Starting phenix.real_space_refine
on Wed Jun  4 16:17:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qjy_14026/06_2025/7qjy_14026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qjy_14026/06_2025/7qjy_14026.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qjy_14026/06_2025/7qjy_14026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qjy_14026/06_2025/7qjy_14026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qjy_14026/06_2025/7qjy_14026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qjy_14026/06_2025/7qjy_14026.cif"
  }
  resolution = 3.14
  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=   0.004
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    2160      2.51       5
     N     636      2.21       5
     O     642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3444
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "B"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 2.85, per 1000 atoms: 0.83
  Number of scatterers: 3444
  At special positions: 0
  Unit cell: (98.1, 132.98, 45.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     642      8.00
     N     636      7.00
     C    2160      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: 0.67
  Conformation dependent library (CDL) restraints added in 380.3 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 16 sheets defined
      0.0% alpha, 48.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.853A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325
      removed outlier: 6.733A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   SER D 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLY B 323 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 342
      removed outlier: 6.594A  pdb=" N   VAL A 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   LYS D 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL A 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   GLU D 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   SER A 341 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   GLU B 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   SER D 341 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LYS B 340 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 346
      removed outlier: 6.621A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 354
    Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 354
      removed outlier: 9.075A  pdb=" N   VAL B 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 10.402A  pdb=" N   LYS D 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 8.946A  pdb=" N   SER B 352 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 10.297A  pdb=" N   GLY D 355 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 8.954A  pdb=" N   ILE B 354 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 9.805A  pdb=" N   LEU D 357 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   SER B 356 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   ASN D 359 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   THR D 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ILE B 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377
      removed outlier: 6.435A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 306 through 310
    Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.820A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 325
      removed outlier: 6.014A  pdb=" N   LYS C 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   SER E 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   THR C 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   CYS E 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS C 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   SER E 324 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLY C 323 " --> pdb=" O   SER E 324 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   VAL C 318 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   LYS F 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   SER C 320 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   GLY F 323 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   CYS C 322 " --> pdb=" O   GLY F 323 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   LEU F 325 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   SER C 324 " --> pdb=" O   LEU F 325 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342
    Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346
      removed outlier: 6.573A  pdb=" N   ASP C 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 351
      removed outlier: 6.234A  pdb=" N   VAL C 350 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 358
      removed outlier: 6.748A  pdb=" N   LEU C 357 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 377
      removed outlier: 6.525A  pdb=" N   LYS C 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   GLU E 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE C 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   HIS E 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   THR C 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   LEU E 376 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   LYS C 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)

    73 hydrogen bonds defined for protein.
    216 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: 0.82

