Starting phenix.real_space_refine
on Tue Feb 11 11:45:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8seh_40411/02_2025/8seh_40411_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8seh_40411/02_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_40411/02_2025/8seh_40411.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8seh_40411/02_2025/8seh_40411.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8seh_40411/02_2025/8seh_40411_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8seh_40411/02_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-5592/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: 2.23, per 1000 atoms: 0.40
  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: 1.19
  Conformation dependent library (CDL) restraints added in 690.5 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: 0.80
  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: 1.60

  Time building geometry restraints manager: 1.41 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:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     15.120
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.140
-------------------------------------------------------------------------------
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  : 0.736 
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: 1.6047
  time to fit residues: 235.3418
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  : 0.655 
-------------------------------------------------------------------------------
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 = 42)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.125469 restraints weight = 5657.369|
|-----------------------------------------------------------------------------|
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  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8305 (tt0) cc_final: 0.7735 (tm-30)
REVERT: A  340 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8051 (ttmm)
REVERT: A  375 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7500 (ttmp)
REVERT: B  331 LYS cc_start: 0.8340 (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: 0.7226 (mptt) cc_final: 0.6982 (mtmt)
REVERT: B  369 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7762 (ttmm)
REVERT: B  375 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7644 (ttmp)
REVERT: C  340 LYS cc_start: 0.7996 (tttt) cc_final: 0.7626 (ttmm)
REVERT: D  343 LYS cc_start: 0.7484 (mptt) cc_final: 0.6887 (tttm)
REVERT: E  343 LYS cc_start: 0.7691 (tptm) cc_final: 0.7435 (tptm)
REVERT: F  336 GLN cc_start: 0.8572 (tt0) cc_final: 0.8291 (mt0)
REVERT: F  343 LYS cc_start: 0.7410 (mptt) cc_final: 0.6842 (mtpp)
REVERT: F  369 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8229 (ttmm)
REVERT: J  319 THR cc_start: 0.8683 (p) cc_final: 0.8361 (t)
REVERT: J  321 LYS cc_start: 0.8377 (mttt) cc_final: 0.7746 (tmtt)
REVERT: J  331 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8407 (mtpm)
  outliers start: 13
  outliers final: 2
  residues processed: 129
  average time/residue: 1.3322
  time to fit residues: 178.7291
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  : 0.708 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.136536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.112766 restraints weight = 6026.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 1.97
r_work: 0.3641 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3523 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.4648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   5660  Z= 0.384
  Angle     :  0.714   5.510   7580  Z= 0.376
  Chirality :  0.051   0.150    860
  Planarity :  0.005   0.042    960
  Dihedral  :  6.184  16.730    740
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 15.62 %
    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: -2.55 (0.27), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 329 
 PHE   0.030   0.005   PHE H 346 
 TYR   0.014   0.003   TYR F 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: 24
    poor density    : 116
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8374 (tt0) cc_final: 0.7871 (tm-30)
REVERT: A  340 LYS cc_start: 0.8500 (ttmm) cc_final: 0.7982 (ttmt)
REVERT: A  375 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7640 (ttmp)
REVERT: B  311 LYS cc_start: 0.7802 (mttt) cc_final: 0.7163 (mmtm)
REVERT: B  316 SER cc_start: 0.8811 (p) cc_final: 0.8602 (p)
REVERT: B  338 GLU cc_start: 0.8532 (tt0) cc_final: 0.8150 (tm-30)
REVERT: B  343 LYS cc_start: 0.7372 (mptt) cc_final: 0.6988 (ttpp)
