Starting phenix.real_space_refine
on Wed Mar  5 20:04:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q7f_18215/03_2025/8q7f_18215.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q7f_18215/03_2025/8q7f_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q7f_18215/03_2025/8q7f_18215.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q7f_18215/03_2025/8q7f_18215.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q7f_18215/03_2025/8q7f_18215.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q7f_18215/03_2025/8q7f_18215.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.90, per 1000 atoms: 1.15
  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: 0.75
  Conformation dependent library (CDL) restraints added in 941.0 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: 0.54
  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: 0.84

  Time building geometry restraints manager: 0.92 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: 0.01
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:             4.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     15.220
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.020
-------------------------------------------------------------------------------
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= 0.765
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.32), 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
 HIS   0.006   0.002   HIS D 362 
 PHE   0.063   0.013   PHE E 346 
 TYR   0.129   0.046   TYR A 310 
 ARG   0.009   0.002   ARG C 349 

*********************** 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  : 0.416 
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: 0.7963 (p)
REVERT: B  338 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7149 (tm-30)
REVERT: B  340 LYS cc_start: 0.7414 (tttt) cc_final: 0.7091 (mttm)
REVERT: B  345 ASP cc_start: 0.7560 (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: 0.8160 (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: 0.7389 (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: 0.7464 (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: 0.7450 (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: 0.6527 (mmm160)
REVERT: A  351 GLN cc_start: 0.6186 (mp10) cc_final: 0.5762 (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: 0.7794 (mtpp)
REVERT: C  349 ARG cc_start: 0.7078 (mmt90) cc_final: 0.6402 (mtm180)
REVERT: C  361 THR cc_start: 0.8773 (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: 0.6205 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2219
  time to fit residues: 37.1620
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  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.7788

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.152691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.141996 restraints weight = 4613.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.144371 restraints weight = 2334.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.145908 restraints weight = 1432.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3456  Z= 0.201
  Angle     :  0.651   5.255   4626  Z= 0.339
  Chirality :  0.052   0.135    522
  Planarity :  0.003   0.028    588
  Dihedral  :  5.930  20.572    456
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  7.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.90 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS B 362 
 PHE   0.015   0.001   PHE F 346 
 TYR   0.013   0.003   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

*********************** 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
  121 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.422 
Fit side-chains
REVERT: B  345 ASP cc_start: 0.8074 (t0) cc_final: 0.7583 (t70)
REVERT: B  375 LYS cc_start: 0.8404 (tttt) cc_final: 0.7864 (tttm)
REVERT: D  315 LEU cc_start: 0.8508 (mp) cc_final: 0.8171 (mt)
REVERT: D  331 LYS cc_start: 0.8254 (mttt) cc_final: 0.7910 (mttm)
REVERT: D  345 ASP cc_start: 0.8198 (t0) cc_final: 0.7973 (t70)
REVERT: D  347 LYS cc_start: 0.7547 (mmtt) cc_final: 0.6574 (mtmm)
REVERT: D  375 LYS cc_start: 0.8297 (tttt) cc_final: 0.8066 (tttp)
REVERT: F  331 LYS cc_start: 0.8117 (mttt) cc_final: 0.7508 (mtpp)
REVERT: F  337 VAL cc_start: 0.8225 (t) cc_final: 0.7967 (m)
REVERT: F  349 ARG cc_start: 0.6971 (mmt90) cc_final: 0.6301 (mmp-170)
REVERT: F  375 LYS cc_start: 0.8430 (tttt) cc_final: 0.8124 (tttm)
REVERT: A  316 SER cc_start: 0.8782 (p) cc_final: 0.8573 (p)
REVERT: A  369 LYS cc_start: 0.7552 (tttt) cc_final: 0.6910 (ttmm)
REVERT: C  369 LYS cc_start: 0.7237 (tttt) cc_final: 0.6757 (ttmm)
REVERT: C  375 LYS cc_start: 0.8150 (tttt) cc_final: 0.7581 (tmtt)
REVERT: E  311 LYS cc_start: 0.7621 (mttt) cc_final: 0.7403 (mmtt)
REVERT: E  349 ARG cc_start: 0.6055 (mmt90) cc_final: 0.5339 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7717 (tttt) cc_final: 0.7135 (mtpt)
  outliers start: 3
  outliers final: 2
  residues processed: 120
  average time/residue: 0.2010
  time to fit residues: 27.9911
Evaluate side-chains
  109 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  353 LYS
Chi-restraints excluded: chain A residue  378 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    5.5788

