Starting phenix.real_space_refine
on Wed Mar 12 02:28:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8z_18266/03_2025/8q8z_18266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8z_18266/03_2025/8q8z_18266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q8z_18266/03_2025/8q8z_18266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8z_18266/03_2025/8q8z_18266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8z_18266/03_2025/8q8z_18266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8z_18266/03_2025/8q8z_18266.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2160      2.51       5
     N     636      2.21       5
     O     642      1.98       5
     H    3588      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7032
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "B"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 4.78, per 1000 atoms: 0.68
  Number of scatterers: 7032
  At special positions: 0
  Unit cell: (146.672, 113.712, 50.264, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     642      8.00
     N     636      7.00
     C    2160      6.00
     H    3588      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 660.2 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:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 51.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.485A  pdb=" N   VAL A 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   VAL E 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE A 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.855A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325
      removed outlier: 6.288A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   SER C 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   SER C 324 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   GLY A 323 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL A 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   LYS E 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   SER A 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   GLY E 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   CYS A 322 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   LEU E 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   SER A 324 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.850A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 333 through 334
      removed outlier: 6.730A  pdb=" N   GLY A 333 " --> pdb=" O   GLY C 334 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 342
      removed outlier: 6.576A  pdb=" N   GLU A 338 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   SER C 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LYS A 340 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 8.259A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   GLU E 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   SER A 341 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354
      removed outlier: 6.375A  pdb=" N   VAL A 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   LYS E 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   SER A 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.226A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   THR C 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE A 360 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 368 through 378
      removed outlier: 6.672A  pdb=" N   LYS A 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   GLU C 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ILE A 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   HIS C 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR A 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   LEU C 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LYS A 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   PHE C 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   THR A 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.508A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.861A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325
      removed outlier: 6.177A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   SER D 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   GLY B 323 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.745A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342
