Starting phenix.real_space_refine
on Wed Mar  5 20:35:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8f_18253/03_2025/8q8f_18253.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8f_18253/03_2025/8q8f_18253.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q8f_18253/03_2025/8q8f_18253.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8f_18253/03_2025/8q8f_18253.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8f_18253/03_2025/8q8f_18253.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8f_18253/03_2025/8q8f_18253.cif"
  }
  resolution = 2.93
  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: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2172      2.51       5
     N     642      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 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: 3468
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "D"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "F"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 3.60, per 1000 atoms: 1.04
  Number of scatterers: 3468
  At special positions: 0
  Unit cell: (111.24, 124.424, 36.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     648      8.00
     N     642      7.00
     C    2172      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 412.3 milliseconds
  

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 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 19 sheets defined
      0.0% alpha, 47.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.520A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   VAL A 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   VAL E 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE A 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.853A  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 322
      removed outlier: 6.441A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   SER C 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.537A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.441A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   SER C 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.537A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.302A  pdb=" N   ILE A 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 340
      removed outlier: 6.614A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 346
      removed outlier: 6.267A  pdb=" N   LYS A 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   PHE C 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 351 through 354
      removed outlier: 6.409A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.357A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   THR C 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ILE A 360 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.379A  pdb=" N   LYS A 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLU C 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ILE A 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   HIS C 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   THR A 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   LEU C 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   LYS A 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   PHE C 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   THR A 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LYS A 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   THR E 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   GLU A 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   LYS E 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   HIS A 374 " --> pdb=" O   LYS E 375 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   THR E 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU A 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.492A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.783A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 321
      removed outlier: 6.245A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.653A  pdb=" N   HIS B 329 " --> pdb=" O   HIS F 330 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 336 through 340
      removed outlier: 6.410A  pdb=" N   VAL B 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   LYS F 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL B 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 343 through 348
      removed outlier: 6.831A  pdb=" N   ASP D 348 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 8.998A  pdb=" N   LYS B 343 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 10.105A  pdb=" N   PHE F 346 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 9.035A  pdb=" N   ASP B 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
      removed outlier: 9.309A  pdb=" N   ASP F 348 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   LYS B 347 " --> pdb=" O   ASP F 348 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 351 through 354
