Starting phenix.real_space_refine
on Wed Feb 12 02:46:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8z_18266/02_2025/8q8z_18266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8z_18266/02_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_18266/02_2025/8q8z_18266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8z_18266/02_2025/8q8z_18266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8z_18266/02_2025/8q8z_18266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8z_18266/02_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-5592/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: 4.52, per 1000 atoms: 0.64
  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: 1.51
  Conformation dependent library (CDL) restraints added in 635.1 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: 0.69
  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: 2.39

  Time building geometry restraints manager: 1.88 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:             3.070
  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:             0.120
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.330
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  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:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.230
-------------------------------------------------------------------------------
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  : 0.568 
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: 0.6511
  time to fit residues: 89.8845
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  : 0.763 
-------------------------------------------------------------------------------
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 = 0.119067 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: 0.8303
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  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8262 (tttt) cc_final: 0.7790 (ttmt)
REVERT: A  375 LYS cc_start: 0.8147 (tttt) cc_final: 0.7798 (tttm)
REVERT: C  311 LYS cc_start: 0.8715 (mttt) cc_final: 0.8296 (mtmt)
REVERT: C  375 LYS cc_start: 0.8549 (tttt) cc_final: 0.8251 (tttp)
REVERT: E  311 LYS cc_start: 0.8161 (mttt) cc_final: 0.7442 (tppt)
REVERT: E  348 ASP cc_start: 0.8088 (t0) cc_final: 0.7836 (t0)
REVERT: E  349 ARG cc_start: 0.6691 (mtm180) cc_final: 0.6278 (mmp-170)
REVERT: B  348 ASP cc_start: 0.8841 (t0) cc_final: 0.8633 (t70)
REVERT: B  351 GLN cc_start: 0.8202 (tt0) cc_final: 0.7945 (mt0)
REVERT: B  375 LYS cc_start: 0.8353 (tttt) cc_final: 0.8014 (ttmt)
REVERT: D  311 LYS cc_start: 0.8547 (mttt) cc_final: 0.8032 (pttp)
REVERT: F  311 LYS cc_start: 0.8228 (mttt) cc_final: 0.7821 (mmtm)
REVERT: F  351 GLN cc_start: 0.8241 (tt0) cc_final: 0.8027 (mt0)
  outliers start: 3
  outliers final: 2
  residues processed: 79
  average time/residue: 0.7337
  time to fit residues: 63.7564
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  : 0.528 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.127250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.111634 restraints weight = 13858.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 1.87
r_work: 0.3711 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.4490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3498  Z= 0.373
  Angle     :  0.562   4.188   4680  Z= 0.291
  Chirality :  0.052   0.126    528
  Planarity :  0.004   0.033    594
  Dihedral  :  4.953  12.437    462
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  6.57 %
    Favored  : 92.68 %
  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: -1.67 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.27 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 374 
 PHE   0.012   0.002   PHE B 346 
 TYR   0.017   0.004   TYR F 310 
 ARG   0.007   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
  86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8274 (tttt) cc_final: 0.7784 (ttmt)