      removed outlier: 6.542A  pdb=" N   VAL B 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   LYS F 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   VAL B 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   GLU F 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   SER B 341 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.667A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.469A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   ILE D 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 359 through 362
    Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 378
      removed outlier: 6.473A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)

    67 hydrogen bonds defined for protein.
    201 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.34

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 3582
        1.12 -     1.29: 570
        1.29 -     1.47: 1140
        1.47 -     1.64: 1788
        1.64 -     1.81: 6
  Bond restraints: 7086
  Sorted by residual:
  bond pdb=" N   SER A 305 "
       pdb=" H   SER A 305 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   SER E 305 "
       pdb=" H   SER E 305 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" NE2 HIS D 330 "
       pdb=" HE2 HIS D 330 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CD2 HIS E 362 "
       pdb=" HD2 HIS E 362 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   LYS C 311 "
       pdb=" H   LYS C 311 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  ... (remaining 7081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 10591
        2.36 -     4.71: 1720
        4.71 -     7.07: 565
        7.07 -     9.42: 30
        9.42 -    11.78: 6
  Bond angle restraints: 12912
  Sorted by residual:
  angle pdb=" CA  ASP B 358 "
        pdb=" CB  ASP B 358 "
        pdb=" CG  ASP B 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.37   -5.77 1.00e+00 1.00e+00 3.33e+01
  angle pdb=" CA  ASP E 358 "
        pdb=" CB  ASP E 358 "
        pdb=" CG  ASP E 358 "
      ideal   model   delta    sigma   weight residual
     112.60  117.10   -4.50 1.00e+00 1.00e+00 2.03e+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  117.06   -4.46 1.00e+00 1.00e+00 1.99e+01
  angle pdb=" CB  HIS E 329 "
        pdb=" CG  HIS E 329 "
        pdb=" CD2 HIS E 329 "
      ideal   model   delta    sigma   weight residual
     131.20  125.44    5.76 1.30e+00 5.92e-01 1.96e+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  117.03   -4.43 1.00e+00 1.00e+00 1.96e+01
  ... (remaining 12907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 2936
       17.39 -    34.77: 164
       34.77 -    52.16: 71
       52.16 -    69.54: 87
       69.54 -    86.93: 6
  Dihedral angle restraints: 3264
    sinusoidal: 1866
      harmonic: 1398
  Sorted by residual:
  dihedral pdb=" C   LYS F 331 "
           pdb=" N   LYS F 331 "
           pdb=" CA  LYS F 331 "
           pdb=" CB  LYS F 331 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.47    9.87     0      2.50e+00 1.60e-01 1.56e+01
  dihedral pdb=" C   LYS B 331 "
           pdb=" N   LYS B 331 "
           pdb=" CA  LYS B 331 "
           pdb=" CB  LYS B 331 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.81    9.21     0      2.50e+00 1.60e-01 1.36e+01
  dihedral pdb=" C   LYS E 331 "
           pdb=" N   LYS E 331 "
           pdb=" CA  LYS E 331 "
           pdb=" CB  LYS E 331 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.71    9.11     0      2.50e+00 1.60e-01 1.33e+01
  ... (remaining 3261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.067: 314
       0.067 -    0.133: 173
       0.133 -    0.199: 29
       0.199 -    0.265: 5
       0.265 -    0.332: 7
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  LYS F 331 "
            pdb=" N   LYS F 331 "
            pdb=" C   LYS F 331 "
            pdb=" CB  LYS F 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" CA  LYS B 331 "
            pdb=" N   LYS B 331 "
            pdb=" C   LYS B 331 "
            pdb=" CB  LYS B 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  LYS E 331 "
            pdb=" N   LYS E 331 "
            pdb=" C   LYS E 331 "
            pdb=" CB  LYS E 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.65e+00
  ... (remaining 525 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.141 2.00e-02 2.50e+03   6.19e-02 1.15e+02
        pdb=" CG  TYR F 310 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.129 2.00e-02 2.50e+03
