t) cc_final: 0.7994 (p)
REVERT: F  369 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8183 (ttmt)
REVERT: F  375 LYS cc_start: 0.8377 (tttt) cc_final: 0.8142 (mtpp)
  outliers start: 12
  outliers final: 7
  residues processed: 87
  average time/residue: 2.9445
  time to fit residues: 262.0812
Evaluate side-chains
  92 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain F residue  342 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 336 GLN
E 351 GLN
B 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.150249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.120015 restraints weight = 11590.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 1.64
r_work: 0.3720 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3396  Z= 0.340
  Angle     :  0.613   4.329   4548  Z= 0.324
  Chirality :  0.051   0.140    516
  Planarity :  0.003   0.017    576
  Dihedral  :  5.279  16.769    444
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.89 %
    Favored  : 81.25 %
  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: -2.24 (0.32), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.24), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 374 
 PHE   0.009   0.002   PHE E 378 
 TYR   0.011   0.003   TYR C 310 
 ARG   0.003   0.001   ARG C 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7937 (mttm)
REVERT: A  347 LYS cc_start: 0.7829 (mttt) cc_final: 0.7463 (mmmm)
REVERT: C  321 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8435 (mttp)
REVERT: C  345 ASP cc_start: 0.7672 (t0) cc_final: 0.7405 (t70)
REVERT: C  347 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7244 (mmmm)
REVERT: C  349 ARG cc_start: 0.7593 (mtt180) cc_final: 0.5784 (mmp-170)
REVERT: E  336 GLN cc_start: 0.7777 (tt0) cc_final: 0.7153 (tt0)
REVERT: E  338 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6373 (mt-10)
REVERT: E  347 LYS cc_start: 0.7817 (mttt) cc_final: 0.7043 (pmtt)
REVERT: E  375 LYS cc_start: 0.8519 (tttp) cc_final: 0.8049 (ttmm)
REVERT: B  320 SER cc_start: 0.8540 (t) cc_final: 0.8220 (p)
REVERT: B  321 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7935 (mttt)
REVERT: B  336 GLN cc_start: 0.6905 (tt0) cc_final: 0.6622 (tt0)
REVERT: B  342 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6334 (tt0)
REVERT: B  375 LYS cc_start: 0.8216 (tttt) cc_final: 0.7982 (mtpp)
REVERT: D  349 ARG cc_start: 0.7319 (mtt180) cc_final: 0.6157 (mmp-170)
REVERT: F  345 ASP cc_start: 0.5946 (OUTLIER) cc_final: 0.5690 (p0)
REVERT: F  375 LYS cc_start: 0.8412 (tttt) cc_final: 0.8162 (mtpp)
  outliers start: 11
  outliers final: 6
  residues processed: 81
  average time/residue: 3.0110
  time to fit residues: 249.5768
Evaluate side-chains
  87 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    2.7986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.151609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.121307 restraints weight = 11437.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 1.64
r_work: 0.3779 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.4877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3396  Z= 0.247
  Angle     :  0.555   4.307   4548  Z= 0.290
  Chirality :  0.050   0.139    516
  Planarity :  0.002   0.016    576
  Dihedral  :  5.041  16.425    444
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 1.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.45 %
    Favored  : 80.47 %
  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: -2.22 (0.32), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.24), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.006   0.001   PHE C 346 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.002   0.001   ARG C 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7800 (mttt) cc_final: 0.7433 (mmmm)
REVERT: C  311 LYS cc_start: 0.6735 (mmtm) cc_final: 0.6483 (mmtm)
REVERT: C  321 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8444 (mttp)
REVERT: C  347 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7260 (mmmm)
REVERT: C  349 ARG cc_start: 0.7542 (mtt180) cc_final: 0.5791 (mmp-170)
REVERT: E  336 GLN cc_start: 0.7867 (tt0) cc_final: 0.7009 (tt0)
REVERT: E  338 GLU cc_start: 0.6983 (tt0) cc_final: 0.6403 (mt-10)
REVERT: E  347 LYS cc_start: 0.7825 (mttt) cc_final: 0.7059 (pmtt)
REVERT: B  320 SER cc_start: 0.8500 (t) cc_final: 0.8258 (p)