REVERT: B  369 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7857 (ttmt)
REVERT: C  340 LYS cc_start: 0.7992 (tttt) cc_final: 0.7705 (ttmm)
REVERT: D  343 LYS cc_start: 0.7495 (mptt) cc_final: 0.7072 (mtpp)
REVERT: D  347 LYS cc_start: 0.7260 (pttm) cc_final: 0.6912 (ptpt)
REVERT: D  369 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8066 (mtpt)
REVERT: E  342 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7669 (mp0)
REVERT: E  369 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8262 (mtpt)
REVERT: E  378 PHE cc_start: 0.7036 (t80) cc_final: 0.6765 (t80)
REVERT: F  343 LYS cc_start: 0.7739 (mptt) cc_final: 0.6987 (mtpp)
REVERT: F  346 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.7106 (p90)
REVERT: F  347 LYS cc_start: 0.7520 (pttt) cc_final: 0.7058 (pttm)
REVERT: G  338 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8087 (tt0)
REVERT: G  343 LYS cc_start: 0.7778 (mptt) cc_final: 0.6814 (tttp)
REVERT: G  369 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8042 (ttmm)
REVERT: H  321 LYS cc_start: 0.8710 (mttp) cc_final: 0.8379 (mttp)
REVERT: H  340 LYS cc_start: 0.7789 (tttt) cc_final: 0.6810 (mppt)
REVERT: H  343 LYS cc_start: 0.7795 (mptt) cc_final: 0.6947 (ttmm)
REVERT: H  347 LYS cc_start: 0.7533 (pttt) cc_final: 0.7177 (pttt)
REVERT: H  352 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8495 (t)
REVERT: H  369 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7718 (mtmm)
REVERT: H  375 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7201 (ttpt)
REVERT: I  311 LYS cc_start: 0.7999 (ttpp) cc_final: 0.7702 (ttmt)
REVERT: J  342 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6996 (mm-30)
REVERT: J  352 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (p)
REVERT: J  357 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8602 (tt)
REVERT: J  378 PHE cc_start: 0.6378 (m-80) cc_final: 0.6131 (m-80)
  outliers start: 24
  outliers final: 13
  residues processed: 132
  average time/residue: 1.4821
  time to fit residues: 202.5992
Evaluate side-chains
  123 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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  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 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:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.138663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.115041 restraints weight = 6095.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 1.99
r_work: 0.3680 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5660  Z= 0.292
  Angle     :  0.621   4.879   7580  Z= 0.326
  Chirality :  0.050   0.128    860
  Planarity :  0.004   0.043    960
  Dihedral  :  5.896  15.644    740
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 16.41 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (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   0.003   0.001   HIS E 329 
 PHE   0.021   0.004   PHE G 346 
 TYR   0.012   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
  126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8330 (tt0) cc_final: 0.7881 (tm-30)
REVERT: A  340 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8066 (ttmt)
REVERT: B  311 LYS cc_start: 0.7821 (mttt) cc_final: 0.7212 (mttm)
REVERT: B  331 LYS cc_start: 0.8369 (mtmt) cc_final: 0.8035 (mtpm)
REVERT: B  338 GLU cc_start: 0.8556 (tt0) cc_final: 0.8172 (tm-30)
REVERT: B  343 LYS cc_start: 0.7356 (mptt) cc_final: 0.6947 (ttpp)
REVERT: B  369 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7898 (ttmm)
REVERT: C  340 LYS cc_start: 0.7977 (tttt) cc_final: 0.7769 (ttmm)
REVERT: C  346 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6721 (p90)
REVERT: C  357 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8635 (tt)
REVERT: D  343 LYS cc_start: 0.7417 (mptt) cc_final: 0.7024 (mmmt)
REVERT: D  347 LYS cc_start: 0.7341 (pttm) cc_final: 0.6964 (ptpt)
REVERT: D  369 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8065 (mtpt)
REVERT: E  375 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7957 (ttmm)
REVERT: F  343 LYS cc_start: 0.7834 (mptt) cc_final: 0.7019 (mtpp)
REVERT: F  347 LYS cc_start: 0.7484 (pttt) cc_final: 0.7042 (pttm)
REVERT: F  357 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8587 (tt)
REVERT: G  317 LYS cc_start: 0.7780 (ptmt) cc_final: 0.7517 (pttt)
REVERT: G  340 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.6991 (mtmt)
REVERT: G  370 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8127 (tttp)
