Starting phenix.real_space_refine
on Fri Aug 22 17:59:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q99_18272/08_2025/8q99_18272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q99_18272/08_2025/8q99_18272.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q99_18272/08_2025/8q99_18272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q99_18272/08_2025/8q99_18272.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q99_18272/08_2025/8q99_18272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q99_18272/08_2025/8q99_18272.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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    2046      2.51       5
     N     588      2.21       5
     O     606      1.98       5
     H    3396      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6642
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
      Conformer: "B"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
          bond proxies already assigned to first conformer: 1110
    Chain: "D"
      Number of atoms: 1107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
      Conformer: "B"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
          bond proxies already assigned to first conformer: 1110
    Chain: "C"
      Number of atoms: 1107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
      Conformer: "B"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
          bond proxies already assigned to first conformer: 1110
    Chain: "B"
      Number of atoms: 1107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
      Conformer: "B"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
          bond proxies already assigned to first conformer: 1110
    Chain: "E"
      Number of atoms: 1107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
      Conformer: "B"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
          bond proxies already assigned to first conformer: 1110
    Chain: "F"
      Number of atoms: 1107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
      Conformer: "B"
        Number of residues, atoms: 71, 1104
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
          bond proxies already assigned to first conformer: 1110
  Time building chain proxies: 2.11, per 1000 atoms: 0.32
  Number of scatterers: 6642
  At special positions: 0
  Unit cell: (114.536, 96.408, 37.904, 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     606      8.00
     N     588      7.00
     C    2046      6.00
     H    3396      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: 0.42
  Conformation dependent library (CDL) restraints added in 387.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 49.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 309 through 310
      removed outlier: 6.695A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.710A  pdb=" N   VAL A 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325
      removed outlier: 6.288A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   LYS C 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   SER A 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   GLY C 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   CYS A 322 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LEU C 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   SER A 324 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.500A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 342
      removed outlier: 6.538A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   GLU C 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   SER A 341 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.531A  pdb=" N   ASP A 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.560A  pdb=" N   GLN A 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   ILE D 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   LYS A 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 357 through 361
      removed outlier: 6.711A  pdb=" N   LEU A 357 " --> pdb=" O   ASP C 358 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   ILE C 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ASN A 359 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 368 through 377
      removed outlier: 6.562A  pdb=" N   LYS A 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   GLU D 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ILE A 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   HIS D 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   THR A 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   LEU D 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LYS A 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310
      removed outlier: 6.431A  pdb=" N   VAL B 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.633A  pdb=" N   VAL B 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325
      removed outlier: 6.319A  pdb=" N   VAL B 318 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   LYS F 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   SER B 320 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   GLY F 323 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   CYS B 322 " --> pdb=" O   GLY F 323 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU F 325 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   SER B 324 " --> pdb=" O   LEU F 325 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330
      removed outlier: 6.654A  pdb=" N   ILE B 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 337 through 342
    Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346
      removed outlier: 6.614A  pdb=" N   ASP B 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 350 through 354
      removed outlier: 6.513A  pdb=" N   GLN B 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   ILE E 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LYS B 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 357 through 361
    Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 377
      removed outlier: 6.537A  pdb=" N   LYS B 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   GLU E 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ILE B 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   HIS E 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   THR B 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   LEU E 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LYS B 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)

    79 hydrogen bonds defined for protein.
    237 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        0.95 -     2.22: 6681
        2.22 -     3.49: 3
        3.49 -     4.76: 6
        4.76 -     6.03: 3
        6.03 -     7.29: 3
  Warning: very large bond lengths.
