Starting phenix.real_space_refine
on Sat May 10 09:59:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b4o_44187/05_2025/9b4o_44187.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b4o_44187/05_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_44187/05_2025/9b4o_44187.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b4o_44187/05_2025/9b4o_44187.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b4o_44187/05_2025/9b4o_44187.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b4o_44187/05_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-5687/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: 2.79, per 1000 atoms: 0.48
  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: 1.24
  Conformation dependent library (CDL) restraints added in 704.7 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: 0.98
  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: 1.34

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.22 -     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:             5.820
  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:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     15.560
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.650
-------------------------------------------------------------------------------
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  : 0.733 
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: 0.2799
  time to fit residues: 112.6677
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  : 0.686 
-------------------------------------------------------------------------------
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 = 31)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.126779 restraints weight = 9782.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.129761 restraints weight = 4570.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.131665 restraints weight = 2761.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
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       6.87885 (  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  : 0.682 
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: 0.8743 (tt)
REVERT: A  343 LYS cc_start: 0.8638 (tppt) cc_final: 0.7475 (pptt)
REVERT: A  379 ARG cc_start: 0.7654 (mmt90) cc_final: 0.7059 (pmt-80)
REVERT: B  311 LYS cc_start: 0.8910 (mttt) cc_final: 0.8570 (mtmt)
REVERT: B  315 LEU cc_start: 0.9227 (mp) cc_final: 0.8799 (tt)
REVERT: B  336 GLN cc_start: 0.8922 (tp40) cc_final: 0.8637 (tp40)
REVERT: B  340 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8294 (tttt)
REVERT: B  345 ASP cc_start: 0.8653 (m-30) cc_final: 0.8361 (t0)
REVERT: C  314 ASP cc_start: 0.8515 (t0) cc_final: 0.8271 (t0)
REVERT: C  315 LEU cc_start: 0.9282 (mp) cc_final: 0.8843 (tt)
REVERT: C  343 LYS cc_start: 0.8516 (tppt) cc_final: 0.7480 (pptt)
REVERT: C  379 ARG cc_start: 0.7468 (mmt90) cc_final: 0.6816 (pmt-80)
REVERT: D  311 LYS cc_start: 0.9023 (mttt) cc_final: 0.8369 (mtmm)
REVERT: D  315 LEU cc_start: 0.9362 (mp) cc_final: 0.8872 (tt)
REVERT: D  342 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7742 (mm-30)
REVERT: D  345 ASP cc_start: 0.8775 (m-30) cc_final: 0.8275 (t0)
REVERT: E  314 ASP cc_start: 0.8364 (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: 0.7854 (mm-30) cc_final: 0.7487 (mm-30)
REVERT: E  343 LYS cc_start: 0.8100 (tppt) cc_final: 0.7724 (mmmt)
REVERT: E  345 ASP cc_start: 0.8439 (m-30) cc_final: 0.8146 (t0)
REVERT: E  370 LYS cc_start: 0.8902 (tttm) cc_final: 0.8267 (tttm)
REVERT: E  372 GLU cc_start: 0.8726 (tt0) cc_final: 0.8362 (mt-10)
REVERT: E  375 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8774 (tttp)
REVERT: E  379 ARG cc_start: 0.7407 (mmt90) cc_final: 0.6898 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9324 (mp) cc_final: 0.8825 (tt)
