Starting phenix.real_space_refine
on Tue Feb 11 21:02:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q97_18270/02_2025/8q97_18270.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q97_18270/02_2025/8q97_18270.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q97_18270/02_2025/8q97_18270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q97_18270/02_2025/8q97_18270.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q97_18270/02_2025/8q97_18270.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q97_18270/02_2025/8q97_18270.cif"
  }
  resolution = 2.99
  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 15 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: 6.31, per 1000 atoms: 0.95
  Number of scatterers: 6642
  At special positions: 0
  Unit cell: (99.704, 139.256, 39.552, 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: 1.51
  Conformation dependent library (CDL) restraints added in 923.9 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 16 sheets defined
      0.0% alpha, 46.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 309 through 310
      removed outlier: 6.520A  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: 6.750A  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
    Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 342
      removed outlier: 6.621A  pdb=" N   GLU A 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   SER D 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LYS A 340 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.629A  pdb=" N   ASP A 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.657A  pdb=" N   GLN A 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   ILE D 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LYS A 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 357 through 361
      removed outlier: 6.162A  pdb=" N   ASP A 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   THR D 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE A 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 377
      removed outlier: 6.612A  pdb=" N   LYS A 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   GLU D 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ILE A 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   HIS D 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   THR A 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   LEU D 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   LYS A 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 309 through 310
      removed outlier: 6.463A  pdb=" N   VAL B 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.770A  pdb=" N   VAL B 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 325
      removed outlier: 6.335A  pdb=" N   LYS B 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   SER E 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   THR B 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.274A  pdb=" N   CYS E 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   LYS B 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   SER E 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   GLY B 323 " --> pdb=" O   SER E 324 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342
    Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346
      removed outlier: 6.683A  pdb=" N   ASP B 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 354
      removed outlier: 6.602A  pdb=" N   GLN B 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ILE E 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LYS B 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 361
      removed outlier: 6.192A  pdb=" N   ASP B 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   THR E 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ILE B 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 377
      removed outlier: 6.656A  pdb=" N   LYS B 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   GLU E 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ILE B 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   HIS E 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   THR B 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   LEU E 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.439A  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: 1.84

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        0.90 -     1.33: 4134
        1.33 -     1.76: 2546
        1.76 -     2.18: 10
        2.18 -     2.61: 0
        2.61 -     3.04: 6
  Bond restraints: 6696
  Sorted by residual:
  bond pdb=" N   LYS A 343 "
       pdb=" H  BLYS A 343 "
    ideal  model  delta    sigma   weight residual
    0.860  3.040 -2.180 2.00e-02 2.50e+03 1.19e+04
  bond pdb=" N   LYS B 343 "
       pdb=" H  BLYS B 343 "
    ideal  model  delta    sigma   weight residual
    0.860  3.013 -2.153 2.00e-02 2.50e+03 1.16e+04
  bond pdb=" N   LYS E 343 "
       pdb=" H  BLYS E 343 "
    ideal  model  delta    sigma   weight residual
    0.860  2.872 -2.012 2.00e-02 2.50e+03 1.01e+04
  bond pdb=" N   LYS D 343 "
       pdb=" H  BLYS D 343 "
    ideal  model  delta    sigma   weight residual