        pdb=" HD1 TYR F 310 "   -0.013 2.00e-02 2.50e+03
        pdb=" HD2 TYR F 310 "   -0.040 2.00e-02 2.50e+03
        pdb=" HE1 TYR F 310 "   -0.027 2.00e-02 2.50e+03
        pdb=" HE2 TYR F 310 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 310 "    0.123 2.00e-02 2.50e+03   5.16e-02 7.98e+01
        pdb=" CG  TYR D 310 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 310 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 310 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 310 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D 310 "    0.096 2.00e-02 2.50e+03
        pdb=" HD1 TYR D 310 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD2 TYR D 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" HE1 TYR D 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" HE2 TYR D 310 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 336 "    0.071 2.00e-02 2.50e+03   6.87e-02 7.08e+01
        pdb=" CD  GLN A 336 "   -0.018 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 336 "   -0.053 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 336 "   -0.061 2.00e-02 2.50e+03
        pdb="HE21 GLN A 336 "   -0.056 2.00e-02 2.50e+03
        pdb="HE22 GLN A 336 "    0.116 2.00e-02 2.50e+03
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 597
        2.17 -     2.78: 12050
        2.78 -     3.39: 18264
        3.39 -     3.99: 25160
        3.99 -     4.60: 34497
  Nonbonded interactions: 90568
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.565 2.450
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.583 2.450
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.589 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.616 2.450
  ... (remaining 90563 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.140
  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:             0.110
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.910
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
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   0.036   3498  Z= 0.732
  Angle     :  1.876   7.705   4680  Z= 1.233
  Chirality :  0.083   0.332    528
  Planarity :  0.010   0.072    594
  Dihedral  : 10.800  86.926   1344
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.003   HIS B 362 
 PHE   0.033   0.009   PHE B 346 
 TYR   0.127   0.043   TYR F 310 
 ARG   0.006   0.002   ARG B 379 

*********************** 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
  125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.7490 (tttt) cc_final: 0.7017 (ttmt)
REVERT: A  375 LYS cc_start: 0.7480 (tttt) cc_final: 0.7117 (tttm)
REVERT: C  311 LYS cc_start: 0.8435 (mttt) cc_final: 0.8036 (mtmt)
REVERT: C  317 LYS cc_start: 0.7723 (mttt) cc_final: 0.7465 (mtpt)
REVERT: C  327 ASN cc_start: 0.8060 (m-40) cc_final: 0.7756 (m110)
REVERT: C  340 LYS cc_start: 0.8217 (tttt) cc_final: 0.7634 (ttmt)
REVERT: C  370 LYS cc_start: 0.7845 (tttm) cc_final: 0.7622 (tttt)
REVERT: C  372 GLU cc_start: 0.7660 (tt0) cc_final: 0.7373 (tt0)
REVERT: C  375 LYS cc_start: 0.8195 (tttt) cc_final: 0.7866 (tttp)
REVERT: E  311 LYS cc_start: 0.7968 (mttt) cc_final: 0.7280 (tppt)
REVERT: E  349 ARG cc_start: 0.6304 (mtm180) cc_final: 0.5911 (mmm160)
REVERT: B  348 ASP cc_start: 0.8291 (t0) cc_final: 0.8003 (t0)
REVERT: B  351 GLN cc_start: 0.7106 (tt0) cc_final: 0.6608 (mt0)
REVERT: B  375 LYS cc_start: 0.7659 (tttt) cc_final: 0.7363 (ttmt)
REVERT: D  311 LYS cc_start: 0.8023 (mttt) cc_final: 0.7754 (pttp)
REVERT: D  317 LYS cc_start: 0.7895 (mttt) cc_final: 0.7331 (mtmt)
REVERT: D  340 LYS cc_start: 0.7997 (tttt) cc_final: 0.7583 (mtpt)
REVERT: D  351 GLN cc_start: 0.8048 (tt0) cc_final: 0.7480 (mt0)
REVERT: D  375 LYS cc_start: 0.8017 (tttt) cc_final: 0.7771 (ttmt)
REVERT: F  311 LYS cc_start: 0.7765 (mttt) cc_final: 0.7268 (mmtm)
REVERT: F  351 GLN cc_start: 0.7375 (tt0) cc_final: 0.6880 (mt0)
REVERT: F  375 LYS cc_start: 0.7960 (tttt) cc_final: 0.7660 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.6308
  time to fit residues: 87.3852
Evaluate side-chains
  87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 330 HIS
B 327 ASN
D 327 ASN
F 327 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.136120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.119066 restraints weight = 12857.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 1.97
