Starting phenix.real_space_refine
on Tue Feb 11 01:01:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qjy_14026/02_2025/7qjy_14026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qjy_14026/02_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_14026/02_2025/7qjy_14026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qjy_14026/02_2025/7qjy_14026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qjy_14026/02_2025/7qjy_14026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qjy_14026/02_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-5592/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: 2.89, per 1000 atoms: 0.84
  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: 0.80
  Conformation dependent library (CDL) restraints added in 367.3 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: 0.58
  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: 0.77

  Time building geometry restraints manager: 0.94 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:             0.720
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.950
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.060
-------------------------------------------------------------------------------
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= 0.740
  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 

*********************** 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  : 0.379 
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: 0.3154
  time to fit residues: 53.8312
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  : 0.392 
-------------------------------------------------------------------------------
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 = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.108203 restraints weight = 4825.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.68
r_work: 0.3503 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
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= 0.255
  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 

*********************** 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  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8765 (mttt) cc_final: 0.8499 (mttp)
REVERT: A  347 LYS cc_start: 0.8211 (mttt) cc_final: 0.7898 (mmmt)
REVERT: B  311 LYS cc_start: 0.8552 (mttt) cc_final: 0.7695 (mmtt)
REVERT: B  342 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6963 (mp0)
REVERT: B  347 LYS cc_start: 0.7582 (mttt) cc_final: 0.7280 (mmtt)
REVERT: B  375 LYS cc_start: 0.8505 (tttm) cc_final: 0.8039 (ttmt)
REVERT: C  347 LYS cc_start: 0.8234 (mttt) cc_final: 0.7995 (mmtt)
REVERT: C  349 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7497 (ttm110)
REVERT: C  370 LYS cc_start: 0.8600 (tttp) cc_final: 0.8374 (tttt)
REVERT: C  375 LYS cc_start: 0.8521 (tttt) cc_final: 0.8279 (tttm)
REVERT: D  347 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7842 (mmmt)
REVERT: E  343 LYS cc_start: 0.8002 (tttt) cc_final: 0.7418 (ttpt)
REVERT: E  349 ARG cc_start: 0.7974 (ttm170) cc_final: 0.6227 (ptt-90)
REVERT: F  340 LYS cc_start: 0.8360 (mmtt) cc_final: 0.7835 (mtpp)
REVERT: F  343 LYS cc_start: 0.6752 (mmtt) cc_final: 0.6540 (mmpt)
  outliers start: 7
  outliers final: 4
  residues processed: 110
  average time/residue: 0.2972
  time to fit residues: 36.2464
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  : 0.388 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   overall best weight:    6.3990

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.115610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.105926 restraints weight = 4824.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.66
r_work: 0.3434 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   3498  Z= 0.490
  Angle     :  0.757   8.620   4680  Z= 0.386
  Chirality :  0.051   0.161    528
  Planarity :  0.005   0.050    594
  Dihedral  :  6.301  23.857    462
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.12 %
    Favored  : 84.85 %
  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 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 330 
 PHE   0.014   0.002   PHE F 346 
 TYR   0.018   0.004   TYR F 310 
 ARG   0.005   0.001   ARG C 379 

*********************** 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
  104 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8795 (mttt) cc_final: 0.8520 (mttt)
REVERT: A  347 LYS cc_start: 0.8200 (mttt) cc_final: 0.7961 (mmtt)
REVERT: A  349 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7923 (ttm170)
REVERT: A  372 GLU cc_start: 0.7805 (tp30) cc_final: 0.7378 (tt0)
REVERT: B  311 LYS cc_start: 0.8749 (mttt) cc_final: 0.7788 (mmtt)
REVERT: B  347 LYS cc_start: 0.7593 (mttt) cc_final: 0.7339 (mmtt)
REVERT: B  375 LYS cc_start: 0.8483 (tttm) cc_final: 0.7992 (ttmt)
REVERT: C  343 LYS cc_start: 0.8420 (mtpp) cc_final: 0.8176 (mtmt)
REVERT: C  347 LYS cc_start: 0.8364 (mttt) cc_final: 0.8122 (mmtt)
REVERT: C  349 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7190 (ttm110)
REVERT: C  351 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7212 (mp10)
REVERT: C  370 LYS cc_start: 0.8564 (tttp) cc_final: 0.8362 (tttt)
REVERT: C  375 LYS cc_start: 0.8551 (tttt) cc_final: 0.8278 (tttm)
REVERT: D  347 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7692 (mmmt)
REVERT: E  343 LYS cc_start: 0.8143 (tttt) cc_final: 0.7444 (ttpt)
REVERT: E  349 ARG cc_start: 0.7911 (ttm170) cc_final: 0.6157 (ptt-90)
REVERT: F  311 LYS cc_start: 0.6446 (mmtm) cc_final: 0.4529 (ptpt)
REVERT: F  369 LYS cc_start: 0.8309 (mttm) cc_final: 0.7726 (mtpt)
  outliers start: 12
  outliers final: 9
  residues processed: 96
  average time/residue: 0.3215
  time to fit residues: 34.0909
Evaluate side-chains
  96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
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:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0030
   chunk 22 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    3.9998

