Starting phenix.real_space_refine
on Sun Apr 27 14:11:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b4o_44187/04_2025/9b4o_44187.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b4o_44187/04_2025/9b4o_44187.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b4o_44187/04_2025/9b4o_44187.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b4o_44187/04_2025/9b4o_44187.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b4o_44187/04_2025/9b4o_44187.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b4o_44187/04_2025/9b4o_44187.cif"
  }
  resolution = 3.5
  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=   1.000
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    3670      2.51       5
     N    1080      2.21       5
     O    1110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 3.11, per 1000 atoms: 0.53
  Number of scatterers: 5870
  At special positions: 0
  Unit cell: (137.5, 107.8, 46.2, 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    1110      8.00
     N    1080      7.00
     C    3670      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: 1.18
  Conformation dependent library (CDL) restraints added in 683.0 milliseconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 35.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 308
      removed outlier: 6.223A  pdb=" N   VAL A 306 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   VAL D 306 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   VAL F 306 " --> pdb=" O   GLN H 307 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   VAL H 306 " --> pdb=" O   GLN J 307 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318
    Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 328
      removed outlier: 7.038A  pdb=" N   CYS D 322 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY A 323 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ILE D 328 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   CYS F 322 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY D 323 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ILE F 328 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   CYS H 322 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY F 323 " --> pdb=" O   CYS H 322 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   ILE H 328 " --> pdb=" O   ASN F 327 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   CYS J 322 " --> pdb=" O   LYS H 321 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY H 323 " --> pdb=" O   CYS J 322 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ILE J 328 " --> pdb=" O   ASN H 327 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338
      removed outlier: 6.706A  pdb=" N   VAL A 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL D 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL F 337 " --> pdb=" O   GLU H 338 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL H 337 " --> pdb=" O   GLU J 338 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 362
      removed outlier: 7.084A  pdb=" N   GLY A 355 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   ASP D 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LEU A 357 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   ILE D 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ASN A 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   HIS D 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   THR A 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   GLY D 355 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   ASP F 358 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU D 357 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   ILE F 360 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ASN D 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   HIS F 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   THR D 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   GLY F 355 " --> pdb=" O   SER H 356 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   ASP H 358 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LEU F 357 " --> pdb=" O   ASP H 358 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   ILE H 360 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ASN F 359 " --> pdb=" O   ILE H 360 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   HIS H 362 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   THR F 361 " --> pdb=" O   HIS H 362 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   GLY H 355 " --> pdb=" O   SER J 356 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   ASP J 358 " --> pdb=" O   GLY H 355 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU H 357 " --> pdb=" O   ASP J 358 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   ILE J 360 " --> pdb=" O   LEU H 357 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ASN H 359 " --> pdb=" O   ILE J 360 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   HIS J 362 " --> pdb=" O   ASN H 359 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   THR H 361 " --> pdb=" O   HIS J 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 373
      removed outlier: 6.524A  pdb=" N   LYS A 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   THR D 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLU A 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LYS D 370 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   THR F 373 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLU D 372 " --> pdb=" O   THR F 373 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LYS F 370 " --> pdb=" O   ILE H 371 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   THR H 373 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLU F 372 " --> pdb=" O   THR H 373 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS H 370 " --> pdb=" O   ILE J 371 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   THR J 373 " --> pdb=" O   LYS H 370 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLU H 372 " --> pdb=" O   THR J 373 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 378
      removed outlier: 6.738A  pdb=" N   LEU A 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU D 376 " --> pdb=" O   THR F 377 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU F 376 " --> pdb=" O   THR H 377 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU H 376 " --> pdb=" O   THR J 377 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 308
      removed outlier: 6.223A  pdb=" N   VAL B 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   VAL E 306 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   VAL G 306 " --> pdb=" O   GLN I 307 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.907A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 318
      removed outlier: 6.695A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 321 through 328
      removed outlier: 6.056A  pdb=" N   CYS B 322 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   LEU C 325 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   SER B 324 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ASN C 327 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 9.076A  pdb=" N   GLY B 326 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   CYS E 322 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY B 323 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ILE E 328 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   CYS G 322 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY E 323 " --> pdb=" O   CYS G 322 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ILE G 328 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   CYS I 322 " --> pdb=" O   LYS G 321 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY G 323 " --> pdb=" O   CYS I 322 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ILE I 328 " --> pdb=" O   ASN G 327 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 338
      removed outlier: 6.707A  pdb=" N   VAL B 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL E 337 " --> pdb=" O   GLU G 338 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL G 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.499A  pdb=" N   ASP B 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 362
      removed outlier: 7.108A  pdb=" N   GLY C 355 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   GLY B 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   ASP E 358 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU B 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   ILE E 360 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ASN B 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   HIS E 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   THR B 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   GLY E 355 " --> pdb=" O   SER G 356 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   ASP G 358 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LEU E 357 " --> pdb=" O   ASP G 358 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   ILE G 360 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ASN E 359 " --> pdb=" O   ILE G 360 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   HIS G 362 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   THR E 361 " --> pdb=" O   HIS G 362 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   GLY G 355 " --> pdb=" O   SER I 356 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   ASP I 358 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU G 357 " --> pdb=" O   ASP I 358 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   ILE I 360 " --> pdb=" O   LEU G 357 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ASN G 359 " --> pdb=" O   ILE I 360 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   HIS I 362 " --> pdb=" O   ASN G 359 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   THR G 361 " --> pdb=" O   HIS I 362 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 369 through 373
      removed outlier: 6.525A  pdb=" N   LYS B 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   THR E 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLU B 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LYS E 370 " --> pdb=" O   ILE G 371 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   THR G 373 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLU E 372 " --> pdb=" O   THR G 373 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LYS G 370 " --> pdb=" O   ILE I 371 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   THR I 373 " --> pdb=" O   LYS G 370 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLU G 372 " --> pdb=" O   THR I 373 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 376 through 378
      removed outlier: 6.737A  pdb=" N   LEU B 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU E 376 " --> pdb=" O   THR G 377 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU G 376 " --> pdb=" O   THR I 377 " (cutoff:3.500A)

    65 hydrogen bonds defined for protein.