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.142144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.131632 restraints weight = 4818.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.133566 restraints weight = 2533.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.134969 restraints weight = 1640.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3456  Z= 0.431
  Angle     :  0.760   5.087   4626  Z= 0.401
  Chirality :  0.055   0.171    522
  Planarity :  0.004   0.049    588
  Dihedral  :  6.023  21.660    456
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.54 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (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
 HIS   0.008   0.002   HIS B 362 
 PHE   0.023   0.003   PHE F 346 
 TYR   0.024   0.005   TYR A 310 
 ARG   0.004   0.001   ARG A 349 

*********************** 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
  109 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.372 
Fit side-chains
REVERT: B  345 ASP cc_start: 0.8160 (t0) cc_final: 0.7719 (t70)
REVERT: B  375 LYS cc_start: 0.8448 (tttt) cc_final: 0.8022 (tttm)
REVERT: D  315 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8470 (mt)
REVERT: D  331 LYS cc_start: 0.8344 (mttt) cc_final: 0.8088 (mttm)
REVERT: D  340 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7728 (mtmt)
REVERT: D  375 LYS cc_start: 0.8364 (tttt) cc_final: 0.8044 (tttp)
REVERT: F  337 VAL cc_start: 0.8285 (t) cc_final: 0.8076 (m)
REVERT: F  349 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6355 (mmp-170)
REVERT: F  375 LYS cc_start: 0.8518 (tttt) cc_final: 0.8236 (tttm)
REVERT: A  316 SER cc_start: 0.9037 (p) cc_final: 0.8813 (p)
REVERT: A  369 LYS cc_start: 0.7947 (tttt) cc_final: 0.7213 (ttmm)
REVERT: C  342 GLU cc_start: 0.8045 (pm20) cc_final: 0.7721 (mt-10)
REVERT: C  369 LYS cc_start: 0.7829 (tttt) cc_final: 0.7196 (ttmm)
REVERT: E  349 ARG cc_start: 0.6690 (mmt90) cc_final: 0.5370 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7941 (tttt) cc_final: 0.7384 (mtpt)
  outliers start: 7
  outliers final: 5
  residues processed: 104
  average time/residue: 0.1689
  time to fit residues: 20.8181
Evaluate side-chains
  100 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  315 LEU
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    4.1588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.143544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.132936 restraints weight = 4844.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.134970 restraints weight = 2511.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.136406 restraints weight = 1600.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3456  Z= 0.335
  Angle     :  0.687   6.190   4626  Z= 0.353
  Chirality :  0.052   0.158    522
  Planarity :  0.003   0.040    588
  Dihedral  :  5.647  18.029    456
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.36 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.10 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 362 
 PHE   0.015   0.002   PHE F 346 
 TYR   0.017   0.003   TYR A 310 
 ARG   0.002   0.000   ARG A 349 

*********************** 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  : 0.405 
Fit side-chains
REVERT: B  315 LEU cc_start: 0.8549 (mp) cc_final: 0.8124 (mt)
REVERT: B  331 LYS cc_start: 0.8282 (mttt) cc_final: 0.7933 (mttm)
REVERT: B  345 ASP cc_start: 0.8132 (t0) cc_final: 0.7712 (t70)
REVERT: B  375 LYS cc_start: 0.8441 (tttt) cc_final: 0.8025 (tttm)
REVERT: D  315 LEU cc_start: 0.8748 (mp) cc_final: 0.8397 (mt)
REVERT: D  331 LYS cc_start: 0.8314 (mttt) cc_final: 0.8070 (mttm)
REVERT: D  340 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7687 (mtmt)
REVERT: D  347 LYS cc_start: 0.7998 (mmtt) cc_final: 0.6734 (mtmm)
REVERT: D  375 LYS cc_start: 0.8318 (tttt) cc_final: 0.8028 (tttp)
REVERT: F  331 LYS cc_start: 0.8102 (mttt) cc_final: 0.7535 (mtpp)
REVERT: F  337 VAL cc_start: 0.8282 (t) cc_final: 0.8071 (m)
REVERT: F  349 ARG cc_start: 0.7473 (mmt90) cc_final: 0.6190 (mmm160)
REVERT: F  375 LYS cc_start: 0.8556 (tttt) cc_final: 0.8267 (tttm)
REVERT: A  369 LYS cc_start: 0.7912 (tttt) cc_final: 0.7165 (ttmm)
REVERT: C  342 GLU cc_start: 0.7962 (pm20) cc_final: 0.7675 (mt-10)
REVERT: C  369 LYS cc_start: 0.7767 (tttt) cc_final: 0.7126 (ttmm)
REVERT: E  336 GLN cc_start: 0.7763 (mp10) cc_final: 0.7285 (mp10)
REVERT: E  349 ARG cc_start: 0.6629 (mmt90) cc_final: 0.5347 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7894 (tttt) cc_final: 0.7262 (mtpt)
  outliers start: 9
  outliers final: 6
  residues processed: 106
  average time/residue: 0.2019
  time to fit residues: 24.7758
Evaluate side-chains
  103 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 37 optimal weight:    0.0980
   chunk 36 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    4.4188