REVERT: A  375 LYS cc_start: 0.8275 (tttt) cc_final: 0.8017 (tttm)
REVERT: C  311 LYS cc_start: 0.8714 (mttt) cc_final: 0.8464 (mttt)
REVERT: C  340 LYS cc_start: 0.8455 (tttt) cc_final: 0.8014 (ttmt)
REVERT: C  347 LYS cc_start: 0.8529 (mppt) cc_final: 0.8313 (mppt)
REVERT: E  311 LYS cc_start: 0.8194 (mttt) cc_final: 0.7490 (tppt)
REVERT: E  347 LYS cc_start: 0.8493 (mppt) cc_final: 0.7847 (mptt)
REVERT: E  348 ASP cc_start: 0.8145 (t0) cc_final: 0.7934 (t0)
REVERT: E  349 ARG cc_start: 0.6679 (mtm180) cc_final: 0.6205 (mmm160)
REVERT: B  321 LYS cc_start: 0.8188 (mttt) cc_final: 0.7736 (mtpt)
REVERT: B  340 LYS cc_start: 0.7773 (tttt) cc_final: 0.7397 (mtpt)
REVERT: B  351 GLN cc_start: 0.8402 (tt0) cc_final: 0.8060 (mt0)
REVERT: B  375 LYS cc_start: 0.8483 (tttt) cc_final: 0.8165 (ttmt)
REVERT: D  311 LYS cc_start: 0.8583 (mttt) cc_final: 0.8098 (pttp)
REVERT: D  317 LYS cc_start: 0.8095 (mttt) cc_final: 0.7676 (mtmt)
REVERT: D  321 LYS cc_start: 0.8572 (mttt) cc_final: 0.8010 (mtpt)
REVERT: D  340 LYS cc_start: 0.8209 (tttt) cc_final: 0.7835 (mtpt)
REVERT: D  375 LYS cc_start: 0.8597 (tttt) cc_final: 0.8304 (ttmt)
REVERT: F  311 LYS cc_start: 0.8308 (mttt) cc_final: 0.7862 (mmtt)
REVERT: F  375 LYS cc_start: 0.8474 (tttt) cc_final: 0.8106 (ttmt)
  outliers start: 3
  outliers final: 3
  residues processed: 86
  average time/residue: 0.8995
  time to fit residues: 84.3836
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  : 0.721 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 10 optimal weight:    0.1980
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0040
   chunk 16 optimal weight:    0.9980
   overall best weight:    1.2396

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.125840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.109569 restraints weight = 13849.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 1.95
r_work: 0.3765 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3676 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.5010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3498  Z= 0.153
  Angle     :  0.470   3.783   4680  Z= 0.235
  Chirality :  0.051   0.128    528
  Planarity :  0.003   0.037    594
  Dihedral  :  4.498  10.782    462
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.08 %
    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: -1.60 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.21 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 362 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.008   0.001   TYR A 310 
 ARG   0.008   0.001   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
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7288 (mtp85)
REVERT: A  375 LYS cc_start: 0.8266 (tttt) cc_final: 0.7976 (tttm)
REVERT: C  311 LYS cc_start: 0.8654 (mttt) cc_final: 0.8257 (ttpt)
REVERT: C  349 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7532 (mtt90)
REVERT: E  311 LYS cc_start: 0.8117 (mttt) cc_final: 0.7490 (tppt)
REVERT: E  347 LYS cc_start: 0.8433 (mppt) cc_final: 0.7974 (mmtm)
REVERT: E  348 ASP cc_start: 0.8054 (t0) cc_final: 0.7830 (t0)
REVERT: E  349 ARG cc_start: 0.6683 (mtm180) cc_final: 0.6279 (mmp-170)
REVERT: B  321 LYS cc_start: 0.8157 (mttt) cc_final: 0.7673 (mtpt)
REVERT: B  340 LYS cc_start: 0.7765 (tttt) cc_final: 0.7380 (mtpt)
REVERT: B  351 GLN cc_start: 0.8295 (tt0) cc_final: 0.8084 (mt0)
REVERT: B  358 ASP cc_start: 0.7644 (m-30) cc_final: 0.7346 (t0)
REVERT: B  375 LYS cc_start: 0.8425 (tttt) cc_final: 0.8092 (ttmt)
REVERT: D  311 LYS cc_start: 0.8516 (mttt) cc_final: 0.7972 (pttp)
REVERT: D  353 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8389 (tttp)
REVERT: F  311 LYS cc_start: 0.8203 (mttt) cc_final: 0.7653 (mmtm)
REVERT: F  353 LYS cc_start: 0.8406 (tttp) cc_final: 0.8170 (tttm)
REVERT: F  375 LYS cc_start: 0.8337 (tttt) cc_final: 0.7959 (ttmt)
  outliers start: 4
  outliers final: 2
  residues processed: 68
  average time/residue: 0.8473