  Bond restraints: 6696
  Sorted by residual:
  bond pdb=" N   LYS B 343 "
       pdb=" H  BLYS B 343 "
    ideal  model  delta    sigma   weight residual
    0.860  7.294 -6.434 2.00e-02 2.50e+03 1.04e+05
  bond pdb=" N   LYS F 343 "
       pdb=" H  BLYS F 343 "
    ideal  model  delta    sigma   weight residual
    0.860  7.174 -6.314 2.00e-02 2.50e+03 9.97e+04
  bond pdb=" N   LYS E 343 "
       pdb=" H  BLYS E 343 "
    ideal  model  delta    sigma   weight residual
    0.860  7.088 -6.228 2.00e-02 2.50e+03 9.70e+04
  bond pdb=" N   SER B 341 "
       pdb=" H  BSER B 341 "
    ideal  model  delta    sigma   weight residual
    0.860  5.496 -4.636 2.00e-02 2.50e+03 5.37e+04
  bond pdb=" N   SER F 341 "
       pdb=" H  BSER F 341 "
    ideal  model  delta    sigma   weight residual
    0.860  5.442 -4.582 2.00e-02 2.50e+03 5.25e+04
  ... (remaining 6691 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    19.71: 12195
       19.71 -    39.42: 8
       39.42 -    59.13: 4
       59.13 -    78.84: 7
       78.84 -    98.55: 8
  Bond angle restraints: 12222
  Sorted by residual:
  angle pdb=" C   LYS A 340 "
        pdb=" N   SER A 341 "
        pdb=" H  BSER A 341 "
      ideal   model   delta    sigma   weight residual
     123.65   25.10   98.55 3.00e+00 1.11e-01 1.08e+03
  angle pdb=" C   LYS D 340 "
        pdb=" N   SER D 341 "
        pdb=" H  BSER D 341 "
      ideal   model   delta    sigma   weight residual
     123.65   25.59   98.06 3.00e+00 1.11e-01 1.07e+03
  angle pdb=" C   LYS C 340 "
        pdb=" N   SER C 341 "
        pdb=" H  BSER C 341 "
      ideal   model   delta    sigma   weight residual
     123.65   30.04   93.61 3.00e+00 1.11e-01 9.74e+02
  angle pdb=" C   LYS E 340 "
        pdb=" N   SER E 341 "
        pdb=" H  BSER E 341 "
      ideal   model   delta    sigma   weight residual
     123.65   32.01   91.64 3.00e+00 1.11e-01 9.33e+02
  angle pdb=" C   LYS B 340 "
        pdb=" N   SER B 341 "
        pdb=" H  BSER B 341 "
      ideal   model   delta    sigma   weight residual
     123.65   35.85   87.80 3.00e+00 1.11e-01 8.57e+02
  ... (remaining 12217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.64: 2745
       16.64 -    33.29: 192
       33.29 -    49.93: 70
       49.93 -    66.57: 71
       66.57 -    83.21: 18
  Dihedral angle restraints: 3096
    sinusoidal: 1770
      harmonic: 1326
  Sorted by residual:
  dihedral pdb=" CA  LYS E 347 "
           pdb=" C   LYS E 347 "
           pdb=" N   ASP E 348 "
           pdb=" CA  ASP E 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.94  -26.06     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  ASP A 358 "
           pdb=" C   ASP A 358 "
           pdb=" N   ASN A 359 "
           pdb=" CA  ASN A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.13   24.87     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ASP D 358 "
           pdb=" C   ASP D 358 "
           pdb=" N   ASN D 359 "
           pdb=" CA  ASN D 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.24   24.76     0      5.00e+00 4.00e-02 2.45e+01
  ... (remaining 3093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 267
       0.066 -    0.132: 165
       0.132 -    0.198: 38
       0.198 -    0.263: 17
       0.263 -    0.329: 11
  Chirality restraints: 498
  Sorted by residual:
  chirality pdb=" CA  LEU B 325 "
            pdb=" N   LEU B 325 "
            pdb=" C   LEU B 325 "
            pdb=" CB  LEU B 325 "
    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  GLN A 351 "
            pdb=" N   GLN A 351 "
            pdb=" C   GLN A 351 "
            pdb=" CB  GLN A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  LEU A 325 "
            pdb=" N   LEU A 325 "
            pdb=" C   LEU A 325 "
            pdb=" CB  LEU A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.63e+00
  ... (remaining 495 not shown)

  Planarity restraints: 978
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 338 "   -0.240 2.00e-02 2.50e+03   2.69e-01 7.23e+02
        pdb=" N   VAL A 339 "    0.436 2.00e-02 2.50e+03
        pdb=" CA  VAL A 339 "   -0.204 2.00e-02 2.50e+03
        pdb=" H  BVAL A 339 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 338 "   -0.237 2.00e-02 2.50e+03   2.68e-01 7.16e+02
        pdb=" N   VAL C 339 "    0.434 2.00e-02 2.50e+03
        pdb=" CA  VAL C 339 "   -0.203 2.00e-02 2.50e+03
        pdb=" H  BVAL C 339 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 338 "   -0.222 2.00e-02 2.50e+03   2.65e-01 7.04e+02
        pdb=" N   VAL D 339 "    0.437 2.00e-02 2.50e+03
        pdb=" CA  VAL D 339 "   -0.201 2.00e-02 2.50e+03
        pdb=" H  BVAL D 339 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 975 not shown)

  Histogram of nonbonded interaction distances:
        0.89 -     1.63: 17
        1.63 -     2.38: 1491
        2.38 -     3.12: 20164
        3.12 -     3.86: 24635
        3.86 -     4.60: 38145
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 84452
  Sorted by model distance:
  nonbonded pdb=" H  BSER B 341 "
            pdb=" C   LYS E 340 "
     model   vdw
     0.892 2.750
  nonbonded pdb=" C   LYS B 340 "
            pdb=" H  BSER F 341 "
     model   vdw
     1.115 2.750
  nonbonded pdb=" H  BSER B 341 "
            pdb=" CA  LYS E 340 "
     model   vdw
     1.168 2.750
  nonbonded pdb=" HB2 LYS A 340 "
            pdb=" H  BSER A 341 "
     model   vdw
     1.431 2.270
  nonbonded pdb=" H  BLYS B 343 "
            pdb=" HB2 GLU E 342 "
     model   vdw
     1.443 2.270
