Starting phenix.real_space_refine
on Fri Dec 27 08:02:58 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qku_14053/12_2024/7qku_14053.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qku_14053/12_2024/7qku_14053.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qku_14053/12_2024/7qku_14053.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qku_14053/12_2024/7qku_14053.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qku_14053/12_2024/7qku_14053.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qku_14053/12_2024/7qku_14053.cif"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2166      2.51       5
     N     639      2.21       5
     O     645      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 4.06, per 1000 atoms: 1.17
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (117.008, 120.304, 35.432, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     645      8.00
     N     639      7.00
     C    2166      6.00
    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: 1.05
  Conformation dependent library (CDL) restraints added in 498.8 milliseconds
  

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 50.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.709A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322
      removed outlier: 6.310A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.465A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330
      removed outlier: 5.817A  pdb=" N   GLY A 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.579A  pdb=" N   HIS D 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   GLY D 326 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ASN B 327 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.547A  pdb=" N   GLN B 336 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   VAL D 339 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   GLU B 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346
      removed outlier: 6.550A  pdb=" N   LEU A 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354
      removed outlier: 6.522A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   ILE D 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 362
      removed outlier: 6.281A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   THR D 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ILE B 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 378
      removed outlier: 6.433A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 307 through 310
      removed outlier: 6.606A  pdb=" N   GLN C 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   TYR E 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL C 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: 6.872A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 323
      removed outlier: 6.317A  pdb=" N   LYS C 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   SER E 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   THR C 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   CYS E 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS C 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 333 through 334
    Processing sheet with id=AB5, first strand: chain 'E' and resid 337 through 342
      removed outlier: 6.557A  pdb=" N   GLU C 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   SER E 341 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LYS C 340 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346
      removed outlier: 6.402A  pdb=" N   ASP C 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 350 through 362
      removed outlier: 9.068A  pdb=" N   VAL C 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 10.217A  pdb=" N   LYS E 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
      removed outlier: 8.940A  pdb=" N   SER C 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 10.373A  pdb=" N   GLY E 355 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   ILE C 354 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 10.078A  pdb=" N   LEU E 357 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   SER C 356 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   ASN E 359 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ASP C 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   THR E 361 " --> pdb=" O   ASP C 358 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE C 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLN C 351 " --> pdb=" O   VAL F 350 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   SER F 352 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LYS C 353 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE F 354 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLY C 355 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   SER F 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 368 through 377