REVERT: H  321 LYS cc_start: 0.8738 (mttp) cc_final: 0.8389 (mttp)
REVERT: H  352 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8541 (t)
REVERT: I  342 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7916 (mt-10)
REVERT: J  331 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8483 (mtpm)
REVERT: J  342 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6978 (mm-30)
REVERT: J  352 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8648 (p)
  outliers start: 28
  outliers final: 11
  residues processed: 120
  average time/residue: 1.3513
  time to fit residues: 168.7893
Evaluate side-chains
  111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain B residue  356 SER
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  340 LYS
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
Chi-restraints excluded: chain J residue  356 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0870
   overall best weight:    0.9360

-------------------------------------------------------------------------------
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 = 0.4123 r_free = 0.4123 target = 0.140734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.117107 restraints weight = 6015.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 1.99
r_work: 0.3713 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3593 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.5134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5660  Z= 0.226
  Angle     :  0.565   4.479   7580  Z= 0.296
  Chirality :  0.049   0.126    860
  Planarity :  0.004   0.041    960
  Dihedral  :  5.554  14.575    740
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 18.75 %
    Favored  : 76.72 %
  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 A 362 
 PHE   0.017   0.003   PHE G 346 
 TYR   0.010   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
  129 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8295 (tt0) cc_final: 0.7809 (tm-30)
REVERT: A  340 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8109 (ttmt)
REVERT: B  311 LYS cc_start: 0.7782 (mttt) cc_final: 0.7147 (mttm)
REVERT: B  331 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8050 (mtpm)
REVERT: B  338 GLU cc_start: 0.8553 (tt0) cc_final: 0.8172 (tm-30)
REVERT: B  343 LYS cc_start: 0.7372 (mptt) cc_final: 0.6978 (ttpp)
REVERT: B  352 SER cc_start: 0.8844 (p) cc_final: 0.8546 (t)
REVERT: B  369 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7894 (ttmm)
REVERT: C  340 LYS cc_start: 0.8059 (tttt) cc_final: 0.7694 (ttmm)
REVERT: C  346 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6553 (p90)
REVERT: D  314 ASP cc_start: 0.8308 (t0) cc_final: 0.8098 (t0)
REVERT: D  343 LYS cc_start: 0.7417 (mptt) cc_final: 0.7094 (mmmt)
REVERT: D  347 LYS cc_start: 0.7281 (pttm) cc_final: 0.6867 (ptpt)
REVERT: D  369 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8083 (mtpt)
REVERT: E  343 LYS cc_start: 0.7643 (tptm) cc_final: 0.7203 (tptp)
REVERT: E  357 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8896 (tt)
REVERT: E  369 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8199 (mtpt)
REVERT: F  317 LYS cc_start: 0.8063 (ptmt) cc_final: 0.7787 (pttt)
REVERT: F  343 LYS cc_start: 0.7873 (mptt) cc_final: 0.7044 (mtpp)
REVERT: F  357 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8649 (tt)
REVERT: G  317 LYS cc_start: 0.7698 (ptmt) cc_final: 0.7434 (tttt)
REVERT: G  340 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7053 (mppt)
REVERT: H  321 LYS cc_start: 0.8756 (mttp) cc_final: 0.8414 (mttp)
REVERT: I  342 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7820 (mt-10)
REVERT: J  308 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8197 (mp)
REVERT: J  331 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8398 (mtpm)
REVERT: J  342 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7040 (mm-30)
REVERT: J  352 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8614 (p)
REVERT: J  357 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8568 (tt)
  outliers start: 29
  outliers final: 12
  residues processed: 120
  average time/residue: 1.4096
  time to fit residues: 175.4499
Evaluate side-chains
  115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A 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  346 PHE
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  357 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain G residue  340 LYS
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
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  308 ILE