  Time building geometry restraints manager: 0.84 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: 988
        1.33 -     1.45: 430
        1.45 -     1.57: 2074
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 3498
  Sorted by residual:
  bond pdb=" CZ  ARG E 349 "
       pdb=" NH2 ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.08e+00
  bond pdb=" CZ  ARG C 349 "
       pdb=" NH2 ARG C 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.54e+00
  bond pdb=" C   GLY D 323 "
       pdb=" O   GLY D 323 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.014 5.30e-03 3.56e+04 6.52e+00
  bond pdb=" CZ  ARG D 349 "
       pdb=" NH2 ARG D 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.33e+00
  bond pdb=" CZ  ARG D 379 "
       pdb=" NH2 ARG D 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.20e+00
  ... (remaining 3493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 3030
        1.69 -     3.39: 1328
        3.39 -     5.08: 282
        5.08 -     6.77: 35
        6.77 -     8.46: 5
  Bond angle restraints: 4680
  Sorted by residual:
  angle pdb=" OD1 ASN D 327 "
        pdb=" CG  ASN D 327 "
        pdb=" ND2 ASN D 327 "
      ideal   model   delta    sigma   weight residual
     122.60  117.87    4.73 1.00e+00 1.00e+00 2.24e+01
  angle pdb=" N   GLY A 367 "
        pdb=" CA  GLY A 367 "
        pdb=" C   GLY A 367 "
      ideal   model   delta    sigma   weight residual
     114.61  121.51   -6.90 1.49e+00 4.50e-01 2.14e+01
  angle pdb=" C   ASP B 348 "
        pdb=" N   ARG B 349 "
        pdb=" CA  ARG B 349 "
      ideal   model   delta    sigma   weight residual
     121.56  128.34   -6.78 1.56e+00 4.11e-01 1.89e+01
  angle pdb=" C   ASP F 348 "
        pdb=" N   ARG F 349 "
        pdb=" CA  ARG F 349 "
      ideal   model   delta    sigma   weight residual
     121.05  127.23   -6.18 1.43e+00 4.89e-01 1.87e+01
  angle pdb=" OD1 ASN A 327 "
        pdb=" CG  ASN A 327 "
        pdb=" ND2 ASN A 327 "
      ideal   model   delta    sigma   weight residual
     122.60  118.30    4.30 1.00e+00 1.00e+00 1.85e+01
  ... (remaining 4675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 1967
       16.44 -    32.88: 143
       32.88 -    49.32: 18
       49.32 -    65.75: 3
       65.75 -    82.19: 5
  Dihedral angle restraints: 2136
    sinusoidal: 894
      harmonic: 1242
  Sorted by residual:
  dihedral pdb=" CA  GLY B 366 "
           pdb=" C   GLY B 366 "
           pdb=" N   GLY B 367 "
           pdb=" CA  GLY B 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.55   29.45     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  GLY A 366 "
           pdb=" C   GLY A 366 "
           pdb=" N   GLY A 367 "
           pdb=" CA  GLY A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.88   29.12     0      5.00e+00 4.00e-02 3.39e+01
  dihedral pdb=" CA  GLY D 366 "
           pdb=" C   GLY D 366 "
           pdb=" N   GLY D 367 "
           pdb=" CA  GLY D 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.44   28.56     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 2133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 314
       0.070 -    0.140: 174
       0.140 -    0.211: 33
       0.211 -    0.281: 4
       0.281 -    0.351: 3
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  HIS C 329 "
            pdb=" N   HIS C 329 "
            pdb=" C   HIS C 329 "
            pdb=" CB  HIS C 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CA  HIS D 329 "
            pdb=" N   HIS D 329 "
            pdb=" C   HIS D 329 "
            pdb=" CB  HIS D 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CA  HIS A 329 "
            pdb=" N   HIS A 329 "
            pdb=" C   HIS A 329 "
            pdb=" CB  HIS A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.26e+00
  ... (remaining 525 not shown)

  Planarity restraints: 594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.139 2.00e-02 2.50e+03   7.57e-02 1.15e+02
        pdb=" CG  TYR F 310 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.070 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "   -0.047 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.114 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 310 "   -0.115 2.00e-02 2.50e+03   6.66e-02 8.88e+01
        pdb=" CG  TYR D 310 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 310 "    0.042 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 310 "    0.058 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 310 "    0.049 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 310 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 310 "    0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR D 310 "   -0.112 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "    0.106 2.00e-02 2.50e+03   6.04e-02 7.29e+01
        pdb=" CG  TYR C 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "   -0.052 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "    0.100 2.00e-02 2.50e+03
  ... (remaining 591 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 1660
        3.00 -     3.47: 2701
        3.47 -     3.95: 5423
        3.95 -     4.42: 5462
        4.42 -     4.90: 10569
  Nonbonded interactions: 25815
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.519 3.040
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.525 3.040
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.536 3.040
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.543 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.548 3.040
  ... (remaining 25810 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:             3.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.160
  Find NCS groups from input model:        0.120
  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:3.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
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   0.039   3498  Z= 0.706
  Angle     :  1.870   8.465   4680  Z= 1.233
  Chirality :  0.085   0.351    528
  Planarity :  0.013   0.095    594
  Dihedral  : 12.320  82.193   1344
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.53 %
    Favored  : 97.22 %
  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: -2.50 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.005   HIS F 330 
 PHE   0.055   0.013   PHE F 346 
 TYR   0.139   0.043   TYR F 310 
 ARG   0.004   0.001   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07429 (   68)
  hydrogen bonds       : angle       7.99598 (  216)
  covalent geometry    : bond        0.01096 ( 3498)
  covalent geometry    : angle       1.86969 ( 4680)

