Starting phenix.real_space_refine
on Tue Feb  3 13:55:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q7f_18215/02_2026/8q7f_18215.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q7f_18215/02_2026/8q7f_18215.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q7f_18215/02_2026/8q7f_18215.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q7f_18215/02_2026/8q7f_18215.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q7f_18215/02_2026/8q7f_18215.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q7f_18215/02_2026/8q7f_18215.map"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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    2136      2.51       5
     N     618      2.21       5
     O     642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3402
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 567
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 567
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 567
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "A"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 567
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 567
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 567
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 0.98, per 1000 atoms: 0.29
  Number of scatterers: 3402
  At special positions: 0
  Unit cell: (106.142, 107.596, 37.804, 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     642      8.00
     N     618      7.00
     C    2136      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: 0.23
  Conformation dependent library (CDL) restraints added in 131.4 milliseconds
  

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 53.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 305 through 310
      removed outlier: 6.581A  pdb=" N   SER B 305 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   ILE D 308 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL B 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: 6.992A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325
      removed outlier: 6.326A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   SER D 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   GLY B 323 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.448A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 342
      removed outlier: 6.652A  pdb=" N   VAL B 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   LYS F 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL B 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   GLU F 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   SER B 341 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.687A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE B 346 " --> pdb=" O   ASP F 345 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.612A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   ILE D 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 357 through 362
      removed outlier: 6.715A  pdb=" N   LEU B 357 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   ILE F 360 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ASN B 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   HIS F 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   THR B 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 368 through 377
      removed outlier: 6.555A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 305 through 310
      removed outlier: 6.581A  pdb=" N   SER A 305 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   ILE C 308 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.991A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 325
      removed outlier: 6.326A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   SER C 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   SER C 324 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   GLY A 323 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.448A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 342
      removed outlier: 6.653A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   GLU E 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   SER A 341 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.823A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354
      removed outlier: 6.381A  pdb=" N   VAL A 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   LYS E 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   SER A 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.732A  pdb=" N   LEU A 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   ILE E 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASN A 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   HIS E 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 377

    88 hydrogen bonds defined for protein.
    264 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: 0.47

  Time building geometry restraints manager: 0.32 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: 708
        1.33 -     1.45: 664
        1.45 -     1.57: 2078
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 3456