      removed outlier: 6.744A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.286A  pdb=" N   ILE D 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 362
      removed outlier: 6.580A  pdb=" N   THR B 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 378
      removed outlier: 6.410A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    159 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.83

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1030
        1.33 -     1.45: 405
        1.45 -     1.58: 2081
        1.58 -     1.70: 0
        1.70 -     1.82: 6
  Bond restraints: 3522
  Sorted by residual:
  bond pdb=" CZ  ARG E 349 "
       pdb=" NH2 ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.24e+00
  bond pdb=" CZ  ARG A 349 "
       pdb=" NH2 ARG A 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.49e+00
  bond pdb=" CZ  ARG C 349 "
       pdb=" NH2 ARG C 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.40e+00
  bond pdb=" CZ  ARG B 379 "
       pdb=" NH2 ARG B 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.11e+00
  bond pdb=" CZ  ARG D 379 "
       pdb=" NH2 ARG D 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.91e+00
  ... (remaining 3517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 3406
        1.92 -     3.83: 1137
        3.83 -     5.75: 150
        5.75 -     7.66: 12
        7.66 -     9.58: 5
  Bond angle restraints: 4710
  Sorted by residual:
  angle pdb=" O   CYS D 322 "
        pdb=" C   CYS D 322 "
        pdb=" N   GLY D 323 "
      ideal   model   delta    sigma   weight residual
     123.25  115.67    7.58 1.14e+00 7.69e-01 4.43e+01
  angle pdb=" O   CYS B 322 "
        pdb=" C   CYS B 322 "
        pdb=" N   GLY B 323 "
      ideal   model   delta    sigma   weight residual
     123.17  115.44    7.73 1.21e+00 6.83e-01 4.08e+01
  angle pdb=" CA  CYS D 322 "
        pdb=" C   CYS D 322 "
        pdb=" N   GLY D 323 "
      ideal   model   delta    sigma   weight residual
     115.36  124.74   -9.38 1.48e+00 4.57e-01 4.01e+01
  angle pdb=" CA  CYS B 322 "
        pdb=" C   CYS B 322 "
        pdb=" N   GLY B 323 "
      ideal   model   delta    sigma   weight residual
     115.36  124.94   -9.58 1.53e+00 4.27e-01 3.92e+01
  angle pdb=" CA  PHE E 346 "
        pdb=" CB  PHE E 346 "
        pdb=" CG  PHE E 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.35   -5.55 1.00e+00 1.00e+00 3.08e+01
  ... (remaining 4705 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.81: 1899
       12.81 -    25.62: 176
       25.62 -    38.43: 42
       38.43 -    51.24: 12
       51.24 -    64.05: 13
  Dihedral angle restraints: 2142
    sinusoidal: 894
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CA  SER A 341 "
           pdb=" C   SER A 341 "
           pdb=" N   GLU A 342 "
           pdb=" CA  GLU A 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.23   28.77     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  SER C 341 "
           pdb=" C   SER C 341 "
           pdb=" N   GLU C 342 "
           pdb=" CA  GLU C 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.61   28.39     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" CA  LEU C 325 "
           pdb=" C   LEU C 325 "
           pdb=" N   GLY C 326 "
           pdb=" CA  GLY C 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.64  -28.36     0      5.00e+00 4.00e-02 3.22e+01
  ... (remaining 2139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 275
       0.061 -    0.122: 188
       0.122 -    0.183: 52
       0.183 -    0.243: 9
       0.243 -    0.304: 4
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  LYS B 347 "
            pdb=" N   LYS B 347 "
            pdb=" C   LYS B 347 "
            pdb=" CB  LYS B 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CA  LYS E 347 "
            pdb=" N   LYS E 347 "
            pdb=" C   LYS E 347 "
            pdb=" CB  LYS E 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.05e+00
  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    2.24    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 525 not shown)

  Planarity restraints: 600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.161 2.00e-02 2.50e+03   9.29e-02 1.73e+02
        pdb=" CG  TYR E 310 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.075 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.064 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "   -0.017 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.156 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.112 2.00e-02 2.50e+03   6.20e-02 7.69e+01
        pdb=" CG  TYR A 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.055 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.097 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 310 "   -0.085 2.00e-02 2.50e+03   4.92e-02 4.84e+01