*********************** 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
  156 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8249 (mttt) cc_final: 0.8028 (mttm)
REVERT: A  340 LYS cc_start: 0.7560 (mmmm) cc_final: 0.6774 (mtmm)
REVERT: A  347 LYS cc_start: 0.8276 (mttt) cc_final: 0.8005 (mmmt)
REVERT: B  311 LYS cc_start: 0.8084 (mttt) cc_final: 0.7603 (mmtt)
REVERT: B  321 LYS cc_start: 0.7909 (mttt) cc_final: 0.7456 (mtpt)
REVERT: B  347 LYS cc_start: 0.7604 (mttt) cc_final: 0.7164 (mmtt)
REVERT: B  373 THR cc_start: 0.9195 (m) cc_final: 0.8945 (m)
REVERT: C  343 LYS cc_start: 0.8288 (tttt) cc_final: 0.7702 (tptt)
REVERT: C  347 LYS cc_start: 0.8331 (mttt) cc_final: 0.8078 (mmtt)
REVERT: C  349 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7959 (ttm110)
REVERT: C  375 LYS cc_start: 0.8260 (tttt) cc_final: 0.7919 (mttt)
REVERT: E  343 LYS cc_start: 0.8336 (tttt) cc_final: 0.7998 (pttp)
REVERT: E  347 LYS cc_start: 0.8601 (mttt) cc_final: 0.7805 (pttm)
REVERT: E  375 LYS cc_start: 0.8279 (tttt) cc_final: 0.7995 (mttt)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.3010
  time to fit residues: 51.3641
Evaluate side-chains
  119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
B 374 HIS
C 359 ASN
C 374 HIS
D 307 GLN
D 374 HIS
E 327 ASN
E 329 HIS
E 359 ASN
F 374 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.117738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.108202 restraints weight = 4825.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.68
r_work: 0.3502 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3498  Z= 0.166
  Angle     :  0.705   7.451   4680  Z= 0.359
  Chirality :  0.050   0.132    528
  Planarity :  0.005   0.048    594
  Dihedral  :  6.312  22.616    462
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.36 %
    Favored  : 86.87 %
  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: -2.42 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 374 
 PHE   0.011   0.002   PHE F 378 
 TYR   0.011   0.003   TYR E 310 
 ARG   0.003   0.001   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02273 (   68)
  hydrogen bonds       : angle       6.11803 (  216)
  covalent geometry    : bond        0.00383 ( 3498)
  covalent geometry    : angle       0.70536 ( 4680)

*********************** 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
  114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8765 (mttt) cc_final: 0.8500 (mttp)
REVERT: A  347 LYS cc_start: 0.8219 (mttt) cc_final: 0.7892 (mmmt)
REVERT: B  311 LYS cc_start: 0.8558 (mttt) cc_final: 0.7697 (mmtt)
REVERT: B  342 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6965 (mp0)
REVERT: B  347 LYS cc_start: 0.7583 (mttt) cc_final: 0.7273 (mmtt)
REVERT: B  375 LYS cc_start: 0.8501 (tttm) cc_final: 0.8034 (ttmt)
REVERT: C  347 LYS cc_start: 0.8249 (mttt) cc_final: 0.7989 (mmtt)
REVERT: C  349 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7491 (ttm110)
REVERT: C  370 LYS cc_start: 0.8601 (tttp) cc_final: 0.8372 (tttt)
REVERT: C  375 LYS cc_start: 0.8519 (tttt) cc_final: 0.8276 (tttm)
REVERT: D  347 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7834 (mmmt)
REVERT: E  343 LYS cc_start: 0.8000 (tttt) cc_final: 0.7412 (ttpt)
REVERT: E  349 ARG cc_start: 0.7975 (ttm170) cc_final: 0.6214 (ptt-90)
REVERT: F  340 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7833 (mtpp)
REVERT: F  343 LYS cc_start: 0.6745 (mmtt) cc_final: 0.6534 (mmpt)
  outliers start: 7
  outliers final: 4
  residues processed: 110
  average time/residue: 0.3111
  time to fit residues: 38.1074
Evaluate side-chains
  97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
B 329 HIS
C 359 ASN
E 359 ASN
E 374 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.114613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.104737 restraints weight = 4843.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.72
r_work: 0.3406 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.066   3498  Z= 0.413
  Angle     :  0.837   9.048   4680  Z= 0.429
  Chirality :  0.052   0.178    528
  Planarity :  0.006   0.053    594
  Dihedral  :  6.507  25.845    462
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.63 %
    Favored  : 84.34 %
  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: -2.46 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS E 330 
 PHE   0.018   0.003   PHE F 346 
 TYR   0.021   0.005   TYR F 310 
 ARG   0.005   0.001   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02640 (   68)
  hydrogen bonds       : angle       5.80428 (  216)
  covalent geometry    : bond        0.00955 ( 3498)
  covalent geometry    : angle       0.83652 ( 4680)