    195 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1950
        1.34 -     1.45: 668
        1.45 -     1.57: 3332
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 5960
  Sorted by residual:
  bond pdb=" N   LYS G 370 "
       pdb=" CA  LYS G 370 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.026 1.20e-02 6.94e+03 4.76e+00
  bond pdb=" N   LYS B 370 "
       pdb=" CA  LYS B 370 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.20e-02 6.94e+03 4.73e+00
  bond pdb=" N   LYS E 370 "
       pdb=" CA  LYS E 370 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.20e-02 6.94e+03 4.66e+00
  bond pdb=" N   LYS F 370 "
       pdb=" CA  LYS F 370 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.20e-02 6.94e+03 4.65e+00
  bond pdb=" N   LYS D 370 "
       pdb=" CA  LYS D 370 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.20e-02 6.94e+03 4.63e+00
  ... (remaining 5955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 7138
        1.23 -     2.47: 702
        2.47 -     3.70: 100
        3.70 -     4.94: 20
        4.94 -     6.17: 10
  Bond angle restraints: 7970
  Sorted by residual:
  angle pdb=" C   LYS C 370 "
        pdb=" CA  LYS C 370 "
        pdb=" CB  LYS C 370 "
      ideal   model   delta    sigma   weight residual
     110.24  105.83    4.41 1.46e+00 4.69e-01 9.14e+00
  angle pdb=" C   LYS I 370 "
        pdb=" CA  LYS I 370 "
        pdb=" CB  LYS I 370 "
      ideal   model   delta    sigma   weight residual
     110.24  105.84    4.40 1.46e+00 4.69e-01 9.08e+00
  angle pdb=" C   LYS D 370 "
        pdb=" CA  LYS D 370 "
        pdb=" CB  LYS D 370 "
      ideal   model   delta    sigma   weight residual
     110.24  105.85    4.39 1.46e+00 4.69e-01 9.05e+00
  angle pdb=" C   LYS J 370 "
        pdb=" CA  LYS J 370 "
        pdb=" CB  LYS J 370 "
      ideal   model   delta    sigma   weight residual
     110.24  105.85    4.39 1.46e+00 4.69e-01 9.04e+00
  angle pdb=" C   LYS A 370 "
        pdb=" CA  LYS A 370 "
        pdb=" CB  LYS A 370 "
      ideal   model   delta    sigma   weight residual
     110.24  105.85    4.39 1.46e+00 4.69e-01 9.03e+00
  ... (remaining 7965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.97: 2634
        6.97 -    13.94: 525
       13.94 -    20.91: 281
       20.91 -    27.88: 160
       27.88 -    34.85: 30
  Dihedral angle restraints: 3630
    sinusoidal: 1520
      harmonic: 2110
  Sorted by residual:
  dihedral pdb=" CA  LYS G 347 "
           pdb=" C   LYS G 347 "
           pdb=" N   ASP G 348 "
           pdb=" CA  ASP G 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.20   15.80     0      5.00e+00 4.00e-02 9.98e+00
  dihedral pdb=" CA  LYS I 347 "
           pdb=" C   LYS I 347 "
           pdb=" N   ASP I 348 "
           pdb=" CA  ASP I 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.21   15.79     0      5.00e+00 4.00e-02 9.97e+00
  dihedral pdb=" CA  LYS D 347 "
           pdb=" C   LYS D 347 "
           pdb=" N   ASP D 348 "
           pdb=" CA  ASP D 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.22   15.78     0      5.00e+00 4.00e-02 9.96e+00
  ... (remaining 3627 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 515
       0.033 -    0.065: 205
       0.065 -    0.098: 46
       0.098 -    0.130: 104
       0.130 -    0.163: 20
  Chirality restraints: 890
  Sorted by residual:
  chirality pdb=" CA  GLU G 372 "
            pdb=" N   GLU G 372 "
            pdb=" C   GLU G 372 "
            pdb=" CB  GLU G 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.61e-01
  chirality pdb=" CA  GLU B 372 "
            pdb=" N   GLU B 372 "
            pdb=" C   GLU B 372 "
            pdb=" CB  GLU B 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.61e-01
  chirality pdb=" CA  GLU J 372 "
            pdb=" N   GLU J 372 "
            pdb=" C   GLU J 372 "
            pdb=" CB  GLU J 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.58e-01
  ... (remaining 887 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 331 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.54e+00
        pdb=" N   PRO H 332 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO H 332 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO H 332 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 331 "    0.021 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO E 332 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO E 332 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E 332 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS I 331 "    0.021 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO I 332 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO I 332 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO I 332 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 1788
        2.85 -     3.36: 4924
        3.36 -     3.87: 8663
        3.87 -     4.39: 8823
        4.39 -     4.90: 16939
  Nonbonded interactions: 41137
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP I 348 "
            pdb=" N   ARG I 349 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OD1 ASP B 348 "
            pdb=" N   ARG B 349 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OD1 ASP C 348 "
            pdb=" N   ARG C 349 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OD1 ASP H 348 "
            pdb=" N   ARG H 349 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OD1 ASP J 348 "
            pdb=" N   ARG J 349 "
     model   vdw
     2.333 3.120
  ... (remaining 41132 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 group one per residue
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:             29.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.170
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
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      :  0.006   0.035   5960  Z= 0.281
  Angle     :  0.771   6.169   7970  Z= 0.440
  Chirality :  0.054   0.163    890
  Planarity :  0.004   0.031   1020
  Dihedral  : 11.064  34.846   2290
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.00 %
    Favored  : 88.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  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: -4.02 (0.20), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.15), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.008   0.002   PHE D 346 
 TYR   0.014   0.004   TYR B 310 
 ARG   0.001   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.38848 (   65)
  hydrogen bonds       : angle       9.78238 (  195)
  covalent geometry    : bond        0.00601 ( 5960)
  covalent geometry    : angle       0.77067 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 341
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9282 (mp) cc_final: 0.8823 (tt)
REVERT: A  340 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8334 (mtpt)
REVERT: A  343 LYS cc_start: 0.8040 (tppt) cc_final: 0.7682 (pttm)
REVERT: A  351 GLN cc_start: 0.9409 (tt0) cc_final: 0.9118 (tt0)
REVERT: A  379 ARG cc_start: 0.7543 (mmt90) cc_final: 0.7283 (pmt-80)
REVERT: B  340 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8422 (tttt)
REVERT: B  344 LEU cc_start: 0.9486 (mt) cc_final: 0.9277 (mt)
REVERT: B  345 ASP cc_start: 0.8726 (m-30) cc_final: 0.8306 (t0)
REVERT: B  370 LYS cc_start: 0.8893 (tttm) cc_final: 0.8670 (ttmm)
REVERT: B  372 GLU cc_start: 0.8628 (tt0) cc_final: 0.8390 (mt-10)
REVERT: C  308 ILE cc_start: 0.8967 (mt) cc_final: 0.8733 (mt)
REVERT: C  315 LEU cc_start: 0.9260 (mp) cc_final: 0.8825 (tt)
REVERT: C  343 LYS cc_start: 0.8188 (tppt) cc_final: 0.7871 (pttp)
REVERT: C  379 ARG cc_start: 0.7346 (mmt90) cc_final: 0.6968 (pmt-80)