  time to fit residues: 62.8620
Evaluate side-chains
  66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  353 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 29 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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 = 0.4061 r_free = 0.4061 target = 0.126261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.110146 restraints weight = 13852.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 1.88
r_work: 0.3716 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.5204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3498  Z= 0.241
  Angle     :  0.483   3.896   4680  Z= 0.244
  Chirality :  0.051   0.122    528
  Planarity :  0.003   0.029    594
  Dihedral  :  4.440  10.668    462
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  6.82 %
    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: -1.70 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 374 
 PHE   0.007   0.001   PHE B 346 
 TYR   0.011   0.002   TYR F 310 
 ARG   0.007   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
  81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.571 
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: 0.8202 (tttt) cc_final: 0.7744 (ttmt)
REVERT: A  349 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7397 (mtp85)
REVERT: A  375 LYS cc_start: 0.8341 (tttt) cc_final: 0.8071 (tttm)
REVERT: C  311 LYS cc_start: 0.8681 (mttt) cc_final: 0.8315 (ttpt)
REVERT: C  340 LYS cc_start: 0.8433 (tttt) cc_final: 0.7993 (ttmt)
REVERT: E  311 LYS cc_start: 0.8140 (mttt) cc_final: 0.7496 (tppt)
REVERT: E  348 ASP cc_start: 0.8125 (t0) cc_final: 0.7915 (t0)
REVERT: E  349 ARG cc_start: 0.6676 (mtm180) cc_final: 0.6171 (mmm160)
REVERT: B  321 LYS cc_start: 0.8184 (mttt) cc_final: 0.7721 (mtpt)
REVERT: B  340 LYS cc_start: 0.7792 (tttt) cc_final: 0.7453 (mtpt)
REVERT: B  358 ASP cc_start: 0.7814 (m-30) cc_final: 0.7488 (t0)
REVERT: B  375 LYS cc_start: 0.8472 (tttt) cc_final: 0.8137 (ttmt)
REVERT: D  311 LYS cc_start: 0.8506 (mttt) cc_final: 0.7998 (pttp)
REVERT: D  321 LYS cc_start: 0.8529 (mttt) cc_final: 0.7939 (mtpt)
REVERT: D  340 LYS cc_start: 0.8285 (tttt) cc_final: 0.7926 (mtpt)
REVERT: D  375 LYS cc_start: 0.8552 (tttt) cc_final: 0.8266 (ttmt)
REVERT: F  311 LYS cc_start: 0.8261 (mttt) cc_final: 0.7814 (mmtt)
REVERT: F  340 LYS cc_start: 0.7976 (tttt) cc_final: 0.7573 (mtpt)
REVERT: F  375 LYS cc_start: 0.8417 (tttt) cc_final: 0.8050 (ttmt)
  outliers start: 6
  outliers final: 4
  residues processed: 78
  average time/residue: 0.9465
  time to fit residues: 80.0087
Evaluate side-chains
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain F residue  348 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   overall best weight:    3.0588

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.124790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.108901 restraints weight = 14074.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 1.86
r_work: 0.3679 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.5444

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= 0.293
  Angle     :  0.501   3.923   4680  Z= 0.255
  Chirality :  0.051   0.125    528
  Planarity :  0.004   0.047    594
  Dihedral  :  4.529  11.357    462
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  6.82 %
    Favored  : 91.92 %
  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: -1.98 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.50 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.007   0.001   PHE B 346 
 TYR   0.011   0.003   TYR F 310 
 ARG   0.009   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
  79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.459 
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: 0.8238 (tttt) cc_final: 0.7798 (ttmt)
REVERT: A  375 LYS cc_start: 0.8383 (tttt) cc_final: 0.8113 (tttm)
REVERT: C  311 LYS cc_start: 0.8691 (mttt) cc_final: 0.8330 (ttpt)