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.142000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.131427 restraints weight = 5012.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.133589 restraints weight = 2581.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.134996 restraints weight = 1626.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3456  Z= 0.351
  Angle     :  0.693   7.651   4626  Z= 0.355
  Chirality :  0.052   0.155    522
  Planarity :  0.004   0.047    588
  Dihedral  :  5.585  16.322    456
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.90 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (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
 HIS   0.004   0.001   HIS D 362 
 PHE   0.013   0.002   PHE F 346 
 TYR   0.024   0.004   TYR B 310 
 ARG   0.002   0.000   ARG D 349 

*********************** 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
  110 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  331 LYS cc_start: 0.8304 (mttt) cc_final: 0.7981 (mttm)
REVERT: B  345 ASP cc_start: 0.8047 (t0) cc_final: 0.7686 (t70)
REVERT: D  337 VAL cc_start: 0.9088 (p) cc_final: 0.8862 (m)
REVERT: D  347 LYS cc_start: 0.7836 (mmtt) cc_final: 0.6626 (mtmm)
REVERT: D  375 LYS cc_start: 0.8314 (tttt) cc_final: 0.7948 (tttp)
REVERT: F  331 LYS cc_start: 0.8219 (mttt) cc_final: 0.7668 (mtpp)
REVERT: F  337 VAL cc_start: 0.8269 (t) cc_final: 0.8050 (m)
REVERT: F  349 ARG cc_start: 0.7531 (mmt90) cc_final: 0.6212 (mmm160)
REVERT: A  369 LYS cc_start: 0.7844 (tttt) cc_final: 0.7265 (ttmm)
REVERT: C  311 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8134 (mtpp)
REVERT: C  342 GLU cc_start: 0.7940 (pm20) cc_final: 0.7704 (mt-10)
REVERT: C  369 LYS cc_start: 0.7813 (tttt) cc_final: 0.7135 (ttmm)
REVERT: E  349 ARG cc_start: 0.6609 (mmt90) cc_final: 0.5566 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7897 (tttt) cc_final: 0.7247 (ttmm)
REVERT: E  375 LYS cc_start: 0.8650 (tttt) cc_final: 0.8126 (tmtt)
  outliers start: 8
  outliers final: 7
  residues processed: 105
  average time/residue: 0.1946
  time to fit residues: 23.8033
Evaluate side-chains
  106 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.139592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.129098 restraints weight = 5068.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.131126 restraints weight = 2647.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.132512 restraints weight = 1676.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4889

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= 0.478
  Angle     :  0.767   8.163   4626  Z= 0.398
  Chirality :  0.054   0.153    522
  Planarity :  0.004   0.050    588
  Dihedral  :  5.860  17.466    456
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.41 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (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
 HIS   0.004   0.002   HIS D 329 
 PHE   0.012   0.002   PHE C 346 
 TYR   0.020   0.004   TYR A 310 
 ARG   0.002   0.000   ARG D 349 