REVERT: D  311 LYS cc_start: 0.8861 (mttt) cc_final: 0.8644 (mttt)
REVERT: D  314 ASP cc_start: 0.8463 (t0) cc_final: 0.8207 (t0)
REVERT: D  315 LEU cc_start: 0.9443 (mp) cc_final: 0.8918 (tt)
REVERT: D  343 LYS cc_start: 0.8249 (tppt) cc_final: 0.8014 (mmmm)
REVERT: D  345 ASP cc_start: 0.8785 (m-30) cc_final: 0.8393 (t0)
REVERT: D  351 GLN cc_start: 0.9347 (tt0) cc_final: 0.9118 (tt0)
REVERT: D  370 LYS cc_start: 0.8873 (tttm) cc_final: 0.8392 (ttmm)
REVERT: E  315 LEU cc_start: 0.9335 (mp) cc_final: 0.8800 (tt)
REVERT: E  343 LYS cc_start: 0.8242 (tppt) cc_final: 0.8014 (mmmm)
REVERT: E  345 ASP cc_start: 0.8603 (m-30) cc_final: 0.8196 (t0)
REVERT: E  370 LYS cc_start: 0.8952 (tttm) cc_final: 0.8599 (tttm)
REVERT: E  372 GLU cc_start: 0.8763 (tt0) cc_final: 0.8525 (tt0)
REVERT: E  379 ARG cc_start: 0.7405 (mmt90) cc_final: 0.7038 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9351 (mp) cc_final: 0.8760 (tt)
REVERT: F  345 ASP cc_start: 0.8729 (m-30) cc_final: 0.8255 (t0)
REVERT: F  379 ARG cc_start: 0.7314 (mmt90) cc_final: 0.7028 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8853 (mttt) cc_final: 0.8570 (mtmt)
REVERT: G  345 ASP cc_start: 0.8844 (m-30) cc_final: 0.8340 (t0)
REVERT: G  372 GLU cc_start: 0.8701 (tt0) cc_final: 0.8388 (mt-10)
REVERT: G  379 ARG cc_start: 0.7221 (mmt90) cc_final: 0.6894 (mmm-85)
REVERT: H  311 LYS cc_start: 0.8964 (mttt) cc_final: 0.8731 (mttt)
REVERT: H  314 ASP cc_start: 0.8585 (t0) cc_final: 0.8279 (t0)
REVERT: H  315 LEU cc_start: 0.9394 (mp) cc_final: 0.8790 (tt)
REVERT: H  343 LYS cc_start: 0.8267 (tppt) cc_final: 0.7842 (mmmm)
REVERT: H  344 LEU cc_start: 0.9471 (mt) cc_final: 0.9199 (mt)
REVERT: H  345 ASP cc_start: 0.8853 (m-30) cc_final: 0.8351 (t0)
REVERT: H  347 LYS cc_start: 0.8892 (pttm) cc_final: 0.8686 (ptpp)
REVERT: H  351 GLN cc_start: 0.9430 (tt0) cc_final: 0.9185 (tt0)
REVERT: H  379 ARG cc_start: 0.7540 (mmt90) cc_final: 0.7293 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9265 (mp) cc_final: 0.8777 (tt)
REVERT: I  331 LYS cc_start: 0.9334 (mtmt) cc_final: 0.9039 (mttt)
REVERT: I  345 ASP cc_start: 0.8795 (m-30) cc_final: 0.8151 (t0)
REVERT: I  358 ASP cc_start: 0.7976 (m-30) cc_final: 0.7697 (m-30)
REVERT: I  378 PHE cc_start: 0.8372 (t80) cc_final: 0.8169 (t80)
REVERT: I  379 ARG cc_start: 0.7274 (mmt90) cc_final: 0.6652 (mmp-170)
REVERT: J  331 LYS cc_start: 0.9321 (mtmt) cc_final: 0.9118 (mttt)
REVERT: J  340 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8466 (mtpt)
REVERT: J  345 ASP cc_start: 0.8810 (m-30) cc_final: 0.8262 (t0)
REVERT: J  379 ARG cc_start: 0.7060 (mmt90) cc_final: 0.6678 (mmp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 341
  average time/residue: 0.2737
  time to fit residues: 110.0296
Evaluate side-chains
  282 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0770
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    1.8146

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 327 ASN
F 307 GLN
F 327 ASN
G 327 ASN
H 327 ASN
I 327 ASN
I 330 HIS
J 307 GLN
J 330 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.147947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.126767 restraints weight = 9782.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.129734 restraints weight = 4580.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.131630 restraints weight = 2774.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5960  Z= 0.156
  Angle     :  0.676   6.311   7970  Z= 0.351
  Chirality :  0.049   0.148    890
  Planarity :  0.003   0.032   1020
  Dihedral  :  5.638  17.402    790
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.37 %
    Favored  : 82.84 %
  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: -3.64 (0.22), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.16), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.017   0.003   PHE A 346 
 TYR   0.013   0.002   TYR I 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07588 (   65)
  hydrogen bonds       : angle       6.87884 (  195)
  covalent geometry    : bond        0.00401 ( 5960)
  covalent geometry    : angle       0.67577 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 304
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9078 (mp) cc_final: 0.8742 (tt)
REVERT: A  343 LYS cc_start: 0.8639 (tppt) cc_final: 0.7474 (pptt)
REVERT: A  379 ARG cc_start: 0.7652 (mmt90) cc_final: 0.7056 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8909 (mttt) cc_final: 0.8570 (mtmt)
REVERT: B  315 LEU cc_start: 0.9227 (mp) cc_final: 0.8798 (tt)
REVERT: B  336 GLN cc_start: 0.8923 (tp40) cc_final: 0.8638 (tp40)
REVERT: B  340 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8293 (tttt)
REVERT: B  345 ASP cc_start: 0.8656 (m-30) cc_final: 0.8360 (t0)
REVERT: C  314 ASP cc_start: 0.8516 (t0) cc_final: 0.8271 (t0)
REVERT: C  315 LEU cc_start: 0.9283 (mp) cc_final: 0.8843 (tt)
REVERT: C  343 LYS cc_start: 0.8517 (tppt) cc_final: 0.7481 (pptt)
REVERT: C  379 ARG cc_start: 0.7467 (mmt90) cc_final: 0.6814 (pmt-80)
REVERT: D  311 LYS cc_start: 0.9024 (mttt) cc_final: 0.8370 (mtmm)
REVERT: D  315 LEU cc_start: 0.9363 (mp) cc_final: 0.8873 (tt)
REVERT: D  342 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7744 (mm-30)
REVERT: D  345 ASP cc_start: 0.8774 (m-30) cc_final: 0.8273 (t0)
REVERT: E  314 ASP cc_start: 0.8368 (t0) cc_final: 0.8043 (t0)
REVERT: E  315 LEU cc_start: 0.9228 (mp) cc_final: 0.8778 (tt)
REVERT: E  342 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7490 (mm-30)
REVERT: E  343 LYS cc_start: 0.8100 (tppt) cc_final: 0.7724 (mmmt)
REVERT: E  345 ASP cc_start: 0.8438 (m-30) cc_final: 0.8143 (t0)
REVERT: E  370 LYS cc_start: 0.8903 (tttm) cc_final: 0.8264 (tttm)
REVERT: E  372 GLU cc_start: 0.8728 (tt0) cc_final: 0.8359 (mt-10)
REVERT: E  375 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8772 (tttp)
REVERT: E  379 ARG cc_start: 0.7406 (mmt90) cc_final: 0.6896 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9323 (mp) cc_final: 0.8824 (tt)
REVERT: F  321 LYS cc_start: 0.8807 (mtmm) cc_final: 0.8606 (ttmm)
REVERT: F  345 ASP cc_start: 0.8715 (m-30) cc_final: 0.8323 (t0)
REVERT: F  379 ARG cc_start: 0.7496 (mmt90) cc_final: 0.6947 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8946 (mttt) cc_final: 0.8499 (mtmt)
REVERT: G  315 LEU cc_start: 0.9335 (mp) cc_final: 0.8869 (tt)
REVERT: G  340 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8269 (tttt)
REVERT: G  342 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7783 (mm-30)
REVERT: G  345 ASP cc_start: 0.8705 (m-30) cc_final: 0.8183 (t0)
REVERT: G  372 GLU cc_start: 0.8598 (tt0) cc_final: 0.8395 (mt-10)
REVERT: G  379 ARG cc_start: 0.7299 (mmt90) cc_final: 0.6743 (mmm-85)
REVERT: H  311 LYS cc_start: 0.8959 (mttt) cc_final: 0.8550 (mtmm)
REVERT: H  315 LEU cc_start: 0.9356 (mp) cc_final: 0.8926 (tt)
REVERT: H  342 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7681 (mm-30)
REVERT: H  344 LEU cc_start: 0.9463 (mt) cc_final: 0.9206 (mt)
REVERT: H  345 ASP cc_start: 0.8712 (m-30) cc_final: 0.8186 (t0)
REVERT: H  379 ARG cc_start: 0.7391 (mmt90) cc_final: 0.6987 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9222 (mp) cc_final: 0.8675 (tt)
REVERT: I  331 LYS cc_start: 0.9288 (mtmt) cc_final: 0.9046 (mttt)
REVERT: I  358 ASP cc_start: 0.8034 (m-30) cc_final: 0.7735 (m-30)
REVERT: I  375 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8610 (ttmm)
REVERT: I  379 ARG cc_start: 0.7202 (mmt90) cc_final: 0.6404 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8739 (mmtt)
REVERT: J  315 LEU cc_start: 0.9340 (mp) cc_final: 0.8832 (tt)