REVERT: C  340 LYS cc_start: 0.8412 (tttt) cc_final: 0.8011 (ttmt)
REVERT: E  311 LYS cc_start: 0.8068 (mttt) cc_final: 0.7494 (tppt)
REVERT: E  349 ARG cc_start: 0.6637 (mtm180) cc_final: 0.6128 (mmm160)
REVERT: B  321 LYS cc_start: 0.8193 (mttt) cc_final: 0.7758 (mtpt)
REVERT: B  340 LYS cc_start: 0.7842 (tttt) cc_final: 0.7498 (mtpt)
REVERT: B  358 ASP cc_start: 0.7956 (m-30) cc_final: 0.7559 (t0)
REVERT: B  375 LYS cc_start: 0.8469 (tttt) cc_final: 0.8140 (ttmt)
REVERT: D  311 LYS cc_start: 0.8584 (mttt) cc_final: 0.8138 (pttp)
REVERT: D  317 LYS cc_start: 0.8093 (mttt) cc_final: 0.7713 (mtmt)
REVERT: D  321 LYS cc_start: 0.8559 (mttt) cc_final: 0.7996 (mtpt)
REVERT: D  340 LYS cc_start: 0.8308 (tttt) cc_final: 0.7898 (mttt)
REVERT: D  375 LYS cc_start: 0.8620 (tttt) cc_final: 0.8315 (ttmt)
REVERT: F  311 LYS cc_start: 0.8335 (mttt) cc_final: 0.7859 (mmtt)
REVERT: F  340 LYS cc_start: 0.8089 (tttt) cc_final: 0.7679 (mtpt)
REVERT: F  375 LYS cc_start: 0.8424 (tttt) cc_final: 0.8055 (ttmt)
  outliers start: 5
  outliers final: 3
  residues processed: 76
  average time/residue: 0.9751
  time to fit residues: 80.0207
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain F residue  348 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0970
   chunk 12 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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 = 0.4070 r_free = 0.4070 target = 0.127565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.111761 restraints weight = 13798.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 1.85
r_work: 0.3725 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.5518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3498  Z= 0.157
  Angle     :  0.458   4.074   4680  Z= 0.227
  Chirality :  0.051   0.125    528
  Planarity :  0.003   0.046    594
  Dihedral  :  4.243  10.744    462
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  8.84 %
    Favored  : 90.66 %
  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 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (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   0.008   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
  70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8232 (tttt) cc_final: 0.7798 (ttmt)
REVERT: A  375 LYS cc_start: 0.8444 (tttt) cc_final: 0.8128 (tttp)
REVERT: C  311 LYS cc_start: 0.8641 (mttt) cc_final: 0.8286 (ttpt)
REVERT: C  375 LYS cc_start: 0.8640 (tttt) cc_final: 0.8356 (tttp)
REVERT: E  311 LYS cc_start: 0.8052 (mttt) cc_final: 0.7453 (tppt)
REVERT: E  349 ARG cc_start: 0.6691 (mtm180) cc_final: 0.6272 (mmp-170)
REVERT: B  358 ASP cc_start: 0.7969 (m-30) cc_final: 0.7577 (t0)
REVERT: B  375 LYS cc_start: 0.8459 (tttt) cc_final: 0.8146 (ttmt)
REVERT: D  311 LYS cc_start: 0.8548 (mttt) cc_final: 0.8061 (pttp)
REVERT: D  321 LYS cc_start: 0.8503 (mttt) cc_final: 0.7934 (mtpt)
REVERT: D  340 LYS cc_start: 0.8298 (tttt) cc_final: 0.7901 (mttt)
REVERT: D  375 LYS cc_start: 0.8575 (tttt) cc_final: 0.8296 (ttmt)
REVERT: F  311 LYS cc_start: 0.8294 (mttt) cc_final: 0.7829 (mmtt)
REVERT: F  340 LYS cc_start: 0.8088 (tttt) cc_final: 0.7704 (mtpt)
REVERT: F  353 LYS cc_start: 0.8400 (tttp) cc_final: 0.8192 (tttm)
REVERT: F  375 LYS cc_start: 0.8390 (tttt) cc_final: 0.8041 (ttmt)
  outliers start: 2
  outliers final: 2
  residues processed: 69
  average time/residue: 0.8908
  time to fit residues: 67.0842
Evaluate side-chains
  66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain F residue  348 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.4076 r_free = 0.4076 target = 0.127984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.112251 restraints weight = 13917.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 1.86
r_work: 0.3735 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.5661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3498  Z= 0.159
  Angle     :  0.460   4.480   4680  Z= 0.226
  Chirality :  0.051   0.126    528