      removed outlier: 6.299A  pdb=" N   LYS C 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   GLU E 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ILE C 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   HIS E 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   THR C 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   LEU E 376 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LYS C 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)

    73 hydrogen bonds defined for protein.
    219 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: 0.85

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1028
        1.33 -     1.45: 388
        1.45 -     1.57: 2088
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 3510
  Sorted by residual:
  bond pdb=" CZ  ARG E 349 "
       pdb=" NH2 ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.35e+00
  bond pdb=" CZ  ARG C 349 "
       pdb=" NH2 ARG C 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.98e+00
  bond pdb=" CZ  ARG B 379 "
       pdb=" NH2 ARG B 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.87e+00
  bond pdb=" CZ  ARG D 379 "
       pdb=" NH2 ARG D 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.64e+00
  bond pdb=" CZ  ARG A 379 "
       pdb=" NH2 ARG A 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.41e+00
  ... (remaining 3505 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 3002
        1.57 -     3.15: 1297
        3.15 -     4.72: 314
        4.72 -     6.30: 79
        6.30 -     7.87: 3
  Bond angle restraints: 4695
  Sorted by residual:
  angle pdb=" CA  GLY F 355 "
        pdb=" C   GLY F 355 "
        pdb=" N   SER F 356 "
      ideal   model   delta    sigma   weight residual
     114.58  119.13   -4.55 8.60e-01 1.35e+00 2.80e+01
  angle pdb=" CA  ASP D 348 "
        pdb=" CB  ASP D 348 "
        pdb=" CG  ASP D 348 "
      ideal   model   delta    sigma   weight residual
     112.60  117.65   -5.05 1.00e+00 1.00e+00 2.55e+01
  angle pdb=" CA  PHE D 346 "
        pdb=" CB  PHE D 346 "
        pdb=" CG  PHE D 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.62   -4.82 1.00e+00 1.00e+00 2.32e+01
  angle pdb=" CA  PHE A 346 "
        pdb=" CB  PHE A 346 "
        pdb=" CG  PHE A 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.54   -4.74 1.00e+00 1.00e+00 2.25e+01
  angle pdb=" CA  PHE B 346 "
        pdb=" CB  PHE B 346 "
        pdb=" CG  PHE B 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.54   -4.74 1.00e+00 1.00e+00 2.25e+01
  ... (remaining 4690 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.46: 1864
       12.46 -    24.93: 214
       24.93 -    37.39: 40
       37.39 -    49.86: 15
       49.86 -    62.32: 6
  Dihedral angle restraints: 2139
    sinusoidal: 894
      harmonic: 1245
  Sorted by residual:
  dihedral pdb=" C   LEU E 325 "
           pdb=" N   LEU E 325 "
           pdb=" CA  LEU E 325 "
           pdb=" CB  LEU E 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.42   15.82     0      2.50e+00 1.60e-01 4.00e+01
  dihedral pdb=" C   ARG D 349 "
           pdb=" N   ARG D 349 "
           pdb=" CA  ARG D 349 "
           pdb=" CB  ARG D 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.80   15.20     0      2.50e+00 1.60e-01 3.70e+01
  dihedral pdb=" C   ARG A 349 "
           pdb=" N   ARG A 349 "
           pdb=" CA  ARG A 349 "
           pdb=" CB  ARG A 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.80   15.20     0      2.50e+00 1.60e-01 3.70e+01
  ... (remaining 2136 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.121: 436
       0.121 -    0.240: 77
       0.240 -    0.359: 10
       0.359 -    0.479: 1
       0.479 -    0.598: 4
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  LEU E 325 "
            pdb=" N   LEU E 325 "
            pdb=" C   LEU E 325 "
            pdb=" CB  LEU E 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.94e+00
  chirality pdb=" CA  ARG A 349 "
            pdb=" N   ARG A 349 "
            pdb=" C   ARG A 349 "