REVERT: B  321 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7938 (mttt)
REVERT: B  375 LYS cc_start: 0.8177 (tttt) cc_final: 0.7942 (mtpp)
REVERT: D  349 ARG cc_start: 0.7306 (mtt180) cc_final: 0.6153 (mmp-170)
REVERT: D  369 LYS cc_start: 0.8413 (ttmm) cc_final: 0.8182 (ttmt)
REVERT: F  345 ASP cc_start: 0.6024 (OUTLIER) cc_final: 0.5789 (p0)
REVERT: F  369 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8219 (ttmt)
REVERT: F  375 LYS cc_start: 0.8400 (tttt) cc_final: 0.8165 (mtpp)
  outliers start: 8
  outliers final: 5
  residues processed: 85
  average time/residue: 3.1500
  time to fit residues: 273.6134
Evaluate side-chains
  85 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.5784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.153964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.124398 restraints weight = 11391.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 1.61
r_work: 0.3784 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3710 rms_B_bonded: 2.55 restraints_weight: 0.2500
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.5028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3396  Z= 0.179
  Angle     :  0.522   4.229   4548  Z= 0.267
  Chirality :  0.050   0.138    516
  Planarity :  0.002   0.015    576
  Dihedral  :  4.761  15.855    444
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 1.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.45 %
    Favored  : 80.47 %
  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: -2.22 (0.32), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 330 
 PHE   0.005   0.001   PHE D 346 
 TYR   0.007   0.002   TYR B 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7788 (mttt) cc_final: 0.7409 (mmmm)
REVERT: C  311 LYS cc_start: 0.6703 (mmtm) cc_final: 0.6455 (mmtm)
REVERT: C  321 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8452 (mttp)
REVERT: C  338 GLU cc_start: 0.6795 (tp30) cc_final: 0.6484 (tp30)
REVERT: C  349 ARG cc_start: 0.7540 (mtt180) cc_final: 0.5704 (mmp-170)
REVERT: E  336 GLN cc_start: 0.7912 (tt0) cc_final: 0.7018 (tt0)
REVERT: E  338 GLU cc_start: 0.7023 (tt0) cc_final: 0.6519 (mt-10)
REVERT: E  347 LYS cc_start: 0.7820 (mttt) cc_final: 0.7044 (pmtt)
REVERT: E  375 LYS cc_start: 0.8504 (tttp) cc_final: 0.8038 (ttmm)
REVERT: B  320 SER cc_start: 0.8519 (t) cc_final: 0.8296 (p)
REVERT: B  321 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7916 (mttt)
REVERT: B  375 LYS cc_start: 0.8193 (tttt) cc_final: 0.7954 (mtpp)
REVERT: D  349 ARG cc_start: 0.7306 (mtt180) cc_final: 0.6160 (mmp-170)
REVERT: D  369 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8172 (ttmt)
REVERT: F  375 LYS cc_start: 0.8373 (tttt) cc_final: 0.8117 (mtpp)
  outliers start: 8
  outliers final: 5
  residues processed: 80
  average time/residue: 3.2045
  time to fit residues: 261.9999
Evaluate side-chains
  82 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  342 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   overall best weight:    2.2984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.152113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.121996 restraints weight = 11306.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 1.63
r_work: 0.3754 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.5042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3396  Z= 0.219
  Angle     :  0.545   4.710   4548  Z= 0.282
  Chirality :  0.050   0.137    516
  Planarity :  0.002   0.016    576
  Dihedral  :  4.758  15.910    444
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.23 %
    Favored  : 79.95 %
  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: -2.30 (0.32), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.24), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 330 
 PHE   0.006   0.001   PHE C 346 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.002   0.000   ARG C 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.568 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7803 (mttt) cc_final: 0.7408 (mmmm)
REVERT: C  311 LYS cc_start: 0.6670 (mmtm) cc_final: 0.6423 (mmtm)
REVERT: C  321 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8451 (mttp)
REVERT: C  338 GLU cc_start: 0.6826 (tp30) cc_final: 0.6504 (tp30)
REVERT: C  349 ARG cc_start: 0.7546 (mtt180) cc_final: 0.5772 (mmp-170)
REVERT: E  336 GLN cc_start: 0.7903 (tt0) cc_final: 0.7124 (tt0)