*********************** 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
  106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8745 (mttt) cc_final: 0.8492 (mttt)
REVERT: A  321 LYS cc_start: 0.8445 (mttt) cc_final: 0.7956 (mtpt)
REVERT: A  347 LYS cc_start: 0.8195 (mttt) cc_final: 0.7933 (mmtt)
REVERT: A  372 GLU cc_start: 0.7853 (tp30) cc_final: 0.7453 (tt0)
REVERT: B  311 LYS cc_start: 0.8791 (mttt) cc_final: 0.7865 (mmtt)
REVERT: B  347 LYS cc_start: 0.7602 (mttt) cc_final: 0.7385 (mmtt)
REVERT: B  375 LYS cc_start: 0.8527 (tttm) cc_final: 0.8062 (ttmt)
REVERT: C  343 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8219 (mtmt)
REVERT: C  349 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7293 (ttm110)
REVERT: C  351 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7343 (mp10)
REVERT: C  375 LYS cc_start: 0.8601 (tttt) cc_final: 0.8336 (tttm)
REVERT: D  347 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7724 (mmmt)
REVERT: E  343 LYS cc_start: 0.8174 (tttt) cc_final: 0.7461 (ttpt)
REVERT: E  349 ARG cc_start: 0.7921 (ttm170) cc_final: 0.6162 (ptt-90)
REVERT: F  311 LYS cc_start: 0.6368 (mmtm) cc_final: 0.4584 (ptpt)
REVERT: F  369 LYS cc_start: 0.8358 (mttm) cc_final: 0.7786 (mtpt)
  outliers start: 12
  outliers final: 9
  residues processed: 100
  average time/residue: 0.3358
  time to fit residues: 37.0234
Evaluate side-chains
  91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  379 ARG
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    9.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
B 329 HIS
C 359 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 = 0.3741 r_free = 0.3741 target = 0.118905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.109731 restraints weight = 4822.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.62
r_work: 0.3496 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3498  Z= 0.154
  Angle     :  0.609   6.925   4680  Z= 0.305
  Chirality :  0.048   0.127    528
  Planarity :  0.004   0.051    594
  Dihedral  :  5.720  21.494    462
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 13.13 %
    Favored  : 83.59 %
  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: -2.23 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 330 
 PHE   0.010   0.001   PHE C 346 
 TYR   0.015   0.003   TYR D 310 
 ARG   0.003   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01840 (   68)
  hydrogen bonds       : angle       5.29625 (  216)
  covalent geometry    : bond        0.00353 ( 3498)
  covalent geometry    : angle       0.60908 ( 4680)