REVERT: J  340 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8400 (mtpt)
REVERT: J  379 ARG cc_start: 0.7141 (mmt90) cc_final: 0.6520 (mmp-170)
  outliers start: 12
  outliers final: 9
  residues processed: 307
  average time/residue: 0.2720
  time to fit residues: 98.8179
Evaluate side-chains
  288 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 279
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain J residue  373 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 46 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 336 GLN
** C 362 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 = 0.4268 r_free = 0.4268 target = 0.149550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.128000 restraints weight = 9830.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.131028 restraints weight = 4694.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.132999 restraints weight = 2842.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5960  Z= 0.145
  Angle     :  0.642   5.940   7970  Z= 0.336
  Chirality :  0.048   0.137    890
  Planarity :  0.003   0.028   1020
  Dihedral  :  5.496  16.056    790
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.00 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.22), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.17), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 362 
 PHE   0.015   0.003   PHE A 346 
 TYR   0.013   0.002   TYR I 310 
 ARG   0.001   0.000   ARG H 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06351 (   65)
  hydrogen bonds       : angle       6.42370 (  195)
  covalent geometry    : bond        0.00377 ( 5960)
  covalent geometry    : angle       0.64229 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 298
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8585 (pttm)
REVERT: A  315 LEU cc_start: 0.9060 (mp) cc_final: 0.8710 (tt)
REVERT: A  379 ARG cc_start: 0.7549 (mmt90) cc_final: 0.6918 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8948 (mttt) cc_final: 0.8692 (mtmt)
REVERT: B  315 LEU cc_start: 0.9229 (mp) cc_final: 0.8765 (tt)
REVERT: B  340 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8136 (tttt)
REVERT: B  345 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8366 (t0)
REVERT: C  315 LEU cc_start: 0.9246 (mp) cc_final: 0.8795 (tt)
REVERT: C  343 LYS cc_start: 0.8499 (tppt) cc_final: 0.7428 (pptt)
REVERT: C  375 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8784 (tttp)
REVERT: C  379 ARG cc_start: 0.7504 (mmt90) cc_final: 0.6802 (pmt-80)
REVERT: D  311 LYS cc_start: 0.8942 (mttt) cc_final: 0.8598 (mtmm)
REVERT: D  315 LEU cc_start: 0.9372 (mp) cc_final: 0.8852 (tt)
REVERT: D  327 ASN cc_start: 0.9518 (t0) cc_final: 0.9030 (t0)
REVERT: D  345 ASP cc_start: 0.8767 (m-30) cc_final: 0.8305 (t0)
REVERT: D  375 LYS cc_start: 0.8983 (tttt) cc_final: 0.8686 (tttp)
REVERT: E  314 ASP cc_start: 0.8316 (t0) cc_final: 0.7950 (t0)
REVERT: E  315 LEU cc_start: 0.9194 (mp) cc_final: 0.8789 (tt)
REVERT: E  343 LYS cc_start: 0.8101 (tppt) cc_final: 0.7835 (mmmm)
REVERT: E  345 ASP cc_start: 0.8583 (m-30) cc_final: 0.8087 (t0)
REVERT: E  370 LYS cc_start: 0.8862 (tttm) cc_final: 0.8247 (tttm)
REVERT: E  372 GLU cc_start: 0.8681 (tt0) cc_final: 0.8390 (mt-10)
REVERT: E  375 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8770 (ttmm)
REVERT: E  379 ARG cc_start: 0.7325 (mmt90) cc_final: 0.6780 (mmm-85)
REVERT: F  311 LYS cc_start: 0.9073 (pttm) cc_final: 0.8856 (pttm)
REVERT: F  314 ASP cc_start: 0.8419 (t0) cc_final: 0.7982 (t0)
REVERT: F  315 LEU cc_start: 0.9288 (mp) cc_final: 0.8845 (tt)
REVERT: F  345 ASP cc_start: 0.8660 (m-30) cc_final: 0.8331 (t0)
REVERT: F  379 ARG cc_start: 0.7396 (mmt90) cc_final: 0.6880 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8978 (mttt) cc_final: 0.8473 (mtmt)
REVERT: G  315 LEU cc_start: 0.9390 (mp) cc_final: 0.8870 (tt)
REVERT: G  345 ASP cc_start: 0.8657 (m-30) cc_final: 0.8111 (t0)
REVERT: G  379 ARG cc_start: 0.7339 (mmt90) cc_final: 0.6718 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9328 (mp) cc_final: 0.8919 (tt)
REVERT: H  343 LYS cc_start: 0.8213 (tppt) cc_final: 0.7962 (mmmm)
REVERT: H  345 ASP cc_start: 0.8709 (m-30) cc_final: 0.8152 (t0)
REVERT: H  379 ARG cc_start: 0.7398 (mmt90) cc_final: 0.6990 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9286 (mp) cc_final: 0.8770 (tt)
REVERT: I  331 LYS cc_start: 0.9259 (mtmt) cc_final: 0.9029 (mttt)
REVERT: I  358 ASP cc_start: 0.7916 (m-30) cc_final: 0.7495 (m-30)
REVERT: I  375 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8519 (ttmm)
REVERT: I  379 ARG cc_start: 0.7242 (mmt90) cc_final: 0.6443 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8782 (mmtt)
REVERT: J  315 LEU cc_start: 0.9273 (mp) cc_final: 0.8617 (tt)
REVERT: J  340 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8151 (tttt)
REVERT: J  379 ARG cc_start: 0.7210 (mmt90) cc_final: 0.6644 (mmp-170)
  outliers start: 18
  outliers final: 14
  residues processed: 303
  average time/residue: 0.2553
  time to fit residues: 91.8478
Evaluate side-chains
  293 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 278
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain H residue  339 VAL
Chi-restraints excluded: chain I residue  322 CYS
Chi-restraints excluded: chain J residue  373 THR
Chi-restraints excluded: chain J residue  375 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN
I 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.146606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.125201 restraints weight = 10060.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.128178 restraints weight = 4757.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.130038 restraints weight = 2888.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5960  Z= 0.182
  Angle     :  0.681   5.529   7970  Z= 0.358
  Chirality :  0.049   0.136    890
  Planarity :  0.004   0.049   1020
  Dihedral  :  5.755  18.152    790
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.85 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.22), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.65 (0.17), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 330 
 PHE   0.015   0.003   PHE A 346 
 TYR   0.015   0.003   TYR F 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06729 (   65)
  hydrogen bonds       : angle       6.37698 (  195)
  covalent geometry    : bond        0.00460 ( 5960)
  covalent geometry    : angle       0.68132 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 285
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9097 (mp) cc_final: 0.8748 (tt)
REVERT: A  378 PHE cc_start: 0.8588 (t80) cc_final: 0.8385 (t80)
REVERT: A  379 ARG cc_start: 0.7559 (mmt90) cc_final: 0.6969 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8949 (mttt) cc_final: 0.8673 (mtmt)
REVERT: B  315 LEU cc_start: 0.9265 (mp) cc_final: 0.8788 (tt)
REVERT: B  340 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8273 (tttt)
REVERT: B  345 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8388 (t0)
REVERT: C  311 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8632 (mtmm)
REVERT: C  315 LEU cc_start: 0.9276 (mp) cc_final: 0.8840 (tt)
REVERT: C  343 LYS cc_start: 0.8535 (tppt) cc_final: 0.7529 (pttp)
REVERT: C  375 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8772 (tttm)
REVERT: C  379 ARG cc_start: 0.7567 (mmt90) cc_final: 0.6866 (pmt-80)
REVERT: D  311 LYS cc_start: 0.9068 (mttt) cc_final: 0.8554 (mtmm)
REVERT: D  315 LEU cc_start: 0.9344 (mp) cc_final: 0.8838 (tt)
REVERT: D  343 LYS cc_start: 0.7986 (tppt) cc_final: 0.7683 (mmmm)