            pdb=" CB  ARG A 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.91e+00
  chirality pdb=" CA  ARG D 349 "
            pdb=" N   ARG D 349 "
            pdb=" C   ARG D 349 "
            pdb=" CB  ARG D 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.33e+00
  ... (remaining 525 not shown)

  Planarity restraints: 597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "   -0.046 2.00e-02 2.50e+03   2.70e-02 1.46e+01
        pdb=" CG  TYR F 310 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 330 "    0.032 2.00e-02 2.50e+03   2.60e-02 1.02e+01
        pdb=" CG  HIS D 330 "   -0.020 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 330 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 330 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 330 "    0.027 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 330 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 346 "   -0.038 2.00e-02 2.50e+03   2.37e-02 9.87e+00
        pdb=" CG  PHE E 346 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 346 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 346 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 346 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 346 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 346 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 594 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 1607
        2.99 -     3.47: 2760
        3.47 -     3.95: 5501
        3.95 -     4.42: 5742
        4.42 -     4.90: 10651
  Nonbonded interactions: 26261
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.516 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.539 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.600 3.040
  nonbonded pdb=" OD2 ASP D 314 "
            pdb=" NZ  LYS D 370 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   SER C 316 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.632 3.040
  ... (remaining 26256 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 305 through 379)
  selection = (chain 'B' and resid 305 through 379)
  selection = chain 'C'
  selection = (chain 'D' and resid 305 through 379)
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.000
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     14.690
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.035   3510  Z= 0.728
  Angle     :  1.831   7.874   4695  Z= 1.211
  Chirality :  0.105   0.598    528
  Planarity :  0.009   0.030    597
  Dihedral  : 11.695  62.321   1347
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Cbeta Deviations :  1.26 %
  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 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.004   HIS D 330 
 PHE   0.038   0.012   PHE E 346 
 TYR   0.046   0.014   TYR F 310 
 ARG   0.002   0.000   ARG B 349 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLN cc_start: 0.8094 (tt0) cc_final: 0.7628 (tt0)
REVERT: A  345 ASP cc_start: 0.8280 (t0) cc_final: 0.8063 (t0)
REVERT: B  311 LYS cc_start: 0.8643 (ptmt) cc_final: 0.7412 (mmtm)
REVERT: B  351 GLN cc_start: 0.7814 (tt0) cc_final: 0.7591 (tt0)
REVERT: B  375 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7823 (ttmm)
REVERT: B  379 ARG cc_start: 0.7911 (ttm170) cc_final: 0.6900 (mmt-90)
REVERT: C  342 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7636 (mp0)
REVERT: D  311 LYS cc_start: 0.8722 (ptmt) cc_final: 0.8265 (pttm)
REVERT: D  375 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7742 (ttmm)
REVERT: D  379 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7334 (ttm170)
REVERT: F  347 LYS cc_start: 0.9014 (mttt) cc_final: 0.8318 (mmmt)
REVERT: F  349 ARG cc_start: 0.8457 (ttm170) cc_final: 0.7040 (mmp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 1.5723
  time to fit residues: 285.4468
Evaluate side-chains
  118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
A 368 ASN
B 307 GLN
** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
D 336 GLN
E 307 GLN
E 329 HIS
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3510  Z= 0.177
  Angle     :  0.622   6.392   4695  Z= 0.314
  Chirality :  0.051   0.170    528
  Planarity :  0.003   0.024    597
  Dihedral  :  6.050  20.092    465
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.18 %
    Favored  : 79.04 %
  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: -1.81 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.37 (0.24), residues: 441

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