r_work: 0.3813 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3498  Z= 0.283
  Angle     :  0.555   4.200   4680  Z= 0.285
  Chirality :  0.052   0.132    528
  Planarity :  0.004   0.036    594
  Dihedral  :  5.016  13.399    462
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  4.29 %
    Favored  : 94.95 %
  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: -1.38 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.04 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 374 
 PHE   0.012   0.002   PHE F 346 
 TYR   0.013   0.003   TYR D 310 
 ARG   0.005   0.001   ARG C 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
  80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8260 (tttt) cc_final: 0.7786 (ttmt)
REVERT: A  342 GLU cc_start: 0.7448 (mp0) cc_final: 0.7248 (mp0)
REVERT: A  375 LYS cc_start: 0.8145 (tttt) cc_final: 0.7794 (tttm)
REVERT: C  311 LYS cc_start: 0.8712 (mttt) cc_final: 0.8294 (mtmt)
REVERT: C  375 LYS cc_start: 0.8548 (tttt) cc_final: 0.8249 (tttp)
REVERT: E  311 LYS cc_start: 0.8160 (mttt) cc_final: 0.7438 (tppt)
REVERT: E  348 ASP cc_start: 0.8085 (t0) cc_final: 0.7831 (t0)
REVERT: E  349 ARG cc_start: 0.6683 (mtm180) cc_final: 0.6268 (mmp-170)
REVERT: B  348 ASP cc_start: 0.8838 (t0) cc_final: 0.8631 (t70)
REVERT: B  351 GLN cc_start: 0.8203 (tt0) cc_final: 0.7945 (mt0)
REVERT: B  375 LYS cc_start: 0.8350 (tttt) cc_final: 0.8010 (ttmt)
REVERT: D  311 LYS cc_start: 0.8546 (mttt) cc_final: 0.8030 (pttp)
REVERT: F  311 LYS cc_start: 0.8228 (mttt) cc_final: 0.7819 (mmtm)
REVERT: F  351 GLN cc_start: 0.8242 (tt0) cc_final: 0.8027 (mt0)
  outliers start: 3
  outliers final: 2
  residues processed: 79
  average time/residue: 0.7201
  time to fit residues: 62.8000
Evaluate side-chains
  65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain C residue  324 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
C 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.129010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.113265 restraints weight = 13671.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 1.89
r_work: 0.3740 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3648 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.4430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3498  Z= 0.294
  Angle     :  0.518   4.088   4680  Z= 0.266
  Chirality :  0.051   0.127    528
  Planarity :  0.004   0.041    594
  Dihedral  :  4.810  12.075    462
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.57 %
    Favored  : 92.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.15 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 330 
 PHE   0.009   0.001   PHE B 346 
 TYR   0.016   0.003   TYR F 310 
 ARG   0.008   0.001   ARG C 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
  84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8176 (tttt) cc_final: 0.7723 (ttmt)
REVERT: A  349 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7340 (mtp85)
REVERT: A  375 LYS cc_start: 0.8264 (tttt) cc_final: 0.8023 (tttm)
REVERT: C  311 LYS cc_start: 0.8705 (mttt) cc_final: 0.8298 (ttpt)
REVERT: C  340 LYS cc_start: 0.8462 (tttt) cc_final: 0.8015 (ttmt)
REVERT: C  349 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7599 (mtt90)
REVERT: E  311 LYS cc_start: 0.8180 (mttt) cc_final: 0.7507 (tppt)
REVERT: E  347 LYS cc_start: 0.8515 (mppt) cc_final: 0.8183 (mmtp)
REVERT: E  348 ASP cc_start: 0.8128 (t0) cc_final: 0.7907 (t0)
REVERT: E  349 ARG cc_start: 0.6695 (mtm180) cc_final: 0.6306 (mmp-170)
REVERT: B  351 GLN cc_start: 0.8352 (tt0) cc_final: 0.8035 (mt0)
REVERT: B  375 LYS cc_start: 0.8447 (tttt) cc_final: 0.8113 (ttmt)
REVERT: D  311 LYS cc_start: 0.8566 (mttt) cc_final: 0.8058 (pttp)
REVERT: D  321 LYS cc_start: 0.8529 (mttt) cc_final: 0.7952 (mtpt)
REVERT: D  340 LYS cc_start: 0.8172 (tttt) cc_final: 0.7820 (mtpt)
REVERT: D  351 GLN cc_start: 0.8362 (tt0) cc_final: 0.8155 (mt0)
REVERT: D  375 LYS cc_start: 0.8555 (tttt) cc_final: 0.8254 (ttmt)
REVERT: F  311 LYS cc_start: 0.8304 (mttt) cc_final: 0.7859 (mmtt)
REVERT: F  351 GLN cc_start: 0.8300 (tt0) cc_final: 0.8041 (mt0)
REVERT: F  375 LYS cc_start: 0.8470 (tttt) cc_final: 0.8118 (ttmt)
  outliers start: 4
  outliers final: 3
  residues processed: 83
  average time/residue: 0.8126
  time to fit residues: 73.5114
Evaluate side-chains