        pdb=" CG  TYR B 310 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 310 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 310 "    0.043 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 310 "    0.037 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 310 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 310 "    0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR B 310 "   -0.081 2.00e-02 2.50e+03
  ... (remaining 597 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1592
        2.98 -     3.46: 2729
        3.46 -     3.94: 5654
        3.94 -     4.42: 5646
        4.42 -     4.90: 10814
  Nonbonded interactions: 26435
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.504 3.040
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.505 3.040
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.520 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.528 3.040
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.556 3.040
  ... (remaining 26430 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:             3.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.990
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:17.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
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   0.037   3522  Z= 0.745
  Angle     :  1.823   9.579   4710  Z= 1.219
  Chirality :  0.082   0.304    528
  Planarity :  0.010   0.093    600
  Dihedral  : 12.076  64.052   1350
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  1.77 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.21 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.018   0.003   HIS F 330 
 PHE   0.032   0.011   PHE B 346 
 TYR   0.161   0.039   TYR E 310 
 ARG   0.004   0.001   ARG E 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 139
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 SER cc_start: 0.8664 (p) cc_final: 0.8446 (p)
REVERT: A  321 LYS cc_start: 0.7354 (mttt) cc_final: 0.6833 (tttm)
REVERT: A  338 GLU cc_start: 0.7668 (tt0) cc_final: 0.7362 (mt-10)
REVERT: A  343 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7459 (mtpp)
REVERT: A  375 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7600 (tttt)
REVERT: B  321 LYS cc_start: 0.7366 (mttt) cc_final: 0.7128 (mttm)
REVERT: B  369 LYS cc_start: 0.7593 (tttt) cc_final: 0.7187 (tttt)
REVERT: C  314 ASP cc_start: 0.8341 (t0) cc_final: 0.7734 (t0)
REVERT: C  321 LYS cc_start: 0.8086 (mttt) cc_final: 0.7591 (tttm)
REVERT: C  375 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8156 (ttmt)
REVERT: D  310 TYR cc_start: 0.8866 (t80) cc_final: 0.8620 (t80)
REVERT: D  316 SER cc_start: 0.8442 (p) cc_final: 0.8225 (p)
REVERT: D  321 LYS cc_start: 0.7992 (mttt) cc_final: 0.7697 (mttm)
REVERT: E  321 LYS cc_start: 0.7487 (mttt) cc_final: 0.6983 (tttt)
REVERT: E  370 LYS cc_start: 0.8138 (tttt) cc_final: 0.7936 (tttm)
REVERT: E  372 GLU cc_start: 0.8334 (tt0) cc_final: 0.8110 (tt0)
REVERT: F  321 LYS cc_start: 0.7752 (mttt) cc_final: 0.7520 (mtmm)
  outliers start: 3
  outliers final: 0
  residues processed: 139
  average time/residue: 1.3703
  time to fit residues: 194.9628
Evaluate side-chains
  109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0770
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 24 optimal weight:    7.9990
   chunk 38 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.9144

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
C 336 GLN
C 359 ASN
C 362 HIS
E 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.130188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.110890 restraints weight = 4612.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.90
r_work: 0.3579 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3522  Z= 0.239
  Angle     :  0.654   7.202   4710  Z= 0.322
  Chirality :  0.050   0.150    528
  Planarity :  0.003   0.026    600
  Dihedral  :  5.917  20.719    468
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.15 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -1.68 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.27 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 330 
 PHE   0.016   0.002   PHE E 378 
 TYR   0.019   0.003   TYR F 310 
 ARG   0.003   0.000   ARG B 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.8241 (mttt) cc_final: 0.7966 (tttm)
REVERT: A  343 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7821 (tttt)
REVERT: B  321 LYS cc_start: 0.8492 (mttt) cc_final: 0.8256 (mttm)
REVERT: B  342 GLU cc_start: 0.5947 (pm20) cc_final: 0.5432 (tp30)
REVERT: B  369 LYS cc_start: 0.8584 (tttt) cc_final: 0.8347 (tttp)
REVERT: C  343 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8037 (tttt)
REVERT: D  321 LYS cc_start: 0.8670 (mttt) cc_final: 0.8424 (mttm)
REVERT: E  321 LYS cc_start: 0.8215 (mttt) cc_final: 0.8011 (tttt)
REVERT: E  343 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7906 (tttt)
REVERT: E  349 ARG cc_start: 0.7278 (mtm180) cc_final: 0.6788 (mpt90)