  ... (remaining 84447 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ 
ough 378))
  selection = (chain 'B' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ 
ough 378))
  selection = (chain 'C' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ 
ough 378))
  selection = (chain 'D' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ 
ough 378))
  selection = (chain 'E' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ 
ough 378))
  selection = (chain 'F' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ 
ough 378))
}

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=0.50 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:                  0.010
  Normalize map: mean=0, sd=1:             4.610
  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:             0.050
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.470
  Find NCS groups from input model:        0.080
  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:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
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   0.033   3300  Z= 0.694
  Angle     :  1.825   7.507   4416  Z= 1.206
  Chirality :  0.096   0.329    498
  Planarity :  0.010   0.067    558
  Dihedral  : 11.757  83.213   1260
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.40 (0.33), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.26), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 349 
 TYR   0.123   0.037   TYR F 310 
 PHE   0.037   0.011   PHE B 346 
 HIS   0.007   0.002   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.01091 ( 3300)
  covalent geometry    : angle       1.82451 ( 4416)
  hydrogen bonds       : bond        0.05453 (   79)
  hydrogen bonds       : angle       7.18686 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.192 
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: D  349 ARG cc_start: 0.8031 (mtp180) cc_final: 0.6841 (pmt-80)
REVERT: C  349 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7038 (mmp-170)
REVERT: F  311 LYS cc_start: 0.7624 (mttt) cc_final: 0.7217 (mmpt)
REVERT: F  349 ARG cc_start: 0.8506 (mtp180) cc_final: 0.7319 (mtt-85)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 1.1069
  time to fit residues: 120.3701
Evaluate side-chains
  70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
D 336 GLN
C 336 GLN
E 327 ASN
E 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.141519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.134584 restraints weight = 25548.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 2.23
r_work: 0.3908 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3814 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3822 r_free = 0.3822    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3821 r_free = 0.3821    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3300  Z= 0.159
  Angle     :  0.741   9.500   4416  Z= 0.397
  Chirality :  0.049   0.129    498
  Planarity :  0.003   0.027    558
  Dihedral  :  6.672  19.701    432
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.10 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.36), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.50 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 349 
 TYR   0.015   0.003   TYR B 310 
 PHE   0.009   0.001   PHE E 346 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3300)
  covalent geometry    : angle       0.74057 ( 4416)
  hydrogen bonds       : bond        0.02494 (   79)
  hydrogen bonds       : angle       5.12343 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.212 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.6587 (pttt)
REVERT: D  324 SER cc_start: 0.8762 (m) cc_final: 0.8547 (m)
REVERT: C  311 LYS cc_start: 0.8261 (mttt) cc_final: 0.7833 (mmtt)
REVERT: C  349 ARG cc_start: 0.8017 (mtp180) cc_final: 0.6953 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8188 (mttt) cc_final: 0.7386 (mmpt)
REVERT: F  349 ARG cc_start: 0.8266 (mtp180) cc_final: 0.7186 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8158 (m-30) cc_final: 0.7843 (m-30)
  outliers start: 12
  outliers final: 4
  residues processed: 78
  average time/residue: 0.9586
  time to fit residues: 76.9508
Evaluate side-chains
  65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  325 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0270
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.9842

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
E 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.137615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.130628 restraints weight = 25514.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.17
r_work: 0.3852 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.4577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3300  Z= 0.150
  Angle     :  0.632   9.352   4416  Z= 0.350
  Chirality :  0.050   0.129    498
  Planarity :  0.003   0.028    558
  Dihedral  :  5.722  17.957    432
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.17 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.86 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.41 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.013   0.003   TYR F 310 
 PHE   0.008   0.001   PHE F 346 
 HIS   0.004   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3300)
  covalent geometry    : angle       0.63164 ( 4416)
  hydrogen bonds       : bond        0.02150 (   79)
  hydrogen bonds       : angle       4.69412 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.136 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.6769 (pttt)