  83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  324 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   overall best weight:    2.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.127957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.111932 restraints weight = 13828.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 1.92
r_work: 0.3746 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3657 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.4865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3498  Z= 0.214
  Angle     :  0.475   3.825   4680  Z= 0.240
  Chirality :  0.051   0.125    528
  Planarity :  0.003   0.025    594
  Dihedral  :  4.558  11.578    462
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  7.83 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.36), 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   0.002   0.001   HIS E 374 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.004   0.000   ARG C 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
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8185 (tttt) cc_final: 0.7725 (ttmt)
REVERT: A  349 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7423 (mtp85)
REVERT: A  375 LYS cc_start: 0.8324 (tttt) cc_final: 0.8039 (tttm)
REVERT: C  311 LYS cc_start: 0.8676 (mttt) cc_final: 0.8312 (ttpt)
REVERT: E  311 LYS cc_start: 0.8174 (mttt) cc_final: 0.7556 (tppt)
REVERT: E  347 LYS cc_start: 0.8486 (mppt) cc_final: 0.7908 (mptt)
REVERT: E  348 ASP cc_start: 0.8111 (t0) cc_final: 0.7878 (t0)
REVERT: E  349 ARG cc_start: 0.6650 (mtm180) cc_final: 0.6149 (mmm160)
REVERT: B  321 LYS cc_start: 0.8167 (mttt) cc_final: 0.7694 (mtpt)
REVERT: B  349 ARG cc_start: 0.8318 (mtt180) cc_final: 0.8085 (mtp180)
REVERT: B  351 GLN cc_start: 0.8333 (tt0) cc_final: 0.8117 (mt0)
REVERT: B  358 ASP cc_start: 0.7643 (m-30) cc_final: 0.7364 (t0)
REVERT: B  375 LYS cc_start: 0.8457 (tttt) cc_final: 0.8128 (ttmt)
REVERT: D  311 LYS cc_start: 0.8526 (mttt) cc_final: 0.8008 (pttp)
REVERT: F  311 LYS cc_start: 0.8254 (mttt) cc_final: 0.7805 (mmtt)
REVERT: F  351 GLN cc_start: 0.8259 (tt0) cc_final: 0.8000 (mt0)
REVERT: F  375 LYS cc_start: 0.8366 (tttt) cc_final: 0.7990 (ttmt)
  outliers start: 3
  outliers final: 3
  residues processed: 72
  average time/residue: 0.7860
  time to fit residues: 61.9893
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  324 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.129328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.113142 restraints weight = 13613.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 1.93
r_work: 0.3740 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3651 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.5116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3498  Z= 0.205
  Angle     :  0.467   4.122   4680  Z= 0.234
  Chirality :  0.051   0.127    528
  Planarity :  0.003   0.043    594
  Dihedral  :  4.401  10.621    462
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  7.07 %
    Favored  : 91.67 %
  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: -1.62 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 374 
 PHE   0.005   0.001   PHE B 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.009   0.001   ARG C 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
  73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8172 (tttt) cc_final: 0.7727 (ttmt)
REVERT: A  375 LYS cc_start: 0.8336 (tttt) cc_final: 0.8063 (tttm)
REVERT: C  311 LYS cc_start: 0.8679 (mttt) cc_final: 0.8322 (ttpt)
REVERT: C  349 ARG cc_start: 0.7809 (mtt90) cc_final: 0.7603 (mtt90)
REVERT: E  311 LYS cc_start: 0.8112 (mttt) cc_final: 0.7508 (tppt)
REVERT: E  348 ASP cc_start: 0.8117 (t0) cc_final: 0.7903 (t0)
REVERT: E  349 ARG cc_start: 0.6601 (mtm180) cc_final: 0.6219 (mmp-170)
REVERT: B  321 LYS cc_start: 0.8166 (mttt) cc_final: 0.7701 (mtpt)
REVERT: B  340 LYS cc_start: 0.7778 (tttt) cc_final: 0.7445 (mtpt)
REVERT: B  349 ARG cc_start: 0.8369 (mtt180) cc_final: 0.8153 (mtp180)
REVERT: B  358 ASP cc_start: 0.7764 (m-30) cc_final: 0.7447 (t0)
REVERT: B  375 LYS cc_start: 0.8482 (tttt) cc_final: 0.8141 (ttmt)
REVERT: D  311 LYS cc_start: 0.8501 (mttt) cc_final: 0.7989 (pttp)
REVERT: F  311 LYS cc_start: 0.8268 (mttt) cc_final: 0.7811 (mmtt)
REVERT: F  351 GLN cc_start: 0.8249 (tt0) cc_final: 0.7951 (mt0)
REVERT: F  375 LYS cc_start: 0.8378 (tttt) cc_final: 0.8046 (ttmt)
  outliers start: 5
  outliers final: 3
  residues processed: 71