REVERT: E  369 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8410 (mttt)
REVERT: E  379 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6422 (mmp80)
REVERT: F  316 SER cc_start: 0.9162 (p) cc_final: 0.8936 (p)
  outliers start: 6
  outliers final: 1
  residues processed: 114
  average time/residue: 1.4872
  time to fit residues: 173.2715
Evaluate side-chains
  94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0000
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   overall best weight:    3.5992

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.125831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.105613 restraints weight = 4638.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 1.90
r_work: 0.3507 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3522  Z= 0.362
  Angle     :  0.682   7.897   4710  Z= 0.336
  Chirality :  0.049   0.139    528
  Planarity :  0.003   0.027    600
  Dihedral  :  5.843  20.809    468
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.96 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F 330 
 PHE   0.011   0.002   PHE E 378 
 TYR   0.020   0.003   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.8344 (mttt) cc_final: 0.7970 (tttt)
REVERT: A  343 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7956 (tttt)
REVERT: A  379 ARG cc_start: 0.7603 (mmm-85) cc_final: 0.6961 (mpt-90)
REVERT: B  342 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5801 (tp30)
REVERT: B  369 LYS cc_start: 0.8709 (tttt) cc_final: 0.8407 (tppt)
REVERT: C  321 LYS cc_start: 0.8591 (mttt) cc_final: 0.8277 (tttm)
REVERT: C  343 LYS cc_start: 0.8382 (mtpp) cc_final: 0.8057 (tttt)
REVERT: D  347 LYS cc_start: 0.7719 (tttt) cc_final: 0.6227 (mtmt)
REVERT: D  379 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.4494 (mtm180)
REVERT: E  321 LYS cc_start: 0.8266 (mttt) cc_final: 0.8027 (ttpt)
REVERT: E  343 LYS cc_start: 0.8333 (mtpp) cc_final: 0.7977 (tttt)
REVERT: E  348 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7838 (p0)
REVERT: E  349 ARG cc_start: 0.7442 (mtm180) cc_final: 0.6961 (mpt180)
REVERT: E  369 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8415 (mttt)
REVERT: E  379 ARG cc_start: 0.7753 (mtt180) cc_final: 0.6909 (mmp80)
REVERT: F  379 ARG cc_start: 0.5615 (mmp-170) cc_final: 0.5066 (mmt180)
  outliers start: 15
  outliers final: 4
  residues processed: 98
  average time/residue: 1.6331
  time to fit residues: 163.3881
Evaluate side-chains
  98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  373 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    0.0070
   chunk 0 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 36 optimal weight:    0.2980
   chunk 17 optimal weight:    8.9990
   overall best weight:    3.4604

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
C 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.126346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.106049 restraints weight = 4676.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.89
r_work: 0.3517 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3522  Z= 0.354
  Angle     :  0.665   8.564   4710  Z= 0.325
  Chirality :  0.048   0.130    528
  Planarity :  0.003   0.036    600
  Dihedral  :  5.649  22.396    468
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 21.46 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -1.93 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.46 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F 330 
 PHE   0.008   0.002   PHE E 378 
 TYR   0.019   0.003   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8404 (mttt) cc_final: 0.8003 (ttpt)
REVERT: A  343 LYS cc_start: 0.8351 (mtmt) cc_final: 0.7875 (tttt)
REVERT: A  379 ARG cc_start: 0.7608 (mmm-85) cc_final: 0.7125 (mpt-90)
REVERT: B  342 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5949 (mm-30)
REVERT: B  351 GLN cc_start: 0.7956 (tt0) cc_final: 0.7007 (mp10)
REVERT: B  369 LYS cc_start: 0.8713 (tttt) cc_final: 0.8501 (tppt)
REVERT: C  321 LYS cc_start: 0.8617 (mttt) cc_final: 0.8233 (ttpp)
REVERT: C  343 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8128 (tttt)
REVERT: D  379 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.5323 (mtm-85)
REVERT: E  321 LYS cc_start: 0.8293 (mttt) cc_final: 0.7998 (tttm)
REVERT: E  343 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8041 (tttt)
REVERT: E  348 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7880 (p0)
REVERT: E  349 ARG cc_start: 0.7431 (mtm180) cc_final: 0.6954 (mpt90)
REVERT: E  369 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8419 (mttt)
REVERT: E  379 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7158 (mmp80)
  outliers start: 15
  outliers final: 5
  residues processed: 98
  average time/residue: 1.6046
  time to fit residues: 160.4961
Evaluate side-chains
  94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  338 GLU