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.8154 (tt0) cc_final: 0.7668 (tt0)
REVERT: A  345 ASP cc_start: 0.8207 (t0) cc_final: 0.7978 (t70)
REVERT: A  348 ASP cc_start: 0.7535 (p0) cc_final: 0.7238 (p0)
REVERT: A  353 LYS cc_start: 0.8718 (mttt) cc_final: 0.8490 (mttm)
REVERT: A  373 THR cc_start: 0.8799 (m) cc_final: 0.8462 (p)
REVERT: A  375 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8362 (ttmm)
REVERT: B  311 LYS cc_start: 0.8775 (ptmt) cc_final: 0.7493 (mmpt)
REVERT: B  319 THR cc_start: 0.8660 (m) cc_final: 0.8384 (p)
REVERT: B  349 ARG cc_start: 0.7170 (ptt180) cc_final: 0.6948 (mtm180)
REVERT: B  373 THR cc_start: 0.8972 (m) cc_final: 0.8594 (p)
REVERT: B  379 ARG cc_start: 0.7921 (ttm170) cc_final: 0.6660 (mmt-90)
REVERT: C  342 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7686 (mp0)
REVERT: D  311 LYS cc_start: 0.8709 (ptmt) cc_final: 0.8301 (pttm)
REVERT: D  359 ASN cc_start: 0.9054 (m-40) cc_final: 0.8777 (m110)
REVERT: D  375 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7738 (ttmm)
REVERT: D  379 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7341 (mtt180)
REVERT: F  338 GLU cc_start: 0.8543 (tt0) cc_final: 0.8092 (tt0)
REVERT: F  349 ARG cc_start: 0.8391 (ttm170) cc_final: 0.7183 (mmp-170)
  outliers start: 11
  outliers final: 1
  residues processed: 134
  average time/residue: 1.4056
  time to fit residues: 192.6788
Evaluate side-chains
  123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0570
   chunk 28 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    5.6106

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN
B 307 GLN
C 307 GLN
C 359 ASN
D 307 GLN
D 351 GLN
E 307 GLN
E 359 ASN
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049   3510  Z= 0.538
  Angle     :  0.745   9.263   4695  Z= 0.372
  Chirality :  0.054   0.180    528
  Planarity :  0.003   0.020    597
  Dihedral  :  6.453  23.137    465
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.18 %
    Favored  : 78.28 %
  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: -2.13 (0.31), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS E 362 
 PHE   0.010   0.003   PHE F 346 
 TYR   0.015   0.003   TYR B 310 
 ARG   0.005   0.001   ARG E 379 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  345 ASP cc_start: 0.8164 (t0) cc_final: 0.7926 (t70)
REVERT: A  348 ASP cc_start: 0.7867 (p0) cc_final: 0.7651 (p0)
REVERT: A  351 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7744 (tt0)
REVERT: A  353 LYS cc_start: 0.8761 (mttt) cc_final: 0.8550 (mttp)
REVERT: A  373 THR cc_start: 0.9040 (m) cc_final: 0.8686 (p)
REVERT: A  379 ARG cc_start: 0.8045 (ttm170) cc_final: 0.7547 (mtt180)
REVERT: B  311 LYS cc_start: 0.8740 (ptmt) cc_final: 0.7617 (mmtt)
REVERT: B  373 THR cc_start: 0.8956 (m) cc_final: 0.8535 (p)
REVERT: D  311 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8301 (pttt)
REVERT: D  340 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7885 (mtpp)
REVERT: D  375 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7878 (ttmm)
REVERT: D  379 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7407 (mtt180)
REVERT: E  340 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8359 (mtpt)
REVERT: F  338 GLU cc_start: 0.8551 (tt0) cc_final: 0.8091 (tt0)
REVERT: F  349 ARG cc_start: 0.8511 (ttm170) cc_final: 0.7276 (mmp-170)
  outliers start: 14
  outliers final: 4
  residues processed: 113
  average time/residue: 1.5277
  time to fit residues: 176.4634
Evaluate side-chains
  108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain E residue  340 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
C 307 GLN
** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
D 351 GLN
E 307 GLN
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3510  Z= 0.307
  Angle     :  0.623   7.748   4695  Z= 0.305
  Chirality :  0.050   0.137    528
  Planarity :  0.002   0.013    597
  Dihedral  :  5.848  19.745    465
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.46 %
    Favored  : 76.26 %
  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: -2.19 (0.31), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.006   0.002   PHE F 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.004   0.001   ARG E 379 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8349 (ptmm) cc_final: 0.8123 (ptmm)
REVERT: A  348 ASP cc_start: 0.7853 (p0) cc_final: 0.7651 (p0)
REVERT: A  351 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7754 (tt0)