  Sorted by residual:
  bond pdb=" CZ  ARG C 349 "
       pdb=" NH2 ARG C 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.30e-02 5.92e+03 1.17e+01
  bond pdb=" CZ  ARG A 349 "
       pdb=" NH2 ARG A 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.72e+00
  bond pdb=" CZ  ARG E 349 "
       pdb=" NH2 ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.51e+00
  bond pdb=" CA  ASP F 345 "
       pdb=" C   ASP F 345 "
    ideal  model  delta    sigma   weight residual
    1.521  1.552 -0.031 1.20e-02 6.94e+03 6.76e+00
  bond pdb=" CZ  ARG B 349 "
       pdb=" NH2 ARG B 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.73e+00
  ... (remaining 3451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 2859
        1.59 -     3.17: 1338
        3.17 -     4.76: 361
        4.76 -     6.35: 62
        6.35 -     7.93: 6
  Bond angle restraints: 4626
  Sorted by residual:
  angle pdb=" CA  PHE F 346 "
        pdb=" CB  PHE F 346 "
        pdb=" CG  PHE F 346 "
      ideal   model   delta    sigma   weight residual
     113.80  121.73   -7.93 1.00e+00 1.00e+00 6.29e+01
  angle pdb=" CA  ASP F 358 "
        pdb=" CB  ASP F 358 "
        pdb=" CG  ASP F 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.20   -5.60 1.00e+00 1.00e+00 3.14e+01
  angle pdb=" CA  PHE E 346 "
        pdb=" CB  PHE E 346 "
        pdb=" CG  PHE E 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.13   -5.33 1.00e+00 1.00e+00 2.84e+01
  angle pdb=" CA  ASP B 358 "
        pdb=" CB  ASP B 358 "
        pdb=" CG  ASP B 358 "
      ideal   model   delta    sigma   weight residual
     112.60  117.89   -5.29 1.00e+00 1.00e+00 2.79e+01
  angle pdb=" CA  ASP C 358 "
        pdb=" CB  ASP C 358 "
        pdb=" CG  ASP C 358 "
      ideal   model   delta    sigma   weight residual
     112.60  117.82   -5.22 1.00e+00 1.00e+00 2.72e+01
  ... (remaining 4621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 1972
       17.23 -    34.47: 82
       34.47 -    51.70: 28
       51.70 -    68.93: 4
       68.93 -    86.17: 8
  Dihedral angle restraints: 2094
    sinusoidal: 864
      harmonic: 1230
  Sorted by residual:
  dihedral pdb=" CA  SER E 356 "
           pdb=" C   SER E 356 "
           pdb=" N   LEU E 357 "
           pdb=" CA  LEU E 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.39   28.61     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  LYS C 347 "
           pdb=" C   LYS C 347 "
           pdb=" N   ASP C 348 "
           pdb=" CA  ASP C 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.73  -28.27     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  LYS D 347 "
           pdb=" C   LYS D 347 "
           pdb=" N   ASP D 348 "
           pdb=" CA  ASP D 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.77  -28.23     0      5.00e+00 4.00e-02 3.19e+01
  ... (remaining 2091 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 362
       0.088 -    0.175: 129
       0.175 -    0.263: 17
       0.263 -    0.350: 11
       0.350 -    0.437: 3
  Chirality restraints: 522
  Sorted by residual:
  chirality pdb=" CA  LYS E 343 "
            pdb=" N   LYS E 343 "
            pdb=" C   LYS E 343 "
            pdb=" CB  LYS E 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.78e+00
  chirality pdb=" CA  LYS F 343 "
            pdb=" N   LYS F 343 "
            pdb=" C   LYS F 343 "
            pdb=" CB  LYS F 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.37e+00
  chirality pdb=" CA  PHE F 346 "
            pdb=" N   PHE F 346 "
            pdb=" C   PHE F 346 "
            pdb=" CB  PHE F 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.31e+00
  ... (remaining 519 not shown)

  Planarity restraints: 588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.129 2.00e-02 2.50e+03   7.14e-02 1.02e+02
        pdb=" CG  TYR A 310 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.061 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.111 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 310 "   -0.117 2.00e-02 2.50e+03   6.38e-02 8.15e+01
        pdb=" CG  TYR B 310 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 310 "    0.052 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 310 "    0.055 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 310 "    0.039 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 310 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 310 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 310 "   -0.097 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "   -0.110 2.00e-02 2.50e+03   6.25e-02 7.81e+01
        pdb=" CG  TYR F 310 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "    0.054 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "    0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "   -0.102 2.00e-02 2.50e+03
  ... (remaining 585 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 1477
        2.97 -     3.46: 2642
        3.46 -     3.94: 5446
        3.94 -     4.42: 5403
        4.42 -     4.90: 10518
  Nonbonded interactions: 25486
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.492 3.040