  average time/residue: 0.8201
  time to fit residues: 63.9677
Evaluate side-chains
  67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  324 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    2.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.127006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.111115 restraints weight = 13859.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 1.88
r_work: 0.3710 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.5323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3498  Z= 0.235
  Angle     :  0.471   3.800   4680  Z= 0.238
  Chirality :  0.051   0.124    528
  Planarity :  0.003   0.035    594
  Dihedral  :  4.374  10.564    462
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  7.58 %
    Favored  : 91.16 %
  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: -1.75 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 374 
 PHE   0.005   0.001   PHE B 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.006   0.001   ARG C 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
  82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8214 (tttt) cc_final: 0.7758 (ttmt)
REVERT: A  375 LYS cc_start: 0.8376 (tttt) cc_final: 0.8113 (tttm)
REVERT: C  311 LYS cc_start: 0.8698 (mttt) cc_final: 0.8270 (ttpt)
REVERT: C  340 LYS cc_start: 0.8411 (tttt) cc_final: 0.7979 (ttmt)
REVERT: E  311 LYS cc_start: 0.8111 (mttt) cc_final: 0.7438 (tppt)
REVERT: E  349 ARG cc_start: 0.6673 (mtm180) cc_final: 0.6249 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5072 (ptt90) cc_final: 0.4688 (ptt90)
REVERT: B  321 LYS cc_start: 0.8200 (mttt) cc_final: 0.7738 (mtpt)
REVERT: B  340 LYS cc_start: 0.7815 (tttt) cc_final: 0.7472 (mtpt)
REVERT: B  349 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8128 (mtp180)
REVERT: B  358 ASP cc_start: 0.7908 (m-30) cc_final: 0.7578 (t0)
REVERT: B  375 LYS cc_start: 0.8514 (tttt) cc_final: 0.8153 (ttmt)
REVERT: D  311 LYS cc_start: 0.8552 (mttt) cc_final: 0.8079 (pttp)
REVERT: D  321 LYS cc_start: 0.8506 (mttt) cc_final: 0.7934 (mtpt)
REVERT: D  340 LYS cc_start: 0.8287 (tttt) cc_final: 0.7958 (mtpt)
REVERT: D  375 LYS cc_start: 0.8545 (tttt) cc_final: 0.8255 (ttmt)
REVERT: F  311 LYS cc_start: 0.8298 (mttt) cc_final: 0.7811 (mmtt)
REVERT: F  340 LYS cc_start: 0.8091 (tttt) cc_final: 0.7697 (mtpt)
REVERT: F  351 GLN cc_start: 0.8241 (tt0) cc_final: 0.7934 (mt0)
REVERT: F  375 LYS cc_start: 0.8414 (tttt) cc_final: 0.8049 (ttmt)
  outliers start: 5
  outliers final: 3
  residues processed: 81
  average time/residue: 0.8747
  time to fit residues: 77.0008
Evaluate side-chains
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  324 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.130833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.114953 restraints weight = 13513.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.89
r_work: 0.3769 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3680 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.5443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3498  Z= 0.125
  Angle     :  0.438   3.811   4680  Z= 0.216
  Chirality :  0.051   0.125    528
  Planarity :  0.003   0.051    594
  Dihedral  :  4.057  10.196    462
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  8.84 %
    Favored  : 90.91 %
  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 : -1.20 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 362 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.007   0.001   TYR A 310 
 ARG   0.009   0.001   ARG C 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
  71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8192 (tttt) cc_final: 0.7756 (ttmt)
REVERT: A  375 LYS cc_start: 0.8421 (tttt) cc_final: 0.8143 (tttm)
REVERT: C  311 LYS cc_start: 0.8661 (mttt) cc_final: 0.8178 (ttpt)
REVERT: E  311 LYS cc_start: 0.8042 (mttt) cc_final: 0.7392 (tppt)
REVERT: E  349 ARG cc_start: 0.6642 (mtm180) cc_final: 0.6212 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5103 (ptt90) cc_final: 0.4726 (ptt90)
REVERT: B  321 LYS cc_start: 0.8169 (mttt) cc_final: 0.7701 (mtpt)
REVERT: B  340 LYS cc_start: 0.7725 (tttt) cc_final: 0.7414 (mtpt)
REVERT: B  349 ARG cc_start: 0.8370 (mtt180) cc_final: 0.8145 (mtp180)
REVERT: B  358 ASP cc_start: 0.7914 (m-30) cc_final: 0.7553 (t0)
REVERT: B  375 LYS cc_start: 0.8448 (tttt) cc_final: 0.8137 (ttmt)