REVERT: E  338 GLU cc_start: 0.6989 (tt0) cc_final: 0.6384 (mt-10)
REVERT: E  347 LYS cc_start: 0.7834 (mttt) cc_final: 0.7057 (pmtt)
REVERT: B  320 SER cc_start: 0.8547 (t) cc_final: 0.8266 (p)
REVERT: B  321 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7947 (mttt)
REVERT: B  375 LYS cc_start: 0.8216 (tttt) cc_final: 0.7970 (mtpp)
REVERT: D  349 ARG cc_start: 0.7325 (mtt180) cc_final: 0.6156 (mmp-170)
REVERT: D  369 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8173 (ttmt)
REVERT: F  375 LYS cc_start: 0.8387 (tttt) cc_final: 0.8142 (mtpp)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 3.2598
  time to fit residues: 249.8733
Evaluate side-chains
  79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  342 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 36 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 2 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    2.0784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.153137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.123075 restraints weight = 11408.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 1.64
r_work: 0.3768 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.5086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3396  Z= 0.204
  Angle     :  0.533   4.828   4548  Z= 0.276
  Chirality :  0.050   0.137    516
  Planarity :  0.002   0.018    576
  Dihedral  :  4.703  15.941    444
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.71 %
    Favored  : 80.21 %
  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: -2.29 (0.32), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 330 
 PHE   0.006   0.001   PHE C 346 
 TYR   0.011   0.002   TYR B 310 
 ARG   0.001   0.000   ARG C 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.536 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7800 (mttt) cc_final: 0.7430 (mmmm)
REVERT: C  311 LYS cc_start: 0.6628 (mmtm) cc_final: 0.6379 (mmtm)
REVERT: C  321 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8451 (mttp)
REVERT: C  338 GLU cc_start: 0.6828 (tp30) cc_final: 0.6497 (tp30)
REVERT: C  347 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7239 (mmmm)
REVERT: C  349 ARG cc_start: 0.7543 (mtt180) cc_final: 0.5780 (mmp-170)
REVERT: E  336 GLN cc_start: 0.7898 (tt0) cc_final: 0.7105 (tt0)
REVERT: E  338 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6403 (mt-10)
REVERT: E  347 LYS cc_start: 0.7818 (mttt) cc_final: 0.7041 (pmtt)
REVERT: B  320 SER cc_start: 0.8543 (t) cc_final: 0.8278 (p)
REVERT: B  321 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7945 (mttt)
REVERT: B  375 LYS cc_start: 0.8229 (tttt) cc_final: 0.7987 (mtpp)
REVERT: D  349 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6145 (mmp-170)
REVERT: D  369 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8171 (ttmt)
REVERT: F  375 LYS cc_start: 0.8385 (tttt) cc_final: 0.8133 (mtpp)
  outliers start: 8
  outliers final: 5
  residues processed: 76
  average time/residue: 3.2374
  time to fit residues: 251.5374
Evaluate side-chains
  81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  342 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    2.1786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.152529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.122332 restraints weight = 11390.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 1.63
r_work: 0.3760 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3396  Z= 0.207
  Angle     :  0.530   4.421   4548  Z= 0.276
  Chirality :  0.050   0.137    516
  Planarity :  0.002   0.018    576
  Dihedral  :  4.686  15.916    444
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.97 %
    Favored  : 80.47 %
  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: -2.29 (0.32), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 330 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.011   0.002   TYR B 310 
 ARG   0.001   0.000   ARG C 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7811 (mttt) cc_final: 0.7438 (mmmm)
REVERT: C  311 LYS cc_start: 0.6631 (mmtm) cc_final: 0.6208 (mmtm)
REVERT: C  321 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8450 (mttp)
REVERT: C  338 GLU cc_start: 0.6820 (tp30) cc_final: 0.6518 (tp30)
REVERT: C  349 ARG cc_start: 0.7559 (mtt180) cc_final: 0.5817 (mmp-170)