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.504 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.508 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.508 3.040
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.567 3.040
  ... (remaining 25481 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             3.540
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.410
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
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   0.044   3456  Z= 0.708
  Angle     :  1.876   7.933   4626  Z= 1.252
  Chirality :  0.099   0.437    522
  Planarity :  0.011   0.071    588
  Dihedral  : 12.868  86.167   1314
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.51 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG C 349 
 TYR   0.129   0.046   TYR A 310 
 PHE   0.063   0.013   PHE E 346 
 HIS   0.006   0.002   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01121 ( 3456)
  covalent geometry    : angle       1.87618 ( 4626)
  hydrogen bonds       : bond        0.10371 (   88)
  hydrogen bonds       : angle       7.62140 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.152 
Fit side-chains
REVERT: B  325 LEU cc_start: 0.7851 (mp) cc_final: 0.7613 (mt)
REVERT: B  337 VAL cc_start: 0.8207 (t) cc_final: 0.7962 (p)
REVERT: B  338 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7148 (tm-30)
REVERT: B  340 LYS cc_start: 0.7414 (tttt) cc_final: 0.7091 (mttm)
REVERT: B  345 ASP cc_start: 0.7561 (t0) cc_final: 0.6947 (t70)
REVERT: B  347 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7402 (mmtt)
REVERT: B  375 LYS cc_start: 0.7749 (tttt) cc_final: 0.7047 (tttm)
REVERT: D  311 LYS cc_start: 0.8161 (mttt) cc_final: 0.7846 (mttp)
REVERT: D  331 LYS cc_start: 0.8258 (mttt) cc_final: 0.7683 (mtpt)
REVERT: D  340 LYS cc_start: 0.7824 (tttt) cc_final: 0.7336 (mtpt)
REVERT: D  375 LYS cc_start: 0.8314 (tttt) cc_final: 0.7801 (tttp)
REVERT: F  311 LYS cc_start: 0.7388 (mttt) cc_final: 0.6788 (tppt)
REVERT: F  331 LYS cc_start: 0.8102 (mttt) cc_final: 0.7335 (mtpp)
REVERT: F  338 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6972 (tt0)
REVERT: F  340 LYS cc_start: 0.7463 (tttt) cc_final: 0.6987 (mttm)
REVERT: F  349 ARG cc_start: 0.6727 (mmt90) cc_final: 0.5364 (mmp-170)
REVERT: F  362 HIS cc_start: 0.7671 (t-170) cc_final: 0.7449 (m-70)
REVERT: F  375 LYS cc_start: 0.7625 (tttt) cc_final: 0.7056 (tttm)
REVERT: A  331 LYS cc_start: 0.8133 (mttt) cc_final: 0.7763 (mttp)
REVERT: A  349 ARG cc_start: 0.7415 (mmt90) cc_final: 0.6465 (mmm160)
REVERT: A  351 GLN cc_start: 0.6185 (mp10) cc_final: 0.5765 (mt0)
REVERT: A  369 LYS cc_start: 0.7461 (tttt) cc_final: 0.6668 (ttmm)
REVERT: C  311 LYS cc_start: 0.8106 (mttt) cc_final: 0.7793 (mtpp)
REVERT: C  349 ARG cc_start: 0.7079 (mmt90) cc_final: 0.6402 (mtm180)
REVERT: C  361 THR cc_start: 0.8774 (m) cc_final: 0.8568 (m)
REVERT: C  369 LYS cc_start: 0.7628 (tttt) cc_final: 0.6976 (ttmm)
REVERT: C  375 LYS cc_start: 0.7418 (tttt) cc_final: 0.6951 (tttm)
REVERT: E  311 LYS cc_start: 0.7634 (mttt) cc_final: 0.6977 (mmtt)
REVERT: E  342 GLU cc_start: 0.7776 (pt0) cc_final: 0.6898 (mm-30)
REVERT: E  369 LYS cc_start: 0.7369 (tttt) cc_final: 0.6375 (mtpt)
REVERT: E  375 LYS cc_start: 0.6512 (tttt) cc_final: 0.6206 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0927
  time to fit residues: 15.5694
Evaluate side-chains
  108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0980
   chunk 22 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.6188

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

Flipped N/Q/H residues before XYZ refinement:
B 329 HIS
F 329 HIS
C 327 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.150878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.140180 restraints weight = 4674.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.142640 restraints weight = 2340.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.144166 restraints weight = 1424.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.145202 restraints weight = 994.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.145893 restraints weight = 767.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3456  Z= 0.164
  Angle     :  0.671   5.055   4626  Z= 0.351
  Chirality :  0.053   0.152    522
  Planarity :  0.004   0.028    588
  Dihedral  :  5.985  21.147    456
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  7.18 %
    Favored  : 91.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.89 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 349 
 TYR   0.009   0.003   TYR A 310 
 PHE   0.015   0.002   PHE F 346 
 HIS   0.007   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3456)
  covalent geometry    : angle       0.67103 ( 4626)
  hydrogen bonds       : bond        0.02632 (   88)
  hydrogen bonds       : angle       6.10342 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: B  345 ASP cc_start: 0.8086 (t0) cc_final: 0.7572 (t70)
REVERT: B  375 LYS cc_start: 0.8384 (tttt) cc_final: 0.7861 (tttm)
