Starting phenix.real_space_refine
on Thu Mar  6 08:23:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8seh_40411/03_2025/8seh_40411_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8seh_40411/03_2025/8seh_40411.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8seh_40411/03_2025/8seh_40411.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8seh_40411/03_2025/8seh_40411.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8seh_40411/03_2025/8seh_40411_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8seh_40411/03_2025/8seh_40411_neut.cif"
  }
  resolution = 2.9
  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=   0.003
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      10      5.16       5
     C    3510      2.51       5
     N    1010      2.21       5
     O    1040      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5570
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 2.01, per 1000 atoms: 0.36
  Number of scatterers: 5570
  At special positions: 0
  Unit cell: (79.05, 144.398, 44.268, 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      10     16.00
     O    1040      8.00
     N    1010      7.00
     C    3510      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: 1.21
  Conformation dependent library (CDL) restraints added in 699.0 milliseconds
  

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1280

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 54.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310
      removed outlier: 6.485A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   GLN C 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   TYR E 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL C 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   GLN E 307 " --> pdb=" O   ILE G 308 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   TYR G 310 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL E 309 " --> pdb=" O   TYR G 310 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   GLN G 307 " --> pdb=" O   ILE I 308 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   TYR I 310 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL G 309 " --> pdb=" O   TYR I 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 324
      removed outlier: 6.734A  pdb=" N   SER C 324 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   SER E 324 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   SER G 324 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   SER I 324 " --> pdb=" O   GLY G 323 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330
      removed outlier: 6.416A  pdb=" N   HIS A 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   HIS C 329 " --> pdb=" O   HIS E 330 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   HIS E 329 " --> pdb=" O   HIS G 330 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   HIS G 329 " --> pdb=" O   HIS I 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340
    Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347
      removed outlier: 6.187A  pdb=" N   LYS A 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE C 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   LYS C 343 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE E 346 " --> pdb=" O   LYS C 343 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP C 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LYS E 343 " --> pdb=" O   LEU G 344 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE G 346 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP E 345 " --> pdb=" O   PHE G 346 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LYS G 343 " --> pdb=" O   LEU I 344 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE I 346 " --> pdb=" O   LYS G 343 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ASP G 345 " --> pdb=" O   PHE I 346 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 356
      removed outlier: 6.623A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   SER C 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   GLY A 355 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLN C 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE E 354 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS C 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   SER E 356 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   GLY C 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLN E 351 " --> pdb=" O   SER G 352 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE G 354 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LYS E 353 " --> pdb=" O   ILE G 354 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   SER G 356 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   GLY E 355 " --> pdb=" O   SER G 356 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLN G 351 " --> pdb=" O   SER I 352 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE I 354 " --> pdb=" O   GLN G 351 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS G 353 " --> pdb=" O   ILE I 354 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   SER I 356 " --> pdb=" O   LYS G 353 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   GLY G 355 " --> pdb=" O   SER I 356 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377
    Processing sheet with id=AA9, first strand: chain 'B' and resid 307 through 310
      removed outlier: 6.485A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   GLN D 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   TYR F 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL D 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   GLN F 307 " --> pdb=" O   ILE H 308 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   TYR H 310 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL F 309 " --> pdb=" O   TYR H 310 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   GLN H 307 " --> pdb=" O   ILE J 308 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   TYR J 310 " --> pdb=" O   GLN H 307 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   VAL H 309 " --> pdb=" O   TYR J 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 314 through 324
      removed outlier: 6.734A  pdb=" N   SER D 324 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   SER F 324 " --> pdb=" O   GLY D 323 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   SER H 324 " --> pdb=" O   GLY F 323 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   SER J 324 " --> pdb=" O   GLY H 323 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.416A  pdb=" N   HIS B 329 " --> pdb=" O   HIS D 330 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   HIS D 329 " --> pdb=" O   HIS F 330 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   HIS F 329 " --> pdb=" O   HIS H 330 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   HIS H 329 " --> pdb=" O   HIS J 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340
    Processing sheet with id=AB4, first strand: chain 'B' and resid 343 through 347
      removed outlier: 6.187A  pdb=" N   LYS B 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE D 346 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LYS D 343 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   PHE F 346 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP D 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LYS F 343 " --> pdb=" O   LEU H 344 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   PHE H 346 " --> pdb=" O   LYS F 343 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP F 345 " --> pdb=" O   PHE H 346 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   LYS H 343 " --> pdb=" O   LEU J 344 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   PHE J 346 " --> pdb=" O   LYS H 343 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP H 345 " --> pdb=" O   PHE J 346 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 356
      removed outlier: 6.624A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE D 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   SER D 356 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   GLY B 355 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   GLN D 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE F 354 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LYS D 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   SER F 356 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   GLY D 355 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLN F 351 " --> pdb=" O   SER H 352 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE H 354 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS F 353 " --> pdb=" O   ILE H 354 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   SER H 356 " --> pdb=" O   LYS F 353 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   GLY F 355 " --> pdb=" O   SER H 356 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLN H 351 " --> pdb=" O   SER J 352 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ILE J 354 " --> pdb=" O   GLN H 351 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LYS H 353 " --> pdb=" O   ILE J 354 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   SER J 356 " --> pdb=" O   LYS H 353 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   GLY H 355 " --> pdb=" O   SER J 356 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 359 through 362
    Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 377

    192 hydrogen bonds defined for protein.