REVERT: D  345 ASP cc_start: 0.8749 (m-30) cc_final: 0.8349 (t0)
REVERT: D  375 LYS cc_start: 0.9039 (tttt) cc_final: 0.8693 (tttp)
REVERT: E  314 ASP cc_start: 0.8277 (t0) cc_final: 0.8075 (t0)
REVERT: E  315 LEU cc_start: 0.9208 (mp) cc_final: 0.8796 (tt)
REVERT: E  345 ASP cc_start: 0.8576 (m-30) cc_final: 0.8071 (t0)
REVERT: E  370 LYS cc_start: 0.8867 (tttm) cc_final: 0.8240 (tttm)
REVERT: E  372 GLU cc_start: 0.8814 (tt0) cc_final: 0.8505 (mt-10)
REVERT: E  375 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8753 (ttmm)
REVERT: E  379 ARG cc_start: 0.7319 (mmt90) cc_final: 0.6769 (mmm-85)
REVERT: F  314 ASP cc_start: 0.8385 (t0) cc_final: 0.8021 (t0)
REVERT: F  315 LEU cc_start: 0.9335 (mp) cc_final: 0.8868 (tt)
REVERT: F  345 ASP cc_start: 0.8660 (m-30) cc_final: 0.8336 (t0)
REVERT: F  379 ARG cc_start: 0.7465 (mmt90) cc_final: 0.6919 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8927 (mttt) cc_final: 0.8425 (mtmt)
REVERT: G  315 LEU cc_start: 0.9409 (mp) cc_final: 0.8901 (tt)
REVERT: G  340 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8271 (tttt)
REVERT: G  345 ASP cc_start: 0.8704 (m-30) cc_final: 0.8120 (t0)
REVERT: G  379 ARG cc_start: 0.7363 (mmt90) cc_final: 0.6721 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9332 (mp) cc_final: 0.8873 (tt)
REVERT: H  343 LYS cc_start: 0.8292 (tppt) cc_final: 0.8004 (mmmm)
REVERT: H  345 ASP cc_start: 0.8732 (m-30) cc_final: 0.8097 (t0)
REVERT: H  379 ARG cc_start: 0.7378 (mmt90) cc_final: 0.6952 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9276 (mp) cc_final: 0.8791 (tt)
REVERT: I  331 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8980 (mttt)
REVERT: I  358 ASP cc_start: 0.7956 (m-30) cc_final: 0.7594 (m-30)
REVERT: I  375 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8471 (ttmm)
REVERT: I  379 ARG cc_start: 0.7292 (mmt90) cc_final: 0.6469 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8794 (mmtt)
REVERT: J  315 LEU cc_start: 0.9340 (mp) cc_final: 0.8644 (tt)
REVERT: J  340 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8179 (tttt)
REVERT: J  379 ARG cc_start: 0.7209 (mmt90) cc_final: 0.6664 (mmp-170)
  outliers start: 19
  outliers final: 16
  residues processed: 290
  average time/residue: 0.2765
  time to fit residues: 94.6957
Evaluate side-chains
  293 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 276
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  369 LYS
Chi-restraints excluded: chain H residue  339 VAL
Chi-restraints excluded: chain I residue  322 CYS
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  373 THR
Chi-restraints excluded: chain J residue  375 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.144107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.122464 restraints weight = 9865.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.125341 restraints weight = 4799.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.127173 restraints weight = 2962.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   5960  Z= 0.267
  Angle     :  0.767   6.142   7970  Z= 0.404
  Chirality :  0.050   0.135    890
  Planarity :  0.004   0.037   1020
  Dihedral  :  6.288  20.893    790
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.30 %
    Favored  : 76.12 %
  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: -3.54 (0.21), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.16), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J 330 
 PHE   0.015   0.003   PHE A 346 
 TYR   0.021   0.004   TYR I 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07933 (   65)
  hydrogen bonds       : angle       6.65491 (  195)
  covalent geometry    : bond        0.00657 ( 5960)
  covalent geometry    : angle       0.76679 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 270
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9122 (mp) cc_final: 0.8711 (tt)
REVERT: A  340 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8120 (mtpt)
REVERT: A  343 LYS cc_start: 0.8692 (tppt) cc_final: 0.8380 (mmmm)
REVERT: A  379 ARG cc_start: 0.7558 (mmt90) cc_final: 0.7049 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8970 (mttt) cc_final: 0.8711 (mtmt)
REVERT: B  315 LEU cc_start: 0.9265 (mp) cc_final: 0.8879 (tt)
REVERT: B  340 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8336 (tttt)
REVERT: B  345 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8363 (t0)
REVERT: C  311 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8647 (mtmm)
REVERT: C  315 LEU cc_start: 0.9279 (mp) cc_final: 0.8828 (tt)
REVERT: C  343 LYS cc_start: 0.8438 (tppt) cc_final: 0.8211 (mmmm)
REVERT: C  379 ARG cc_start: 0.7558 (mmt90) cc_final: 0.6923 (pmt-80)
REVERT: D  311 LYS cc_start: 0.9009 (mttt) cc_final: 0.8511 (mtmm)
REVERT: D  315 LEU cc_start: 0.9397 (mp) cc_final: 0.8853 (tt)
REVERT: D  343 LYS cc_start: 0.8146 (tppt) cc_final: 0.7777 (mmmm)
REVERT: D  345 ASP cc_start: 0.8714 (m-30) cc_final: 0.8403 (t0)
REVERT: D  375 LYS cc_start: 0.9115 (tttt) cc_final: 0.8768 (tttp)
REVERT: E  315 LEU cc_start: 0.9223 (mp) cc_final: 0.8818 (tt)
REVERT: E  342 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7743 (mm-30)
REVERT: E  345 ASP cc_start: 0.8643 (m-30) cc_final: 0.8155 (t0)
REVERT: E  370 LYS cc_start: 0.8882 (tttm) cc_final: 0.8506 (tttm)
REVERT: E  372 GLU cc_start: 0.8854 (tt0) cc_final: 0.8502 (mt-10)
REVERT: E  379 ARG cc_start: 0.7403 (mmt90) cc_final: 0.6849 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9298 (mp) cc_final: 0.8852 (tt)
REVERT: F  345 ASP cc_start: 0.8722 (m-30) cc_final: 0.8349 (t0)
REVERT: F  379 ARG cc_start: 0.7524 (mmt90) cc_final: 0.6989 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8950 (mttt) cc_final: 0.8452 (mtmt)
REVERT: G  315 LEU cc_start: 0.9431 (mp) cc_final: 0.8926 (tt)
REVERT: G  340 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8319 (tttt)
REVERT: G  342 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7654 (mm-30)
REVERT: G  345 ASP cc_start: 0.8686 (m-30) cc_final: 0.8203 (t0)
REVERT: G  379 ARG cc_start: 0.7421 (mmt90) cc_final: 0.6741 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9384 (mp) cc_final: 0.8997 (tt)
REVERT: H  343 LYS cc_start: 0.8355 (tppt) cc_final: 0.8069 (mmmm)
REVERT: H  345 ASP cc_start: 0.8768 (m-30) cc_final: 0.8101 (t0)
REVERT: H  379 ARG cc_start: 0.7481 (mmt90) cc_final: 0.7127 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9317 (mp) cc_final: 0.8804 (tt)
REVERT: I  331 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8888 (mttt)
REVERT: I  343 LYS cc_start: 0.8636 (mmmm) cc_final: 0.8135 (mmmt)
REVERT: I  358 ASP cc_start: 0.8080 (m-30) cc_final: 0.7733 (m-30)
REVERT: I  379 ARG cc_start: 0.7381 (mmt90) cc_final: 0.6537 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8845 (mmtt)
REVERT: J  379 ARG cc_start: 0.7260 (mmt90) cc_final: 0.6731 (mmp-170)
  outliers start: 24
  outliers final: 18
  residues processed: 279
  average time/residue: 0.2756
  time to fit residues: 90.4607
Evaluate side-chains
  284 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 265
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  369 LYS
Chi-restraints excluded: chain H residue  339 VAL
Chi-restraints excluded: chain H residue  344 LEU
Chi-restraints excluded: chain I residue  322 CYS
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  373 THR
Chi-restraints excluded: chain J residue  375 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 336 GLN
E 336 GLN