    0.860  2.852 -1.992 2.00e-02 2.50e+03 9.92e+03
  bond pdb=" N   LYS F 343 "
       pdb=" H  BLYS F 343 "
    ideal  model  delta    sigma   weight residual
    0.860  2.840 -1.980 2.00e-02 2.50e+03 9.80e+03
  ... (remaining 6691 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    22.33: 12204
       22.33 -    44.65: 0
       44.65 -    66.98: 6
       66.98 -    89.31: 2
       89.31 -   111.64: 10
  Bond angle restraints: 12222
  Sorted by residual:
  angle pdb=" C   LYS E 340 "
        pdb=" N   SER E 341 "
        pdb=" H  BSER E 341 "
      ideal   model   delta    sigma   weight residual
     123.78   12.14  111.64 3.00e+00 1.11e-01 1.38e+03
  angle pdb=" C   LYS B 340 "
        pdb=" N   SER B 341 "
        pdb=" H  BSER B 341 "
      ideal   model   delta    sigma   weight residual
     123.78   12.97  110.81 3.00e+00 1.11e-01 1.36e+03
  angle pdb=" C   LYS D 340 "
        pdb=" N   SER D 341 "
        pdb=" H  BSER D 341 "
      ideal   model   delta    sigma   weight residual
     123.78   14.67  109.11 3.00e+00 1.11e-01 1.32e+03
  angle pdb=" C   LYS F 340 "
        pdb=" N   SER F 341 "
        pdb=" H  BSER F 341 "
      ideal   model   delta    sigma   weight residual
     123.78   15.25  108.53 3.00e+00 1.11e-01 1.31e+03
  angle pdb=" C   LYS A 340 "
        pdb=" N   SER A 341 "
        pdb=" H  BSER A 341 "
      ideal   model   delta    sigma   weight residual
     123.65   15.28  108.37 3.00e+00 1.11e-01 1.30e+03
  ... (remaining 12217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.98: 2728
       14.98 -    29.96: 164
       29.96 -    44.93: 92
       44.93 -    59.91: 56
       59.91 -    74.89: 56
  Dihedral angle restraints: 3096
    sinusoidal: 1770
      harmonic: 1326
  Sorted by residual:
  dihedral pdb=" CA  GLY A 355 "
           pdb=" C   GLY A 355 "
           pdb=" N   SER A 356 "
           pdb=" CA  SER A 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.60   24.40     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  VAL A 318 "
           pdb=" C   VAL A 318 "
           pdb=" N   THR A 319 "
           pdb=" CA  THR A 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.85  -22.15     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  VAL A 350 "
           pdb=" C   VAL A 350 "
           pdb=" N   GLN A 351 "
           pdb=" CA  GLN A 351 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 3093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 283
       0.072 -    0.144: 157
       0.144 -    0.216: 37
       0.216 -    0.287: 13
       0.287 -    0.359: 8
  Chirality restraints: 498
  Sorted by residual:
  chirality pdb=" CA  HIS C 329 "
            pdb=" N   HIS C 329 "
            pdb=" C   HIS C 329 "
            pdb=" CB  HIS C 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" CA  HIS D 329 "
            pdb=" N   HIS D 329 "
            pdb=" C   HIS D 329 "
            pdb=" CB  HIS D 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" CA  HIS F 329 "
            pdb=" N   HIS F 329 "
            pdb=" C   HIS F 329 "
            pdb=" CB  HIS F 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 495 not shown)

  Planarity restraints: 978
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 338 "    0.198 2.00e-02 2.50e+03   2.62e-01 6.87e+02
        pdb=" N   VAL A 339 "   -0.443 2.00e-02 2.50e+03
        pdb=" CA  VAL A 339 "    0.189 2.00e-02 2.50e+03
        pdb=" H  BVAL A 339 "    0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU F 338 "    0.199 2.00e-02 2.50e+03   2.61e-01 6.83e+02
        pdb=" N   VAL F 339 "   -0.442 2.00e-02 2.50e+03
        pdb=" CA  VAL F 339 "    0.189 2.00e-02 2.50e+03
        pdb=" H  BVAL F 339 "    0.053 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 338 "    0.199 2.00e-02 2.50e+03   2.61e-01 6.80e+02
        pdb=" N   VAL C 339 "   -0.441 2.00e-02 2.50e+03
        pdb=" CA  VAL C 339 "    0.188 2.00e-02 2.50e+03
        pdb=" H  BVAL C 339 "    0.053 2.00e-02 2.50e+03
  ... (remaining 975 not shown)

  Histogram of nonbonded interaction distances:
        0.53 -     1.34: 8
        1.34 -     2.16: 448
        2.16 -     2.97: 16746
        2.97 -     3.79: 26158
        3.79 -     4.60: 42109
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 85469
  Sorted by model distance:
  nonbonded pdb=" O   LYS C 340 "
            pdb=" H  BSER C 341 "
     model   vdw
     0.527 1.960
  nonbonded pdb=" O   LYS A 340 "
            pdb=" H  BSER A 341 "
     model   vdw
     0.551 1.960
  nonbonded pdb=" O   LYS F 340 "
            pdb=" H  BSER F 341 "
     model   vdw
     0.589 1.960
  nonbonded pdb=" O   LYS B 340 "
            pdb=" H  BSER B 341 "
     model   vdw
     0.604 1.960
  nonbonded pdb=" O   LYS D 340 "
            pdb=" H  BSER D 341 "
     model   vdw
     0.748 1.960
  ... (remaining 85464 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:             2.810
  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:             0.180
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.790
  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:10.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