REVERT: F  321 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8605 (ttmm)
REVERT: F  345 ASP cc_start: 0.8716 (m-30) cc_final: 0.8325 (t0)
REVERT: F  379 ARG cc_start: 0.7496 (mmt90) cc_final: 0.6949 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8945 (mttt) cc_final: 0.8499 (mtmt)
REVERT: G  315 LEU cc_start: 0.9335 (mp) cc_final: 0.8868 (tt)
REVERT: G  340 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8270 (tttt)
REVERT: G  342 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7780 (mm-30)
REVERT: G  345 ASP cc_start: 0.8704 (m-30) cc_final: 0.8185 (t0)
REVERT: G  372 GLU cc_start: 0.8596 (tt0) cc_final: 0.8396 (mt-10)
REVERT: G  379 ARG cc_start: 0.7301 (mmt90) cc_final: 0.6746 (mmm-85)
REVERT: H  311 LYS cc_start: 0.8960 (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: 0.7936 (mm-30) cc_final: 0.7679 (mm-30)
REVERT: H  344 LEU cc_start: 0.9464 (mt) cc_final: 0.9207 (mt)
REVERT: H  345 ASP cc_start: 0.8713 (m-30) cc_final: 0.8187 (t0)
REVERT: H  379 ARG cc_start: 0.7391 (mmt90) cc_final: 0.6989 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9222 (mp) cc_final: 0.8674 (tt)
REVERT: I  331 LYS cc_start: 0.9288 (mtmt) cc_final: 0.9046 (mttt)
REVERT: I  358 ASP cc_start: 0.8035 (m-30) cc_final: 0.7735 (m-30)
REVERT: I  375 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8612 (ttmm)
REVERT: I  379 ARG cc_start: 0.7204 (mmt90) cc_final: 0.6408 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8740 (mmtt)
REVERT: J  315 LEU cc_start: 0.9340 (mp) cc_final: 0.8832 (tt)
REVERT: J  340 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8401 (mtpt)
REVERT: J  379 ARG cc_start: 0.7142 (mmt90) cc_final: 0.6524 (mmp-170)
  outliers start: 12
  outliers final: 9
  residues processed: 307
  average time/residue: 0.2541
  time to fit residues: 92.5184
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  : 0.706 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0370
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.0062

-------------------------------------------------------------------------------
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 = 0.4277 r_free = 0.4277 target = 0.150359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.128955 restraints weight = 9829.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.131961 restraints weight = 4728.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.133887 restraints weight = 2871.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2884

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= 0.121
  Angle     :  0.609   5.921   7970  Z= 0.318
  Chirality :  0.048   0.134    890
  Planarity :  0.003   0.026   1020
  Dihedral  :  5.220  15.260    790
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.30 %
    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: -3.42 (0.22), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.17), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 362 
 PHE   0.013   0.002   PHE D 346 
 TYR   0.010   0.002   TYR F 310 
 ARG   0.001   0.000   ARG H 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05330 (   65)
  hydrogen bonds       : angle       6.27020 (  195)
  covalent geometry    : bond        0.00320 ( 5960)
  covalent geometry    : angle       0.60913 ( 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
  330 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 314
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8601 (ptpp)
REVERT: A  315 LEU cc_start: 0.9025 (mp) cc_final: 0.8682 (tt)
REVERT: A  379 ARG cc_start: 0.7538 (mmt90) cc_final: 0.6962 (pmt-80)
REVERT: B  315 LEU cc_start: 0.9200 (mp) cc_final: 0.8745 (tt)
REVERT: B  340 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8075 (tttt)