  Planarity :  0.004   0.051    594
  Dihedral  :  4.150  10.344    462
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.08 %
    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: -1.77 (0.37), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.34 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B 362 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.008   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
  71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.629 
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: A  340 LYS cc_start: 0.8228 (tttt) cc_final: 0.7788 (ttmt)
REVERT: A  375 LYS cc_start: 0.8447 (tttt) cc_final: 0.7945 (ttmm)
REVERT: C  311 LYS cc_start: 0.8638 (mttt) cc_final: 0.8285 (ttpt)
REVERT: C  340 LYS cc_start: 0.8431 (tttt) cc_final: 0.7996 (ttmt)
REVERT: E  311 LYS cc_start: 0.8092 (mttt) cc_final: 0.7433 (tppt)
REVERT: E  349 ARG cc_start: 0.6690 (mtm180) cc_final: 0.6254 (mmp-170)
REVERT: E  379 ARG cc_start: 0.4953 (ptt90) cc_final: 0.4712 (ptt90)
REVERT: B  358 ASP cc_start: 0.7974 (m-30) cc_final: 0.7547 (t0)
REVERT: B  375 LYS cc_start: 0.8437 (tttt) cc_final: 0.8102 (ttmt)
REVERT: D  311 LYS cc_start: 0.8542 (mttt) cc_final: 0.8057 (pttp)
REVERT: D  321 LYS cc_start: 0.8494 (mttt) cc_final: 0.7918 (mtpt)
REVERT: D  340 LYS cc_start: 0.8269 (tttt) cc_final: 0.7891 (mttt)
REVERT: D  375 LYS cc_start: 0.8586 (tttt) cc_final: 0.8294 (ttmt)
REVERT: F  311 LYS cc_start: 0.8288 (mttt) cc_final: 0.7816 (mmtt)
REVERT: F  340 LYS cc_start: 0.8118 (tttt) cc_final: 0.7742 (mtpt)
REVERT: F  375 LYS cc_start: 0.8390 (tttt) cc_final: 0.8037 (ttmt)
  outliers start: 4
  outliers final: 3
  residues processed: 69
  average time/residue: 0.9212
  time to fit residues: 69.1244
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  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain F residue  348 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 15 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 39 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.131666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.115307 restraints weight = 13524.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 1.87
r_work: 0.3808 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.5737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3498  Z= 0.121
  Angle     :  0.437   3.623   4680  Z= 0.214
  Chirality :  0.051   0.124    528
  Planarity :  0.004   0.051    594
  Dihedral  :  3.912  10.862    462
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.84 %
    Favored  : 90.15 %
  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: -1.63 (0.38), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 362 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.006   0.001   TYR A 310 
 ARG   0.008   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
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.658 
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: A  311 LYS cc_start: 0.8012 (mttm) cc_final: 0.7797 (mtpp)
REVERT: A  340 LYS cc_start: 0.8193 (tttt) cc_final: 0.7759 (ttmt)
REVERT: A  375 LYS cc_start: 0.8440 (tttt) cc_final: 0.7938 (ttmm)
REVERT: C  311 LYS cc_start: 0.8567 (mttt) cc_final: 0.8237 (ttpt)
REVERT: C  340 LYS cc_start: 0.8439 (tttt) cc_final: 0.7999 (ttmt)
REVERT: E  311 LYS cc_start: 0.8024 (mttt) cc_final: 0.7363 (tppt)
REVERT: E  349 ARG cc_start: 0.6692 (mtm180) cc_final: 0.6078 (mmm160)
REVERT: E  379 ARG cc_start: 0.5133 (ptt90) cc_final: 0.4899 (ptt90)
REVERT: B  358 ASP cc_start: 0.7944 (m-30) cc_final: 0.7522 (t0)
REVERT: B  375 LYS cc_start: 0.8438 (tttt) cc_final: 0.8120 (ttmt)
REVERT: D  311 LYS cc_start: 0.8496 (mttt) cc_final: 0.8016 (pttp)
REVERT: F  311 LYS cc_start: 0.8236 (mttt) cc_final: 0.7746 (mmtt)
REVERT: F  340 LYS cc_start: 0.8144 (tttt) cc_final: 0.7757 (mtpt)
REVERT: F  349 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7835 (mtp180)
REVERT: F  353 LYS cc_start: 0.8383 (tttp) cc_final: 0.8171 (tttm)