REVERT: D  315 LEU cc_start: 0.8572 (mp) cc_final: 0.8207 (mt)
REVERT: D  331 LYS cc_start: 0.8265 (mttt) cc_final: 0.7927 (mttm)
REVERT: D  345 ASP cc_start: 0.8244 (t0) cc_final: 0.8043 (t70)
REVERT: D  347 LYS cc_start: 0.7611 (mmtt) cc_final: 0.6594 (mtmm)
REVERT: D  375 LYS cc_start: 0.8330 (tttt) cc_final: 0.8087 (tttp)
REVERT: F  331 LYS cc_start: 0.8118 (mttt) cc_final: 0.7519 (mtpp)
REVERT: F  337 VAL cc_start: 0.8240 (t) cc_final: 0.8013 (m)
REVERT: F  349 ARG cc_start: 0.7049 (mmt90) cc_final: 0.6394 (mmp-170)
REVERT: A  316 SER cc_start: 0.8860 (p) cc_final: 0.8647 (p)
REVERT: A  369 LYS cc_start: 0.7678 (tttt) cc_final: 0.6980 (ttmm)
REVERT: C  369 LYS cc_start: 0.7423 (tttt) cc_final: 0.6892 (ttmm)
REVERT: C  375 LYS cc_start: 0.8212 (tttt) cc_final: 0.7632 (tmtt)
REVERT: E  311 LYS cc_start: 0.7738 (mttt) cc_final: 0.7213 (mmmt)
REVERT: E  349 ARG cc_start: 0.6097 (mmt90) cc_final: 0.5237 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7765 (tttt) cc_final: 0.7120 (mtpt)
  outliers start: 5
  outliers final: 4
  residues processed: 120
  average time/residue: 0.0911
  time to fit residues: 12.7604
Evaluate side-chains
  112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain F residue  353 LYS
Chi-restraints excluded: chain A residue  378 PHE
Chi-restraints excluded: chain C residue  378 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
D 368 ASN
F 362 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.144173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.133426 restraints weight = 4867.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.135506 restraints weight = 2539.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.136924 restraints weight = 1618.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.137909 restraints weight = 1171.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.138462 restraints weight = 925.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3456  Z= 0.219
  Angle     :  0.702   5.109   4626  Z= 0.367
  Chirality :  0.053   0.156    522
  Planarity :  0.004   0.033    588
  Dihedral  :  5.801  19.747    456
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.56 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.91 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 349 
 TYR   0.024   0.005   TYR A 310 
 PHE   0.021   0.002   PHE F 346 
 HIS   0.007   0.002   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 3456)
  covalent geometry    : angle       0.70159 ( 4626)
  hydrogen bonds       : bond        0.02691 (   88)
  hydrogen bonds       : angle       5.81871 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.144 
Fit side-chains
REVERT: B  315 LEU cc_start: 0.8600 (mp) cc_final: 0.8130 (mt)
REVERT: B  345 ASP cc_start: 0.8137 (t0) cc_final: 0.7668 (t70)
REVERT: B  375 LYS cc_start: 0.8436 (tttt) cc_final: 0.8008 (tttm)
REVERT: D  315 LEU cc_start: 0.8729 (mp) cc_final: 0.8392 (mt)
REVERT: D  331 LYS cc_start: 0.8318 (mttt) cc_final: 0.8047 (mttm)
REVERT: D  340 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7655 (mtmt)
REVERT: D  347 LYS cc_start: 0.7741 (mmtt) cc_final: 0.6876 (mtmm)
REVERT: D  349 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7278 (mtt90)
REVERT: D  375 LYS cc_start: 0.8376 (tttt) cc_final: 0.8073 (tttp)
REVERT: F  337 VAL cc_start: 0.8250 (t) cc_final: 0.8045 (m)
REVERT: F  349 ARG cc_start: 0.7312 (mmt90) cc_final: 0.6390 (mmp-170)
REVERT: F  373 THR cc_start: 0.9026 (m) cc_final: 0.8817 (m)
REVERT: F  375 LYS cc_start: 0.8511 (tttt) cc_final: 0.8228 (tttm)
REVERT: A  316 SER cc_start: 0.9011 (p) cc_final: 0.8777 (p)
REVERT: A  349 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7103 (mmt180)
REVERT: A  369 LYS cc_start: 0.7904 (tttt) cc_final: 0.7217 (ttmm)
REVERT: C  369 LYS cc_start: 0.7816 (tttt) cc_final: 0.7323 (mtpt)
REVERT: E  348 ASP cc_start: 0.7610 (t0) cc_final: 0.7316 (t0)
REVERT: E  349 ARG cc_start: 0.6517 (mmt90) cc_final: 0.5394 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7899 (tttt) cc_final: 0.7323 (mtpt)
  outliers start: 6
  outliers final: 6
  residues processed: 108
  average time/residue: 0.0814
  time to fit residues: 10.2388
Evaluate side-chains
  108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  378 PHE
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain E residue  378 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    3.7988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.145020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.134485 restraints weight = 4861.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.136472 restraints weight = 2558.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.137888 restraints weight = 1653.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.138637 restraints weight = 1201.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.139257 restraints weight = 989.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3456  Z= 0.194
  Angle     :  0.655   5.350   4626  Z= 0.340
  Chirality :  0.052   0.155    522
  Planarity :  0.003   0.040    588
  Dihedral  :  5.532  18.095    456