    576 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: 1.36

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.20 -     1.31: 1358
        1.31 -     1.43: 1055
        1.43 -     1.55: 3207
        1.55 -     1.67: 30
        1.67 -     1.79: 10
  Bond restraints: 5660
  Sorted by residual:
  bond pdb=" CB  HIS E 374 "
       pdb=" CG  HIS E 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.419  0.078 1.40e-02 5.10e+03 3.11e+01
  bond pdb=" CB  HIS H 374 "
       pdb=" CG  HIS H 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.419  0.078 1.40e-02 5.10e+03 3.08e+01
  bond pdb=" CB  HIS A 374 "
       pdb=" CG  HIS A 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.420  0.077 1.40e-02 5.10e+03 3.06e+01
  bond pdb=" CB  HIS D 374 "
       pdb=" CG  HIS D 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.420  0.077 1.40e-02 5.10e+03 3.03e+01
  bond pdb=" CB  HIS F 374 "
       pdb=" CG  HIS F 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.420  0.077 1.40e-02 5.10e+03 3.03e+01
  ... (remaining 5655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 5357
        1.82 -     3.64: 1565
        3.64 -     5.47: 468
        5.47 -     7.29: 140
        7.29 -     9.11: 50
  Bond angle restraints: 7580
  Sorted by residual:
  angle pdb=" CA  PHE H 346 "
        pdb=" CB  PHE H 346 "
        pdb=" CG  PHE H 346 "
      ideal   model   delta    sigma   weight residual
     113.80  122.53   -8.73 1.00e+00 1.00e+00 7.63e+01
  angle pdb=" CA  PHE C 346 "
        pdb=" CB  PHE C 346 "
        pdb=" CG  PHE C 346 "
      ideal   model   delta    sigma   weight residual
     113.80  122.53   -8.73 1.00e+00 1.00e+00 7.62e+01
  angle pdb=" CA  PHE D 346 "
        pdb=" CB  PHE D 346 "
        pdb=" CG  PHE D 346 "
      ideal   model   delta    sigma   weight residual
     113.80  122.53   -8.73 1.00e+00 1.00e+00 7.62e+01
  angle pdb=" CA  PHE B 346 "
        pdb=" CB  PHE B 346 "
        pdb=" CG  PHE B 346 "
      ideal   model   delta    sigma   weight residual
     113.80  122.52   -8.72 1.00e+00 1.00e+00 7.60e+01
  angle pdb=" CA  PHE E 346 "
        pdb=" CB  PHE E 346 "
        pdb=" CG  PHE E 346 "
      ideal   model   delta    sigma   weight residual
     113.80  122.49   -8.69 1.00e+00 1.00e+00 7.54e+01
  ... (remaining 7575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.66: 3280
       15.66 -    31.31: 110
       31.31 -    46.96: 20
       46.96 -    62.62: 20
       62.62 -    78.27: 10
  Dihedral angle restraints: 3440
    sinusoidal: 1430
      harmonic: 2010
  Sorted by residual:
  dihedral pdb=" C   PHE A 346 "
           pdb=" N   PHE A 346 "
           pdb=" CA  PHE A 346 "
           pdb=" CB  PHE A 346 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.33   10.73     0      2.50e+00 1.60e-01 1.84e+01
  dihedral pdb=" C   PHE F 346 "
           pdb=" N   PHE F 346 "
           pdb=" CA  PHE F 346 "
           pdb=" CB  PHE F 346 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.33   10.73     0      2.50e+00 1.60e-01 1.84e+01
  dihedral pdb=" C   PHE E 346 "
           pdb=" N   PHE E 346 "
           pdb=" CA  PHE E 346 "
           pdb=" CB  PHE E 346 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.30   10.70     0      2.50e+00 1.60e-01 1.83e+01
  ... (remaining 3437 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 590
       0.103 -    0.206: 238
       0.206 -    0.309: 22
       0.309 -    0.412: 0
       0.412 -    0.515: 10
  Chirality restraints: 860
  Sorted by residual:
  chirality pdb=" CA  PHE F 346 "
            pdb=" N   PHE F 346 "
            pdb=" C   PHE F 346 "
            pdb=" CB  PHE F 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.63e+00
  chirality pdb=" CA  PHE E 346 "
            pdb=" N   PHE E 346 "
            pdb=" C   PHE E 346 "
            pdb=" CB  PHE E 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.62e+00
  chirality pdb=" CA  PHE D 346 "
            pdb=" N   PHE D 346 "
            pdb=" C   PHE D 346 "
            pdb=" CB  PHE D 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.61e+00
  ... (remaining 857 not shown)

  Planarity restraints: 960
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G 346 "    0.048 2.00e-02 2.50e+03   2.97e-02 1.54e+01
        pdb=" CG  PHE G 346 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE G 346 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE G 346 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE G 346 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE G 346 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE G 346 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE I 346 "    0.048 2.00e-02 2.50e+03   2.97e-02 1.54e+01
        pdb=" CG  PHE I 346 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE I 346 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE I 346 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE I 346 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE I 346 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE I 346 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F 346 "   -0.048 2.00e-02 2.50e+03   2.96e-02 1.53e+01