*********************** 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
  105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8721 (mttt) cc_final: 0.8474 (mttt)
REVERT: A  347 LYS cc_start: 0.8183 (mttt) cc_final: 0.7902 (mmtt)
REVERT: B  311 LYS cc_start: 0.8733 (mttt) cc_final: 0.7781 (mmtt)
REVERT: B  321 LYS cc_start: 0.8232 (mttt) cc_final: 0.7690 (mtpt)
REVERT: B  347 LYS cc_start: 0.7536 (mttt) cc_final: 0.7314 (mmtt)
REVERT: B  375 LYS cc_start: 0.8413 (tttm) cc_final: 0.7974 (ttmt)
REVERT: C  317 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8360 (mttp)
REVERT: C  343 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8203 (mtmt)
REVERT: C  349 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7228 (ttm110)
REVERT: C  351 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7213 (mp10)
REVERT: C  375 LYS cc_start: 0.8534 (tttt) cc_final: 0.8300 (tttm)
REVERT: D  347 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7831 (mmmt)
REVERT: D  378 PHE cc_start: 0.8851 (t80) cc_final: 0.8601 (t80)
REVERT: E  343 LYS cc_start: 0.8219 (tttt) cc_final: 0.7512 (ttpt)
REVERT: F  311 LYS cc_start: 0.6247 (mmtm) cc_final: 0.4269 (ptpt)
REVERT: F  340 LYS cc_start: 0.8435 (mptt) cc_final: 0.7792 (mtpp)
REVERT: F  349 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7296 (mtp180)
REVERT: F  369 LYS cc_start: 0.8411 (mttm) cc_final: 0.7835 (mtpt)
  outliers start: 13
  outliers final: 6
  residues processed: 100
  average time/residue: 0.2915
  time to fit residues: 32.5443
Evaluate side-chains
  88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 329 HIS
C 359 ASN
F 327 ASN
F 359 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.113755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.104475 restraints weight = 4924.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.66
r_work: 0.3423 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.4724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   3498  Z= 0.360
  Angle     :  0.754   7.931   4680  Z= 0.384
  Chirality :  0.050   0.155    528
  Planarity :  0.005   0.049    594
  Dihedral  :  6.112  24.891    462
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 13.89 %
    Favored  : 82.07 %
  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: -2.43 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS E 330 
 PHE   0.016   0.002   PHE C 346 
 TYR   0.020   0.004   TYR F 310 
 ARG   0.004   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02230 (   68)
  hydrogen bonds       : angle       5.30407 (  216)
  covalent geometry    : bond        0.00828 ( 3498)
  covalent geometry    : angle       0.75449 ( 4680)

*********************** 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
  100 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8757 (mttt) cc_final: 0.8466 (mttt)
REVERT: A  340 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7958 (mptt)
REVERT: A  347 LYS cc_start: 0.8158 (mttt) cc_final: 0.7923 (mmmt)
REVERT: B  311 LYS cc_start: 0.8757 (mttt) cc_final: 0.7807 (mmtt)
REVERT: B  347 LYS cc_start: 0.7517 (mttt) cc_final: 0.7295 (mmtt)
REVERT: B  375 LYS cc_start: 0.8446 (tttm) cc_final: 0.7973 (ttmt)
REVERT: C  317 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8376 (mttp)
REVERT: C  343 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8237 (mtmt)
REVERT: C  349 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7255 (ttm110)
REVERT: C  351 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7234 (mp10)
REVERT: C  375 LYS cc_start: 0.8540 (tttt) cc_final: 0.8283 (tttm)
REVERT: D  347 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7757 (mmtt)
REVERT: D  378 PHE cc_start: 0.8967 (t80) cc_final: 0.8648 (t80)
REVERT: E  343 LYS cc_start: 0.8212 (tttt) cc_final: 0.7486 (ttpt)
REVERT: F  311 LYS cc_start: 0.6265 (mmtm) cc_final: 0.4230 (ptpt)
REVERT: F  340 LYS cc_start: 0.8430 (mptt) cc_final: 0.8095 (mptt)
REVERT: F  349 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7357 (mtp180)
REVERT: F  369 LYS cc_start: 0.8346 (mttm) cc_final: 0.7758 (mtpt)
  outliers start: 16
  outliers final: 9
  residues processed: 93
  average time/residue: 0.2904
  time to fit residues: 30.0436
Evaluate side-chains
  92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.120964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.111832 restraints weight = 4857.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 1.66
r_work: 0.3535 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.4795