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.59 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.04 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 349 
 TYR   0.016   0.003   TYR A 310 
 PHE   0.014   0.002   PHE F 346 
 HIS   0.004   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 3456)
  covalent geometry    : angle       0.65495 ( 4626)
  hydrogen bonds       : bond        0.02388 (   88)
  hydrogen bonds       : angle       5.56064 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B  331 LYS cc_start: 0.8272 (mttt) cc_final: 0.7920 (mttm)
REVERT: B  345 ASP cc_start: 0.8125 (t0) cc_final: 0.7711 (t70)
REVERT: B  375 LYS cc_start: 0.8422 (tttt) cc_final: 0.8022 (tttm)
REVERT: D  315 LEU cc_start: 0.8690 (mp) cc_final: 0.8396 (mt)
REVERT: D  331 LYS cc_start: 0.8335 (mttt) cc_final: 0.8100 (mttm)
REVERT: D  347 LYS cc_start: 0.7993 (mmtt) cc_final: 0.6768 (mtmm)
REVERT: D  375 LYS cc_start: 0.8356 (tttt) cc_final: 0.8077 (tttp)
REVERT: F  331 LYS cc_start: 0.8084 (mttt) cc_final: 0.7523 (mtpp)
REVERT: F  349 ARG cc_start: 0.7396 (mmt90) cc_final: 0.6141 (mmm160)
REVERT: F  375 LYS cc_start: 0.8523 (tttt) cc_final: 0.8242 (tttm)
REVERT: A  349 ARG cc_start: 0.7615 (mtt180) cc_final: 0.6894 (mtp85)
REVERT: A  369 LYS cc_start: 0.7902 (tttt) cc_final: 0.7231 (ttmm)
REVERT: C  311 LYS cc_start: 0.8284 (mmmt) cc_final: 0.8001 (mtpp)
REVERT: C  369 LYS cc_start: 0.7759 (tttt) cc_final: 0.7107 (ttmm)
REVERT: E  336 GLN cc_start: 0.7741 (mp10) cc_final: 0.7274 (mp10)
REVERT: E  342 GLU cc_start: 0.4341 (mm-30) cc_final: 0.3849 (pt0)
REVERT: E  349 ARG cc_start: 0.6578 (mmt90) cc_final: 0.5366 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7902 (tttt) cc_final: 0.7294 (mtpt)
  outliers start: 9
  outliers final: 7
  residues processed: 105
  average time/residue: 0.0983
  time to fit residues: 11.9297
Evaluate side-chains
  102 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  378 PHE
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain E residue  378 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    3.7990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.144174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.133315 restraints weight = 4895.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.135447 restraints weight = 2558.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.136889 restraints weight = 1628.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.137521 restraints weight = 1177.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.138305 restraints weight = 991.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3456  Z= 0.196
  Angle     :  0.666   8.004   4626  Z= 0.341
  Chirality :  0.052   0.154    522
  Planarity :  0.004   0.045    588
  Dihedral  :  5.464  16.245    456
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.87 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.15 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 349 
 TYR   0.023   0.004   TYR B 310 
 PHE   0.013   0.002   PHE F 346 
 HIS   0.004   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 3456)
  covalent geometry    : angle       0.66628 ( 4626)
  hydrogen bonds       : bond        0.02397 (   88)
  hydrogen bonds       : angle       5.48028 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B  315 LEU cc_start: 0.8602 (mp) cc_final: 0.8195 (mt)
REVERT: B  331 LYS cc_start: 0.8274 (mttt) cc_final: 0.7955 (mttm)
REVERT: B  345 ASP cc_start: 0.8051 (t0) cc_final: 0.7702 (t70)
REVERT: B  375 LYS cc_start: 0.8398 (tttt) cc_final: 0.8001 (tttm)
REVERT: D  315 LEU cc_start: 0.8746 (mp) cc_final: 0.8385 (mt)
REVERT: D  340 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7660 (mtmt)
REVERT: D  347 LYS cc_start: 0.7978 (mmtt) cc_final: 0.6685 (mtmm)
REVERT: D  375 LYS cc_start: 0.8346 (tttt) cc_final: 0.8037 (tttp)
REVERT: F  331 LYS cc_start: 0.8188 (mttt) cc_final: 0.7630 (mtpp)
REVERT: F  349 ARG cc_start: 0.7481 (mmt90) cc_final: 0.6176 (mmm160)
REVERT: F  375 LYS cc_start: 0.8525 (tttt) cc_final: 0.8275 (tttm)
REVERT: A  369 LYS cc_start: 0.7903 (tttt) cc_final: 0.7159 (ttmm)
REVERT: C  369 LYS cc_start: 0.7770 (tttt) cc_final: 0.7128 (ttmm)
REVERT: E  336 GLN cc_start: 0.7650 (mp10) cc_final: 0.7264 (mp10)
REVERT: E  342 GLU cc_start: 0.4579 (mm-30) cc_final: 0.3651 (pm20)
REVERT: E  349 ARG cc_start: 0.6580 (mmt90) cc_final: 0.5442 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7902 (tttt) cc_final: 0.7313 (mtpt)
REVERT: E  375 LYS cc_start: 0.8637 (tttt) cc_final: 0.8166 (tttm)
  outliers start: 10
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0864
  time to fit residues: 10.4952
Evaluate side-chains
  107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  378 PHE
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain E residue  378 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.0970
   chunk 8 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    3.0186

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

Flipped N/Q/H residues before XYZ refinement:
B 362 HIS
A 329 HIS
C 359 ASN