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  357 LEU
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:    0.1980
   chunk 69 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.140087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.116666 restraints weight = 5957.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 1.96
r_work: 0.3703 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3582 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.5265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5660  Z= 0.243
  Angle     :  0.579   6.044   7580  Z= 0.304
  Chirality :  0.049   0.125    860
  Planarity :  0.004   0.041    960
  Dihedral  :  5.592  14.825    740
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 19.22 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.26), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.20), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS D 374 
 PHE   0.017   0.003   PHE G 346 
 TYR   0.010   0.002   TYR H 310 
 ARG   0.002   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
  122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8315 (tt0) cc_final: 0.7880 (tm-30)
REVERT: A  340 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8139 (ttmt)
REVERT: B  311 LYS cc_start: 0.7806 (mttt) cc_final: 0.7169 (mttm)
REVERT: B  331 LYS cc_start: 0.8312 (mtmt) cc_final: 0.8018 (mtpm)
REVERT: B  338 GLU cc_start: 0.8564 (tt0) cc_final: 0.8147 (tm-30)
REVERT: B  343 LYS cc_start: 0.7394 (mptt) cc_final: 0.6998 (ttpp)
REVERT: B  369 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7980 (ttmm)
REVERT: C  340 LYS cc_start: 0.8182 (tttt) cc_final: 0.7753 (ttmt)
REVERT: C  346 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6547 (p90)
REVERT: D  319 THR cc_start: 0.7903 (p) cc_final: 0.7671 (m)
REVERT: D  343 LYS cc_start: 0.7446 (mptt) cc_final: 0.7026 (mmmt)
REVERT: D  347 LYS cc_start: 0.7212 (pttm) cc_final: 0.6800 (ptpt)
REVERT: D  369 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8117 (mtpt)
REVERT: F  317 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7788 (pttt)
REVERT: F  343 LYS cc_start: 0.7890 (mptt) cc_final: 0.7059 (mtpp)
REVERT: F  346 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6828 (p90)
REVERT: F  357 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8648 (tt)
REVERT: G  340 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7060 (mtmt)
REVERT: H  321 LYS cc_start: 0.8773 (mttp) cc_final: 0.8425 (mttp)
REVERT: I  342 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7802 (mt-10)
REVERT: I  378 PHE cc_start: 0.6891 (m-80) cc_final: 0.6659 (m-80)
REVERT: J  308 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8273 (mp)
REVERT: J  331 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8428 (mtpm)
REVERT: J  342 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7065 (mm-30)
REVERT: J  352 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8637 (p)
REVERT: J  357 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8581 (tt)
  outliers start: 27
  outliers final: 12
  residues processed: 116
  average time/residue: 1.3719
  time to fit residues: 165.3544
Evaluate side-chains
  113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A 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  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  340 LYS
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
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  308 ILE
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  357 LEU
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:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    3.0988

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.130426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.107039 restraints weight = 6139.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 1.93
r_work: 0.3586 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.5363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.054   5660  Z= 0.585
  Angle     :  0.802   7.020   7580  Z= 0.426
  Chirality :  0.056   0.213    860
  Planarity :  0.006   0.050    960
  Dihedral  :  6.598  24.827    740
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 18.91 %
    Favored  : 76.25 %
  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: -3.28 (0.24), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.18), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS G 362 
 PHE   0.034   0.007   PHE G 346 
 TYR   0.017   0.004   TYR D 310 
 ARG   0.003   0.001   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