REVERT: B  345 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8386 (t0)
REVERT: C  311 LYS cc_start: 0.8722 (mttt) cc_final: 0.8095 (mtmm)
REVERT: C  315 LEU cc_start: 0.9229 (mp) cc_final: 0.8794 (tt)
REVERT: C  372 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8205 (mt-10)
REVERT: C  375 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8419 (tttp)
REVERT: C  379 ARG cc_start: 0.7471 (mmt90) cc_final: 0.6804 (pmt-80)
REVERT: D  311 LYS cc_start: 0.8928 (mttt) cc_final: 0.8488 (mtmm)
REVERT: D  315 LEU cc_start: 0.9372 (mp) cc_final: 0.8839 (tt)
REVERT: D  327 ASN cc_start: 0.9455 (t0) cc_final: 0.9227 (t0)
REVERT: D  345 ASP cc_start: 0.8772 (m-30) cc_final: 0.8280 (t0)
REVERT: D  375 LYS cc_start: 0.8971 (tttt) cc_final: 0.8676 (tttp)
REVERT: E  315 LEU cc_start: 0.9199 (mp) cc_final: 0.8781 (tt)
REVERT: E  342 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7633 (mm-30)
REVERT: E  343 LYS cc_start: 0.8056 (tppt) cc_final: 0.7697 (mmmm)
REVERT: E  345 ASP cc_start: 0.8476 (m-30) cc_final: 0.8070 (t0)
REVERT: E  370 LYS cc_start: 0.8850 (tttm) cc_final: 0.8226 (tttm)
REVERT: E  372 GLU cc_start: 0.8650 (tt0) cc_final: 0.8355 (mt-10)
REVERT: E  375 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8754 (tttp)
REVERT: E  379 ARG cc_start: 0.7307 (mmt90) cc_final: 0.6774 (mmm-85)
REVERT: F  314 ASP cc_start: 0.8390 (t0) cc_final: 0.7976 (t0)
REVERT: F  315 LEU cc_start: 0.9269 (mp) cc_final: 0.8836 (tt)
REVERT: F  321 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8595 (ttmm)
REVERT: F  345 ASP cc_start: 0.8618 (m-30) cc_final: 0.8318 (t0)
REVERT: F  379 ARG cc_start: 0.7366 (mmt90) cc_final: 0.6842 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8963 (mttt) cc_final: 0.8463 (mtmt)
REVERT: G  315 LEU cc_start: 0.9369 (mp) cc_final: 0.8853 (tt)
REVERT: G  340 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8268 (tttt)
REVERT: G  345 ASP cc_start: 0.8629 (m-30) cc_final: 0.8147 (t0)
REVERT: G  379 ARG cc_start: 0.7321 (mmt90) cc_final: 0.6713 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9311 (mp) cc_final: 0.8936 (tt)
REVERT: H  342 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: H  344 LEU cc_start: 0.9438 (mt) cc_final: 0.9141 (mt)
REVERT: H  345 ASP cc_start: 0.8657 (m-30) cc_final: 0.8084 (t0)
REVERT: H  379 ARG cc_start: 0.7359 (mmt90) cc_final: 0.6941 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9258 (mp) cc_final: 0.8761 (tt)
REVERT: I  358 ASP cc_start: 0.7921 (m-30) cc_final: 0.7597 (m-30)
REVERT: I  375 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8556 (ttmm)
REVERT: I  379 ARG cc_start: 0.7182 (mmt90) cc_final: 0.6391 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8784 (mmtt)
REVERT: J  315 LEU cc_start: 0.9222 (mp) cc_final: 0.8700 (tt)
REVERT: J  340 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8189 (tttt)
REVERT: J  379 ARG cc_start: 0.7218 (mmt90) cc_final: 0.6629 (mmp-170)
  outliers start: 16
  outliers final: 9
  residues processed: 319
  average time/residue: 0.2465
  time to fit residues: 93.7652
Evaluate side-chains
  296 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 286
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 ASP
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 D residue  363 VAL
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 I residue  322 CYS
Chi-restraints excluded: chain J residue  373 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.4244 r_free = 0.4244 target = 0.146138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.124559 restraints weight = 10113.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.127549 restraints weight = 4820.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.129471 restraints weight = 2931.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3084