-------------------------------------------------------------------------------
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
E 327 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.118059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.108741 restraints weight = 4859.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.62
r_work: 0.3469 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.4552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3498  Z= 0.320
  Angle     :  0.656   7.332   4680  Z= 0.330
  Chirality :  0.048   0.128    528
  Planarity :  0.005   0.048    594
  Dihedral  :  5.917  22.639    462
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 12.63 %
    Favored  : 84.09 %
  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: -2.31 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 330 
 PHE   0.010   0.002   PHE C 346 
 TYR   0.020   0.004   TYR D 310 
 ARG   0.003   0.000   ARG C 379 

*********************** 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
  106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8778 (mttt) cc_final: 0.8508 (mttt)
REVERT: A  347 LYS cc_start: 0.8213 (mttt) cc_final: 0.7928 (mmtt)
REVERT: B  311 LYS cc_start: 0.8753 (mttt) cc_final: 0.7812 (mmtt)
REVERT: B  321 LYS cc_start: 0.8220 (mttt) cc_final: 0.7674 (mtpt)
REVERT: B  347 LYS cc_start: 0.7568 (mttt) cc_final: 0.7332 (mmtt)
REVERT: B  375 LYS cc_start: 0.8484 (tttm) cc_final: 0.8027 (ttmt)
REVERT: C  317 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8383 (mttp)
REVERT: C  343 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8211 (mtmt)
REVERT: C  347 LYS cc_start: 0.8326 (mttt) cc_final: 0.8125 (mmtt)
REVERT: C  349 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7236 (ttm110)
REVERT: C  351 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7231 (mp10)
REVERT: C  370 LYS cc_start: 0.8589 (tttp) cc_final: 0.8359 (tttt)
REVERT: C  375 LYS cc_start: 0.8539 (tttt) cc_final: 0.8302 (tttm)
REVERT: D  347 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7877 (mmmt)
REVERT: D  372 GLU cc_start: 0.7901 (tp30) cc_final: 0.7653 (tt0)
REVERT: D  378 PHE cc_start: 0.8917 (t80) cc_final: 0.8681 (t80)
REVERT: E  343 LYS cc_start: 0.8173 (tttt) cc_final: 0.7473 (ttpt)
REVERT: F  311 LYS cc_start: 0.6298 (mmtm) cc_final: 0.4313 (ptpt)
REVERT: F  340 LYS cc_start: 0.8439 (mptt) cc_final: 0.7832 (mtpp)
REVERT: F  349 ARG cc_start: 0.7688 (ttm170) cc_final: 0.7301 (mtp180)
REVERT: F  369 LYS cc_start: 0.8365 (mttm) cc_final: 0.7782 (mtpt)
  outliers start: 13
  outliers final: 9
  residues processed: 100
  average time/residue: 0.3101
  time to fit residues: 34.4125
Evaluate side-chains
  98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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  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  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:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0570
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    5.2106

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.115636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.105968 restraints weight = 4824.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.72
r_work: 0.3434 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3498  Z= 0.412
  Angle     :  0.686   7.497   4680  Z= 0.348
  Chirality :  0.049   0.136    528
  Planarity :  0.005   0.048    594
  Dihedral  :  5.935  23.055    462
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 13.13 %
    Favored  : 83.08 %
  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: -2.37 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 330 
 PHE   0.012   0.002   PHE F 346 
 TYR   0.017   0.003   TYR F 310 
 ARG   0.003   0.001   ARG C 379 