        pdb=" CG  PHE F 346 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE F 346 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE F 346 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE F 346 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE F 346 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE F 346 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 957 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 3119
        2.99 -     3.46: 4765
        3.46 -     3.94: 8642
        3.94 -     4.42: 10487
        4.42 -     4.90: 20246
  Nonbonded interactions: 47259
  Sorted by model distance:
  nonbonded pdb=" CB  GLU E 372 "
            pdb=" OE1 GLU E 372 "
     model   vdw
     2.507 2.752
  nonbonded pdb=" CB  GLU J 372 "
            pdb=" OE1 GLU J 372 "
     model   vdw
     2.507 2.752
  nonbonded pdb=" CB  GLU G 372 "
            pdb=" OE1 GLU G 372 "
     model   vdw
     2.507 2.752
  nonbonded pdb=" CB  GLU B 372 "
            pdb=" OE1 GLU B 372 "
     model   vdw
     2.507 2.752
  nonbonded pdb=" CB  GLU H 372 "
            pdb=" OE1 GLU H 372 "
     model   vdw
     2.507 2.752
  ... (remaining 47254 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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:             0.940
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.480
  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:10.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
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      :  0.026   0.138   5660  Z= 1.751
  Angle     :  2.088   9.108   7580  Z= 1.335
  Chirality :  0.117   0.515    860
  Planarity :  0.010   0.035    960
  Dihedral  : 10.929  78.268   2160
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  1.56 %
  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: -2.29 (0.26), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.004   HIS E 362 
 PHE   0.051   0.015   PHE G 346 
 TYR   0.013   0.008   TYR A 310 
 ARG   0.002   0.001   ARG C 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
REVERT: C  342 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7075 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 1.5448
  time to fit residues: 226.6710
Evaluate side-chains
  88 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
B 368 ASN
C 327 ASN
C 368 ASN
D 368 ASN
F 336 GLN
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 368 ASN
J 368 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.148353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.125468 restraints weight = 5657.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.04
r_work: 0.3824 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5660  Z= 0.248
  Angle     :  0.657   5.585   7580  Z= 0.341
  Chirality :  0.050   0.132    860
  Planarity :  0.004   0.031    960
  Dihedral  :  5.926  17.325    740
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.19 %
    Favored  : 85.78 %
  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: -2.16 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 374 
 PHE   0.019   0.003   PHE F 346 
 TYR   0.010   0.002   TYR H 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8306 (tt0) cc_final: 0.7735 (tm-30)
REVERT: A  340 LYS cc_start: 0.8372 (ttmm) cc_final: 0.8054 (ttmm)
REVERT: A  375 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7501 (ttmp)
REVERT: B  331 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7918 (mtpm)
REVERT: B  338 GLU cc_start: 0.8387 (tt0) cc_final: 0.8012 (tm-30)
REVERT: B  343 LYS cc_start: 0.7227 (mptt) cc_final: 0.6984 (mtmt)
REVERT: B  369 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7763 (ttmm)
REVERT: B  375 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7645 (ttmp)
REVERT: C  340 LYS cc_start: 0.7998 (tttt) cc_final: 0.7628 (ttmm)
REVERT: D  343 LYS cc_start: 0.7485 (mptt) cc_final: 0.6889 (tttm)
REVERT: E  343 LYS cc_start: 0.7693 (tptm) cc_final: 0.7438 (tptm)
REVERT: F  336 GLN cc_start: 0.8573 (tt0) cc_final: 0.8292 (mt0)
REVERT: F  343 LYS cc_start: 0.7412 (mptt) cc_final: 0.6844 (mtpp)
REVERT: F  369 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8229 (ttmm)
REVERT: J  319 THR cc_start: 0.8684 (p) cc_final: 0.8362 (t)
REVERT: J  321 LYS cc_start: 0.8379 (mttt) cc_final: 0.7747 (tmtt)
REVERT: J  331 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8408 (mtpm)
  outliers start: 13
  outliers final: 2
  residues processed: 129
  average time/residue: 1.2835
  time to fit residues: 172.2476
Evaluate side-chains
  104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain G residue  357 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
B 336 GLN
D 362 HIS
F 336 GLN
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 336 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.135754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.112207 restraints weight = 6038.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.98
r_work: 0.3644 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3525 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.4560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   5660  Z= 0.385
  Angle     :  0.709   5.337   7580  Z= 0.373
  Chirality :  0.051   0.149    860
  Planarity :  0.005   0.042    960