*********************** 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
  112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.446 
Fit side-chains
REVERT: B  345 ASP cc_start: 0.7985 (t0) cc_final: 0.7562 (t70)
REVERT: B  347 LYS cc_start: 0.8443 (mmtt) cc_final: 0.7852 (mmtt)
REVERT: B  375 LYS cc_start: 0.8442 (tttt) cc_final: 0.8224 (tttp)
REVERT: D  337 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8868 (m)
REVERT: D  347 LYS cc_start: 0.8165 (mmtt) cc_final: 0.6995 (mtmt)
REVERT: D  375 LYS cc_start: 0.8307 (tttt) cc_final: 0.7951 (tttp)
REVERT: D  376 LEU cc_start: 0.8932 (tp) cc_final: 0.8611 (tt)
REVERT: F  331 LYS cc_start: 0.8190 (mttt) cc_final: 0.7776 (mttm)
REVERT: F  337 VAL cc_start: 0.8291 (t) cc_final: 0.8083 (m)
REVERT: F  349 ARG cc_start: 0.7598 (mmt90) cc_final: 0.6220 (mmm160)
REVERT: F  375 LYS cc_start: 0.8536 (tttt) cc_final: 0.8328 (tttp)
REVERT: A  369 LYS cc_start: 0.7892 (tttt) cc_final: 0.7262 (ttmm)
REVERT: C  342 GLU cc_start: 0.7939 (pm20) cc_final: 0.7706 (mt-10)
REVERT: C  369 LYS cc_start: 0.7850 (tttt) cc_final: 0.7174 (ttmm)
REVERT: E  349 ARG cc_start: 0.6609 (mmt90) cc_final: 0.5531 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7909 (tttt) cc_final: 0.7273 (ttmm)
  outliers start: 9
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1963
  time to fit residues: 24.3460
Evaluate side-chains
  108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
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  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 9 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.142029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.131483 restraints weight = 4942.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.133638 restraints weight = 2549.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.134933 restraints weight = 1599.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
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      :  0.004   0.036   3456  Z= 0.300
  Angle     :  0.690   7.475   4626  Z= 0.348
  Chirality :  0.052   0.142    522
  Planarity :  0.004   0.058    588
  Dihedral  :  5.545  16.965    456
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (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
 HIS   0.004   0.001   HIS D 362 
 PHE   0.012   0.002   PHE F 346 
 TYR   0.015   0.003   TYR A 310 
 ARG   0.001   0.000   ARG D 349 

*********************** 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
  113 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: B  315 LEU cc_start: 0.8631 (mp) cc_final: 0.8076 (mt)
REVERT: B  331 LYS cc_start: 0.8334 (mttt) cc_final: 0.8040 (mttm)
REVERT: B  336 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8057 (mm110)
REVERT: B  345 ASP cc_start: 0.7925 (t0) cc_final: 0.7634 (t70)
REVERT: B  347 LYS cc_start: 0.8406 (mmtt) cc_final: 0.7862 (mmtt)
REVERT: B  375 LYS cc_start: 0.8461 (tttt) cc_final: 0.8082 (tttm)
REVERT: D  315 LEU cc_start: 0.8709 (mp) cc_final: 0.8298 (mt)
REVERT: D  337 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8818 (m)
REVERT: D  347 LYS cc_start: 0.8178 (mmtt) cc_final: 0.6977 (mtmt)
REVERT: D  375 LYS cc_start: 0.8255 (tttt) cc_final: 0.8002 (tttp)
REVERT: F  331 LYS cc_start: 0.8136 (mttt) cc_final: 0.7735 (mttm)
REVERT: F  337 VAL cc_start: 0.8219 (t) cc_final: 0.8000 (m)
REVERT: F  349 ARG cc_start: 0.7521 (mmt90) cc_final: 0.6170 (mmt-90)
REVERT: F  375 LYS cc_start: 0.8545 (tttt) cc_final: 0.8288 (tttm)
REVERT: A  369 LYS cc_start: 0.7881 (tttt) cc_final: 0.7272 (ttmm)
REVERT: C  342 GLU cc_start: 0.7873 (pm20) cc_final: 0.7666 (mt-10)
REVERT: C  369 LYS cc_start: 0.7827 (tttt) cc_final: 0.7133 (ttmm)
REVERT: E  349 ARG cc_start: 0.6531 (mmt90) cc_final: 0.5529 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7917 (tttt) cc_final: 0.7272 (ttmm)
REVERT: E  375 LYS cc_start: 0.8664 (tttt) cc_final: 0.8109 (tmtt)
  outliers start: 10
  outliers final: 8
  residues processed: 105
  average time/residue: 0.2055
  time to fit residues: 24.8738
Evaluate side-chains
  109 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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  338 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 8 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 23 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    3.2988