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= 0.749
  Angle     :  2.017   9.222   4416  Z= 1.331
  Chirality :  0.099   0.359    498
  Planarity :  0.012   0.107    558
  Dihedral  : 12.244  74.889   1260
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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: -2.45 (0.32), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.24), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.017   0.005   HIS B 374 
 PHE   0.044   0.015   PHE B 346 
 TYR   0.192   0.059   TYR B 310 
 ARG   0.003   0.001   ARG C 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
  91 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.8224 (m-30) cc_final: 0.7960 (t0)
REVERT: D  345 ASP cc_start: 0.8509 (m-30) cc_final: 0.8220 (t0)
REVERT: D  349 ARG cc_start: 0.8006 (mtp180) cc_final: 0.6879 (ppt90)
REVERT: C  370 LYS cc_start: 0.6995 (tttt) cc_final: 0.6400 (mttt)
REVERT: B  345 ASP cc_start: 0.8449 (m-30) cc_final: 0.8052 (OUTLIER)
REVERT: E  349 ARG cc_start: 0.8049 (mtp180) cc_final: 0.6872 (pmt-80)
REVERT: F  345 ASP cc_start: 0.8292 (m-30) cc_final: 0.7904 (t0)
REVERT: F  370 LYS cc_start: 0.7061 (tttt) cc_final: 0.6629 (mttt)
  outliers start: 0
  outliers final: 1
  residues processed: 91
  average time/residue: 3.0851
  time to fit residues: 287.0490
Evaluate side-chains
  64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
E 336 GLN
F 368 ASN
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.152306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.138538 restraints weight = 21546.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.4291 rms_B_bonded: 2.78
r_work: 0.4188 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.4090 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4091 r_free = 0.4091    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4091 r_free = 0.4091    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3300  Z= 0.280
  Angle     :  0.882  12.286   4416  Z= 0.484
  Chirality :  0.050   0.130    498
  Planarity :  0.003   0.021    558
  Dihedral  :  6.183  18.106    432
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 15.32 %
    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: -2.03 (0.33), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.25), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS F 374 
 PHE   0.013   0.002   PHE F 346 
 TYR   0.016   0.004   TYR A 310 
 ARG   0.002   0.001   ARG D 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
  67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.7815 (mttm) cc_final: 0.7591 (mttm)
REVERT: A  345 ASP cc_start: 0.7657 (m-30) cc_final: 0.7369 (t0)
REVERT: A  347 LYS cc_start: 0.8628 (mttp) cc_final: 0.8137 (mtpm)
REVERT: A  353 LYS cc_start: 0.8373 (tttt) cc_final: 0.8092 (tttp)
REVERT: C  370 LYS cc_start: 0.8035 (tttt) cc_final: 0.6740 (mttt)
REVERT: B  345 ASP cc_start: 0.7761 (m-30) cc_final: 0.7488 (OUTLIER)
REVERT: E  342 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7836 (tt0)
REVERT: E  353 LYS cc_start: 0.8946 (tttt) cc_final: 0.8741 (tttp)
REVERT: F  370 LYS cc_start: 0.8241 (tttt) cc_final: 0.6826 (mttt)
  outliers start: 3
  outliers final: 3
  residues processed: 64
  average time/residue: 2.7027
  time to fit residues: 177.6078
Evaluate side-chains
  62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
D 327 ASN
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 327 ASN
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.153490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.139558 restraints weight = 22475.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.4290 rms_B_bonded: 2.83
r_work: 0.4194 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.4101 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4105 r_free = 0.4105    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4105 r_free = 0.4105    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3300  Z= 0.221
  Angle     :  0.801  11.987   4416  Z= 0.443
  Chirality :  0.049   0.127    498
  Planarity :  0.002   0.015    558
  Dihedral  :  5.899  16.579    432
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.59 %
    Favored  : 82.80 %
  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: -1.79 (0.35), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.26), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 374 
 PHE   0.011   0.001   PHE F 346 
 TYR   0.012   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 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
  66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.7867 (mttm) cc_final: 0.7583 (mttm)
REVERT: A  353 LYS cc_start: 0.8452 (tttt) cc_final: 0.8150 (tttp)
REVERT: C  349 ARG cc_start: 0.7672 (mtp180) cc_final: 0.5941 (mmp-170)
REVERT: C  370 LYS cc_start: 0.8044 (tttt) cc_final: 0.6754 (mttt)
REVERT: E  342 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7828 (tt0)
REVERT: E  348 ASP cc_start: 0.8315 (t0) cc_final: 0.8115 (t70)
REVERT: E  349 ARG cc_start: 0.7985 (mtp180) cc_final: 0.6705 (pmt-80)
REVERT: F  370 LYS cc_start: 0.8069 (tttt) cc_final: 0.6814 (mttt)
  outliers start: 6
  outliers final: 0
  residues processed: 61
  average time/residue: 3.2371