  Dihedral  :  6.160  16.722    740
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 15.47 %
    Favored  : 80.62 %
  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: -2.52 (0.27), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 374 
 PHE   0.030   0.005   PHE H 346 
 TYR   0.013   0.003   TYR D 310 
 ARG   0.002   0.000   ARG J 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8368 (tt0) cc_final: 0.7858 (tm-30)
REVERT: A  340 LYS cc_start: 0.8487 (ttmm) cc_final: 0.7967 (ttmt)
REVERT: A  375 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7636 (ttmp)
REVERT: B  311 LYS cc_start: 0.7794 (mttt) cc_final: 0.7154 (mmtm)
REVERT: B  316 SER cc_start: 0.8831 (p) cc_final: 0.8605 (p)
REVERT: B  338 GLU cc_start: 0.8533 (tt0) cc_final: 0.8150 (tm-30)
REVERT: B  343 LYS cc_start: 0.7331 (mptt) cc_final: 0.6945 (ttpp)
REVERT: B  369 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7851 (ttmt)
REVERT: C  340 LYS cc_start: 0.7980 (tttt) cc_final: 0.7694 (ttmm)
REVERT: D  343 LYS cc_start: 0.7496 (mptt) cc_final: 0.7100 (mtpp)
REVERT: D  347 LYS cc_start: 0.7245 (pttm) cc_final: 0.6888 (ptpt)
REVERT: D  369 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8064 (mtpt)
REVERT: E  342 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7550 (mp0)
REVERT: E  369 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8254 (mtpt)
REVERT: E  378 PHE cc_start: 0.7023 (t80) cc_final: 0.6743 (t80)
REVERT: F  343 LYS cc_start: 0.7676 (mptt) cc_final: 0.6942 (mtpp)
REVERT: F  347 LYS cc_start: 0.7553 (pttt) cc_final: 0.7078 (pttm)
REVERT: G  338 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8078 (tt0)
REVERT: G  340 LYS cc_start: 0.7807 (tttt) cc_final: 0.7598 (tmtp)
REVERT: G  343 LYS cc_start: 0.7770 (mptt) cc_final: 0.6805 (tttp)
REVERT: G  369 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8053 (ttmm)
REVERT: G  375 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7579 (ttmt)
REVERT: H  321 LYS cc_start: 0.8721 (mttp) cc_final: 0.8393 (mttp)
REVERT: H  340 LYS cc_start: 0.7723 (tttt) cc_final: 0.6798 (mppt)
REVERT: H  343 LYS cc_start: 0.7769 (mptt) cc_final: 0.6930 (ttmm)
REVERT: H  347 LYS cc_start: 0.7536 (pttt) cc_final: 0.7184 (pttt)
REVERT: H  352 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8498 (t)
REVERT: H  369 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7704 (mtmm)
REVERT: I  311 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7690 (ttmt)
REVERT: J  308 ILE cc_start: 0.7970 (mt) cc_final: 0.7765 (mt)
REVERT: J  342 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6962 (mm-30)
REVERT: J  357 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8596 (tt)
REVERT: J  378 PHE cc_start: 0.6443 (m-80) cc_final: 0.6169 (m-80)
  outliers start: 25
  outliers final: 14
  residues processed: 131
  average time/residue: 1.4164
  time to fit residues: 192.2144
Evaluate side-chains
  121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  331 LYS
Chi-restraints excluded: chain I residue  352 SER
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C 362 HIS
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 362 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.142260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.118755 restraints weight = 6082.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.01
r_work: 0.3727 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3606 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.4898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5660  Z= 0.215
  Angle     :  0.573   4.520   7580  Z= 0.299
  Chirality :  0.049   0.125    860
  Planarity :  0.004   0.040    960
  Dihedral  :  5.618  15.066    740
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.34 %
    Favored  : 79.53 %
  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: -2.65 (0.26), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 374 
 PHE   0.016   0.003   PHE G 346 
 TYR   0.011   0.002   TYR H 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8377 (tt0) cc_final: 0.7872 (tm-30)
REVERT: A  340 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8034 (ttmt)
REVERT: B  311 LYS cc_start: 0.7809 (mttt) cc_final: 0.7183 (mttm)
REVERT: B  331 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8031 (mtpm)
REVERT: B  338 GLU cc_start: 0.8506 (tt0) cc_final: 0.8108 (tm-30)
REVERT: B  343 LYS cc_start: 0.7366 (mptt) cc_final: 0.6959 (ttpp)
REVERT: B  352 SER cc_start: 0.8833 (p) cc_final: 0.8558 (t)
REVERT: B  369 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7777 (ttmm)
REVERT: C  340 LYS cc_start: 0.8018 (tttt) cc_final: 0.7677 (ttmm)
REVERT: C  346 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6611 (p90)
REVERT: C  357 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8602 (tt)
REVERT: D  343 LYS cc_start: 0.7405 (mptt) cc_final: 0.7086 (mmmt)
REVERT: D  347 LYS cc_start: 0.7365 (pttm) cc_final: 0.6973 (ptpt)
REVERT: D  369 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8053 (mtpt)
REVERT: E  378 PHE cc_start: 0.6868 (t80) cc_final: 0.6667 (t80)
REVERT: F  343 LYS cc_start: 0.7872 (mptt) cc_final: 0.7054 (mtpp)
REVERT: F  357 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8561 (tt)