*********************** 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
  103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8729 (mttt) cc_final: 0.8471 (mttt)
REVERT: A  347 LYS cc_start: 0.8163 (mttt) cc_final: 0.7867 (mmmt)
REVERT: A  349 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7947 (ttm170)
REVERT: B  311 LYS cc_start: 0.8762 (mttt) cc_final: 0.7836 (mmtt)
REVERT: B  347 LYS cc_start: 0.7489 (mttt) cc_final: 0.7271 (mmtt)
REVERT: B  375 LYS cc_start: 0.8425 (tttm) cc_final: 0.7946 (ttmt)
REVERT: C  317 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8391 (mttp)
REVERT: C  343 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8209 (mtmt)
REVERT: C  349 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7435 (ttm110)
REVERT: C  351 GLN cc_start: 0.7507 (tm-30) cc_final: 0.7263 (mp10)
REVERT: C  353 LYS cc_start: 0.8424 (tttp) cc_final: 0.8214 (tptp)
REVERT: C  370 LYS cc_start: 0.8584 (tttp) cc_final: 0.8378 (tttt)
REVERT: C  375 LYS cc_start: 0.8509 (tttt) cc_final: 0.8276 (tttm)
REVERT: D  347 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7995 (mmtt)
REVERT: D  378 PHE cc_start: 0.8930 (t80) cc_final: 0.8646 (t80)
REVERT: E  343 LYS cc_start: 0.8134 (tttt) cc_final: 0.7463 (ttpt)
REVERT: F  311 LYS cc_start: 0.6286 (mmtm) cc_final: 0.4238 (ptpt)
REVERT: F  340 LYS cc_start: 0.8439 (mptt) cc_final: 0.8101 (mptt)
REVERT: F  349 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7317 (mtp180)
REVERT: F  369 LYS cc_start: 0.8332 (mttm) cc_final: 0.7742 (mtpt)
  outliers start: 15
  outliers final: 9
  residues processed: 96
  average time/residue: 0.3376
  time to fit residues: 35.7279
Evaluate side-chains
  92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
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  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  360 ILE
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:   10.0000
   chunk 24 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0770
   chunk 15 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    3.1944

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.116944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.107519 restraints weight = 4953.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.72
r_work: 0.3472 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3498  Z= 0.268
  Angle     :  0.607   6.867   4680  Z= 0.305
  Chirality :  0.047   0.129    528
  Planarity :  0.004   0.048    594
  Dihedral  :  5.609  21.423    462
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 13.64 %
    Favored  : 82.58 %
  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: -2.32 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 330 
 PHE   0.011   0.002   PHE C 346 
 TYR   0.017   0.003   TYR D 310 
 ARG   0.002   0.000   ARG C 379 

*********************** 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
  98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8702 (mttt) cc_final: 0.8439 (mttt)
REVERT: A  347 LYS cc_start: 0.8134 (mttt) cc_final: 0.7849 (mmmt)
REVERT: A  349 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7944 (ttm170)
REVERT: B  311 LYS cc_start: 0.8747 (mttt) cc_final: 0.7792 (mmtt)
REVERT: B  347 LYS cc_start: 0.7464 (mttt) cc_final: 0.7242 (mmtt)
REVERT: B  375 LYS cc_start: 0.8432 (tttm) cc_final: 0.7972 (ttmt)
REVERT: B  379 ARG cc_start: 0.6457 (mmp-170) cc_final: 0.6133 (mmp-170)
REVERT: C  317 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8381 (mttp)
REVERT: C  343 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8240 (mtmt)
REVERT: C  349 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7410 (ttm110)
REVERT: C  351 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7245 (mp10)
REVERT: D  347 LYS cc_start: 0.8295 (mmmt) cc_final: 0.8057 (mmtt)
REVERT: D  378 PHE cc_start: 0.8834 (t80) cc_final: 0.8576 (t80)
REVERT: E  343 LYS cc_start: 0.8169 (tttt) cc_final: 0.7493 (ttpt)
REVERT: F  311 LYS cc_start: 0.6231 (mmtm) cc_final: 0.4247 (ptpt)
REVERT: F  340 LYS cc_start: 0.8493 (mptt) cc_final: 0.8170 (mptt)
REVERT: F  349 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7374 (mtp180)
REVERT: F  369 LYS cc_start: 0.8352 (mttm) cc_final: 0.7753 (mtpt)
  outliers start: 15
  outliers final: 8
  residues processed: 91
  average time/residue: 0.3188
  time to fit residues: 32.1964
Evaluate side-chains
  87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.118700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.109406 restraints weight = 4832.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.70
r_work: 0.3515 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.4874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3498  Z= 0.186
  Angle     :  0.565   6.603   4680  Z= 0.283
  Chirality :  0.047   0.128    528
  Planarity :  0.004   0.048    594
  Dihedral  :  5.247  19.980    462
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.40 %
    Favored  : 81.82 %
  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 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 329 
 PHE   0.007   0.001   PHE F 346 
 TYR   0.018   0.003   TYR D 310 
 ARG   0.002   0.000   ARG C 379 