Chi-restraints excluded: chain F residue  351 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 35 optimal weight:    0.2980
   chunk 19 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
D 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.127781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.107498 restraints weight = 4680.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.91
r_work: 0.3546 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3522  Z= 0.262
  Angle     :  0.618   9.616   4710  Z= 0.299
  Chirality :  0.048   0.119    528
  Planarity :  0.003   0.025    600
  Dihedral  :  5.339  21.086    468
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.22 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -1.96 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 330 
 PHE   0.007   0.001   PHE E 378 
 TYR   0.014   0.002   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8391 (mttt) cc_final: 0.7981 (tttt)
REVERT: A  343 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7875 (tttt)
REVERT: A  379 ARG cc_start: 0.7564 (mmm-85) cc_final: 0.7142 (mmt90)
REVERT: B  342 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5933 (mm-30)
REVERT: B  351 GLN cc_start: 0.8093 (tt0) cc_final: 0.7098 (mp10)
REVERT: B  353 LYS cc_start: 0.8609 (mtpt) cc_final: 0.7816 (tttt)
REVERT: B  369 LYS cc_start: 0.8745 (tttt) cc_final: 0.8531 (ttmt)
REVERT: C  321 LYS cc_start: 0.8571 (mttt) cc_final: 0.8193 (tttm)
REVERT: C  343 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8129 (tttt)
REVERT: D  338 GLU cc_start: 0.4239 (pm20) cc_final: 0.4010 (pm20)
REVERT: D  379 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.5563 (mtm-85)
REVERT: E  321 LYS cc_start: 0.8304 (mttt) cc_final: 0.8032 (tttm)
REVERT: E  343 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8061 (tttt)
REVERT: E  348 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7812 (p0)
REVERT: E  349 ARG cc_start: 0.7520 (mtm180) cc_final: 0.6923 (mpt90)
REVERT: E  369 LYS cc_start: 0.8837 (mtmt) cc_final: 0.8486 (mtpt)
REVERT: E  379 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7288 (mmp80)
  outliers start: 14
  outliers final: 8
  residues processed: 92
  average time/residue: 1.6581
  time to fit residues: 155.6536
Evaluate side-chains
  98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  317 LYS
Chi-restraints excluded: chain F residue  338 GLU
Chi-restraints excluded: chain F residue  351 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0070
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.5604

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.131978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.112012 restraints weight = 4451.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.85
r_work: 0.3586 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3522  Z= 0.187
  Angle     :  0.584   9.764   4710  Z= 0.277
  Chirality :  0.048   0.116    528
  Planarity :  0.002   0.019    600
  Dihedral  :  5.029  19.693    468
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.98 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -1.94 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 330 
 PHE   0.006   0.001   PHE E 378 
 TYR   0.010   0.002   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8392 (mttt) cc_final: 0.7987 (tttt)
REVERT: A  343 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7933 (tttt)
REVERT: A  379 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.7137 (mtp180)
REVERT: B  342 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6007 (mm-30)
REVERT: B  351 GLN cc_start: 0.8073 (tt0) cc_final: 0.7156 (mp10)
REVERT: B  353 LYS cc_start: 0.8562 (mtpt) cc_final: 0.7812 (ttpt)
REVERT: B  369 LYS cc_start: 0.8738 (tttt) cc_final: 0.8535 (ttmt)
REVERT: C  321 LYS cc_start: 0.8528 (mttt) cc_final: 0.8140 (ttmt)
REVERT: C  343 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8146 (tttt)
REVERT: D  379 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5619 (mtm-85)
REVERT: E  311 LYS cc_start: 0.8751 (mtpt) cc_final: 0.7720 (tppt)
REVERT: E  321 LYS cc_start: 0.8300 (mttt) cc_final: 0.8050 (tttm)
REVERT: E  343 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8096 (tttt)
REVERT: E  349 ARG cc_start: 0.7515 (mtm180) cc_final: 0.6950 (mpt90)
REVERT: E  369 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8465 (mtpt)
REVERT: E  379 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7380 (mmp80)
  outliers start: 13
  outliers final: 6
  residues processed: 92
  average time/residue: 1.5985
  time to fit residues: 150.1659
Evaluate side-chains
  95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain F residue  338 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.1980
   chunk 25 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 37 optimal weight:    0.4980
   chunk 23 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
C 336 GLN