REVERT: C  311 LYS cc_start: 0.8133 (mttt) cc_final: 0.7749 (mmtt)
REVERT: C  349 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7096 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8522 (t0) cc_final: 0.8121 (t70)
REVERT: F  311 LYS cc_start: 0.8088 (mttt) cc_final: 0.7461 (mmtt)
REVERT: F  349 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7289 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8109 (m-30) cc_final: 0.7813 (m-30)
  outliers start: 10
  outliers final: 4
  residues processed: 71
  average time/residue: 1.0949
  time to fit residues: 79.7510
Evaluate side-chains
  59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  325 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    2.1586

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.134775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.127939 restraints weight = 24360.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 2.09
r_work: 0.3851 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3767
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3767 r_free = 0.3767    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3767 r_free = 0.3767    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3767
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3300  Z= 0.151
  Angle     :  0.604   9.545   4416  Z= 0.339
  Chirality :  0.050   0.125    498
  Planarity :  0.003   0.031    558
  Dihedral  :  5.376  18.526    432
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.90 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.34 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.012   0.003   TYR F 310 
 PHE   0.009   0.001   PHE E 346 
 HIS   0.005   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3300)
  covalent geometry    : angle       0.60367 ( 4416)
  hydrogen bonds       : bond        0.01942 (   79)
  hydrogen bonds       : angle       4.47262 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.237 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.6507 (pptt)
REVERT: D  349 ARG cc_start: 0.8455 (mtt-85) cc_final: 0.6844 (pmt-80)
REVERT: C  311 LYS cc_start: 0.8170 (mttt) cc_final: 0.7783 (mmtt)
REVERT: C  349 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7100 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8439 (t0) cc_final: 0.8058 (t70)
REVERT: F  311 LYS cc_start: 0.8152 (mttt) cc_final: 0.7391 (mmpt)
REVERT: F  349 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7293 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8087 (m-30) cc_final: 0.7794 (m-30)
  outliers start: 10
  outliers final: 5
  residues processed: 68
  average time/residue: 0.9121
  time to fit residues: 63.9308
Evaluate side-chains
  60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  325 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    3.3990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.130046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.123528 restraints weight = 23058.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 1.99
r_work: 0.3794 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3709 r_free = 0.3709    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3709 r_free = 0.3709    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.5126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3300  Z= 0.219
  Angle     :  0.641   9.559   4416  Z= 0.356
  Chirality :  0.050   0.132    498
  Planarity :  0.003   0.033    558
  Dihedral  :  5.477  18.020    432
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.44 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.79 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.017   0.004   TYR F 310 
 PHE   0.012   0.002   PHE E 346 
 HIS   0.006   0.002   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 3300)
  covalent geometry    : angle       0.64088 ( 4416)
  hydrogen bonds       : bond        0.02089 (   79)
  hydrogen bonds       : angle       4.47638 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.122 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.6560 (pptt)
REVERT: C  311 LYS cc_start: 0.8143 (mttt) cc_final: 0.7677 (mmtm)
REVERT: C  349 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7161 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8462 (t0) cc_final: 0.8043 (t70)
REVERT: E  311 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6774 (pttp)
REVERT: F  311 LYS cc_start: 0.8239 (mttt) cc_final: 0.7549 (mmpt)
REVERT: F  349 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7260 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8093 (m-30) cc_final: 0.7809 (m-30)
  outliers start: 11
  outliers final: 5
  residues processed: 64
  average time/residue: 1.0190
  time to fit residues: 66.9845
Evaluate side-chains
  57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    0.0370
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.1862

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.135145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.128483 restraints weight = 23843.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 1.98
r_work: 0.3864 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3778 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3785
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3785 r_free = 0.3785    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3785 r_free = 0.3785    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3785
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3300  Z= 0.095