*********************** 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
  98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8117 (mttt) cc_final: 0.7817 (mmmt)
REVERT: A  349 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7920 (ttm170)
REVERT: B  311 LYS cc_start: 0.8676 (mttt) cc_final: 0.7756 (mmtt)
REVERT: B  375 LYS cc_start: 0.8437 (tttm) cc_final: 0.7990 (ttmt)
REVERT: B  379 ARG cc_start: 0.6372 (mmp-170) cc_final: 0.6045 (mmp-170)
REVERT: C  349 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7434 (ttm110)
REVERT: C  351 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7240 (mp10)
REVERT: D  378 PHE cc_start: 0.8752 (t80) cc_final: 0.8511 (t80)
REVERT: E  340 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8235 (mmmt)
REVERT: E  343 LYS cc_start: 0.8229 (tttt) cc_final: 0.7552 (ttpt)
REVERT: F  311 LYS cc_start: 0.6173 (mmtm) cc_final: 0.4198 (ptpt)
REVERT: F  340 LYS cc_start: 0.8461 (mptt) cc_final: 0.7637 (mmmt)
REVERT: F  349 ARG cc_start: 0.7702 (ttm170) cc_final: 0.6997 (mtp-110)
REVERT: F  351 GLN cc_start: 0.7862 (tt0) cc_final: 0.7528 (mt0)
REVERT: F  369 LYS cc_start: 0.8385 (mttm) cc_final: 0.7806 (mtpt)
  outliers start: 11
  outliers final: 7
  residues processed: 92
  average time/residue: 0.2895
  time to fit residues: 29.6887
Evaluate side-chains
  80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0570
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   overall best weight:    5.0106

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.115141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.105823 restraints weight = 4933.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 1.69
r_work: 0.3454 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   3498  Z= 0.399
  Angle     :  0.674   7.194   4680  Z= 0.339
  Chirality :  0.049   0.126    528
  Planarity :  0.005   0.046    594
  Dihedral  :  5.637  21.942    462
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.16 %
    Favored  : 80.81 %
  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: -2.32 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E 330 
 PHE   0.012   0.002   PHE C 346 
 TYR   0.019   0.003   TYR A 310 
 ARG   0.003   0.001   ARG F 379 

*********************** 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
  88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8224 (mmmm) cc_final: 0.7979 (mptt)
REVERT: A  347 LYS cc_start: 0.8134 (mttt) cc_final: 0.7884 (mmtt)
REVERT: A  349 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7959 (ttm170)
REVERT: A  379 ARG cc_start: 0.8543 (ttt180) cc_final: 0.7322 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8710 (mttt) cc_final: 0.7743 (mmtm)
REVERT: B  379 ARG cc_start: 0.6429 (mmp-170) cc_final: 0.6102 (mmp-170)
REVERT: C  349 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7432 (ttm110)
REVERT: C  351 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7228 (mp10)
REVERT: D  347 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7960 (mmtt)
REVERT: D  378 PHE cc_start: 0.8870 (t80) cc_final: 0.8531 (t80)
REVERT: E  340 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8130 (mmmt)
REVERT: E  343 LYS cc_start: 0.8225 (tttt) cc_final: 0.7513 (ttpt)
REVERT: F  340 LYS cc_start: 0.8463 (mptt) cc_final: 0.7648 (mmmt)
REVERT: F  349 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7366 (mtp180)
REVERT: F  369 LYS cc_start: 0.8319 (mttm) cc_final: 0.7710 (mtpt)
  outliers start: 12
  outliers final: 9
  residues processed: 83
  average time/residue: 0.3050
  time to fit residues: 28.3478
Evaluate side-chains
  87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.115365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 20)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.106092 restraints weight = 4839.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.67
r_work: 0.3490 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   3498  Z= 0.363
  Angle     :  0.655   7.051   4680  Z= 0.330
  Chirality :  0.048   0.125    528
  Planarity :  0.004   0.045    594
  Dihedral  :  5.653  22.213    462
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.91 %
    Favored  : 81.06 %
  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   0.005   0.001   HIS E 330 
 PHE   0.011   0.002   PHE C 346 
 TYR   0.020   0.003   TYR A 310 
 ARG   0.002   0.000   ARG F 379 