F 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.128529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.108475 restraints weight = 4456.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 1.83
r_work: 0.3534 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3522  Z= 0.285
  Angle     :  0.629  10.031   4710  Z= 0.303
  Chirality :  0.047   0.118    528
  Planarity :  0.003   0.028    600
  Dihedral  :  5.235  21.707    468
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.47 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -1.97 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.49 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 330 
 PHE   0.006   0.001   PHE F 378 
 TYR   0.014   0.003   TYR A 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8369 (mttt) cc_final: 0.7948 (ttpt)
REVERT: A  343 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7898 (tttt)
REVERT: A  379 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7185 (mtp180)
REVERT: B  321 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8535 (mttm)
REVERT: B  342 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5988 (mm-30)
REVERT: B  351 GLN cc_start: 0.8070 (tt0) cc_final: 0.7224 (mp10)
REVERT: B  369 LYS cc_start: 0.8753 (tttt) cc_final: 0.8540 (ttmt)
REVERT: C  321 LYS cc_start: 0.8588 (mttt) cc_final: 0.8222 (ttmt)
REVERT: C  343 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8146 (tttt)
REVERT: D  379 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.5497 (mtm-85)
REVERT: E  321 LYS cc_start: 0.8339 (mttt) cc_final: 0.8058 (tttm)
REVERT: E  343 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8103 (tttt)
REVERT: E  349 ARG cc_start: 0.7527 (mtm180) cc_final: 0.6898 (mpt90)
REVERT: E  369 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8496 (mtpt)
REVERT: E  379 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7205 (tpm170)
  outliers start: 18
  outliers final: 6
  residues processed: 90
  average time/residue: 1.5753
  time to fit residues: 144.8023
Evaluate side-chains
  90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  351 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
C 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.129522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.109285 restraints weight = 4618.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.98
r_work: 0.3517 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.4557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3522  Z= 0.305
  Angle     :  0.627  10.111   4710  Z= 0.301
  Chirality :  0.047   0.116    528
  Planarity :  0.003   0.032    600
  Dihedral  :  5.302  22.755    468
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 22.98 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -2.03 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 330 
 PHE   0.006   0.002   PHE F 378 
 TYR   0.015   0.003   TYR A 310 
 ARG   0.001   0.000   ARG F 379 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8379 (mttt) cc_final: 0.7991 (mtpm)
REVERT: A  343 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7826 (tttt)
REVERT: A  379 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.7176 (mtp180)
REVERT: B  321 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8513 (mttm)
REVERT: B  342 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5956 (mm-30)
REVERT: B  351 GLN cc_start: 0.8029 (tt0) cc_final: 0.7160 (mp10)
REVERT: B  369 LYS cc_start: 0.8760 (tttt) cc_final: 0.8537 (ttmt)
REVERT: C  321 LYS cc_start: 0.8617 (mttt) cc_final: 0.8213 (ttmt)
REVERT: C  343 LYS cc_start: 0.8397 (mtpp) cc_final: 0.8141 (tttt)
REVERT: D  379 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.5440 (mtm-85)
REVERT: E  321 LYS cc_start: 0.8346 (mttt) cc_final: 0.8003 (tttm)
REVERT: E  343 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8078 (tttt)
REVERT: E  348 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7891 (p0)
REVERT: E  349 ARG cc_start: 0.7649 (mtm180) cc_final: 0.6828 (mpt90)
REVERT: E  369 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8492 (mtpt)
REVERT: E  379 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7255 (tpm170)
  outliers start: 17
  outliers final: 10
  residues processed: 91
  average time/residue: 1.5254
  time to fit residues: 141.8785
Evaluate side-chains
  98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  351 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
C 336 GLN
F 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.124228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.104612 restraints weight = 4476.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 1.83
r_work: 0.3502 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3522  Z= 0.324
  Angle     :  0.635  10.108   4710  Z= 0.305
  Chirality :  0.047   0.119    528
  Planarity :  0.003   0.035    600
  Dihedral  :  5.334  22.907    468
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.48 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -2.05 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 330 