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= 0.098
  Angle     :  0.556   6.045   4680  Z= 0.280
  Chirality :  0.048   0.130    528
  Planarity :  0.004   0.051    594
  Dihedral  :  5.323  19.732    462
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 16.67 %
    Favored  : 82.07 %
  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 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.013   0.002   TYR A 310 
 ARG   0.002   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01538 (   68)
  hydrogen bonds       : angle       4.96008 (  216)
  covalent geometry    : bond        0.00219 ( 3498)
  covalent geometry    : angle       0.55638 ( 4680)

*********************** 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
  96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8665 (mttt) cc_final: 0.8403 (mtpp)
REVERT: A  347 LYS cc_start: 0.8133 (mttt) cc_final: 0.7821 (mmmt)
REVERT: B  311 LYS cc_start: 0.8720 (mttt) cc_final: 0.7746 (mmtt)
REVERT: B  347 LYS cc_start: 0.7508 (mttt) cc_final: 0.7267 (mmtt)
REVERT: B  375 LYS cc_start: 0.8361 (tttm) cc_final: 0.7921 (ttmt)
REVERT: B  379 ARG cc_start: 0.6531 (mmp-170) cc_final: 0.6139 (mmp-170)
REVERT: C  343 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8196 (mtmt)
REVERT: C  348 ASP cc_start: 0.8042 (t0) cc_final: 0.7806 (t0)
REVERT: C  349 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7348 (ttm110)
REVERT: C  351 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7214 (mp10)
REVERT: E  340 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8247 (mmmt)
REVERT: E  343 LYS cc_start: 0.8205 (tttt) cc_final: 0.7456 (ttpt)
REVERT: F  311 LYS cc_start: 0.6112 (mmtm) cc_final: 0.4173 (ptpt)
REVERT: F  340 LYS cc_start: 0.8467 (mptt) cc_final: 0.8064 (mptt)
REVERT: F  349 ARG cc_start: 0.7681 (ttm170) cc_final: 0.6960 (mtp-110)
REVERT: F  351 GLN cc_start: 0.7837 (tt0) cc_final: 0.7519 (mt0)
REVERT: F  369 LYS cc_start: 0.8354 (mttm) cc_final: 0.7775 (mtpt)
  outliers start: 5
  outliers final: 2
  residues processed: 94
  average time/residue: 0.2879
  time to fit residues: 30.2638
Evaluate side-chains
  83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain E residue  359 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0870
   chunk 9 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    4.4166

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

Flipped N/Q/H residues before XYZ refinement:
B 329 HIS
C 359 ASN
F 327 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.117042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.107608 restraints weight = 4888.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 1.77
r_work: 0.3465 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.4817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3498  Z= 0.235
  Angle     :  0.656   7.076   4680  Z= 0.328
  Chirality :  0.048   0.125    528
  Planarity :  0.004   0.046    594
  Dihedral  :  5.548  21.630    462
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.42 %
    Favored  : 80.30 %
  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: -2.23 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 374 
 PHE   0.011   0.002   PHE C 346 
 TYR   0.016   0.002   TYR F 310 
 ARG   0.002   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01894 (   68)
  hydrogen bonds       : angle       4.96493 (  216)
  covalent geometry    : bond        0.00534 ( 3498)
  covalent geometry    : angle       0.65642 ( 4680)