G 327 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.146508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.124705 restraints weight = 9860.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.127588 restraints weight = 4782.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.129448 restraints weight = 2970.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5960  Z= 0.195
  Angle     :  0.704   5.809   7970  Z= 0.371
  Chirality :  0.049   0.138    890
  Planarity :  0.004   0.039   1020
  Dihedral  :  5.956  19.465    790
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.69 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.22), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.17), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J 330 
 PHE   0.016   0.003   PHE A 378 
 TYR   0.015   0.003   TYR I 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06608 (   65)
  hydrogen bonds       : angle       6.45897 (  195)
  covalent geometry    : bond        0.00492 ( 5960)
  covalent geometry    : angle       0.70388 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 272
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9124 (mp) cc_final: 0.8742 (tt)
REVERT: A  340 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8072 (mtpt)
REVERT: A  379 ARG cc_start: 0.7535 (mmt90) cc_final: 0.6978 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8984 (mttt) cc_final: 0.8711 (mtmt)
REVERT: B  315 LEU cc_start: 0.9259 (mp) cc_final: 0.8878 (tt)
REVERT: B  340 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8322 (tttt)
REVERT: B  345 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8413 (t0)
REVERT: C  311 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8624 (mtmm)
REVERT: C  315 LEU cc_start: 0.9260 (mp) cc_final: 0.8842 (tt)
REVERT: C  343 LYS cc_start: 0.8311 (tppt) cc_final: 0.7978 (mmmm)
REVERT: C  375 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8828 (tttp)
REVERT: C  379 ARG cc_start: 0.7544 (mmt90) cc_final: 0.6925 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9378 (mp) cc_final: 0.8833 (tt)
REVERT: D  343 LYS cc_start: 0.8039 (tppt) cc_final: 0.7734 (mmmm)
REVERT: D  345 ASP cc_start: 0.8728 (m-30) cc_final: 0.8366 (t0)
REVERT: D  375 LYS cc_start: 0.9100 (tttt) cc_final: 0.8774 (tttp)
REVERT: E  315 LEU cc_start: 0.9216 (mp) cc_final: 0.8788 (tt)
REVERT: E  343 LYS cc_start: 0.8239 (mmmm) cc_final: 0.7812 (mmmm)
REVERT: E  345 ASP cc_start: 0.8495 (m-30) cc_final: 0.8046 (t0)
REVERT: E  370 LYS cc_start: 0.8879 (tttm) cc_final: 0.8510 (tttm)
REVERT: E  372 GLU cc_start: 0.8720 (tt0) cc_final: 0.8423 (mt-10)
REVERT: E  375 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8614 (ttmm)
REVERT: E  379 ARG cc_start: 0.7415 (mmt90) cc_final: 0.6848 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9257 (mp) cc_final: 0.8805 (tt)
REVERT: F  345 ASP cc_start: 0.8640 (m-30) cc_final: 0.8379 (t0)
REVERT: F  379 ARG cc_start: 0.7455 (mmt90) cc_final: 0.6924 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8945 (mttt) cc_final: 0.8455 (mtmt)
REVERT: G  315 LEU cc_start: 0.9409 (mp) cc_final: 0.8946 (tt)
REVERT: G  340 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8324 (tttt)
REVERT: G  342 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7707 (mm-30)
REVERT: G  345 ASP cc_start: 0.8703 (m-30) cc_final: 0.8227 (t0)
REVERT: G  379 ARG cc_start: 0.7413 (mmt90) cc_final: 0.6715 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9332 (mp) cc_final: 0.8997 (tt)
REVERT: H  343 LYS cc_start: 0.8309 (tppt) cc_final: 0.8037 (mmmm)
REVERT: H  345 ASP cc_start: 0.8743 (m-30) cc_final: 0.8129 (t0)
REVERT: H  379 ARG cc_start: 0.7470 (mmt90) cc_final: 0.7045 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9355 (mp) cc_final: 0.8837 (tt)
REVERT: I  331 LYS cc_start: 0.9211 (mtmt) cc_final: 0.8952 (mttp)
REVERT: I  343 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8120 (mmmt)
REVERT: I  358 ASP cc_start: 0.7988 (m-30) cc_final: 0.7633 (m-30)
REVERT: I  379 ARG cc_start: 0.7294 (mmt90) cc_final: 0.6501 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8847 (mmtt)
REVERT: J  379 ARG cc_start: 0.7319 (mmt90) cc_final: 0.6821 (mmp-170)
  outliers start: 23
  outliers final: 18
  residues processed: 281
  average time/residue: 0.2694
  time to fit residues: 89.4327
Evaluate side-chains
  286 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 267
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  369 LYS
Chi-restraints excluded: chain H residue  339 VAL
Chi-restraints excluded: chain I residue  322 CYS
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  373 THR
Chi-restraints excluded: chain J residue  375 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.147311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.125642 restraints weight = 9942.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.128634 restraints weight = 4802.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.130622 restraints weight = 2944.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5960  Z= 0.206
  Angle     :  0.721   5.761   7970  Z= 0.380
  Chirality :  0.049   0.146    890
  Planarity :  0.004   0.037   1020
  Dihedral  :  6.060  20.512    790
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 23.43 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.23), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.17), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J 330 
 PHE   0.015   0.003   PHE A 378 
 TYR   0.016   0.003   TYR I 310 
 ARG   0.001   0.000   ARG H 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06844 (   65)
  hydrogen bonds       : angle       6.49280 (  195)
  covalent geometry    : bond        0.00517 ( 5960)
  covalent geometry    : angle       0.72063 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 272
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8739 (ptpt)
REVERT: A  315 LEU cc_start: 0.9133 (mp) cc_final: 0.8747 (tt)
REVERT: A  340 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8089 (mtpt)
REVERT: A  379 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7060 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8982 (mttt) cc_final: 0.8709 (mtmt)
REVERT: B  315 LEU cc_start: 0.9266 (mp) cc_final: 0.8886 (tt)
REVERT: B  340 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8363 (tttt)
REVERT: B  345 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8413 (t0)
REVERT: C  311 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8588 (mtmm)
REVERT: C  315 LEU cc_start: 0.9270 (mp) cc_final: 0.8853 (tt)
REVERT: C  343 LYS cc_start: 0.8179 (tppt) cc_final: 0.7243 (pttm)
REVERT: C  375 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8821 (tttp)
REVERT: C  379 ARG cc_start: 0.7476 (mmt90) cc_final: 0.6917 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9365 (mp) cc_final: 0.8846 (tt)
REVERT: D  343 LYS cc_start: 0.8061 (tppt) cc_final: 0.7711 (mmmm)
REVERT: D  345 ASP cc_start: 0.8704 (m-30) cc_final: 0.8378 (t0)
REVERT: D  375 LYS cc_start: 0.9075 (tttt) cc_final: 0.8727 (tttp)
REVERT: E  315 LEU cc_start: 0.9241 (mp) cc_final: 0.8787 (tt)
REVERT: E  343 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7839 (mmmm)
REVERT: E  345 ASP cc_start: 0.8518 (m-30) cc_final: 0.8039 (t0)
REVERT: E  370 LYS cc_start: 0.8896 (tttm) cc_final: 0.8513 (tttm)
REVERT: E  372 GLU cc_start: 0.8712 (tt0) cc_final: 0.8459 (mt-10)
REVERT: E  375 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8629 (ttmm)
REVERT: E  379 ARG cc_start: 0.7398 (mmt90) cc_final: 0.6784 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9256 (mp) cc_final: 0.8804 (tt)
REVERT: F  343 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8204 (mmmm)
REVERT: F  345 ASP cc_start: 0.8631 (m-30) cc_final: 0.8413 (t0)