  Angle     :  0.565   9.884   4416  Z= 0.321
  Chirality :  0.049   0.128    498
  Planarity :  0.003   0.027    558
  Dihedral  :  4.910  15.911    432
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 12.90 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.34 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.007   0.002   TYR C 310 
 PHE   0.004   0.001   PHE E 346 
 HIS   0.002   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 3300)
  covalent geometry    : angle       0.56528 ( 4416)
  hydrogen bonds       : bond        0.01642 (   79)
  hydrogen bonds       : angle       4.24936 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.163 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.6434 (pptt)
REVERT: C  311 LYS cc_start: 0.8149 (mttt) cc_final: 0.7811 (mmtt)
REVERT: C  314 ASP cc_start: 0.8610 (t0) cc_final: 0.8357 (t70)
REVERT: C  349 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7113 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8402 (t0) cc_final: 0.8019 (t70)
REVERT: F  311 LYS cc_start: 0.8134 (mttt) cc_final: 0.7452 (mmpt)
REVERT: F  349 ARG cc_start: 0.8341 (mtp180) cc_final: 0.7162 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8015 (m-30) cc_final: 0.7711 (m-30)
  outliers start: 9
  outliers final: 3
  residues processed: 64
  average time/residue: 1.1396
  time to fit residues: 74.8894
Evaluate side-chains
  59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain C residue  325 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.3722

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.130891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.124450 restraints weight = 26713.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 2.10
r_work: 0.3847 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.5399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3300  Z= 0.110
  Angle     :  0.559   9.805   4416  Z= 0.318
  Chirality :  0.049   0.128    498
  Planarity :  0.003   0.028    558
  Dihedral  :  4.785  15.390    432
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.52 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.010   0.002   TYR F 310 
 PHE   0.007   0.001   PHE E 346 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3300)
  covalent geometry    : angle       0.55853 ( 4416)
  hydrogen bonds       : bond        0.01678 (   79)
  hydrogen bonds       : angle       4.11993 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.189 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.6509 (pptt)
REVERT: C  311 LYS cc_start: 0.8173 (mttt) cc_final: 0.7715 (mmpt)
REVERT: C  314 ASP cc_start: 0.8592 (t0) cc_final: 0.8319 (t70)
REVERT: C  349 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7212 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8375 (t0) cc_final: 0.7993 (t70)
REVERT: E  311 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6775 (pttp)
REVERT: E  338 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: F  311 LYS cc_start: 0.8200 (mttt) cc_final: 0.7501 (mmpt)
REVERT: F  349 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7323 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8060 (m-30) cc_final: 0.7717 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 60
  average time/residue: 1.2544
  time to fit residues: 77.2425
Evaluate side-chains
  59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  311 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
D 359 ASN
B 351 GLN
E 351 GLN
F 336 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.130912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.124966 restraints weight = 21645.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 1.87
r_work: 0.3868 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3786 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3783 r_free = 0.3783    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3783 r_free = 0.3783    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.5472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3300  Z= 0.111
  Angle     :  0.551   9.869   4416  Z= 0.315
  Chirality :  0.049   0.127    498
  Planarity :  0.003   0.028    558
  Dihedral  :  4.666  15.157    432
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 15.05 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.010   0.002   TYR F 310 
 PHE   0.006   0.001   PHE E 346 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3300)
  covalent geometry    : angle       0.55130 ( 4416)
  hydrogen bonds       : bond        0.01637 (   79)
  hydrogen bonds       : angle       4.07929 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.210 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.6499 (pptt)
REVERT: C  311 LYS cc_start: 0.8143 (mttt) cc_final: 0.7806 (mmtt)
REVERT: C  314 ASP cc_start: 0.8580 (t0) cc_final: 0.8310 (t70)
REVERT: C  349 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7190 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8354 (t0) cc_final: 0.7977 (t70)
REVERT: E  311 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6761 (pttp)
REVERT: E  338 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: F  311 LYS cc_start: 0.8166 (mttt) cc_final: 0.7488 (mmpt)
REVERT: F  349 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7302 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8009 (m-30) cc_final: 0.7661 (m-30)
  outliers start: 4
  outliers final: 2
  residues processed: 60
  average time/residue: 1.0935
  time to fit residues: 67.3495