E 359 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.145167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.134342 restraints weight = 4792.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.136511 restraints weight = 2485.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.137881 restraints weight = 1577.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.138788 restraints weight = 1149.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.139424 restraints weight = 919.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3456  Z= 0.163
  Angle     :  0.643   8.286   4626  Z= 0.327
  Chirality :  0.051   0.150    522
  Planarity :  0.003   0.052    588
  Dihedral  :  5.282  15.598    456
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.13 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.017   0.003   TYR A 310 
 PHE   0.011   0.001   PHE F 346 
 HIS   0.004   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3456)
  covalent geometry    : angle       0.64298 ( 4626)
  hydrogen bonds       : bond        0.02256 (   88)
  hydrogen bonds       : angle       5.39596 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B  315 LEU cc_start: 0.8598 (mp) cc_final: 0.8190 (mt)
REVERT: B  331 LYS cc_start: 0.8310 (mttt) cc_final: 0.7985 (mttm)
REVERT: B  345 ASP cc_start: 0.8041 (t0) cc_final: 0.7708 (t70)
REVERT: B  375 LYS cc_start: 0.8401 (tttt) cc_final: 0.7998 (tttm)
REVERT: D  315 LEU cc_start: 0.8686 (mp) cc_final: 0.8358 (mt)
REVERT: D  337 VAL cc_start: 0.9050 (p) cc_final: 0.8799 (m)
REVERT: D  340 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7585 (mtmt)
REVERT: D  347 LYS cc_start: 0.7830 (mmtt) cc_final: 0.6589 (mtmm)
REVERT: D  375 LYS cc_start: 0.8312 (tttt) cc_final: 0.8009 (tttp)
REVERT: F  331 LYS cc_start: 0.8142 (mttt) cc_final: 0.7630 (mtpp)
REVERT: F  349 ARG cc_start: 0.7473 (mmt90) cc_final: 0.6158 (mmm160)
REVERT: F  375 LYS cc_start: 0.8525 (tttt) cc_final: 0.8284 (tttm)
REVERT: A  369 LYS cc_start: 0.7790 (tttt) cc_final: 0.7183 (ttmm)
REVERT: C  369 LYS cc_start: 0.7779 (tttt) cc_final: 0.7115 (ttmm)
REVERT: E  342 GLU cc_start: 0.4596 (mm-30) cc_final: 0.3485 (pm20)
REVERT: E  349 ARG cc_start: 0.6520 (mmt90) cc_final: 0.5356 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7906 (tttt) cc_final: 0.7289 (mtpt)
REVERT: E  375 LYS cc_start: 0.8657 (tttt) cc_final: 0.8104 (tmtt)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.1009
  time to fit residues: 11.9034
Evaluate side-chains
  103 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  378 PHE
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain E residue  378 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
D 330 HIS
C 329 HIS
C 359 ASN
E 359 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.139994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.129073 restraints weight = 4995.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.131034 restraints weight = 2624.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.132393 restraints weight = 1699.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.133321 restraints weight = 1256.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.133892 restraints weight = 1007.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.4992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   3456  Z= 0.318
  Angle     :  0.766   8.215   4626  Z= 0.400
  Chirality :  0.055   0.150    522
  Planarity :  0.004   0.052    588
  Dihedral  :  5.898  17.562    456
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.41 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 349 
 TYR   0.019   0.005   TYR A 310 
 PHE   0.012   0.002   PHE C 346 
 HIS   0.005   0.002   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00731 ( 3456)
  covalent geometry    : angle       0.76586 ( 4626)
  hydrogen bonds       : bond        0.02754 (   88)
  hydrogen bonds       : angle       5.65185 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.144 
Fit side-chains
REVERT: B  345 ASP cc_start: 0.7975 (t0) cc_final: 0.7626 (t70)
REVERT: B  347 LYS cc_start: 0.8493 (mmtt) cc_final: 0.7857 (mmtt)
REVERT: B  375 LYS cc_start: 0.8441 (tttt) cc_final: 0.8193 (tttp)
REVERT: D  336 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7553 (mm-40)
REVERT: D  337 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8742 (m)
REVERT: D  340 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7716 (mtmt)
REVERT: D  347 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7062 (mtmt)
REVERT: D  375 LYS cc_start: 0.8327 (tttt) cc_final: 0.7992 (tttp)
REVERT: D  376 LEU cc_start: 0.8929 (tp) cc_final: 0.8608 (tt)
REVERT: F  331 LYS cc_start: 0.8202 (mttt) cc_final: 0.7818 (mttm)
REVERT: F  349 ARG cc_start: 0.7608 (mmt90) cc_final: 0.6222 (mmm160)
REVERT: F  375 LYS cc_start: 0.8520 (tttt) cc_final: 0.8309 (tttm)
REVERT: A  369 LYS cc_start: 0.7828 (tttt) cc_final: 0.7214 (ttmm)
REVERT: C  369 LYS cc_start: 0.7830 (tttt) cc_final: 0.7163 (ttmm)
REVERT: E  349 ARG cc_start: 0.6663 (mmt90) cc_final: 0.5577 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7915 (tttt) cc_final: 0.7333 (ttmm)