REVERT: G  317 LYS cc_start: 0.7734 (ptmt) cc_final: 0.7456 (tttt)
REVERT: G  338 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8111 (tt0)
REVERT: H  342 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7780 (mp0)
REVERT: I  342 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7185 (mp0)
REVERT: J  308 ILE cc_start: 0.8090 (mt) cc_final: 0.7849 (mt)
REVERT: J  331 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8399 (mtpm)
REVERT: J  342 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7033 (mm-30)
REVERT: J  352 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8635 (p)
REVERT: J  378 PHE cc_start: 0.6376 (m-80) cc_final: 0.6115 (m-80)
  outliers start: 20
  outliers final: 7
  residues processed: 116
  average time/residue: 1.3251
  time to fit residues: 159.8333
Evaluate side-chains
  110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  346 PHE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  346 PHE
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain J residue  352 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    0.4980
   chunk 24 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.142280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.118335 restraints weight = 5960.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 2.01
r_work: 0.3725 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5660  Z= 0.215
  Angle     :  0.559   4.430   7580  Z= 0.291
  Chirality :  0.048   0.125    860
  Planarity :  0.004   0.041    960
  Dihedral  :  5.437  14.320    740
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.12 %
    Favored  : 77.97 %
  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: -2.78 (0.26), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 362 
 PHE   0.016   0.003   PHE G 346 
 TYR   0.009   0.002   TYR H 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8346 (tt0) cc_final: 0.7899 (tm-30)
REVERT: A  340 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8064 (ttmt)
REVERT: B  311 LYS cc_start: 0.7781 (mttt) cc_final: 0.7144 (mttm)
REVERT: B  331 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8039 (mtpm)
REVERT: B  338 GLU cc_start: 0.8515 (tt0) cc_final: 0.8132 (tm-30)
REVERT: B  343 LYS cc_start: 0.7364 (mptt) cc_final: 0.6936 (ttpp)
REVERT: B  352 SER cc_start: 0.8846 (p) cc_final: 0.8544 (t)
REVERT: B  369 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7898 (ttmm)
REVERT: C  340 LYS cc_start: 0.8042 (tttt) cc_final: 0.7721 (ttmt)
REVERT: C  346 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6522 (p90)
REVERT: D  343 LYS cc_start: 0.7375 (mptt) cc_final: 0.7035 (mmmt)
REVERT: D  347 LYS cc_start: 0.7291 (pttm) cc_final: 0.7033 (ptpt)
REVERT: D  369 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8075 (mtpt)
REVERT: E  311 LYS cc_start: 0.7647 (ttmt) cc_final: 0.7444 (pttt)
REVERT: E  369 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8177 (mtpt)
REVERT: E  378 PHE cc_start: 0.6900 (t80) cc_final: 0.6689 (t80)
REVERT: F  343 LYS cc_start: 0.7879 (mptt) cc_final: 0.7063 (mtpp)
REVERT: F  357 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8639 (tp)
REVERT: G  317 LYS cc_start: 0.7777 (ptmt) cc_final: 0.7494 (pttt)
REVERT: G  338 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8101 (tt0)
REVERT: H  369 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8003 (mttm)
REVERT: I  342 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7776 (mt-10)
REVERT: J  308 ILE cc_start: 0.8218 (mt) cc_final: 0.7984 (mt)
REVERT: J  331 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8495 (mtpm)
REVERT: J  342 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7002 (mm-30)
REVERT: J  352 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8628 (p)
  outliers start: 25
  outliers final: 13
  residues processed: 111
  average time/residue: 1.2937
  time to fit residues: 149.5069
Evaluate side-chains
  112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  346 PHE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  346 PHE
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  357 LEU
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain I residue  352 SER
Chi-restraints excluded: chain J residue  352 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0770
   chunk 69 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.144231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120439 restraints weight = 5889.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 1.99
r_work: 0.3747 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3624 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.5238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5660  Z= 0.188
  Angle     :  0.534   4.433   7580  Z= 0.279
  Chirality :  0.048   0.124    860
  Planarity :  0.004   0.038    960
  Dihedral  :  5.308  13.588    740
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 20.00 %
    Favored  : 76.88 %
  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: -2.80 (0.26), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 362 
 PHE   0.013   0.002   PHE H 346 
 TYR   0.009   0.002   TYR H 310 
 ARG   0.001   0.000   ARG J 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8319 (tt0) cc_final: 0.7892 (tm-30)