-------------------------------------------------------------------------------
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 = 0.4019 r_free = 0.4019 target = 0.143355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.132749 restraints weight = 4931.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.134900 restraints weight = 2552.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.136284 restraints weight = 1614.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.5075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3456  Z= 0.277
  Angle     :  0.673   7.008   4626  Z= 0.339
  Chirality :  0.051   0.147    522
  Planarity :  0.004   0.057    588
  Dihedral  :  5.345  16.057    456
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.37), 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
 HIS   0.003   0.001   HIS D 362 
 PHE   0.010   0.001   PHE F 346 
 TYR   0.013   0.003   TYR A 310 
 ARG   0.001   0.000   ARG C 349 

*********************** 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
  108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.404 
Fit side-chains
REVERT: B  315 LEU cc_start: 0.8611 (mp) cc_final: 0.8096 (mt)
REVERT: B  331 LYS cc_start: 0.8335 (mttt) cc_final: 0.8048 (mttm)
REVERT: B  345 ASP cc_start: 0.7929 (t0) cc_final: 0.7641 (t70)
REVERT: B  347 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7692 (mmtt)
REVERT: B  375 LYS cc_start: 0.8454 (tttt) cc_final: 0.8072 (tttm)
REVERT: D  315 LEU cc_start: 0.8715 (mp) cc_final: 0.8322 (mt)
REVERT: D  337 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8676 (m)
REVERT: D  347 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7028 (mtmt)
REVERT: D  375 LYS cc_start: 0.8245 (tttt) cc_final: 0.7979 (tttp)
REVERT: F  331 LYS cc_start: 0.8148 (mttt) cc_final: 0.7729 (mttm)
REVERT: F  337 VAL cc_start: 0.8209 (t) cc_final: 0.7970 (m)
REVERT: F  349 ARG cc_start: 0.7498 (mmt90) cc_final: 0.6151 (mmt-90)
REVERT: F  375 LYS cc_start: 0.8532 (tttt) cc_final: 0.8277 (tttm)
REVERT: A  369 LYS cc_start: 0.7872 (tttt) cc_final: 0.7262 (ttmm)
REVERT: C  369 LYS cc_start: 0.7819 (tttt) cc_final: 0.7129 (ttmm)
REVERT: E  349 ARG cc_start: 0.6529 (mmt90) cc_final: 0.5109 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7918 (tttt) cc_final: 0.7267 (ttmm)
REVERT: E  375 LYS cc_start: 0.8651 (tttt) cc_final: 0.8099 (tmtt)
  outliers start: 10
  outliers final: 9
  residues processed: 100
  average time/residue: 0.1994
  time to fit residues: 23.2039
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  : 0.398 
-------------------------------------------------------------------------------
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  349 ARG
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 28 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    0.5980
   chunk 12 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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 = 0.4056 r_free = 0.4056 target = 0.145726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.134949 restraints weight = 4761.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.137239 restraints weight = 2460.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.138720 restraints weight = 1541.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3456  Z= 0.209
  Angle     :  0.645   6.572   4626  Z= 0.322
  Chirality :  0.051   0.149    522
  Planarity :  0.003   0.057    588
  Dihedral  :  5.118  15.687    456
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.46 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.37 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 362 
 PHE   0.010   0.001   PHE F 346 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 349 