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= 0.183
  Angle     :  0.677   5.484   7970  Z= 0.357
  Chirality :  0.048   0.137    890
  Planarity :  0.004   0.050   1020
  Dihedral  :  5.742  17.935    790
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.75 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.22), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (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   0.016   0.003   TYR F 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06922 (   65)
  hydrogen bonds       : angle       6.39298 (  195)
  covalent geometry    : bond        0.00462 ( 5960)
  covalent geometry    : angle       0.67686 ( 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
  295 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 278
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9123 (mp) cc_final: 0.8711 (tt)
REVERT: A  379 ARG cc_start: 0.7577 (mmt90) cc_final: 0.6965 (pmt-80)
REVERT: B  315 LEU cc_start: 0.9267 (mp) cc_final: 0.8807 (tt)
REVERT: B  340 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8224 (tttt)
REVERT: B  345 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8383 (t0)
REVERT: C  311 LYS cc_start: 0.9033 (mttt) cc_final: 0.8507 (mtmm)
REVERT: C  314 ASP cc_start: 0.8379 (t0) cc_final: 0.8102 (t0)
REVERT: C  315 LEU cc_start: 0.9264 (mp) cc_final: 0.8812 (tt)
REVERT: C  343 LYS cc_start: 0.8544 (tppt) cc_final: 0.7536 (pttm)
REVERT: C  375 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8774 (tttm)
REVERT: C  379 ARG cc_start: 0.7568 (mmt90) cc_final: 0.6851 (pmt-80)
REVERT: D  311 LYS cc_start: 0.9008 (mttt) cc_final: 0.8724 (mtmm)
REVERT: D  315 LEU cc_start: 0.9343 (mp) cc_final: 0.8841 (tt)
REVERT: D  345 ASP cc_start: 0.8762 (m-30) cc_final: 0.8332 (t0)
REVERT: D  375 LYS cc_start: 0.8995 (tttt) cc_final: 0.8647 (tttp)
REVERT: E  315 LEU cc_start: 0.9201 (mp) cc_final: 0.8765 (tt)
REVERT: E  343 LYS cc_start: 0.8108 (tppt) cc_final: 0.7868 (mmmm)
REVERT: E  345 ASP cc_start: 0.8594 (m-30) cc_final: 0.8078 (t0)
REVERT: E  370 LYS cc_start: 0.8887 (tttm) cc_final: 0.8282 (tttm)
REVERT: E  372 GLU cc_start: 0.8708 (tt0) cc_final: 0.8439 (mt-10)
REVERT: E  375 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8770 (ttmm)
REVERT: E  379 ARG cc_start: 0.7311 (mmt90) cc_final: 0.6746 (mmm-85)
REVERT: F  314 ASP cc_start: 0.8395 (t0) cc_final: 0.8101 (t0)
REVERT: F  315 LEU cc_start: 0.9337 (mp) cc_final: 0.8869 (tt)
REVERT: F  345 ASP cc_start: 0.8661 (m-30) cc_final: 0.8299 (t0)
REVERT: F  379 ARG cc_start: 0.7444 (mmt90) cc_final: 0.6961 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8918 (mttt) cc_final: 0.8415 (mtmt)
REVERT: G  315 LEU cc_start: 0.9410 (mp) cc_final: 0.8884 (tt)
REVERT: G  340 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8247 (tttt)
REVERT: G  345 ASP cc_start: 0.8691 (m-30) cc_final: 0.8112 (t0)
REVERT: G  379 ARG cc_start: 0.7360 (mmt90) cc_final: 0.6721 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9360 (mp) cc_final: 0.8925 (tt)
REVERT: H  343 LYS cc_start: 0.8208 (tppt) cc_final: 0.7932 (mmmm)
REVERT: H  345 ASP cc_start: 0.8755 (m-30) cc_final: 0.8090 (t0)
REVERT: H  379 ARG cc_start: 0.7395 (mmt90) cc_final: 0.7016 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9274 (mp) cc_final: 0.8796 (tt)
REVERT: I  342 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6931 (mm-30)
REVERT: I  358 ASP cc_start: 0.7923 (m-30) cc_final: 0.7525 (m-30)
REVERT: I  375 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8457 (ttmm)
REVERT: I  379 ARG cc_start: 0.7258 (mmt90) cc_final: 0.6411 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8787 (mmtt)
REVERT: J  315 LEU cc_start: 0.9356 (mp) cc_final: 0.8652 (tt)
REVERT: J  379 ARG cc_start: 0.7181 (mmt90) cc_final: 0.6627 (mmp-170)