REVERT: E  336 GLN cc_start: 0.7858 (tt0) cc_final: 0.7072 (tt0)
REVERT: E  338 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6407 (mt-10)
REVERT: E  347 LYS cc_start: 0.7824 (mttt) cc_final: 0.7064 (pmtt)
REVERT: B  320 SER cc_start: 0.8544 (t) cc_final: 0.8271 (p)
REVERT: B  321 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7955 (mttt)
REVERT: B  345 ASP cc_start: 0.6530 (p0) cc_final: 0.6123 (p0)
REVERT: B  375 LYS cc_start: 0.8231 (tttt) cc_final: 0.7987 (mtpp)
REVERT: D  349 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6164 (mmp-170)
REVERT: D  369 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8187 (ttmt)
REVERT: F  347 LYS cc_start: 0.6999 (mttt) cc_final: 0.6594 (pmtt)
REVERT: F  375 LYS cc_start: 0.8390 (tttt) cc_final: 0.8140 (mtpp)
  outliers start: 6
  outliers final: 5
  residues processed: 77
  average time/residue: 3.2406
  time to fit residues: 254.9138
Evaluate side-chains
  81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  342 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   overall best weight:    3.1788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.150992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.120423 restraints weight = 11554.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 1.64
r_work: 0.3761 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.5125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3396  Z= 0.267
  Angle     :  0.573   4.537   4548  Z= 0.301
  Chirality :  0.050   0.137    516
  Planarity :  0.003   0.017    576
  Dihedral  :  4.903  16.230    444
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.97 %
    Favored  : 80.21 %
  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: -2.32 (0.32), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.24), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 374 
 PHE   0.007   0.001   PHE C 346 
 TYR   0.011   0.002   TYR B 310 
 ARG   0.002   0.001   ARG C 349 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7815 (mttt) cc_final: 0.7445 (mmmm)
REVERT: C  311 LYS cc_start: 0.6653 (mmtm) cc_final: 0.6405 (mmtm)
REVERT: C  321 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8437 (mttp)
REVERT: C  338 GLU cc_start: 0.6764 (tp30) cc_final: 0.6500 (tp30)
REVERT: C  349 ARG cc_start: 0.7546 (mtt180) cc_final: 0.5821 (mmp-170)
REVERT: E  336 GLN cc_start: 0.7850 (tt0) cc_final: 0.7041 (tt0)
REVERT: E  338 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6316 (mt-10)
REVERT: E  347 LYS cc_start: 0.7833 (mttt) cc_final: 0.7102 (pmtt)
REVERT: B  320 SER cc_start: 0.8529 (t) cc_final: 0.8220 (p)
REVERT: B  321 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7929 (mttt)
REVERT: B  345 ASP cc_start: 0.6592 (p0) cc_final: 0.6146 (p0)
REVERT: B  375 LYS cc_start: 0.8237 (tttt) cc_final: 0.8005 (mtpp)
REVERT: D  349 ARG cc_start: 0.7326 (mtt180) cc_final: 0.6202 (mmp-170)
REVERT: D  369 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8203 (ttmt)
REVERT: F  345 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5954 (p0)
REVERT: F  347 LYS cc_start: 0.6969 (mttt) cc_final: 0.6595 (pmtt)
REVERT: F  375 LYS cc_start: 0.8389 (tttt) cc_final: 0.8138 (mtpp)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 3.3117
  time to fit residues: 253.8384
Evaluate side-chains
  81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    2.9788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.151408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.120917 restraints weight = 11468.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 1.64
r_work: 0.3735 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3659 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3396  Z= 0.254
  Angle     :  0.557   4.312   4548  Z= 0.292
  Chirality :  0.050   0.137    516
  Planarity :  0.002   0.017    576
  Dihedral  :  4.880  15.882    444
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.23 %
    Favored  : 79.95 %
  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: -2.31 (0.32), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.24), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 330 
 PHE   0.006   0.001   PHE C 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.002   0.000   ARG C 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7491.44 seconds
wall clock time: 127 minutes 21.77 seconds (7641.77 seconds total)