REVERT: F  379 ARG cc_start: 0.7534 (mmt90) cc_final: 0.6968 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8937 (mttt) cc_final: 0.8421 (mtmt)
REVERT: G  315 LEU cc_start: 0.9416 (mp) cc_final: 0.8957 (tt)
REVERT: G  340 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8301 (tttt)
REVERT: G  342 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7667 (mm-30)
REVERT: G  345 ASP cc_start: 0.8686 (m-30) cc_final: 0.8298 (t0)
REVERT: G  379 ARG cc_start: 0.7372 (mmt90) cc_final: 0.6697 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9305 (mp) cc_final: 0.8958 (tt)
REVERT: H  343 LYS cc_start: 0.8321 (tppt) cc_final: 0.8043 (mmmm)
REVERT: H  345 ASP cc_start: 0.8737 (m-30) cc_final: 0.8134 (t0)
REVERT: H  379 ARG cc_start: 0.7525 (mmt90) cc_final: 0.7047 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9362 (mp) cc_final: 0.8827 (tt)
REVERT: I  331 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8913 (mttp)
REVERT: I  343 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8185 (mmmt)
REVERT: I  358 ASP cc_start: 0.7984 (m-30) cc_final: 0.7647 (m-30)
REVERT: I  379 ARG cc_start: 0.7327 (mmt90) cc_final: 0.6500 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8842 (mmtt)
REVERT: J  379 ARG cc_start: 0.7333 (mmt90) cc_final: 0.6851 (mmp-170)
  outliers start: 18
  outliers final: 16
  residues processed: 277
  average time/residue: 0.2949
  time to fit residues: 96.4421
Evaluate side-chains
  286 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 269
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  369 LYS
Chi-restraints excluded: chain H residue  339 VAL
Chi-restraints excluded: chain I residue  322 CYS
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  373 THR
Chi-restraints excluded: chain J residue  375 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 4 optimal weight:    0.3980
   chunk 69 optimal weight:    0.0050
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.150680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.128851 restraints weight = 9770.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.131878 restraints weight = 4744.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.133825 restraints weight = 2898.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5960  Z= 0.131
  Angle     :  0.648   5.863   7970  Z= 0.343
  Chirality :  0.048   0.126    890
  Planarity :  0.004   0.035   1020
  Dihedral  :  5.449  20.970    790
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 24.48 %
    Favored  : 73.13 %
  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: -3.35 (0.23), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS J 330 
 PHE   0.013   0.003   PHE A 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.003   0.000   ARG G 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04858 (   65)
  hydrogen bonds       : angle       6.05948 (  195)
  covalent geometry    : bond        0.00350 ( 5960)
  covalent geometry    : angle       0.64781 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 285
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9073 (mp) cc_final: 0.8733 (tt)
REVERT: A  340 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7912 (mtpt)
REVERT: A  379 ARG cc_start: 0.7442 (mmt90) cc_final: 0.6821 (pmt-80)
REVERT: B  315 LEU cc_start: 0.9232 (mp) cc_final: 0.8847 (tt)
REVERT: B  340 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8286 (tttt)
REVERT: B  345 ASP cc_start: 0.8692 (m-30) cc_final: 0.8383 (t0)
REVERT: C  315 LEU cc_start: 0.9255 (mp) cc_final: 0.8852 (tt)
REVERT: C  370 LYS cc_start: 0.8779 (ttmm) cc_final: 0.7942 (tppt)
REVERT: C  379 ARG cc_start: 0.7386 (mmt90) cc_final: 0.6776 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9388 (mp) cc_final: 0.8899 (tt)
REVERT: D  345 ASP cc_start: 0.8713 (m-30) cc_final: 0.8343 (t0)
REVERT: D  375 LYS cc_start: 0.9032 (tttt) cc_final: 0.8702 (tttp)
REVERT: E  315 LEU cc_start: 0.9207 (mp) cc_final: 0.8762 (tt)
REVERT: E  343 LYS cc_start: 0.8203 (mmmm) cc_final: 0.7779 (mmmm)
REVERT: E  345 ASP cc_start: 0.8393 (m-30) cc_final: 0.7980 (t0)
REVERT: E  379 ARG cc_start: 0.7386 (mmt90) cc_final: 0.6844 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9278 (mp) cc_final: 0.8843 (tt)
REVERT: F  345 ASP cc_start: 0.8556 (m-30) cc_final: 0.8314 (t0)
REVERT: F  379 ARG cc_start: 0.7539 (mmt90) cc_final: 0.6986 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8911 (mttt) cc_final: 0.8454 (mtmt)
REVERT: G  315 LEU cc_start: 0.9348 (mp) cc_final: 0.8906 (tt)
REVERT: G  340 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8191 (tttt)
REVERT: G  345 ASP cc_start: 0.8644 (m-30) cc_final: 0.8277 (t0)
REVERT: G  379 ARG cc_start: 0.7341 (mmt90) cc_final: 0.6700 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9269 (mp) cc_final: 0.8959 (tt)
REVERT: H  343 LYS cc_start: 0.8248 (tppt) cc_final: 0.7974 (mmmm)
REVERT: H  345 ASP cc_start: 0.8651 (m-30) cc_final: 0.8119 (t0)
REVERT: H  379 ARG cc_start: 0.7524 (mmt90) cc_final: 0.6990 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9321 (mp) cc_final: 0.8830 (tt)
REVERT: I  358 ASP cc_start: 0.7924 (m-30) cc_final: 0.7628 (m-30)
REVERT: I  379 ARG cc_start: 0.7240 (mmt90) cc_final: 0.6433 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8795 (mmtt)
REVERT: J  315 LEU cc_start: 0.9268 (mp) cc_final: 0.8542 (tt)
REVERT: J  349 ARG cc_start: 0.7514 (mtm180) cc_final: 0.6776 (mmm160)
REVERT: J  379 ARG cc_start: 0.7345 (mmt90) cc_final: 0.6837 (mmp-170)
  outliers start: 16
  outliers final: 9
  residues processed: 291
  average time/residue: 0.2576
  time to fit residues: 88.7132
Evaluate side-chains
  283 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 274
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain H residue  339 VAL
Chi-restraints excluded: chain I residue  322 CYS
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  373 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   chunk 7 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.146608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.124932 restraints weight = 10032.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.127839 restraints weight = 4846.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.129770 restraints weight = 2968.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5960  Z= 0.204
  Angle     :  0.718   6.006   7970  Z= 0.380
  Chirality :  0.049   0.139    890
  Planarity :  0.005   0.050   1020
  Dihedral  :  5.930  19.258    790
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 26.12 %
    Favored  : 72.24 %
  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: -3.39 (0.23), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.014   0.003   PHE A 378 
 TYR   0.017   0.003   TYR F 310 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06668 (   65)
  hydrogen bonds       : angle       6.37588 (  195)
  covalent geometry    : bond        0.00515 ( 5960)
  covalent geometry    : angle       0.71783 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 270
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9090 (mp) cc_final: 0.8737 (tt)
REVERT: A  340 LYS cc_start: 0.8299 (ttmm) cc_final: 0.8044 (mtpt)
REVERT: A  379 ARG cc_start: 0.7519 (mmt90) cc_final: 0.6996 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8971 (mttt) cc_final: 0.8657 (mtmt)
REVERT: B  315 LEU cc_start: 0.9254 (mp) cc_final: 0.8869 (tt)
REVERT: B  340 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8324 (tttt)
REVERT: B  345 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8424 (t0)
REVERT: C  315 LEU cc_start: 0.9256 (mp) cc_final: 0.8875 (tt)