*********************** 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
  112 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.373 
Fit side-chains
REVERT: B  315 LEU cc_start: 0.8593 (mp) cc_final: 0.8181 (mt)
REVERT: B  331 LYS cc_start: 0.8328 (mttt) cc_final: 0.8046 (mttm)
REVERT: B  345 ASP cc_start: 0.7901 (t0) cc_final: 0.7627 (t70)
REVERT: B  347 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7742 (mmtt)
REVERT: B  375 LYS cc_start: 0.8411 (tttt) cc_final: 0.8061 (tttm)
REVERT: D  315 LEU cc_start: 0.8640 (mp) cc_final: 0.8244 (mt)
REVERT: D  340 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7987 (mttm)
REVERT: D  347 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7076 (mtmt)
REVERT: D  375 LYS cc_start: 0.8212 (tttt) cc_final: 0.7992 (tttp)
REVERT: F  331 LYS cc_start: 0.8130 (mttt) cc_final: 0.7723 (mttm)
REVERT: F  337 VAL cc_start: 0.8187 (t) cc_final: 0.7951 (m)
REVERT: F  349 ARG cc_start: 0.7484 (mmt90) cc_final: 0.6111 (mmt-90)
REVERT: F  375 LYS cc_start: 0.8543 (tttt) cc_final: 0.8281 (tttm)
REVERT: A  369 LYS cc_start: 0.7849 (tttt) cc_final: 0.7192 (ttmm)
REVERT: C  311 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7965 (mtpp)
REVERT: C  369 LYS cc_start: 0.7783 (tttt) cc_final: 0.7080 (ttmm)
REVERT: E  349 ARG cc_start: 0.6438 (mmt90) cc_final: 0.5160 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7886 (tttt) cc_final: 0.7245 (mtpt)
REVERT: E  375 LYS cc_start: 0.8628 (tttt) cc_final: 0.8122 (tmtt)
  outliers start: 11
  outliers final: 9
  residues processed: 104
  average time/residue: 0.2019
  time to fit residues: 24.3071
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  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  349 ARG
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 12 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 40 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   overall best weight:    5.2186

-------------------------------------------------------------------------------
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 = 0.4010 r_free = 0.4010 target = 0.141344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.130899 restraints weight = 5040.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.132994 restraints weight = 2618.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.134374 restraints weight = 1666.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.5223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   3456  Z= 0.397
  Angle     :  0.738   6.602   4626  Z= 0.379
  Chirality :  0.053   0.150    522
  Planarity :  0.004   0.058    588
  Dihedral  :  5.462  16.282    456
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.74 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.41 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 362 
 PHE   0.012   0.002   PHE F 346 
 TYR   0.016   0.004   TYR A 310 
 ARG   0.003   0.001   ARG A 349 

********************** 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
  106 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.419 
Fit side-chains
REVERT: B  345 ASP cc_start: 0.7892 (t0) cc_final: 0.7635 (t70)
REVERT: B  347 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7708 (mmtt)
REVERT: B  375 LYS cc_start: 0.8419 (tttt) cc_final: 0.8080 (tttm)
REVERT: D  375 LYS cc_start: 0.8315 (tttt) cc_final: 0.8077 (tttp)
REVERT: D  376 LEU cc_start: 0.8887 (tp) cc_final: 0.8561 (tt)
REVERT: F  331 LYS cc_start: 0.8157 (mttt) cc_final: 0.7769 (mttm)
REVERT: F  337 VAL cc_start: 0.8230 (t) cc_final: 0.8029 (m)
REVERT: F  349 ARG cc_start: 0.7522 (mmt90) cc_final: 0.6122 (mmt-90)
REVERT: F  375 LYS cc_start: 0.8541 (tttt) cc_final: 0.8329 (tttp)
REVERT: C  369 LYS cc_start: 0.7862 (tttt) cc_final: 0.7168 (ttmm)
REVERT: E  349 ARG cc_start: 0.6567 (mmt90) cc_final: 0.5178 (mmp-170)
REVERT: E  369 LYS cc_start: 0.7900 (tttt) cc_final: 0.7273 (ttmm)
REVERT: E  375 LYS cc_start: 0.8674 (tttt) cc_final: 0.8201 (tttm)
  outliers start: 9
  outliers final: 8
  residues processed: 99
  average time/residue: 0.2012
  time to fit residues: 23.4119
Evaluate side-chains
  103 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  338 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:    0.4980
   chunk 40 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    3.4988

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.142904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.132372 restraints weight = 4917.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.134578 restraints weight = 2543.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.135996 restraints weight = 1591.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.5246

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= 0.289
  Angle     :  0.690   6.501   4626  Z= 0.347
  Chirality :  0.051   0.147    522
  Planarity :  0.004   0.059    588
  Dihedral  :  5.333  16.649    456
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 20.00 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.41 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 362 
 PHE   0.011   0.002   PHE F 346 
 TYR   0.013   0.003   TYR A 310 
 ARG   0.001   0.000   ARG D 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1518.28 seconds
wall clock time: 27 minutes 18.54 seconds (1638.54 seconds total)