Evaluate side-chains
  59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  311 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0770
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.7744

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.129292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.122896 restraints weight = 28651.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.15
r_work: 0.3831 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3745 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3300  Z= 0.125
  Angle     :  0.557   9.837   4416  Z= 0.318
  Chirality :  0.049   0.128    498
  Planarity :  0.003   0.028    558
  Dihedral  :  4.680  15.143    432
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 15.05 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.011   0.002   TYR F 310 
 PHE   0.008   0.001   PHE E 346 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3300)
  covalent geometry    : angle       0.55716 ( 4416)
  hydrogen bonds       : bond        0.01661 (   79)
  hydrogen bonds       : angle       4.02256 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.119 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.6565 (pptt)
REVERT: C  311 LYS cc_start: 0.8227 (mttt) cc_final: 0.7763 (mmtm)
REVERT: C  314 ASP cc_start: 0.8572 (t0) cc_final: 0.8282 (t70)
REVERT: C  349 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7256 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8385 (t0) cc_final: 0.8000 (t70)
REVERT: E  311 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6780 (pttp)
REVERT: E  338 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8070 (tm-30)
REVERT: F  311 LYS cc_start: 0.8196 (mttt) cc_final: 0.7519 (mmpt)
REVERT: F  349 ARG cc_start: 0.8337 (mtp180) cc_final: 0.7330 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8061 (m-30) cc_final: 0.7740 (m-30)
  outliers start: 4
  outliers final: 2
  residues processed: 56
  average time/residue: 1.0027
  time to fit residues: 57.7312
Evaluate side-chains
  58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  311 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0970
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
D 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.128777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.122590 restraints weight = 26681.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.06
r_work: 0.3831 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3747 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3746 r_free = 0.3746    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3746 r_free = 0.3746    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.5579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3300  Z= 0.125
  Angle     :  0.558   9.866   4416  Z= 0.318
  Chirality :  0.049   0.126    498
  Planarity :  0.003   0.028    558
  Dihedral  :  4.667  15.109    432
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.52 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.010   0.002   TYR F 310 
 PHE   0.007   0.001   PHE E 346 
 HIS   0.004   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3300)
  covalent geometry    : angle       0.55776 ( 4416)
  hydrogen bonds       : bond        0.01660 (   79)
  hydrogen bonds       : angle       3.99155 (  237)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.210 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.6554 (pptt)
REVERT: C  311 LYS cc_start: 0.8230 (mttt) cc_final: 0.7765 (mmtm)
REVERT: C  314 ASP cc_start: 0.8577 (t0) cc_final: 0.8302 (t70)
REVERT: C  349 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7268 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8372 (t0) cc_final: 0.8015 (t70)
REVERT: E  311 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6789 (pttp)
REVERT: E  338 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8074 (tm-30)
REVERT: F  311 LYS cc_start: 0.8187 (mttt) cc_final: 0.7514 (mmpt)
REVERT: F  349 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7346 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8046 (m-30) cc_final: 0.7727 (m-30)
  outliers start: 6
  outliers final: 2
  residues processed: 56
  average time/residue: 1.0513
  time to fit residues: 60.2978
Evaluate side-chains
  60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  338 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 31 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
D 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.129368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.123365 restraints weight = 24360.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 1.96
r_work: 0.3841 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3759 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.5624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3300  Z= 0.112
  Angle     :  0.551   9.890   4416  Z= 0.315
  Chirality :  0.049   0.127    498
  Planarity :  0.003   0.028    558
  Dihedral  :  4.566  15.034    432
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.52 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.010   0.002   TYR F 310 
 PHE   0.006   0.001   PHE E 346 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 3300)
  covalent geometry    : angle       0.55127 ( 4416)
  hydrogen bonds       : bond        0.01588 (   79)
  hydrogen bonds       : angle       3.92076 (  237)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2694.62 seconds
wall clock time: 46 minutes 15.82 seconds (2775.82 seconds total)