REVERT: A  373 THR cc_start: 0.9028 (m) cc_final: 0.8667 (p)
REVERT: A  379 ARG cc_start: 0.8057 (ttm170) cc_final: 0.7587 (mtt180)
REVERT: B  311 LYS cc_start: 0.8780 (ptmt) cc_final: 0.7564 (mmtt)
REVERT: B  324 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8371 (t)
REVERT: B  373 THR cc_start: 0.8956 (m) cc_final: 0.8542 (p)
REVERT: C  338 GLU cc_start: 0.8582 (tt0) cc_final: 0.8205 (tt0)
REVERT: D  311 LYS cc_start: 0.8703 (ptmt) cc_final: 0.8285 (pttm)
REVERT: D  340 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7841 (mtpp)
REVERT: D  375 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7849 (ttmm)
REVERT: D  379 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7429 (mtt180)
REVERT: E  338 GLU cc_start: 0.8654 (tt0) cc_final: 0.8214 (tt0)
REVERT: F  338 GLU cc_start: 0.8576 (tt0) cc_final: 0.8204 (tt0)
REVERT: F  349 ARG cc_start: 0.8479 (ttm170) cc_final: 0.7281 (mmp-170)
  outliers start: 9
  outliers final: 2
  residues processed: 111
  average time/residue: 1.4265
  time to fit residues: 162.1905
Evaluate side-chains
  106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0050
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    2.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
A 359 ASN
B 307 GLN
C 307 GLN
D 307 GLN
D 351 GLN
E 307 GLN
E 359 ASN
F 307 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3510  Z= 0.273
  Angle     :  0.607   7.624   4695  Z= 0.295
  Chirality :  0.050   0.133    528
  Planarity :  0.002   0.025    597
  Dihedral  :  5.608  18.568    465
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.96 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.31), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.005   0.001   PHE F 346 
 TYR   0.011   0.002   TYR B 310 
 ARG   0.004   0.001   ARG F 379 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8329 (ptmm) cc_final: 0.8100 (ptmm)
REVERT: A  373 THR cc_start: 0.9010 (m) cc_final: 0.8652 (p)
REVERT: A  379 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7618 (mtt180)
REVERT: B  311 LYS cc_start: 0.8782 (ptmt) cc_final: 0.7629 (mmtt)
REVERT: B  324 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8377 (t)
REVERT: B  373 THR cc_start: 0.8956 (m) cc_final: 0.8538 (p)
REVERT: C  338 GLU cc_start: 0.8577 (tt0) cc_final: 0.8294 (tt0)
REVERT: D  311 LYS cc_start: 0.8704 (ptmt) cc_final: 0.8291 (pttm)
REVERT: D  340 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7846 (mtpp)
REVERT: D  375 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7852 (ttmm)
REVERT: D  379 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7429 (mtt180)
REVERT: E  338 GLU cc_start: 0.8647 (tt0) cc_final: 0.8387 (tt0)
REVERT: F  338 GLU cc_start: 0.8584 (tt0) cc_final: 0.8215 (tt0)
REVERT: F  349 ARG cc_start: 0.8460 (ttm170) cc_final: 0.7263 (mmp-170)
  outliers start: 15
  outliers final: 5
  residues processed: 114
  average time/residue: 1.4297
  time to fit residues: 166.7141
Evaluate side-chains
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    4.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
D 351 GLN
E 307 GLN
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   3510  Z= 0.431
  Angle     :  0.677   9.524   4695  Z= 0.330
  Chirality :  0.051   0.154    528
  Planarity :  0.003   0.027    597
  Dihedral  :  5.836  20.599    465
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.46 %
    Favored  : 74.49 %
  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: -2.32 (0.31), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E 362 
 PHE   0.007   0.002   PHE F 346 
 TYR   0.013   0.003   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8370 (ptmm) cc_final: 0.8132 (ptmm)
REVERT: A  351 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7935 (tm-30)
REVERT: A  373 THR cc_start: 0.9036 (m) cc_final: 0.8665 (p)
REVERT: A  379 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7663 (mtt180)
REVERT: B  311 LYS cc_start: 0.8763 (ptmt) cc_final: 0.7648 (mmtt)
REVERT: B  373 THR cc_start: 0.8949 (m) cc_final: 0.8518 (p)
REVERT: C  338 GLU cc_start: 0.8545 (tt0) cc_final: 0.8156 (tt0)
REVERT: D  311 LYS cc_start: 0.8697 (ptmt) cc_final: 0.8273 (pttm)
REVERT: D  340 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7905 (mtpp)
REVERT: D  375 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7892 (ttmm)
REVERT: D  379 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7478 (mtt180)
REVERT: E  338 GLU cc_start: 0.8650 (tt0) cc_final: 0.8166 (tt0)