REVERT: D  311 LYS cc_start: 0.8514 (mttt) cc_final: 0.8062 (pttp)
REVERT: F  311 LYS cc_start: 0.8231 (mttt) cc_final: 0.7748 (mmtt)
REVERT: F  351 GLN cc_start: 0.8121 (tt0) cc_final: 0.7877 (mt0)
REVERT: F  375 LYS cc_start: 0.8357 (tttt) cc_final: 0.8039 (ttmt)
  outliers start: 1
  outliers final: 0
  residues processed: 70
  average time/residue: 0.8331
  time to fit residues: 63.8448
Evaluate side-chains
  66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    2.0986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.127399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.111618 restraints weight = 13905.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.88
r_work: 0.3724 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3635 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.5610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3498  Z= 0.219
  Angle     :  0.469   4.454   4680  Z= 0.232
  Chirality :  0.050   0.123    528
  Planarity :  0.003   0.041    594
  Dihedral  :  4.148  10.337    462
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  8.08 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 330 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.008   0.002   TYR F 310 
 ARG   0.009   0.001   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
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8206 (tttt) cc_final: 0.7775 (ttmt)
REVERT: A  375 LYS cc_start: 0.8477 (tttt) cc_final: 0.8196 (tttm)
REVERT: C  311 LYS cc_start: 0.8704 (mttt) cc_final: 0.8239 (ttpt)
REVERT: C  340 LYS cc_start: 0.8429 (tttt) cc_final: 0.8002 (ttmt)
REVERT: E  311 LYS cc_start: 0.8130 (mttt) cc_final: 0.7466 (tppt)
REVERT: E  349 ARG cc_start: 0.6666 (mtm180) cc_final: 0.6151 (mmm160)
REVERT: E  379 ARG cc_start: 0.5158 (ptt90) cc_final: 0.4773 (ptt90)
REVERT: B  321 LYS cc_start: 0.8189 (mttt) cc_final: 0.7734 (mtpt)
REVERT: B  340 LYS cc_start: 0.7813 (tttt) cc_final: 0.7446 (mtpt)
REVERT: B  349 ARG cc_start: 0.8379 (mtt180) cc_final: 0.8147 (mtp180)
REVERT: B  358 ASP cc_start: 0.7970 (m-30) cc_final: 0.7588 (t0)
REVERT: B  375 LYS cc_start: 0.8470 (tttt) cc_final: 0.8166 (ttmt)
REVERT: D  311 LYS cc_start: 0.8555 (mttt) cc_final: 0.8090 (pttp)
REVERT: F  311 LYS cc_start: 0.8299 (mttt) cc_final: 0.7820 (mmtt)
REVERT: F  340 LYS cc_start: 0.8128 (tttt) cc_final: 0.7748 (mtpt)
REVERT: F  351 GLN cc_start: 0.8200 (tt0) cc_final: 0.7940 (mt0)
REVERT: F  375 LYS cc_start: 0.8380 (tttt) cc_final: 0.8060 (ttmt)
  outliers start: 2
  outliers final: 0
  residues processed: 71
  average time/residue: 0.8770
  time to fit residues: 67.6962
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   overall best weight:    2.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.125463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.109712 restraints weight = 13959.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 1.88
r_work: 0.3699 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.5699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3498  Z= 0.251
  Angle     :  0.483   3.826   4680  Z= 0.243
  Chirality :  0.051   0.124    528
  Planarity :  0.003   0.044    594
  Dihedral  :  4.302  10.611    462
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  8.33 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (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   0.002   0.001   HIS D 330 
 PHE   0.005   0.001   PHE B 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.009   0.001   ARG C 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
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8254 (tttt) cc_final: 0.7792 (ttmt)
REVERT: A  349 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7382 (mtm180)
REVERT: A  375 LYS cc_start: 0.8464 (tttt) cc_final: 0.8181 (tttm)
REVERT: C  311 LYS cc_start: 0.8700 (mttt) cc_final: 0.8449 (mttt)
REVERT: C  340 LYS cc_start: 0.8456 (tttt) cc_final: 0.8028 (ttmt)
REVERT: C  349 ARG cc_start: 0.7650 (mtt90) cc_final: 0.5271 (pmt-80)
REVERT: E  311 LYS cc_start: 0.8022 (mttt) cc_final: 0.7410 (tppt)
REVERT: E  349 ARG cc_start: 0.6699 (mtm180) cc_final: 0.6233 (mmp-170)
REVERT: B  321 LYS cc_start: 0.8214 (mttt) cc_final: 0.7728 (mtpt)
REVERT: B  340 LYS cc_start: 0.7833 (tttt) cc_final: 0.7458 (mtpt)
REVERT: B  349 ARG cc_start: 0.8399 (mtt180) cc_final: 0.8158 (mtp180)
REVERT: B  358 ASP cc_start: 0.7980 (m-30) cc_final: 0.7577 (t0)