REVERT: A  340 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8085 (ttmt)
REVERT: B  311 LYS cc_start: 0.7761 (mttt) cc_final: 0.7419 (pttt)
REVERT: B  338 GLU cc_start: 0.8519 (tt0) cc_final: 0.8122 (tm-30)
REVERT: B  343 LYS cc_start: 0.7346 (mptt) cc_final: 0.6930 (ttpp)
REVERT: B  352 SER cc_start: 0.8814 (p) cc_final: 0.8550 (t)
REVERT: C  340 LYS cc_start: 0.8119 (tttt) cc_final: 0.7729 (ttmt)
REVERT: C  346 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6520 (p90)
REVERT: C  357 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8552 (tt)
REVERT: D  343 LYS cc_start: 0.7421 (mptt) cc_final: 0.7034 (mmmt)
REVERT: D  369 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8070 (mtpt)
REVERT: E  311 LYS cc_start: 0.7627 (ttmt) cc_final: 0.7394 (pttt)
REVERT: E  369 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8207 (mtpt)
REVERT: E  371 ILE cc_start: 0.8764 (mt) cc_final: 0.8532 (mp)
REVERT: F  343 LYS cc_start: 0.7866 (mptt) cc_final: 0.7036 (mtpp)
REVERT: F  357 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8528 (tt)
REVERT: G  317 LYS cc_start: 0.7627 (ptmt) cc_final: 0.7370 (tttt)
REVERT: G  338 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8081 (tt0)
REVERT: H  369 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8017 (mtpm)
REVERT: J  308 ILE cc_start: 0.8109 (mt) cc_final: 0.7899 (mt)
REVERT: J  331 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8426 (mtpm)
REVERT: J  342 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6915 (mm-30)
  outliers start: 20
  outliers final: 11
  residues processed: 120
  average time/residue: 1.3576
  time to fit residues: 169.5020
Evaluate side-chains
  116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain C residue  346 PHE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  346 PHE
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  352 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.135420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.111972 restraints weight = 6075.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 1.93
r_work: 0.3646 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3525 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.5292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5660  Z= 0.371
  Angle     :  0.657   5.405   7580  Z= 0.347
  Chirality :  0.051   0.146    860
  Planarity :  0.005   0.045    960
  Dihedral  :  5.973  15.500    740
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 19.69 %
    Favored  : 75.47 %
  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: -2.96 (0.25), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.19), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 362 
 PHE   0.025   0.005   PHE G 346 
 TYR   0.012   0.003   TYR D 310 
 ARG   0.002   0.000   ARG J 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8353 (tt0) cc_final: 0.7862 (tm-30)
REVERT: A  340 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8098 (ttmt)
REVERT: B  311 LYS cc_start: 0.7810 (mttt) cc_final: 0.7161 (mttm)
REVERT: B  338 GLU cc_start: 0.8553 (tt0) cc_final: 0.8207 (tm-30)
REVERT: B  343 LYS cc_start: 0.7413 (mptt) cc_final: 0.6993 (ttpp)
REVERT: B  345 ASP cc_start: 0.7732 (t0) cc_final: 0.7494 (t70)
REVERT: C  340 LYS cc_start: 0.8049 (tttt) cc_final: 0.7781 (ttmm)
REVERT: C  346 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6594 (p90)
REVERT: D  343 LYS cc_start: 0.7421 (mptt) cc_final: 0.7016 (mmmt)
REVERT: D  369 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8126 (mtpt)
REVERT: E  342 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7575 (mp0)
REVERT: E  369 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8340 (mtpt)
REVERT: F  343 LYS cc_start: 0.7875 (mptt) cc_final: 0.7024 (mtpp)
REVERT: F  346 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6944 (p90)
REVERT: G  338 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8131 (tt0)
REVERT: G  369 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8123 (ttmm)
REVERT: G  370 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8140 (tttp)
REVERT: H  340 LYS cc_start: 0.7970 (tttt) cc_final: 0.7650 (mtpm)
REVERT: H  343 LYS cc_start: 0.7875 (mptt) cc_final: 0.7066 (mmmm)
REVERT: H  352 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8478 (t)
REVERT: H  375 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7439 (ttpt)
REVERT: I  342 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7683 (mt-10)
REVERT: I  369 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8380 (ttmm)
REVERT: J  331 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8434 (mtpm)
REVERT: J  342 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7057 (mm-30)
REVERT: J  352 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8633 (p)
REVERT: J  357 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8611 (tt)
  outliers start: 31
  outliers final: 16
  residues processed: 122
  average time/residue: 1.4744
  time to fit residues: 186.4586
Evaluate side-chains
  120 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  346 PHE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  346 PHE
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  346 PHE
