Starting phenix.real_space_refine
on Tue Feb 11 21:06:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q99_18272/02_2025/8q99_18272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q99_18272/02_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_18272/02_2025/8q99_18272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q99_18272/02_2025/8q99_18272.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q99_18272/02_2025/8q99_18272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q99_18272/02_2025/8q99_18272.cif"
  }
  resolution = 2.7
  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    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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.95, per 1000 atoms: 1.05
  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: 1.45
  Conformation dependent library (CDL) restraints added in 944.1 milliseconds
  

  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: 0.75
  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: 2.28

  Time building geometry restraints manager: 1.81 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: 0.01
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:                  0.000
  Normalize map: mean=0, sd=1:             5.440
  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:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.900
  Find NCS groups from input model:        0.230
  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:15.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.830
-------------------------------------------------------------------------------
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= 0.734
  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 (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: -2.40 (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
 HIS   0.007   0.002   HIS A 374 
 PHE   0.037   0.011   PHE B 346 
 TYR   0.123   0.037   TYR F 310 
 ARG   0.004   0.001   ARG D 349 

*********************** 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  : 0.529 
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: D  349 ARG cc_start: 0.8031 (mtp180) cc_final: 0.6840 (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: 2.4766
  time to fit residues: 269.8578
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  : 0.569 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.140995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.134059 restraints weight = 23536.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 2.16
r_work: 0.3905 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3812 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3815
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3815 r_free = 0.3815    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3815 r_free = 0.3815    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3815
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3300  Z= 0.230
  Angle     :  0.756   9.491   4416  Z= 0.405
  Chirality :  0.050   0.133    498
  Planarity :  0.003   0.024    558
  Dihedral  :  6.780  20.376    432
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.63 %
    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 (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: -2.00 (0.36), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 374 
 PHE   0.010   0.001   PHE B 346 
 TYR   0.015   0.003   TYR F 310 
 ARG   0.002   0.001   ARG B 349 

*********************** 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
  81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.616 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.6577 (pttt)
REVERT: D  324 SER cc_start: 0.8739 (m) cc_final: 0.8524 (m)
REVERT: C  349 ARG cc_start: 0.8016 (mtp180) cc_final: 0.6956 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8186 (mttt) cc_final: 0.7388 (mmpt)
REVERT: F  349 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7173 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8113 (m-30) cc_final: 0.7802 (m-30)
  outliers start: 11
  outliers final: 5
  residues processed: 77
  average time/residue: 2.2928
  time to fit residues: 181.7434
Evaluate side-chains
  66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
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
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 30 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
C 327 ASN
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 = 0.4017 r_free = 0.4017 target = 0.135418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.128600 restraints weight = 25151.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 2.12
r_work: 0.3829 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3737 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3756 r_free = 0.3756    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 = 0.3756 r_free = 0.3756    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.4611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3300  Z= 0.283
  Angle     :  0.661   9.270   4416  Z= 0.364
  Chirality :  0.051   0.130    498
  Planarity :  0.003   0.027    558
  Dihedral  :  5.890  18.527    432
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.71 %
    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 (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: -1.83 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.38 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 362 
 PHE   0.012   0.002   PHE F 346 
 TYR   0.014   0.003   TYR F 310 
 ARG   0.001   0.000   ARG C 349 

*********************** 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
  72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.523 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.6513 (pptt)
REVERT: C  311 LYS cc_start: 0.8163 (mttt) cc_final: 0.7761 (mmpt)
REVERT: C  349 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7172 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8504 (t0) cc_final: 0.8092 (t70)
REVERT: F  311 LYS cc_start: 0.8115 (mttt) cc_final: 0.7472 (mmpt)
REVERT: F  349 ARG cc_start: 0.8329 (mtp180) cc_final: 0.7307 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8130 (m-30) cc_final: 0.7837 (m-30)
  outliers start: 9
  outliers final: 5
  residues processed: 70
  average time/residue: 2.7396
  time to fit residues: 196.9329
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  : 0.574 
-------------------------------------------------------------------------------
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
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 22 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0010
   chunk 26 optimal weight:    5.9990
   overall best weight:    2.3590

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.133471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.126822 restraints weight = 21879.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 1.98
r_work: 0.3844 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3300  Z= 0.233
  Angle     :  0.614   9.627   4416  Z= 0.344
  Chirality :  0.049   0.126    498
  Planarity :  0.003   0.032    558
  Dihedral  :  5.499  18.517    432
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.90 %
    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 (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: -1.74 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 362 
 PHE   0.009   0.001   PHE E 346 
 TYR   0.013   0.003   TYR F 310 
 ARG   0.002   0.000   ARG B 349 