  time to fit residues: 202.0082
Evaluate side-chains
  57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.157043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.143782 restraints weight = 18997.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.4349 rms_B_bonded: 2.60
r_work: 0.4247 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.4143 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4158 r_free = 0.4158    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4158 r_free = 0.4158    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.4158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3300  Z= 0.253
  Angle     :  0.767  11.991   4416  Z= 0.435
  Chirality :  0.049   0.123    498
  Planarity :  0.002   0.013    558
  Dihedral  :  5.663  15.839    432
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.47 %
    Favored  : 81.45 %
  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: -1.65 (0.36), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 329 
 PHE   0.008   0.001   PHE F 346 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 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
  61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8502 (tttt) cc_final: 0.8226 (tttp)
REVERT: C  349 ARG cc_start: 0.7710 (mtp180) cc_final: 0.6022 (mmp-170)
REVERT: C  370 LYS cc_start: 0.8080 (tttt) cc_final: 0.6799 (mttt)
REVERT: E  317 LYS cc_start: 0.8602 (mttm) cc_final: 0.8133 (mttm)
REVERT: E  349 ARG cc_start: 0.7951 (mtp180) cc_final: 0.6785 (pmt-80)
REVERT: F  317 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7864 (mttm)
REVERT: F  349 ARG cc_start: 0.7627 (mtp180) cc_final: 0.5803 (mmp-170)
REVERT: F  370 LYS cc_start: 0.8093 (tttt) cc_final: 0.6849 (mttt)
  outliers start: 4
  outliers final: 2
  residues processed: 59
  average time/residue: 3.2390
  time to fit residues: 195.5415
Evaluate side-chains
  59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain F residue  317 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.161297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.147026 restraints weight = 25324.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.4322 rms_B_bonded: 3.09
r_work: 0.4235 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4231 r_free = 0.4231    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4231 r_free = 0.4231    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.4245

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= 0.190
  Angle     :  0.739  12.040   4416  Z= 0.423
  Chirality :  0.049   0.125    498
  Planarity :  0.002   0.015    558
  Dihedral  :  5.383  14.790    432
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 18.82 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.37), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.18 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 374 
 PHE   0.006   0.001   PHE F 346 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.001   0.000   ARG D 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
  60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  348 ASP cc_start: 0.8198 (t0) cc_final: 0.7723 (t70)
REVERT: C  349 ARG cc_start: 0.7663 (mtp180) cc_final: 0.5951 (mmp-170)
REVERT: C  370 LYS cc_start: 0.7919 (tttt) cc_final: 0.6592 (mttt)
REVERT: B  353 LYS cc_start: 0.8700 (tttt) cc_final: 0.8465 (tttp)
REVERT: E  317 LYS cc_start: 0.8519 (mttm) cc_final: 0.8024 (mttm)
REVERT: E  349 ARG cc_start: 0.7836 (mtp180) cc_final: 0.6712 (pmt-80)
REVERT: F  317 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7809 (mttm)
REVERT: F  349 ARG cc_start: 0.7565 (mtp180) cc_final: 0.5764 (mmp-170)
REVERT: F  370 LYS cc_start: 0.7907 (tttt) cc_final: 0.6658 (mttt)
  outliers start: 3
  outliers final: 0
  residues processed: 59
  average time/residue: 3.1655
  time to fit residues: 191.1583
Evaluate side-chains
  57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.0170
   chunk 33 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.9422

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.154498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.141475 restraints weight = 21308.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.4326 rms_B_bonded: 2.71
r_work: 0.4231 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.4139 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.4139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4141 r_free = 0.4141    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4141 r_free = 0.4141    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.4141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.4352

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= 0.148
  Angle     :  0.725  12.060   4416  Z= 0.415
  Chirality :  0.049   0.131    498
  Planarity :  0.002   0.013    558
  Dihedral  :  5.155  14.670    432
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 20.70 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.37), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 374 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.001   0.000   ARG D 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