REVERT: F  338 GLU cc_start: 0.8551 (tt0) cc_final: 0.8171 (tt0)
REVERT: F  349 ARG cc_start: 0.8464 (ttm170) cc_final: 0.7279 (mmp-170)
  outliers start: 16
  outliers final: 5
  residues processed: 114
  average time/residue: 1.4359
  time to fit residues: 167.4119
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   overall best weight:    3.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
D 351 GLN
E 307 GLN
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   3510  Z= 0.401
  Angle     :  0.664   9.219   4695  Z= 0.323
  Chirality :  0.050   0.146    528
  Planarity :  0.003   0.026    597
  Dihedral  :  5.734  20.264    465
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 23.99 %
    Favored  : 73.23 %
  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: -2.35 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.006   0.002   PHE F 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8357 (ptmm) cc_final: 0.8114 (ptmm)
REVERT: A  351 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7927 (tm-30)
REVERT: A  373 THR cc_start: 0.9027 (m) cc_final: 0.8658 (p)
REVERT: A  379 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7719 (mtt180)
REVERT: B  311 LYS cc_start: 0.8772 (ptmt) cc_final: 0.7654 (mmtt)
REVERT: B  373 THR cc_start: 0.8950 (m) cc_final: 0.8521 (p)
REVERT: C  338 GLU cc_start: 0.8545 (tt0) cc_final: 0.8159 (tt0)
REVERT: D  311 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8272 (pttm)
REVERT: D  340 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7890 (mtpp)
REVERT: D  375 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7902 (ttmm)
REVERT: D  379 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7553 (mtt180)
REVERT: E  338 GLU cc_start: 0.8657 (tt0) cc_final: 0.8232 (tt0)
REVERT: F  338 GLU cc_start: 0.8551 (tt0) cc_final: 0.8185 (tt0)
REVERT: F  349 ARG cc_start: 0.8430 (ttm170) cc_final: 0.7213 (mmp-170)
  outliers start: 11
  outliers final: 6
  residues processed: 107
  average time/residue: 1.4766
  time to fit residues: 161.4845
Evaluate side-chains
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0570
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 29 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    2.1504

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
D 351 GLN
F 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.3635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3510  Z= 0.247
  Angle     :  0.599   7.556   4695  Z= 0.289
  Chirality :  0.049   0.132    528
  Planarity :  0.002   0.019    597
  Dihedral  :  5.407  17.314    465
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 23.48 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.004   0.001   PHE F 346 
 TYR   0.010   0.002   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8302 (ptmm) cc_final: 0.8054 (ptmm)
REVERT: A  373 THR cc_start: 0.9002 (m) cc_final: 0.8640 (p)
REVERT: A  379 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7740 (mtt180)
REVERT: B  311 LYS cc_start: 0.8772 (ptmt) cc_final: 0.7615 (mmtm)
REVERT: B  373 THR cc_start: 0.8953 (m) cc_final: 0.8544 (p)
REVERT: C  338 GLU cc_start: 0.8561 (tt0) cc_final: 0.8179 (tt0)
REVERT: D  311 LYS cc_start: 0.8669 (ptmt) cc_final: 0.8262 (pttm)
REVERT: D  340 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7831 (mtpp)
REVERT: D  375 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7923 (ttmm)
REVERT: D  379 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7547 (mtt180)
REVERT: E  338 GLU cc_start: 0.8663 (tt0) cc_final: 0.8230 (tt0)
REVERT: F  338 GLU cc_start: 0.8593 (tt0) cc_final: 0.8235 (tt0)
REVERT: F  349 ARG cc_start: 0.8406 (ttm170) cc_final: 0.7221 (mmp-170)
  outliers start: 11
  outliers final: 4
  residues processed: 112
  average time/residue: 1.4173
  time to fit residues: 162.4595
Evaluate side-chains
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 38 optimal weight:    0.3980
   chunk 33 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
A 359 ASN
B 307 GLN
B 351 GLN
C 307 GLN
C 362 HIS
D 307 GLN
D 351 GLN
E 327 ASN
F 307 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3510  Z= 0.183
  Angle     :  0.570   7.874   4695  Z= 0.271
  Chirality :  0.049   0.127    528
  Planarity :  0.002   0.017    597
  Dihedral  :  5.026  15.289    465
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 25.00 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.33), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8245 (ptmm) cc_final: 0.7993 (ptmm)