*********************** 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
  89 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8705 (mttt) cc_final: 0.8468 (mttt)
REVERT: A  340 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7913 (mptt)
REVERT: A  347 LYS cc_start: 0.8104 (mttt) cc_final: 0.7877 (mmtt)
REVERT: A  379 ARG cc_start: 0.8544 (ttt180) cc_final: 0.7302 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8731 (mttt) cc_final: 0.7799 (mmtt)
REVERT: B  347 LYS cc_start: 0.7530 (mttt) cc_final: 0.7255 (mmtt)
REVERT: B  375 LYS cc_start: 0.8432 (tttm) cc_final: 0.7971 (ttmt)
REVERT: B  379 ARG cc_start: 0.6514 (mmp-170) cc_final: 0.6215 (mmp-170)
REVERT: C  349 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7261 (ttm110)
REVERT: C  351 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7253 (mp10)
REVERT: C  375 LYS cc_start: 0.8551 (tttt) cc_final: 0.8346 (tttm)
REVERT: D  347 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7833 (mmmt)
REVERT: E  340 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8132 (mmmt)
REVERT: E  343 LYS cc_start: 0.8241 (tttt) cc_final: 0.7516 (ttpt)
REVERT: F  311 LYS cc_start: 0.6267 (mmtm) cc_final: 0.4227 (ptpt)
REVERT: F  340 LYS cc_start: 0.8463 (mptt) cc_final: 0.7775 (mmmt)
REVERT: F  349 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7393 (mtp180)
REVERT: F  369 LYS cc_start: 0.8357 (mttm) cc_final: 0.7751 (mtpt)
  outliers start: 9
  outliers final: 5
  residues processed: 84
  average time/residue: 0.3164
  time to fit residues: 29.5712
Evaluate side-chains
  85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 359 ASN
F 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.111638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.101959 restraints weight = 4942.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.81
r_work: 0.3430 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   3498  Z= 0.317
  Angle     :  0.715   7.400   4680  Z= 0.361
  Chirality :  0.049   0.135    528
  Planarity :  0.005   0.044    594
  Dihedral  :  5.822  23.749    462
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.67 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.40 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 330 
 PHE   0.014   0.003   PHE C 346 
 TYR   0.021   0.004   TYR A 310 
 ARG   0.002   0.001   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02117 (   68)
  hydrogen bonds       : angle       5.08434 (  216)
  covalent geometry    : bond        0.00723 ( 3498)
  covalent geometry    : angle       0.71515 ( 4680)

*********************** 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
  93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8719 (mttt) cc_final: 0.8461 (mtpp)
REVERT: A  340 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8029 (mptt)
REVERT: A  347 LYS cc_start: 0.8123 (mttt) cc_final: 0.7914 (mmtt)
REVERT: A  379 ARG cc_start: 0.8603 (ttt180) cc_final: 0.7355 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8758 (mttt) cc_final: 0.7848 (mmtt)
REVERT: B  347 LYS cc_start: 0.7451 (mttt) cc_final: 0.7250 (mmtt)
REVERT: B  375 LYS cc_start: 0.8438 (tttm) cc_final: 0.7957 (ttmt)
REVERT: B  379 ARG cc_start: 0.6523 (mmp-170) cc_final: 0.6223 (mmp-170)
REVERT: C  349 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7252 (ttm110)
REVERT: C  351 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7246 (mp10)
REVERT: C  375 LYS cc_start: 0.8531 (tttt) cc_final: 0.8291 (tttm)
REVERT: D  347 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7779 (mmtt)
REVERT: E  343 LYS cc_start: 0.8269 (tttt) cc_final: 0.7518 (ttpt)
REVERT: F  340 LYS cc_start: 0.8478 (mptt) cc_final: 0.7786 (mmmt)
REVERT: F  349 ARG cc_start: 0.7737 (ttm170) cc_final: 0.7399 (mtp180)
REVERT: F  369 LYS cc_start: 0.8367 (mttm) cc_final: 0.7813 (mtpt)
  outliers start: 11
  outliers final: 6
  residues processed: 87
  average time/residue: 0.2968
  time to fit residues: 28.8388
Evaluate side-chains
  85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 40 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0370
   overall best weight:    4.1264

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.117867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.108540 restraints weight = 4798.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.69
r_work: 0.3462 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.4914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3498  Z= 0.223
  Angle     :  0.654   6.742   4680  Z= 0.329
  Chirality :  0.048   0.127    528
  Planarity :  0.004   0.045    594
  Dihedral  :  5.608  22.408    462
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.17 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.38 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 330 
 PHE   0.010   0.002   PHE D 378 
 TYR   0.018   0.003   TYR A 310 
 ARG   0.002   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01882 (   68)
  hydrogen bonds       : angle       4.94260 (  216)
  covalent geometry    : bond        0.00505 ( 3498)
  covalent geometry    : angle       0.65382 ( 4680)