REVERT: B  375 LYS cc_start: 0.8493 (tttt) cc_final: 0.8133 (ttmt)
REVERT: D  311 LYS cc_start: 0.8555 (mttt) cc_final: 0.8085 (pttp)
REVERT: D  321 LYS cc_start: 0.8550 (mttt) cc_final: 0.7998 (mtpt)
REVERT: D  340 LYS cc_start: 0.8268 (tttt) cc_final: 0.7961 (mtpt)
REVERT: D  375 LYS cc_start: 0.8613 (tttt) cc_final: 0.8317 (ttmt)
REVERT: F  311 LYS cc_start: 0.8299 (mttt) cc_final: 0.7823 (mmtt)
REVERT: F  340 LYS cc_start: 0.8177 (tttt) cc_final: 0.7813 (mtpt)
REVERT: F  351 GLN cc_start: 0.8208 (tt0) cc_final: 0.7918 (mt0)
REVERT: F  375 LYS cc_start: 0.8406 (tttt) cc_final: 0.8055 (ttmt)
  outliers start: 1
  outliers final: 1
  residues processed: 76
  average time/residue: 0.9296
  time to fit residues: 76.6010
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.126599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.110530 restraints weight = 14286.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.91
r_work: 0.3694 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3603 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.5720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3498  Z= 0.252
  Angle     :  0.480   3.825   4680  Z= 0.242
  Chirality :  0.050   0.124    528
  Planarity :  0.004   0.053    594
  Dihedral  :  4.315  10.757    462
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  8.59 %
    Favored  : 91.16 %
  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: -1.88 (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
 HIS   0.002   0.001   HIS D 374 
 PHE   0.005   0.001   PHE B 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.008   0.001   ARG C 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
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8258 (tttt) cc_final: 0.7768 (ttmt)
REVERT: A  349 ARG cc_start: 0.7641 (mtp85) cc_final: 0.7349 (mtm180)
REVERT: A  375 LYS cc_start: 0.8436 (tttt) cc_final: 0.8149 (tttm)
REVERT: C  311 LYS cc_start: 0.8691 (mttt) cc_final: 0.8289 (ttpt)
REVERT: C  340 LYS cc_start: 0.8452 (tttt) cc_final: 0.8028 (ttmt)
REVERT: C  349 ARG cc_start: 0.7657 (mtt90) cc_final: 0.5231 (pmt-80)
REVERT: E  311 LYS cc_start: 0.8096 (mttt) cc_final: 0.7459 (tppt)
REVERT: E  349 ARG cc_start: 0.6720 (mtm180) cc_final: 0.6210 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5060 (ptt90) cc_final: 0.4847 (ptt90)
REVERT: B  321 LYS cc_start: 0.8187 (mttt) cc_final: 0.7699 (mtpt)
REVERT: B  340 LYS cc_start: 0.7797 (tttt) cc_final: 0.7428 (mtpt)
REVERT: B  349 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8133 (mtp180)
REVERT: B  375 LYS cc_start: 0.8434 (tttt) cc_final: 0.8108 (ttmt)
REVERT: D  311 LYS cc_start: 0.8542 (mttt) cc_final: 0.8038 (pttp)
REVERT: D  317 LYS cc_start: 0.8061 (mttt) cc_final: 0.7721 (mtmt)
REVERT: D  321 LYS cc_start: 0.8562 (mttt) cc_final: 0.7999 (mtpt)
REVERT: D  340 LYS cc_start: 0.8279 (tttt) cc_final: 0.7899 (mttt)
REVERT: D  375 LYS cc_start: 0.8628 (tttt) cc_final: 0.8325 (ttmt)
REVERT: F  311 LYS cc_start: 0.8307 (mttt) cc_final: 0.7827 (mmtt)
REVERT: F  340 LYS cc_start: 0.8185 (tttt) cc_final: 0.7816 (mtpt)
REVERT: F  351 GLN cc_start: 0.8197 (tt0) cc_final: 0.7900 (mt0)
REVERT: F  375 LYS cc_start: 0.8402 (tttt) cc_final: 0.8047 (ttmt)
  outliers start: 1
  outliers final: 1
  residues processed: 76
  average time/residue: 0.9311
  time to fit residues: 76.7264
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.128661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.112228 restraints weight = 13933.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 1.88
r_work: 0.3743 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3654 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.5786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3498  Z= 0.184
  Angle     :  0.462   3.800   4680  Z= 0.230
  Chirality :  0.051   0.123    528
  Planarity :  0.004   0.049    594
  Dihedral  :  4.202  11.140    462
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  9.34 %
    Favored  : 90.40 %
  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: -1.84 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.39 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 374 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.007   0.002   TYR F 310 
 ARG   0.008   0.001   ARG C 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4937.00 seconds
wall clock time: 84 minutes 20.29 seconds (5060.29 seconds total)