  133 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8385 (tt0) cc_final: 0.7851 (tm-30)
REVERT: A  340 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8184 (ttmt)
REVERT: B  311 LYS cc_start: 0.7875 (mttt) cc_final: 0.7211 (mttm)
REVERT: B  343 LYS cc_start: 0.7510 (mptt) cc_final: 0.7123 (ttpp)
REVERT: B  347 LYS cc_start: 0.7474 (pttt) cc_final: 0.6835 (ptpt)
REVERT: B  369 LYS cc_start: 0.8348 (ttmt) cc_final: 0.8043 (ttmt)
REVERT: C  346 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6465 (p90)
REVERT: D  343 LYS cc_start: 0.7417 (mptt) cc_final: 0.7040 (mmmt)
REVERT: D  347 LYS cc_start: 0.7184 (pttm) cc_final: 0.6740 (ptpt)
REVERT: E  342 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7728 (mp0)
REVERT: E  375 LYS cc_start: 0.8321 (ttmm) cc_final: 0.8032 (ttmp)
REVERT: F  321 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8528 (mppt)
REVERT: F  340 LYS cc_start: 0.8013 (tttt) cc_final: 0.7610 (ttpt)
REVERT: F  343 LYS cc_start: 0.7934 (mptt) cc_final: 0.7031 (mtpp)
REVERT: F  346 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7058 (p90)
REVERT: G  340 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.6995 (mtmt)
REVERT: G  343 LYS cc_start: 0.7958 (mptt) cc_final: 0.7038 (mtpp)
REVERT: G  369 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8302 (ttmm)
REVERT: G  370 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8183 (tttp)
REVERT: H  321 LYS cc_start: 0.8826 (mttp) cc_final: 0.8496 (mttp)
REVERT: H  340 LYS cc_start: 0.8021 (tttt) cc_final: 0.7688 (mtpm)
REVERT: H  343 LYS cc_start: 0.7892 (mptt) cc_final: 0.6845 (ttmm)
REVERT: H  369 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8081 (mtmt)
REVERT: H  375 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7479 (ttpt)
REVERT: I  311 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7482 (mttt)
REVERT: I  342 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7873 (mt-10)
REVERT: I  369 LYS cc_start: 0.8919 (ttmt) cc_final: 0.8542 (ttmm)
REVERT: J  308 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8220 (mp)
REVERT: J  342 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7117 (mm-30)
REVERT: J  357 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8618 (tt)
  outliers start: 31
  outliers final: 19
  residues processed: 124
  average time/residue: 1.4694
  time to fit residues: 188.7171
Evaluate side-chains
  124 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue  316 SER
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  346 PHE
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  340 LYS
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain G residue  357 LEU
Chi-restraints excluded: chain H 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  308 ILE
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:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
G 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.142786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.119219 restraints weight = 5924.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 1.98
r_work: 0.3741 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.5510

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= 0.178
  Angle     :  0.554   6.713   7580  Z= 0.291
  Chirality :  0.049   0.126    860
  Planarity :  0.004   0.040    960
  Dihedral  :  5.471  14.895    740
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.19 %
    Favored  : 74.69 %
  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: -3.04 (0.25), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.19), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS D 374 
 PHE   0.011   0.002   PHE H 346 
 TYR   0.010   0.001   TYR H 310 
 ARG   0.002   0.000   ARG A 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
  121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8337 (tt0) cc_final: 0.7938 (tm-30)
REVERT: A  340 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8173 (ttmt)
REVERT: A  343 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7847 (ttpp)
REVERT: B  331 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8073 (mtpm)
REVERT: B  338 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8222 (tm-30)
REVERT: B  343 LYS cc_start: 0.7389 (mptt) cc_final: 0.7137 (ttpp)
REVERT: B  352 SER cc_start: 0.8843 (p) cc_final: 0.8540 (t)
REVERT: C  340 LYS cc_start: 0.8064 (tttt) cc_final: 0.7728 (ttmt)
REVERT: C  357 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8603 (tt)