 PHE   0.007   0.002   PHE F 378 
 TYR   0.015   0.003   TYR A 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8402 (mttt) cc_final: 0.8024 (mtpm)
REVERT: A  343 LYS cc_start: 0.8442 (mtmt) cc_final: 0.7861 (tttt)
REVERT: A  379 ARG cc_start: 0.7569 (mmm-85) cc_final: 0.7236 (mtp180)
REVERT: B  321 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8549 (mttm)
REVERT: B  342 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5948 (mm-30)
REVERT: B  351 GLN cc_start: 0.8052 (tt0) cc_final: 0.7255 (mp10)
REVERT: B  369 LYS cc_start: 0.8732 (tttt) cc_final: 0.8508 (ttmt)
REVERT: C  321 LYS cc_start: 0.8630 (mttt) cc_final: 0.8227 (mtpm)
REVERT: C  343 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8163 (tttt)
REVERT: D  379 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.5490 (mtm-85)
REVERT: E  321 LYS cc_start: 0.8358 (mttt) cc_final: 0.8053 (tttm)
REVERT: E  343 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8085 (tttt)
REVERT: E  348 ASP cc_start: 0.8119 (p0) cc_final: 0.7916 (p0)
REVERT: E  349 ARG cc_start: 0.7693 (mtm180) cc_final: 0.6917 (mmt-90)
REVERT: E  369 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8508 (mtpt)
REVERT: E  379 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7255 (tpm170)
REVERT: F  379 ARG cc_start: 0.5447 (mmp-170) cc_final: 0.5162 (mmp-170)
  outliers start: 17
  outliers final: 8
  residues processed: 91
  average time/residue: 1.5826
  time to fit residues: 147.1920
Evaluate side-chains
  93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  351 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 19 optimal weight:    0.4980
   chunk 4 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    4.4988

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
B 330 HIS
C 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.122572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.102810 restraints weight = 4601.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.84
r_work: 0.3465 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.4664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   3522  Z= 0.438
  Angle     :  0.688  10.293   4710  Z= 0.334
  Chirality :  0.048   0.129    528
  Planarity :  0.004   0.050    600
  Dihedral  :  5.540  24.751    468
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.24 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -2.12 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 330 
 PHE   0.008   0.002   PHE F 378 
 TYR   0.019   0.003   TYR A 310 
 ARG   0.001   0.000   ARG B 379 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8444 (mttt) cc_final: 0.8077 (mtpm)
REVERT: A  343 LYS cc_start: 0.8477 (mtmt) cc_final: 0.7932 (tttt)
REVERT: A  379 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7300 (mtp180)
REVERT: B  342 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5996 (mm-30)
REVERT: B  351 GLN cc_start: 0.8088 (tt0) cc_final: 0.7293 (mp10)
REVERT: B  369 LYS cc_start: 0.8775 (tttt) cc_final: 0.8560 (ttmt)
REVERT: C  321 LYS cc_start: 0.8682 (mttt) cc_final: 0.8286 (mtpm)
REVERT: C  343 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8213 (tttt)
REVERT: D  379 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.5383 (mtm-85)
REVERT: E  321 LYS cc_start: 0.8395 (mttt) cc_final: 0.8145 (tttm)
REVERT: E  343 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8071 (tttt)
REVERT: E  348 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7941 (p0)
REVERT: E  349 ARG cc_start: 0.7756 (mtm180) cc_final: 0.6886 (mpt90)
REVERT: E  369 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8546 (mtpt)
REVERT: E  379 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7172 (tpm170)
REVERT: F  379 ARG cc_start: 0.5594 (mmp-170) cc_final: 0.5207 (mmp-170)
  outliers start: 14
  outliers final: 7
  residues processed: 90
  average time/residue: 1.5863
  time to fit residues: 145.8057
Evaluate side-chains
  95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  351 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.126914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.107518 restraints weight = 4540.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.84
r_work: 0.3530 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3522  Z= 0.221
  Angle     :  0.600  10.044   4710  Z= 0.284
  Chirality :  0.047   0.116    528
  Planarity :  0.003   0.022    600
  Dihedral  :  5.098  21.136    468
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 25.76 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    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: -2.10 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 330 
 PHE   0.005   0.001   PHE E 378 
 TYR   0.010   0.002   TYR E 310 
 ARG   0.001   0.000   ARG B 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3872.69 seconds
wall clock time: 66 minutes 45.90 seconds (4005.90 seconds total)