*********************** 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
  92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8780 (mttt) cc_final: 0.8567 (mttt)
REVERT: A  340 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7998 (mptt)
REVERT: A  347 LYS cc_start: 0.8093 (mttt) cc_final: 0.7889 (mmtt)
REVERT: A  379 ARG cc_start: 0.8554 (ttt180) cc_final: 0.7320 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8716 (mttt) cc_final: 0.7822 (mmtt)
REVERT: B  347 LYS cc_start: 0.7499 (mttt) cc_final: 0.7251 (mmtt)
REVERT: B  375 LYS cc_start: 0.8415 (tttm) cc_final: 0.7960 (ttmt)
REVERT: C  349 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7473 (ttm110)
REVERT: C  351 GLN cc_start: 0.7477 (tm-30) cc_final: 0.7250 (mp10)
REVERT: C  375 LYS cc_start: 0.8563 (tttt) cc_final: 0.8356 (tttm)
REVERT: D  347 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7914 (mmmt)
REVERT: E  343 LYS cc_start: 0.8283 (tttt) cc_final: 0.7607 (ttpt)
REVERT: F  340 LYS cc_start: 0.8468 (mptt) cc_final: 0.7686 (mmmt)
REVERT: F  349 ARG cc_start: 0.7724 (ttm170) cc_final: 0.7365 (mtp180)
REVERT: F  369 LYS cc_start: 0.8370 (mttm) cc_final: 0.7823 (mtpt)
  outliers start: 9
  outliers final: 7
  residues processed: 89
  average time/residue: 0.2912
  time to fit residues: 28.9794
Evaluate side-chains
  87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 23 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
C 359 ASN
F 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.115998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.106588 restraints weight = 4878.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 1.73
r_work: 0.3471 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3498  Z= 0.204
  Angle     :  0.642   6.498   4680  Z= 0.324
  Chirality :  0.048   0.127    528
  Planarity :  0.004   0.045    594
  Dihedral  :  5.514  21.833    462
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.17 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS E 330 
 PHE   0.015   0.002   PHE D 378 
 TYR   0.018   0.003   TYR A 310 
 ARG   0.002   0.000   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01773 (   68)
  hydrogen bonds       : angle       4.90778 (  216)
  covalent geometry    : bond        0.00462 ( 3498)
  covalent geometry    : angle       0.64159 ( 4680)

********************** 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
  95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7986 (mptt)
REVERT: A  347 LYS cc_start: 0.7980 (mttt) cc_final: 0.7738 (mmmt)
REVERT: A  379 ARG cc_start: 0.8563 (ttt180) cc_final: 0.7328 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8714 (mttt) cc_final: 0.7793 (mmtt)
REVERT: B  375 LYS cc_start: 0.8425 (tttm) cc_final: 0.7969 (ttmt)
REVERT: C  349 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7472 (ttm110)
REVERT: C  351 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7249 (mp10)
REVERT: D  347 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7922 (mmmt)
REVERT: E  343 LYS cc_start: 0.8247 (tttt) cc_final: 0.7632 (ttpt)
REVERT: F  340 LYS cc_start: 0.8472 (mptt) cc_final: 0.7689 (mmmt)
REVERT: F  349 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7366 (mtp180)
REVERT: F  369 LYS cc_start: 0.8381 (mttm) cc_final: 0.7827 (mtpt)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2683
  time to fit residues: 27.0151
Evaluate side-chains
  85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.0670
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.7322

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.120595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.111539 restraints weight = 4810.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 1.63
r_work: 0.3533 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.5062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3498  Z= 0.118
  Angle     :  0.581   6.270   4680  Z= 0.292
  Chirality :  0.047   0.130    528
  Planarity :  0.005   0.048    594
  Dihedral  :  5.137  19.687    462
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.68 %
    Favored  : 80.30 %
  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: -2.17 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 330 
 PHE   0.009   0.001   PHE D 378 
 TYR   0.017   0.002   TYR A 310 
 ARG   0.010   0.001   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01515 (   68)
  hydrogen bonds       : angle       4.78794 (  216)
  covalent geometry    : bond        0.00269 ( 3498)
  covalent geometry    : angle       0.58107 ( 4680)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2298.33 seconds
wall clock time: 40 minutes 11.80 seconds (2411.80 seconds total)