REVERT: D  319 THR cc_start: 0.7929 (p) cc_final: 0.7692 (m)
REVERT: D  321 LYS cc_start: 0.8588 (mttm) cc_final: 0.8313 (mttm)
REVERT: D  343 LYS cc_start: 0.7443 (mptt) cc_final: 0.7094 (mmmt)
REVERT: D  347 LYS cc_start: 0.7153 (pttm) cc_final: 0.6742 (ptpt)
REVERT: D  369 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8073 (mtpt)
REVERT: E  340 LYS cc_start: 0.8123 (tttt) cc_final: 0.7352 (mtmm)
REVERT: E  375 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7998 (ttmp)
REVERT: F  317 LYS cc_start: 0.7972 (ptmt) cc_final: 0.7661 (pttt)
REVERT: F  343 LYS cc_start: 0.7812 (mptt) cc_final: 0.7040 (mtpp)
REVERT: F  357 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8517 (tt)
REVERT: G  317 LYS cc_start: 0.7718 (ptmt) cc_final: 0.7452 (tttt)
REVERT: G  340 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7012 (mtmt)
REVERT: H  314 ASP cc_start: 0.7890 (t0) cc_final: 0.7622 (t0)
REVERT: H  321 LYS cc_start: 0.8746 (mttp) cc_final: 0.8395 (mttp)
REVERT: I  342 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7807 (mt-10)
REVERT: I  378 PHE cc_start: 0.7177 (m-80) cc_final: 0.6813 (m-80)
REVERT: J  331 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8402 (mtpm)
REVERT: J  342 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7128 (mm-30)
  outliers start: 20
  outliers final: 3
  residues processed: 113
  average time/residue: 1.2889
  time to fit residues: 151.7870
Evaluate side-chains
  104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain G residue  340 LYS
Chi-restraints excluded: chain I residue  342 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.4096 r_free = 0.4096 target = 0.137366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.113873 restraints weight = 6015.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 1.94
r_work: 0.3674 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5660  Z= 0.289
  Angle     :  0.617   6.826   7580  Z= 0.325
  Chirality :  0.050   0.124    860
  Planarity :  0.005   0.047    960
  Dihedral  :  5.768  18.056    740
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 23.91 %
    Favored  : 73.28 %
  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: -3.10 (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   0.000   HIS E 374 
 PHE   0.020   0.004   PHE C 346 
 TYR   0.011   0.002   TYR D 310 
 ARG   0.002   0.000   ARG B 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
  115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.6125 (mmpt) cc_final: 0.5315 (mmpt)
REVERT: A  338 GLU cc_start: 0.8351 (tt0) cc_final: 0.7757 (tm-30)
REVERT: A  340 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8120 (ttmt)
REVERT: B  338 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8337 (tm-30)
REVERT: B  343 LYS cc_start: 0.7444 (mptt) cc_final: 0.7109 (ttpp)
REVERT: C  340 LYS cc_start: 0.8052 (tttt) cc_final: 0.7719 (ttmm)
REVERT: C  346 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6667 (p90)
REVERT: D  343 LYS cc_start: 0.7460 (mptt) cc_final: 0.7030 (mmmt)
REVERT: D  347 LYS cc_start: 0.7073 (pttm) cc_final: 0.6800 (ptpt)
REVERT: D  369 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8121 (mtpt)
REVERT: E  342 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7604 (mp0)
REVERT: E  375 LYS cc_start: 0.8289 (ttmm) cc_final: 0.8003 (ttmp)
REVERT: F  343 LYS cc_start: 0.7840 (mptt) cc_final: 0.7060 (mtpp)
REVERT: G  317 LYS cc_start: 0.7748 (ptmt) cc_final: 0.7467 (tttt)
REVERT: G  340 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7033 (mtmt)
REVERT: G  370 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8242 (tttp)
REVERT: H  314 ASP cc_start: 0.8022 (t0) cc_final: 0.7701 (t0)
REVERT: H  321 LYS cc_start: 0.8756 (mttp) cc_final: 0.8419 (mttp)
REVERT: I  342 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7857 (mt-10)
REVERT: I  378 PHE cc_start: 0.7347 (m-80) cc_final: 0.6914 (m-80)
REVERT: J  342 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7175 (mm-30)
  outliers start: 18
  outliers final: 8
  residues processed: 108
  average time/residue: 1.4686
  time to fit residues: 164.3160
Evaluate side-chains
  108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain B residue  338 GLU
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 F residue  357 LEU
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  340 LYS
Chi-restraints excluded: chain I residue  342 GLU
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:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 65 optimal weight:    0.4980