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  338 GLU
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  357 LEU
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain I residue  352 SER
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  356 SER
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0270
   chunk 69 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.143512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.119881 restraints weight = 5935.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 1.98
r_work: 0.3745 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.5446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5660  Z= 0.180
  Angle     :  0.544   4.497   7580  Z= 0.286
  Chirality :  0.048   0.124    860
  Planarity :  0.004   0.039    960
  Dihedral  :  5.365  14.640    740
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 20.94 %
    Favored  : 75.47 %
  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: -2.88 (0.26), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 374 
 PHE   0.011   0.002   PHE C 346 
 TYR   0.009   0.001   TYR H 310 
 ARG   0.001   0.000   ARG D 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8275 (tt0) cc_final: 0.7886 (tm-30)
REVERT: A  340 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8161 (ttmt)
REVERT: B  338 GLU cc_start: 0.8523 (tt0) cc_final: 0.8080 (tm-30)
REVERT: B  343 LYS cc_start: 0.7474 (mptt) cc_final: 0.7199 (ttpp)
REVERT: B  352 SER cc_start: 0.8842 (p) cc_final: 0.8560 (t)
REVERT: C  340 LYS cc_start: 0.8058 (tttt) cc_final: 0.7763 (ttmt)
REVERT: C  346 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6600 (p90)
REVERT: C  357 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8584 (tt)
REVERT: D  343 LYS cc_start: 0.7483 (mptt) cc_final: 0.7098 (mmmt)
REVERT: D  369 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8100 (mtpt)
REVERT: E  340 LYS cc_start: 0.8155 (tttt) cc_final: 0.7403 (mtmm)
REVERT: E  369 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8158 (mtpt)
REVERT: F  343 LYS cc_start: 0.7877 (mptt) cc_final: 0.7032 (mtpp)
REVERT: F  357 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8542 (tt)
REVERT: G  317 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7495 (tttt)
REVERT: G  338 GLU cc_start: 0.8486 (tt0) cc_final: 0.8094 (tt0)
REVERT: H  321 LYS cc_start: 0.8731 (mttp) cc_final: 0.8381 (mttp)
REVERT: H  369 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7967 (mttm)
REVERT: I  342 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7691 (mt-10)
REVERT: I  357 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8507 (tt)
REVERT: I  378 PHE cc_start: 0.6922 (m-80) cc_final: 0.6625 (m-80)
REVERT: J  331 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8400 (mtpm)
REVERT: J  342 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7074 (mm-30)
REVERT: J  352 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8621 (p)
  outliers start: 23
  outliers final: 11
  residues processed: 116
  average time/residue: 1.3253
  time to fit residues: 160.0842
Evaluate side-chains
  114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  346 PHE
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  346 PHE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain H residue  369 LYS
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain I residue  357 LEU
Chi-restraints excluded: chain J residue  352 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.136538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.113015 restraints weight = 6015.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 1.94
r_work: 0.3660 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3539 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.5397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5660  Z= 0.325
  Angle     :  0.641   6.866   7580  Z= 0.338
  Chirality :  0.050   0.126    860
  Planarity :  0.005   0.046    960
  Dihedral  :  5.819  16.024    740
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.88 %
    Favored  : 74.53 %
  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: -2.97 (0.25), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.19), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 329 
 PHE   0.021   0.004   PHE H 346 
 TYR   0.012   0.002   TYR D 310 
 ARG   0.001   0.000   ARG H 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8350 (tt0) cc_final: 0.7877 (tm-30)
REVERT: A  340 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8132 (ttmt)
REVERT: B  311 LYS cc_start: 0.7828 (mttt) cc_final: 0.7195 (mttm)
REVERT: B  338 GLU cc_start: 0.8573 (tt0) cc_final: 0.8252 (tm-30)
REVERT: B  343 LYS cc_start: 0.7506 (mptt) cc_final: 0.7135 (ttpp)
REVERT: C  340 LYS cc_start: 0.8080 (tttt) cc_final: 0.7770 (ttmt)
REVERT: C  346 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6423 (p90)
REVERT: D  343 LYS cc_start: 0.7498 (mptt) cc_final: 0.7076 (mmmt)
REVERT: D  369 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8108 (mtpt)
REVERT: E  342 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7636 (mp0)
REVERT: F  343 LYS cc_start: 0.7906 (mptt) cc_final: 0.7087 (mtpp)
REVERT: G  369 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8155 (ttmm)