REVERT: F  375 LYS cc_start: 0.8383 (tttt) cc_final: 0.8042 (ttmt)
  outliers start: 4
  outliers final: 4
  residues processed: 67
  average time/residue: 0.8881
  time to fit residues: 64.9760
Evaluate side-chains
  68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain F residue  348 ASP
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:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.4069 r_free = 0.4069 target = 0.127034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.110537 restraints weight = 14198.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 1.90
r_work: 0.3718 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.5738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3498  Z= 0.250
  Angle     :  0.470   3.860   4680  Z= 0.236
  Chirality :  0.050   0.123    528
  Planarity :  0.003   0.042    594
  Dihedral  :  4.153  10.250    462
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  9.34 %
    Favored  : 89.65 %
  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   0.002   0.001   HIS F 330 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.010   0.002   TYR B 310 
 ARG   0.005   0.001   ARG E 379 

********************** 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
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.566 
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  311 LYS cc_start: 0.8097 (mttm) cc_final: 0.7881 (mtpp)
REVERT: A  340 LYS cc_start: 0.8232 (tttt) cc_final: 0.7808 (ttmt)
REVERT: A  375 LYS cc_start: 0.8434 (tttt) cc_final: 0.8152 (tttm)
REVERT: C  311 LYS cc_start: 0.8623 (mttt) cc_final: 0.8273 (ttpt)
REVERT: C  340 LYS cc_start: 0.8462 (tttt) cc_final: 0.8044 (ttmt)
REVERT: E  311 LYS cc_start: 0.8068 (mttt) cc_final: 0.7384 (tppt)
REVERT: E  349 ARG cc_start: 0.6715 (mtm180) cc_final: 0.6220 (mmp-170)
REVERT: E  379 ARG cc_start: 0.5127 (ptt90) cc_final: 0.4900 (ptt90)
REVERT: B  321 LYS cc_start: 0.8160 (mttt) cc_final: 0.7657 (mtpt)
REVERT: B  340 LYS cc_start: 0.7796 (tttt) cc_final: 0.7419 (mtpt)
REVERT: B  375 LYS cc_start: 0.8461 (tttt) cc_final: 0.8131 (ttmt)
REVERT: D  311 LYS cc_start: 0.8524 (mttt) cc_final: 0.8019 (pttp)
REVERT: D  317 LYS cc_start: 0.8069 (mttt) cc_final: 0.7723 (mtmt)
REVERT: D  321 LYS cc_start: 0.8552 (mttt) cc_final: 0.7968 (mtpt)
REVERT: D  340 LYS cc_start: 0.8247 (tttt) cc_final: 0.7919 (mttt)
REVERT: D  375 LYS cc_start: 0.8634 (tttt) cc_final: 0.8331 (ttmt)
REVERT: F  311 LYS cc_start: 0.8290 (mttt) cc_final: 0.7800 (mmtt)
REVERT: F  340 LYS cc_start: 0.8191 (tttt) cc_final: 0.7789 (mtpt)
REVERT: F  375 LYS cc_start: 0.8405 (tttt) cc_final: 0.8052 (ttmt)
  outliers start: 4
  outliers final: 3
  residues processed: 76
  average time/residue: 0.9388
  time to fit residues: 77.0876
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain F residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.0370
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.3464

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.129403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.112850 restraints weight = 13775.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 1.89
r_work: 0.3756 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3667 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.5765

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= 0.156
  Angle     :  0.448   3.783   4680  Z= 0.221
  Chirality :  0.051   0.124    528
  Planarity :  0.003   0.043    594
  Dihedral  :  4.037  11.153    462
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  9.60 %
    Favored  : 89.65 %
  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: -1.76 (0.38), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B 362 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.006   0.001   TYR D 310 
 ARG   0.007   0.001   ARG C 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4910.83 seconds
wall clock time: 86 minutes 56.74 seconds (5216.74 seconds total)