REVERT: A  373 THR cc_start: 0.8902 (m) cc_final: 0.8535 (p)
REVERT: A  379 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7790 (mtt180)
REVERT: B  305 SER cc_start: 0.8356 (m) cc_final: 0.8112 (t)
REVERT: B  311 LYS cc_start: 0.8747 (ptmt) cc_final: 0.7653 (mmtt)
REVERT: B  319 THR cc_start: 0.8612 (m) cc_final: 0.8356 (p)
REVERT: B  331 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8313 (mttt)
REVERT: B  351 GLN cc_start: 0.7997 (tt0) cc_final: 0.7538 (tm-30)
REVERT: B  353 LYS cc_start: 0.8835 (mttm) cc_final: 0.8620 (mttm)
REVERT: B  373 THR cc_start: 0.8980 (m) cc_final: 0.8601 (p)
REVERT: C  338 GLU cc_start: 0.8550 (tt0) cc_final: 0.8179 (tt0)
REVERT: D  311 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8269 (pttm)
REVERT: D  375 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7874 (ttmm)
REVERT: D  379 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7545 (mtt180)
REVERT: E  338 GLU cc_start: 0.8663 (tt0) cc_final: 0.8240 (tt0)
REVERT: F  338 GLU cc_start: 0.8580 (tt0) cc_final: 0.8215 (tt0)
REVERT: F  349 ARG cc_start: 0.8392 (ttm170) cc_final: 0.7238 (mmp-170)
  outliers start: 9
  outliers final: 2
  residues processed: 121
  average time/residue: 1.4497
  time to fit residues: 179.4046
Evaluate side-chains
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 10 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0070
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.9804

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
A 359 ASN
B 307 GLN
C 307 GLN
D 307 GLN
D 351 GLN
F 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3510  Z= 0.228
  Angle     :  0.600   8.388   4695  Z= 0.283
  Chirality :  0.049   0.133    528
  Planarity :  0.002   0.019    597
  Dihedral  :  5.112  16.934    465
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 26.26 %
    Favored  : 72.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.33), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.010   0.002   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8252 (ptmm) cc_final: 0.8007 (ptmm)
REVERT: A  373 THR cc_start: 0.8910 (m) cc_final: 0.8546 (p)
REVERT: A  379 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7797 (mtt180)
REVERT: B  305 SER cc_start: 0.8349 (m) cc_final: 0.8109 (t)
REVERT: B  311 LYS cc_start: 0.8752 (ptmt) cc_final: 0.7662 (mmtt)
REVERT: B  319 THR cc_start: 0.8705 (m) cc_final: 0.8412 (p)
REVERT: B  331 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8319 (mttt)
REVERT: B  351 GLN cc_start: 0.8008 (tt0) cc_final: 0.7534 (tt0)
REVERT: B  373 THR cc_start: 0.8977 (m) cc_final: 0.8563 (p)
REVERT: C  338 GLU cc_start: 0.8536 (tt0) cc_final: 0.8155 (tt0)
REVERT: D  311 LYS cc_start: 0.8676 (ptmt) cc_final: 0.8264 (pttm)
REVERT: D  375 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7892 (ttmm)
REVERT: D  379 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7581 (mtt180)
REVERT: E  338 GLU cc_start: 0.8662 (tt0) cc_final: 0.8224 (tt0)
REVERT: F  338 GLU cc_start: 0.8580 (tt0) cc_final: 0.8216 (tt0)
REVERT: F  349 ARG cc_start: 0.8387 (ttm170) cc_final: 0.7225 (mmp-170)
  outliers start: 5
  outliers final: 2
  residues processed: 107
  average time/residue: 1.4500
  time to fit residues: 158.7401
Evaluate side-chains
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0470
   chunk 26 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   overall best weight:    2.6082

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
A 359 ASN
B 307 GLN
C 307 GLN
D 307 GLN
D 351 GLN
E 307 GLN
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.108151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.095030 restraints weight = 4382.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.62
r_work: 0.3267 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3510  Z= 0.283
  Angle     :  0.631   8.458   4695  Z= 0.299
  Chirality :  0.049   0.134    528
  Planarity :  0.002   0.017    597
  Dihedral  :  5.285  18.257    465
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 26.26 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.33), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 362 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.011   0.002   TYR B 310 
 ARG   0.005   0.001   ARG F 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2917.40 seconds
wall clock time: 52 minutes 38.13 seconds (3158.13 seconds total)