*********************** 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
  71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.562 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.6531 (pptt)
REVERT: D  349 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.6828 (pmt-80)
REVERT: C  311 LYS cc_start: 0.8171 (mttt) cc_final: 0.7730 (mmtm)
REVERT: C  349 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7100 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8448 (t0) cc_final: 0.8052 (t70)
REVERT: F  311 LYS cc_start: 0.8156 (mttt) cc_final: 0.7449 (mmpt)
REVERT: F  349 ARG cc_start: 0.8328 (mtp180) cc_final: 0.7303 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8063 (m-30) cc_final: 0.7779 (m-30)
  outliers start: 11
  outliers final: 6
  residues processed: 67
  average time/residue: 2.4401
  time to fit residues: 168.1786
Evaluate side-chains
  63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
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 C 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 28 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0980
   chunk 9 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.4382

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.139455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.132280 restraints weight = 25886.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 2.20
r_work: 0.3886 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3793 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3818 r_free = 0.3818    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3818 r_free = 0.3818    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.5109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3300  Z= 0.122
  Angle     :  0.556   9.734   4416  Z= 0.316
  Chirality :  0.050   0.132    498
  Planarity :  0.003   0.029    558
  Dihedral  :  4.852  16.567    432
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.78 %
    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 (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: -1.72 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 362 
 PHE   0.002   0.000   PHE C 378 
 TYR   0.007   0.001   TYR A 310 
 ARG   0.001   0.000   ARG B 349 

*********************** 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
  72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.588 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6506 (pptt)
REVERT: D  349 ARG cc_start: 0.8487 (mtt-85) cc_final: 0.6972 (pmt-80)
REVERT: C  311 LYS cc_start: 0.8140 (mttt) cc_final: 0.7752 (mmpt)
REVERT: C  314 ASP cc_start: 0.8569 (t0) cc_final: 0.8258 (t70)
REVERT: C  349 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7130 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8349 (t0) cc_final: 0.7984 (t70)
REVERT: F  311 LYS cc_start: 0.8100 (mttt) cc_final: 0.7422 (mmpt)
REVERT: F  349 ARG cc_start: 0.8272 (mtp180) cc_final: 0.7285 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8068 (m-30) cc_final: 0.7743 (m-30)
  outliers start: 6
  outliers final: 1
  residues processed: 67
  average time/residue: 2.4192
  time to fit residues: 166.8792
Evaluate side-chains
  58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 37 optimal weight:    0.6980
   chunk 12 optimal weight:    0.2980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.4047 r_free = 0.4047 target = 0.133799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.127166 restraints weight = 26003.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 2.15
r_work: 0.3886 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3799 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.5201

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= 0.158
  Angle     :  0.558   9.697   4416  Z= 0.316
  Chirality :  0.049   0.127    498
  Planarity :  0.003   0.030    558
  Dihedral  :  4.751  15.899    432
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.40 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.29), residues: 414

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

*********************** 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
  67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.560 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.6482 (pptt)
REVERT: C  311 LYS cc_start: 0.8176 (mttt) cc_final: 0.7734 (mmpt)
REVERT: C  314 ASP cc_start: 0.8547 (t0) cc_final: 0.8236 (t70)
REVERT: C  349 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7087 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8393 (t0) cc_final: 0.8023 (t70)
REVERT: F  311 LYS cc_start: 0.8112 (mttt) cc_final: 0.7426 (mmpt)
REVERT: F  349 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7248 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8049 (m-30) cc_final: 0.7704 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 64
  average time/residue: 2.4929
  time to fit residues: 164.2593
Evaluate side-chains
  62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 33 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.2186

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.129880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.123229 restraints weight = 28550.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 2.22
r_work: 0.3826 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3737 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.5252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3300  Z= 0.223
  Angle     :  0.577   9.741   4416  Z= 0.325
  Chirality :  0.049   0.127    498
  Planarity :  0.003   0.031    558
  Dihedral  :  4.894  16.067    432
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.25 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 362 
 PHE   0.010   0.001   PHE E 346 
 TYR   0.012   0.003   TYR F 310 
 ARG   0.002   0.000   ARG C 349 

*********************** 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
  66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.518 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.6516 (pptt)
REVERT: C  311 LYS cc_start: 0.8219 (mttt) cc_final: 0.7745 (mmtm)
REVERT: C  349 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7197 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8399 (t0) cc_final: 0.8026 (t70)
REVERT: E  311 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6790 (pttp)
REVERT: F  311 LYS cc_start: 0.8216 (mttt) cc_final: 0.7509 (mmpt)
REVERT: F  349 ARG cc_start: 0.8336 (mtp180) cc_final: 0.7305 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8080 (m-30) cc_final: 0.7763 (m-30)
  outliers start: 9
  outliers final: 3
  residues processed: 58
  average time/residue: 2.4052
  time to fit residues: 143.6866
Evaluate side-chains
  58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
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  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 13 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 351 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.131091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.124984 restraints weight = 23155.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 1.96
r_work: 0.3863 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3779 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3774 r_free = 0.3774    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3774 r_free = 0.3774    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.5338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3300  Z= 0.175
  Angle     :  0.558   9.838   4416  Z= 0.318
  Chirality :  0.049   0.125    498
  Planarity :  0.003   0.029    558
  Dihedral  :  4.737  15.925    432
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.25 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.007   0.001   PHE E 346 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.001   0.000   ARG C 349 