  outliers start: 10
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0733
  time to fit residues: 8.7873
Evaluate side-chains
  106 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain D residue  337 VAL
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  378 PHE
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain E residue  378 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0170
   overall best weight:    3.2026

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.144333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.133431 restraints weight = 4901.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.135583 restraints weight = 2537.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.137021 restraints weight = 1608.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.137825 restraints weight = 1167.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.138496 restraints weight = 953.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.5104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3456  Z= 0.174
  Angle     :  0.665   7.636   4626  Z= 0.340
  Chirality :  0.051   0.146    522
  Planarity :  0.004   0.058    588
  Dihedral  :  5.524  17.718    456
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.44 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.015   0.003   TYR A 310 
 PHE   0.011   0.002   PHE F 346 
 HIS   0.003   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 3456)
  covalent geometry    : angle       0.66459 ( 4626)
  hydrogen bonds       : bond        0.02389 (   88)
  hydrogen bonds       : angle       5.51417 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: B  315 LEU cc_start: 0.8602 (mp) cc_final: 0.8123 (mt)
REVERT: B  336 GLN cc_start: 0.8443 (mm110) cc_final: 0.7924 (mm-40)
REVERT: D  315 LEU cc_start: 0.8652 (mp) cc_final: 0.8333 (mt)
REVERT: D  336 GLN cc_start: 0.7716 (mm-40) cc_final: 0.6727 (pt0)
REVERT: D  337 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8694 (m)
REVERT: D  340 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7572 (mtmt)
REVERT: D  343 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7102 (pptt)
REVERT: D  347 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7017 (mtmt)
REVERT: D  375 LYS cc_start: 0.8236 (tttt) cc_final: 0.7989 (tttp)
REVERT: F  331 LYS cc_start: 0.8148 (mttt) cc_final: 0.7756 (mttm)
REVERT: F  349 ARG cc_start: 0.7517 (mmt90) cc_final: 0.6156 (mmt-90)
REVERT: F  375 LYS cc_start: 0.8523 (tttt) cc_final: 0.8264 (tttm)
REVERT: A  369 LYS cc_start: 0.7797 (tttt) cc_final: 0.7238 (ttmm)
REVERT: C  369 LYS cc_start: 0.7813 (tttt) cc_final: 0.7108 (ttmm)
REVERT: E  349 ARG cc_start: 0.6521 (mmt90) cc_final: 0.5255 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7908 (tttt) cc_final: 0.7272 (ttmm)
REVERT: E  375 LYS cc_start: 0.8646 (tttt) cc_final: 0.8089 (tmtt)
  outliers start: 10
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0969
  time to fit residues: 11.2529
Evaluate side-chains
  106 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain D residue  337 VAL
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  378 PHE
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain E residue  378 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0040
   chunk 31 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.8000

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

Flipped N/Q/H residues before XYZ refinement:
C 359 ASN
E 329 HIS
E 359 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.146377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.135619 restraints weight = 4889.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.137712 restraints weight = 2566.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.139153 restraints weight = 1637.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.140107 restraints weight = 1190.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.140580 restraints weight = 947.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.5171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3456  Z= 0.158
  Angle     :  0.658   7.332   4626  Z= 0.336
  Chirality :  0.051   0.146    522
  Planarity :  0.003   0.056    588
  Dihedral  :  5.299  15.793    456
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.69 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.014   0.003   TYR A 310 
 PHE   0.009   0.001   PHE F 346 
 HIS   0.003   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3456)
  covalent geometry    : angle       0.65791 ( 4626)
  hydrogen bonds       : bond        0.02250 (   88)
  hydrogen bonds       : angle       5.40841 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: B  315 LEU cc_start: 0.8612 (mp) cc_final: 0.8100 (mt)
REVERT: B  331 LYS cc_start: 0.8333 (mttt) cc_final: 0.8009 (mttm)
REVERT: B  336 GLN cc_start: 0.8478 (mm110) cc_final: 0.8113 (mm-40)
REVERT: D  315 LEU cc_start: 0.8613 (mp) cc_final: 0.8305 (mt)
REVERT: D  337 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8720 (m)