REVERT: C  379 ARG cc_start: 0.7479 (mmt90) cc_final: 0.6879 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9380 (mp) cc_final: 0.8846 (tt)
REVERT: D  345 ASP cc_start: 0.8721 (m-30) cc_final: 0.8414 (t0)
REVERT: D  375 LYS cc_start: 0.9119 (tttt) cc_final: 0.8789 (tttp)
REVERT: E  315 LEU cc_start: 0.9249 (mp) cc_final: 0.8837 (tt)
REVERT: E  343 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7839 (mmmm)
REVERT: E  345 ASP cc_start: 0.8458 (m-30) cc_final: 0.8051 (t0)
REVERT: E  379 ARG cc_start: 0.7400 (mmt90) cc_final: 0.6860 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9259 (mp) cc_final: 0.8823 (tt)
REVERT: F  343 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8000 (mmmm)
REVERT: F  372 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8622 (mt-10)
REVERT: F  379 ARG cc_start: 0.7557 (mmt90) cc_final: 0.6962 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8921 (mttt) cc_final: 0.8472 (mtmt)
REVERT: G  315 LEU cc_start: 0.9399 (mp) cc_final: 0.8958 (tt)
REVERT: G  340 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8312 (tttt)
REVERT: G  345 ASP cc_start: 0.8615 (m-30) cc_final: 0.8292 (t0)
REVERT: G  379 ARG cc_start: 0.7329 (mmt90) cc_final: 0.6710 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9322 (mp) cc_final: 0.8997 (tt)
REVERT: H  343 LYS cc_start: 0.8302 (tppt) cc_final: 0.8007 (mmmm)
REVERT: H  345 ASP cc_start: 0.8688 (m-30) cc_final: 0.8132 (t0)
REVERT: H  379 ARG cc_start: 0.7545 (mmt90) cc_final: 0.7043 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9393 (mp) cc_final: 0.8872 (tt)
REVERT: I  343 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8189 (mmmt)
REVERT: I  358 ASP cc_start: 0.8008 (m-30) cc_final: 0.7691 (m-30)
REVERT: I  379 ARG cc_start: 0.7326 (mmt90) cc_final: 0.6504 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9116 (mtmt) cc_final: 0.8842 (mmtt)
REVERT: J  379 ARG cc_start: 0.7339 (mmt90) cc_final: 0.6872 (mmp-170)
  outliers start: 11
  outliers final: 9
  residues processed: 275
  average time/residue: 0.2778
  time to fit residues: 89.8853
Evaluate side-chains
  268 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 258
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain H residue  339 VAL
Chi-restraints excluded: chain I residue  322 CYS
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  373 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.150876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.128904 restraints weight = 9825.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.131953 restraints weight = 4715.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.133947 restraints weight = 2868.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5960  Z= 0.137
  Angle     :  0.679   6.437   7970  Z= 0.358
  Chirality :  0.049   0.129    890
  Planarity :  0.005   0.047   1020
  Dihedral  :  5.546  20.832    790
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 26.57 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS I 330 
 PHE   0.014   0.003   PHE A 378 
 TYR   0.009   0.001   TYR F 310 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04832 (   65)
  hydrogen bonds       : angle       6.04761 (  195)
  covalent geometry    : bond        0.00363 ( 5960)
  covalent geometry    : angle       0.67925 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 264
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9042 (mp) cc_final: 0.8680 (tt)
REVERT: A  340 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7977 (mtpt)
REVERT: A  379 ARG cc_start: 0.7433 (mmt90) cc_final: 0.6793 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8958 (mttt) cc_final: 0.8619 (mtmt)
REVERT: B  315 LEU cc_start: 0.9226 (mp) cc_final: 0.8855 (tt)
REVERT: B  345 ASP cc_start: 0.8765 (m-30) cc_final: 0.8410 (t0)
REVERT: C  315 LEU cc_start: 0.9259 (mp) cc_final: 0.8868 (tt)
REVERT: C  375 LYS cc_start: 0.9252 (tttp) cc_final: 0.9037 (tttm)
REVERT: C  379 ARG cc_start: 0.7442 (mmt90) cc_final: 0.6779 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9383 (mp) cc_final: 0.8920 (tt)
REVERT: D  345 ASP cc_start: 0.8796 (m-30) cc_final: 0.8409 (t0)
REVERT: D  375 LYS cc_start: 0.9077 (tttt) cc_final: 0.8762 (tttp)
REVERT: D  379 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.6905 (mmm-85)
REVERT: E  314 ASP cc_start: 0.8258 (t0) cc_final: 0.8034 (t0)
REVERT: E  315 LEU cc_start: 0.9183 (mp) cc_final: 0.8855 (tt)
REVERT: E  343 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7753 (mmmm)
REVERT: E  345 ASP cc_start: 0.8437 (m-30) cc_final: 0.8020 (t0)
REVERT: E  379 ARG cc_start: 0.7420 (mmt90) cc_final: 0.6831 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9287 (mp) cc_final: 0.8840 (tt)
REVERT: F  379 ARG cc_start: 0.7513 (mmt90) cc_final: 0.6559 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8888 (mttt) cc_final: 0.8417 (mtmt)
REVERT: G  315 LEU cc_start: 0.9340 (mp) cc_final: 0.8906 (tt)
REVERT: G  340 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8194 (tttt)
REVERT: G  345 ASP cc_start: 0.8613 (m-30) cc_final: 0.8286 (t0)
REVERT: G  379 ARG cc_start: 0.7317 (mmt90) cc_final: 0.6670 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9284 (mp) cc_final: 0.8938 (tt)
REVERT: H  343 LYS cc_start: 0.8252 (tppt) cc_final: 0.7974 (mmmm)
REVERT: H  345 ASP cc_start: 0.8784 (m-30) cc_final: 0.8151 (t0)
REVERT: H  349 ARG cc_start: 0.7252 (mtm180) cc_final: 0.6784 (ttm110)
REVERT: H  379 ARG cc_start: 0.7548 (mmt90) cc_final: 0.6900 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9308 (mp) cc_final: 0.8784 (tt)
REVERT: I  358 ASP cc_start: 0.7938 (m-30) cc_final: 0.7634 (m-30)
REVERT: I  379 ARG cc_start: 0.7256 (mmt90) cc_final: 0.6431 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8831 (mmtt)
REVERT: J  349 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6757 (mmm160)
REVERT: J  379 ARG cc_start: 0.7339 (mmt90) cc_final: 0.6870 (mmp-170)
  outliers start: 9
  outliers final: 9
  residues processed: 267
  average time/residue: 0.2660
  time to fit residues: 84.1882
Evaluate side-chains
  264 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 255
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  369 LYS
Chi-restraints excluded: chain H residue  339 VAL
Chi-restraints excluded: chain I residue  322 CYS
Chi-restraints excluded: chain J residue  331 LYS
Chi-restraints excluded: chain J residue  352 SER
Chi-restraints excluded: chain J residue  373 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.148868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.126967 restraints weight = 9980.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.129914 restraints weight = 4794.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.131876 restraints weight = 2934.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5960  Z= 0.171
  Angle     :  0.712   6.591   7970  Z= 0.374
  Chirality :  0.049   0.144    890
  Planarity :  0.005   0.050   1020
  Dihedral  :  5.849  19.802    790
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 27.31 %
    Favored  : 71.19 %
  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: -3.39 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J 330 
 PHE   0.014   0.003   PHE A 378 
 TYR   0.015   0.003   TYR A 310 
 ARG   0.003   0.000   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06009 (   65)
  hydrogen bonds       : angle       6.27427 (  195)
  covalent geometry    : bond        0.00442 ( 5960)
  covalent geometry    : angle       0.71246 ( 7970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2806.78 seconds
wall clock time: 49 minutes 49.62 seconds (2989.62 seconds total)