*********************** 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
  90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8213 (mmmm) cc_final: 0.8001 (mptt)
REVERT: A  379 ARG cc_start: 0.8554 (ttt180) cc_final: 0.7377 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8748 (mttt) cc_final: 0.7823 (mmtm)
REVERT: B  379 ARG cc_start: 0.6487 (mmp-170) cc_final: 0.6150 (mmp-170)
REVERT: C  349 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7561 (ttm110)
REVERT: D  340 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8135 (mmmt)
REVERT: D  347 LYS cc_start: 0.8277 (mmmt) cc_final: 0.8003 (mmtt)
REVERT: D  378 PHE cc_start: 0.8840 (t80) cc_final: 0.8547 (t80)
REVERT: E  343 LYS cc_start: 0.8258 (tttt) cc_final: 0.7610 (ttpt)
REVERT: F  340 LYS cc_start: 0.8482 (mptt) cc_final: 0.7710 (mmmt)
REVERT: F  349 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7408 (mtp180)
REVERT: F  369 LYS cc_start: 0.8297 (mttm) cc_final: 0.7757 (mtpt)
  outliers start: 12
  outliers final: 9
  residues processed: 85
  average time/residue: 0.2756
  time to fit residues: 26.3934
Evaluate side-chains
  79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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 24 optimal weight:   20.0000
   chunk 8 optimal weight:    9.9990
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    5.7588

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.113948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.104596 restraints weight = 4966.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.69
r_work: 0.3436 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.5009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   3498  Z= 0.448
  Angle     :  0.707   7.320   4680  Z= 0.358
  Chirality :  0.049   0.127    528
  Planarity :  0.005   0.044    594
  Dihedral  :  5.808  23.648    462
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.91 %
    Favored  : 81.31 %
  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: -2.49 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS E 330 
 PHE   0.013   0.002   PHE C 346 
 TYR   0.020   0.004   TYR A 310 
 ARG   0.003   0.001   ARG F 379 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7963 (ttm170)
REVERT: A  379 ARG cc_start: 0.8544 (ttt180) cc_final: 0.7319 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8734 (mttt) cc_final: 0.7842 (mmtt)
REVERT: B  379 ARG cc_start: 0.6479 (mmp-170) cc_final: 0.6154 (mmp-170)
REVERT: C  349 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7384 (ttm110)
REVERT: D  340 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8068 (mmmt)
REVERT: D  347 LYS cc_start: 0.8275 (mmmt) cc_final: 0.8004 (mmtt)
REVERT: D  378 PHE cc_start: 0.8886 (t80) cc_final: 0.8542 (t80)
REVERT: E  343 LYS cc_start: 0.8238 (tttt) cc_final: 0.7577 (ttpt)
REVERT: F  320 SER cc_start: 0.8901 (t) cc_final: 0.8677 (p)
REVERT: F  340 LYS cc_start: 0.8464 (mptt) cc_final: 0.7757 (mmmt)
REVERT: F  349 ARG cc_start: 0.7737 (ttm170) cc_final: 0.7374 (mtp180)
REVERT: F  369 LYS cc_start: 0.8276 (mttm) cc_final: 0.7687 (mtpt)
  outliers start: 11
  outliers final: 7
  residues processed: 77
  average time/residue: 0.2779
  time to fit residues: 24.1558
Evaluate side-chains
  79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
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
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:    9.9990
   chunk 35 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.119011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.109942 restraints weight = 4858.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.64
r_work: 0.3492 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.5058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3498  Z= 0.238
  Angle     :  0.603   6.184   4680  Z= 0.302
  Chirality :  0.048   0.128    528
  Planarity :  0.004   0.046    594
  Dihedral  :  5.423  21.110    462
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.16 %
    Favored  : 81.31 %
  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: -2.33 (0.36), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E 330 
 PHE   0.007   0.001   PHE D 346 
 TYR   0.018   0.003   TYR D 310 
 ARG   0.001   0.000   ARG C 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2143.53 seconds
wall clock time: 38 minutes 55.21 seconds (2335.21 seconds total)