  57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  348 ASP cc_start: 0.8231 (t0) cc_final: 0.7732 (t70)
REVERT: C  349 ARG cc_start: 0.7702 (mtp180) cc_final: 0.5964 (mmp-170)
REVERT: C  370 LYS cc_start: 0.8079 (tttt) cc_final: 0.6773 (mttt)
REVERT: B  353 LYS cc_start: 0.8759 (tttt) cc_final: 0.8483 (tttp)
REVERT: E  317 LYS cc_start: 0.8546 (mttm) cc_final: 0.8049 (mttm)
REVERT: E  349 ARG cc_start: 0.7911 (mtp180) cc_final: 0.6723 (pmt-80)
REVERT: F  317 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7858 (mttm)
REVERT: F  349 ARG cc_start: 0.7606 (mtp180) cc_final: 0.5757 (mmp-170)
REVERT: F  370 LYS cc_start: 0.8022 (tttt) cc_final: 0.6822 (mttt)
  outliers start: 1
  outliers final: 2
  residues processed: 57
  average time/residue: 3.1927
  time to fit residues: 186.2692
Evaluate side-chains
  53 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain F residue  321 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.159678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.146588 restraints weight = 20476.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.4224 rms_B_bonded: 2.71
r_work: 0.4121 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.4021 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4030 r_free = 0.4030    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4030 r_free = 0.4030    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.4497

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= 0.187
  Angle     :  0.711  12.044   4416  Z= 0.413
  Chirality :  0.048   0.126    498
  Planarity :  0.002   0.012    558
  Dihedral  :  5.142  14.785    432
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 20.43 %
    Favored  : 78.76 %
  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: -1.51 (0.37), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.14 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 374 
 PHE   0.012   0.001   PHE A 346 
 TYR   0.009   0.002   TYR A 310 
 ARG   0.000   0.000   ARG E 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
  56 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  348 ASP cc_start: 0.8222 (t0) cc_final: 0.7732 (t70)
REVERT: C  349 ARG cc_start: 0.7770 (mtp180) cc_final: 0.6070 (mmp-170)
REVERT: C  370 LYS cc_start: 0.8053 (tttt) cc_final: 0.6792 (mttt)
REVERT: B  353 LYS cc_start: 0.8769 (tttt) cc_final: 0.8512 (tttp)
REVERT: E  317 LYS cc_start: 0.8583 (mttm) cc_final: 0.8127 (mttp)
REVERT: E  349 ARG cc_start: 0.7959 (mtp180) cc_final: 0.6784 (pmt-80)
REVERT: F  317 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7947 (mttm)
REVERT: F  349 ARG cc_start: 0.7703 (mtp180) cc_final: 0.5894 (mmp-170)
REVERT: F  370 LYS cc_start: 0.8023 (tttt) cc_final: 0.6820 (mttt)
  outliers start: 3
  outliers final: 3
  residues processed: 55
  average time/residue: 3.0333
  time to fit residues: 170.9527
Evaluate side-chains
  55 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain F residue  321 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 10 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 327 ASN
** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.157432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.144633 restraints weight = 22544.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.4358 rms_B_bonded: 2.69
r_work: 0.4272 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.4181 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4189 r_free = 0.4189    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4189 r_free = 0.4189    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3300  Z= 0.142
  Angle     :  0.699  12.082   4416  Z= 0.407
  Chirality :  0.049   0.129    498
  Planarity :  0.002   0.010    558
  Dihedral  :  4.927  14.000    432
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 20.43 %
    Favored  : 78.49 %
  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: -1.52 (0.37), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.15 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 374 
 PHE   0.004   0.001   PHE A 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.000   0.000   ARG D 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
  59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  348 ASP cc_start: 0.8219 (t0) cc_final: 0.7721 (t70)
REVERT: C  349 ARG cc_start: 0.7713 (mtp180) cc_final: 0.5949 (mmp-170)
REVERT: C  370 LYS cc_start: 0.8071 (tttt) cc_final: 0.6780 (mttt)
REVERT: B  353 LYS cc_start: 0.8793 (tttt) cc_final: 0.8547 (tttp)
REVERT: E  317 LYS cc_start: 0.8562 (mttm) cc_final: 0.8101 (mttp)
REVERT: E  349 ARG cc_start: 0.7918 (mtp180) cc_final: 0.6700 (pmt-80)
REVERT: F  317 LYS cc_start: 0.8297 (mtpp) cc_final: 0.7869 (mttm)
REVERT: F  349 ARG cc_start: 0.7591 (mtp180) cc_final: 0.5774 (mmp-170)
REVERT: F  370 LYS cc_start: 0.8035 (tttt) cc_final: 0.6785 (mttt)
  outliers start: 4
  outliers final: 2
  residues processed: 56
  average time/residue: 2.9515
  time to fit residues: 169.4474
Evaluate side-chains
  54 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain F residue  321 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.191537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.162633 restraints weight = 24516.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.4309 rms_B_bonded: 2.48