REVERT: D  340 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7550 (mtmt)
REVERT: D  343 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7104 (pptt)
REVERT: D  375 LYS cc_start: 0.8222 (tttt) cc_final: 0.7943 (tttp)
REVERT: F  331 LYS cc_start: 0.8140 (mttt) cc_final: 0.7724 (mttm)
REVERT: F  349 ARG cc_start: 0.7441 (mmt90) cc_final: 0.6146 (mmm160)
REVERT: F  375 LYS cc_start: 0.8517 (tttt) cc_final: 0.8265 (tttm)
REVERT: A  369 LYS cc_start: 0.7807 (tttt) cc_final: 0.7225 (ttmm)
REVERT: C  369 LYS cc_start: 0.7796 (tttt) cc_final: 0.7130 (ttmm)
REVERT: E  349 ARG cc_start: 0.6469 (mmt90) cc_final: 0.5121 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7908 (tttt) cc_final: 0.7315 (ttmm)
REVERT: E  375 LYS cc_start: 0.8652 (tttt) cc_final: 0.8104 (tmtt)
  outliers start: 10
  outliers final: 8
  residues processed: 99
  average time/residue: 0.0811
  time to fit residues: 9.3794
Evaluate side-chains
  107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain D residue  337 VAL
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  378 PHE
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain E residue  378 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    1.1382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.150429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.139445 restraints weight = 4786.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.141737 restraints weight = 2456.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.143189 restraints weight = 1541.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.144165 restraints weight = 1109.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.144724 restraints weight = 879.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   3456  Z= 0.103
  Angle     :  0.610   7.014   4626  Z= 0.306
  Chirality :  0.050   0.149    522
  Planarity :  0.003   0.056    588
  Dihedral  :  4.881  15.401    456
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 19.74 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 349 
 TYR   0.011   0.002   TYR A 310 
 PHE   0.006   0.001   PHE F 346 
 HIS   0.003   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 3456)
  covalent geometry    : angle       0.61005 ( 4626)
  hydrogen bonds       : bond        0.01968 (   88)
  hydrogen bonds       : angle       5.22569 (  264)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.153 
Fit side-chains
REVERT: B  315 LEU cc_start: 0.8587 (mp) cc_final: 0.8324 (mt)
REVERT: B  331 LYS cc_start: 0.8277 (mttt) cc_final: 0.7963 (mttm)
REVERT: B  336 GLN cc_start: 0.8482 (mm110) cc_final: 0.7971 (mm-40)
REVERT: D  315 LEU cc_start: 0.8573 (mp) cc_final: 0.8316 (mt)
REVERT: D  336 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6492 (pt0)
REVERT: D  340 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7853 (mttm)
REVERT: D  347 LYS cc_start: 0.7886 (mmtm) cc_final: 0.6597 (mtmm)
REVERT: D  375 LYS cc_start: 0.8172 (tttt) cc_final: 0.7914 (tttp)
REVERT: F  331 LYS cc_start: 0.8097 (mttt) cc_final: 0.7674 (mttm)
REVERT: F  349 ARG cc_start: 0.7390 (mmt90) cc_final: 0.6091 (mmm160)
REVERT: F  375 LYS cc_start: 0.8537 (tttt) cc_final: 0.8300 (tttm)
REVERT: A  369 LYS cc_start: 0.7673 (tttt) cc_final: 0.7078 (ttmm)
REVERT: C  369 LYS cc_start: 0.7748 (tttt) cc_final: 0.7086 (ttmm)
REVERT: E  349 ARG cc_start: 0.6277 (mmt90) cc_final: 0.5066 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7891 (tttt) cc_final: 0.7234 (mtpt)
REVERT: E  375 LYS cc_start: 0.8601 (tttt) cc_final: 0.8110 (tmtt)
  outliers start: 5
  outliers final: 3
  residues processed: 100
  average time/residue: 0.0804
  time to fit residues: 9.4559
Evaluate side-chains
  99 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain C residue  378 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   overall best weight:    6.1990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.141882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.131037 restraints weight = 4950.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.133088 restraints weight = 2609.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.134496 restraints weight = 1671.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.135253 restraints weight = 1224.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.135912 restraints weight = 1006.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   3456  Z= 0.295
  Angle     :  0.762   7.014   4626  Z= 0.398
  Chirality :  0.054   0.152    522
  Planarity :  0.004   0.057    588
  Dihedral  :  5.573  16.158    456
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 19.49 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 349 
 TYR   0.019   0.005   TYR A 310 
 PHE   0.013   0.002   PHE F 346 
 HIS   0.004   0.002   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 ( 3456)
  covalent geometry    : angle       0.76192 ( 4626)
  hydrogen bonds       : bond        0.02610 (   88)
  hydrogen bonds       : angle       5.44893 (  264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 827.80 seconds
wall clock time: 15 minutes 5.48 seconds (905.48 seconds total)