*********************** 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
  70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.572 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.6462 (pptt)
REVERT: C  311 LYS cc_start: 0.8164 (mttt) cc_final: 0.7719 (mmtm)
REVERT: C  314 ASP cc_start: 0.8555 (t0) cc_final: 0.8263 (t70)
REVERT: C  349 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7172 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8336 (t0) cc_final: 0.7967 (t70)
REVERT: E  311 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6754 (pttp)
REVERT: F  311 LYS cc_start: 0.8176 (mttt) cc_final: 0.7482 (mmpt)
REVERT: F  349 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7277 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8026 (m-30) cc_final: 0.7703 (m-30)
  outliers start: 9
  outliers final: 4
  residues processed: 62
  average time/residue: 2.5917
  time to fit residues: 165.2160
Evaluate side-chains
  64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   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 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 = 0.4005 r_free = 0.4005 target = 0.130431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.123778 restraints weight = 30176.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 2.25
r_work: 0.3840 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3750 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3750
-------------------------------------------------------------------------------
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:        6 |
|-----------------------------------------------------------------------------|
|-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:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3300  Z= 0.193
  Angle     :  0.563   9.805   4416  Z= 0.320
  Chirality :  0.049   0.127    498
  Planarity :  0.003   0.030    558
  Dihedral  :  4.736  15.946    432
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.05 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.30), residues: 414

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

*********************** 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
  65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.534 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6529 (pptt)
REVERT: C  311 LYS cc_start: 0.8205 (mttt) cc_final: 0.7838 (mmtt)
REVERT: C  314 ASP cc_start: 0.8605 (t0) cc_final: 0.8313 (t70)
REVERT: C  349 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7203 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8366 (t0) cc_final: 0.8005 (t70)
REVERT: E  311 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6757 (pttp)
REVERT: E  338 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8100 (tm-30)
REVERT: F  311 LYS cc_start: 0.8225 (mttt) cc_final: 0.7525 (mmpt)
REVERT: F  349 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7297 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8085 (m-30) cc_final: 0.7747 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 60
  average time/residue: 2.5755
  time to fit residues: 159.0646
Evaluate side-chains
  62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
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  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0170
   chunk 31 optimal weight:    0.0070
   overall best weight:    1.0042

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.132596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.126230 restraints weight = 27072.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 2.11
r_work: 0.3877 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3791 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.5496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3300  Z= 0.138
  Angle     :  0.544   9.935   4416  Z= 0.312
  Chirality :  0.049   0.126    498
  Planarity :  0.003   0.028    558
  Dihedral  :  4.514  15.444    432
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.32 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 374 
 PHE   0.005   0.001   PHE E 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.001   0.000   ARG B 349 

********************** 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
  63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.539 
Fit side-chains
REVERT: D  311 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.6531 (pptt)
REVERT: C  311 LYS cc_start: 0.8156 (mttt) cc_final: 0.7713 (mmpt)
REVERT: C  314 ASP cc_start: 0.8528 (t0) cc_final: 0.8249 (t70)
REVERT: C  349 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7187 (mmp-170)
REVERT: B  345 ASP cc_start: 0.8329 (t0) cc_final: 0.7970 (t70)
REVERT: E  311 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6744 (pttp)
REVERT: E  338 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8057 (tm-30)
REVERT: F  311 LYS cc_start: 0.8151 (mttt) cc_final: 0.7488 (mmpt)
REVERT: F  349 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7227 (mtt-85)
REVERT: F  358 ASP cc_start: 0.8044 (m-30) cc_final: 0.7674 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 59
  average time/residue: 2.4990
  time to fit residues: 151.6850
Evaluate side-chains
  60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0030
   chunk 20 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0030
   overall best weight:    1.3804

-------------------------------------------------------------------------------
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 = 0.4019 r_free = 0.4019 target = 0.131183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.125068 restraints weight = 24545.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 1.99
r_work: 0.3869 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3785 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3780 r_free = 0.3780    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3780 r_free = 0.3780    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.5533

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= 0.164
  Angle     :  0.549   9.831   4416  Z= 0.314
  Chirality :  0.049   0.126    498
  Planarity :  0.003   0.029    558
  Dihedral  :  4.536  15.339    432
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.05 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.39), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.22 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.006   0.001   PHE E 346 
 TYR   0.010   0.002   TYR F 310 
 ARG   0.001   0.000   ARG C 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5952.99 seconds
wall clock time: 105 minutes 40.62 seconds (6340.62 seconds total)