REVERT: G  370 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8260 (tttp)
REVERT: H  314 ASP cc_start: 0.8134 (t0) cc_final: 0.7818 (t0)
REVERT: H  369 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8066 (mtmt)
REVERT: I  342 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7621 (mt-10)
REVERT: I  378 PHE cc_start: 0.6874 (m-80) cc_final: 0.6541 (m-80)
REVERT: J  331 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8415 (mtpm)
REVERT: J  342 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7089 (mm-30)
REVERT: J  352 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8605 (p)
REVERT: J  357 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8663 (tt)
  outliers start: 23
  outliers final: 14
  residues processed: 118
  average time/residue: 1.3325
  time to fit residues: 163.3402
Evaluate side-chains
  120 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  346 PHE
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  346 PHE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain H residue  369 LYS
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain I residue  352 SER
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.134943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.111447 restraints weight = 6029.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 1.93
r_work: 0.3640 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.5460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5660  Z= 0.371
  Angle     :  0.682   7.150   7580  Z= 0.360
  Chirality :  0.051   0.140    860
  Planarity :  0.005   0.043    960
  Dihedral  :  6.078  22.054    740
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 22.03 %
    Favored  : 74.53 %
  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: -3.09 (0.25), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.19), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 329 
 PHE   0.023   0.005   PHE H 346 
 TYR   0.013   0.003   TYR D 310 
 ARG   0.001   0.000   ARG C 349 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8349 (tt0) cc_final: 0.7827 (tm-30)
REVERT: A  340 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8208 (ttmt)
REVERT: B  338 GLU cc_start: 0.8542 (tt0) cc_final: 0.8239 (tm-30)
REVERT: B  347 LYS cc_start: 0.7512 (pttt) cc_final: 0.6867 (ptpt)
REVERT: C  340 LYS cc_start: 0.8109 (tttt) cc_final: 0.7848 (ttmm)
REVERT: C  346 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6665 (p90)
REVERT: D  343 LYS cc_start: 0.7428 (mptt) cc_final: 0.7021 (mmmt)
REVERT: D  369 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8128 (mtpt)
REVERT: E  342 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7615 (mp0)
REVERT: E  369 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8339 (mtpt)
REVERT: F  343 LYS cc_start: 0.7923 (mptt) cc_final: 0.7124 (mtpp)
REVERT: F  378 PHE cc_start: 0.7147 (t80) cc_final: 0.6910 (m-80)
REVERT: G  369 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8141 (ttmm)
REVERT: G  370 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8195 (tttp)
REVERT: H  314 ASP cc_start: 0.8146 (t0) cc_final: 0.7807 (t0)
REVERT: H  352 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8515 (t)
REVERT: H  369 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8082 (mtmt)
REVERT: I  342 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7838 (mt-10)
REVERT: I  369 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8384 (mtpp)
REVERT: I  378 PHE cc_start: 0.6748 (m-80) cc_final: 0.6455 (m-80)
REVERT: J  331 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8440 (mtpm)
REVERT: J  342 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7074 (mm-30)
REVERT: J  357 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8634 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 113
  average time/residue: 1.3547
  time to fit residues: 159.1836
Evaluate side-chains
  114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  346 PHE
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  346 PHE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain H residue  369 LYS
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain I residue  352 SER
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 4 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.142363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.118751 restraints weight = 5953.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 1.97
r_work: 0.3736 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3614 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.5567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5660  Z= 0.194
  Angle     :  0.567   7.810   7580  Z= 0.299
  Chirality :  0.048   0.125    860
  Planarity :  0.004   0.042    960
  Dihedral  :  5.401  14.768    740
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.66 %
    Favored  : 74.38 %
  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: -2.96 (0.26), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 362 
 PHE   0.012   0.002   PHE H 346 
 TYR   0.009   0.002   TYR H 310 
 ARG   0.002   0.000   ARG A 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4623.22 seconds
wall clock time: 79 minutes 56.15 seconds (4796.15 seconds total)