r_work: 0.4232 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.4144 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3995
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3995 r_free = 0.3995    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3995 r_free = 0.3995    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3995
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3300  Z= 0.266
  Angle     :  0.732  12.129   4416  Z= 0.425
  Chirality :  0.048   0.120    498
  Planarity :  0.002   0.013    558
  Dihedral  :  5.323  15.011    432
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 20.70 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.06 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 374 
 PHE   0.009   0.002   PHE F 346 
 TYR   0.012   0.002   TYR A 310 
 ARG   0.002   0.000   ARG E 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
  58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASN cc_start: 0.8102 (m110) cc_final: 0.7830 (m-40)
REVERT: D  348 ASP cc_start: 0.8319 (t0) cc_final: 0.7759 (t70)
REVERT: C  349 ARG cc_start: 0.7692 (mtp180) cc_final: 0.5934 (mmp-170)
REVERT: C  370 LYS cc_start: 0.8063 (tttt) cc_final: 0.6765 (mttt)
REVERT: B  353 LYS cc_start: 0.8763 (tttt) cc_final: 0.8495 (tttp)
REVERT: E  349 ARG cc_start: 0.7939 (mtp180) cc_final: 0.6711 (pmt-80)
REVERT: F  317 LYS cc_start: 0.8371 (mtpp) cc_final: 0.7915 (mttm)
REVERT: F  370 LYS cc_start: 0.8145 (tttt) cc_final: 0.6843 (mttt)
  outliers start: 2
  outliers final: 3
  residues processed: 57
  average time/residue: 2.9457
  time to fit residues: 172.2158
Evaluate side-chains
  59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain F residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0370
   chunk 20 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.194991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.167060 restraints weight = 19744.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.4375 rms_B_bonded: 2.12
r_work: 0.4311 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.4231 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4087 r_free = 0.4087    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4087 r_free = 0.4087    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3300  Z= 0.142
  Angle     :  0.712  12.136   4416  Z= 0.414
  Chirality :  0.049   0.123    498
  Planarity :  0.002   0.012    558
  Dihedral  :  5.069  14.420    432
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 20.97 %
    Favored  : 78.49 %
  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: -1.43 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.08 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 330 
 PHE   0.018   0.001   PHE A 346 
 TYR   0.008   0.002   TYR F 310 
 ARG   0.001   0.000   ARG D 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
  54 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  368 ASN cc_start: 0.8219 (m110) cc_final: 0.7977 (m-40)
REVERT: C  349 ARG cc_start: 0.7693 (mtp180) cc_final: 0.6079 (mmm160)
REVERT: C  370 LYS cc_start: 0.8016 (tttt) cc_final: 0.6738 (pttt)
REVERT: B  353 LYS cc_start: 0.8769 (tttt) cc_final: 0.8530 (tttp)
REVERT: E  349 ARG cc_start: 0.7887 (mtp180) cc_final: 0.6770 (pmt-80)
REVERT: F  317 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7975 (mttm)
REVERT: F  349 ARG cc_start: 0.7617 (mtp180) cc_final: 0.5896 (mmp-170)
REVERT: F  370 LYS cc_start: 0.8013 (tttt) cc_final: 0.6785 (mttt)
  outliers start: 2
  outliers final: 2
  residues processed: 53
  average time/residue: 3.0455
  time to fit residues: 165.5143
Evaluate side-chains
  52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain F residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 21 optimal weight:    0.4980
   chunk 29 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0000
   overall best weight:    1.4990

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.194886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.166313 restraints weight = 22648.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.4367 rms_B_bonded: 2.31
r_work: 0.4297 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.4213 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4069 r_free = 0.4069    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4069 r_free = 0.4069    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4918

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= 0.176
  Angle     :  0.703  12.119   4416  Z= 0.411
  Chirality :  0.048   0.121    498
  Planarity :  0.002   0.013    558
  Dihedral  :  4.968  14.436    432
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 20.97 %
    Favored  : 78.23 %
  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: -1.44 (0.38), residues: 414
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.09 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 330 
 PHE   0.008   0.001   PHE A 346 
 TYR   0.010   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6153.17 seconds
wall clock time: 108 minutes 40.10 seconds (6520.10 seconds total)