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 = 0.4093 r_free = 0.4093 target = 0.137254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.113719 restraints weight = 6023.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.94
r_work: 0.3676 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3555 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.5525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5660  Z= 0.281
  Angle     :  0.622   7.110   7580  Z= 0.328
  Chirality :  0.050   0.125    860
  Planarity :  0.005   0.042    960
  Dihedral  :  5.807  18.075    740
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.91 %
    Favored  : 73.44 %
  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: -3.14 (0.25), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.19), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 374 
 PHE   0.019   0.004   PHE C 346 
 TYR   0.010   0.002   TYR H 310 
 ARG   0.001   0.000   ARG B 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
  113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.6105 (mmpt) cc_final: 0.5300 (mmpt)
REVERT: A  338 GLU cc_start: 0.8339 (tt0) cc_final: 0.7787 (tm-30)
REVERT: A  340 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8119 (ttmt)
REVERT: B  338 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8352 (tm-30)
REVERT: B  343 LYS cc_start: 0.7457 (mptt) cc_final: 0.7158 (ttpp)
REVERT: C  340 LYS cc_start: 0.8061 (tttt) cc_final: 0.7728 (ttmt)
REVERT: C  346 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6549 (p90)
REVERT: C  357 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8677 (tt)
REVERT: D  343 LYS cc_start: 0.7458 (mptt) cc_final: 0.7024 (mmmt)
REVERT: D  347 LYS cc_start: 0.7075 (pttm) cc_final: 0.6803 (ptpt)
REVERT: D  369 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8114 (mtpt)
REVERT: E  375 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7998 (ttmp)
REVERT: F  317 LYS cc_start: 0.8127 (ptmt) cc_final: 0.7893 (ptmt)
REVERT: F  343 LYS cc_start: 0.7805 (mptt) cc_final: 0.7058 (mtpp)
REVERT: F  346 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6987 (p90)
REVERT: F  357 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8621 (tt)
REVERT: F  378 PHE cc_start: 0.7382 (m-80) cc_final: 0.7170 (m-80)
REVERT: G  317 LYS cc_start: 0.7789 (ptmt) cc_final: 0.7524 (tttt)
REVERT: G  340 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7006 (mtmt)
REVERT: H  321 LYS cc_start: 0.8766 (mttp) cc_final: 0.8441 (mttp)
REVERT: H  369 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8090 (mtmt)
REVERT: I  342 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7865 (mt-10)
REVERT: I  378 PHE cc_start: 0.6885 (m-80) cc_final: 0.6595 (m-80)
REVERT: J  342 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7153 (mm-30)
REVERT: J  357 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8522 (tt)
  outliers start: 17
  outliers final: 7
  residues processed: 107
  average time/residue: 1.4060
  time to fit residues: 156.2206
Evaluate side-chains
  110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain B residue  338 GLU
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 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  340 LYS
Chi-restraints excluded: chain G residue  352 SER
Chi-restraints excluded: chain H residue  369 LYS
Chi-restraints excluded: chain I residue  331 LYS
Chi-restraints excluded: chain I residue  342 GLU
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:    0.9980
   chunk 13 optimal weight:    0.0060
   chunk 43 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.4199 r_free = 0.4199 target = 0.146370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.122740 restraints weight = 5907.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 1.98
r_work: 0.3794 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.5689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5660  Z= 0.159
  Angle     :  0.531   6.923   7580  Z= 0.279
  Chirality :  0.048   0.128    860
  Planarity :  0.004   0.042    960
  Dihedral  :  5.139  13.911    740
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 24.84 %
    Favored  : 73.44 %
  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 (0.26), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.19), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS D 374 
 PHE   0.010   0.002   PHE C 346 
 TYR   0.009   0.001   TYR H 310 
 ARG   0.001   0.000   ARG B 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4487.82 seconds
wall clock time: 80 minutes 25.17 seconds (4825.17 seconds total)