  outliers start: 17
  outliers final: 15
  residues processed: 284
  average time/residue: 0.2600
  time to fit residues: 87.5820
Evaluate side-chains
  287 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 271
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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 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:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 = 0.4268 r_free = 0.4268 target = 0.148084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.126215 restraints weight = 9805.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.129214 restraints weight = 4826.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.131109 restraints weight = 2974.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5960  Z= 0.168
  Angle     :  0.672   6.069   7970  Z= 0.354
  Chirality :  0.048   0.133    890
  Planarity :  0.004   0.038   1020
  Dihedral  :  5.646  17.643    790
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.09 %
    Favored  : 74.63 %
  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: -3.40 (0.22), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.17), residues: 750

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06181 (   65)
  hydrogen bonds       : angle       6.30261 (  195)
  covalent geometry    : bond        0.00431 ( 5960)
  covalent geometry    : angle       0.67207 ( 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
  304 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 282
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9111 (mp) cc_final: 0.8750 (tt)
REVERT: A  340 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8266 (mtpt)
REVERT: A  379 ARG cc_start: 0.7693 (mmt90) cc_final: 0.6972 (pmt-80)
REVERT: B  311 LYS cc_start: 0.9090 (pttt) cc_final: 0.8794 (ptpp)
REVERT: B  315 LEU cc_start: 0.9227 (mp) cc_final: 0.8855 (tt)
REVERT: B  340 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8205 (tttt)
REVERT: B  345 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8377 (t0)
REVERT: C  311 LYS cc_start: 0.8945 (mttt) cc_final: 0.8704 (mttp)
REVERT: C  314 ASP cc_start: 0.8386 (t0) cc_final: 0.8114 (t0)
REVERT: C  315 LEU cc_start: 0.9241 (mp) cc_final: 0.8801 (tt)
REVERT: C  343 LYS cc_start: 0.8358 (tppt) cc_final: 0.7448 (pttm)
REVERT: C  375 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8734 (tttm)
REVERT: C  379 ARG cc_start: 0.7526 (mmt90) cc_final: 0.6841 (pmt-80)
REVERT: D  311 LYS cc_start: 0.8972 (mttt) cc_final: 0.8500 (mtmm)
REVERT: D  315 LEU cc_start: 0.9375 (mp) cc_final: 0.8794 (tt)
REVERT: D  345 ASP cc_start: 0.8742 (m-30) cc_final: 0.8346 (t0)
REVERT: D  375 LYS cc_start: 0.9080 (tttt) cc_final: 0.8762 (tttp)
REVERT: E  315 LEU cc_start: 0.9188 (mp) cc_final: 0.8771 (tt)
REVERT: E  343 LYS cc_start: 0.8053 (tppt) cc_final: 0.7849 (mmmm)
REVERT: E  345 ASP cc_start: 0.8585 (m-30) cc_final: 0.8097 (t0)
REVERT: E  370 LYS cc_start: 0.8869 (tttm) cc_final: 0.8394 (tttm)
REVERT: E  372 GLU cc_start: 0.8693 (tt0) cc_final: 0.8378 (mt-10)
REVERT: E  375 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8757 (ttmm)
REVERT: E  379 ARG cc_start: 0.7316 (mmt90) cc_final: 0.6754 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9287 (mp) cc_final: 0.8834 (tt)
REVERT: F  343 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8175 (mmmm)
REVERT: F  345 ASP cc_start: 0.8662 (m-30) cc_final: 0.8376 (t0)
REVERT: F  379 ARG cc_start: 0.7471 (mmt90) cc_final: 0.6963 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8885 (mttt) cc_final: 0.8416 (mtmt)
REVERT: G  315 LEU cc_start: 0.9399 (mp) cc_final: 0.8861 (tt)
REVERT: G  340 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8261 (tttt)
REVERT: G  345 ASP cc_start: 0.8687 (m-30) cc_final: 0.8128 (t0)
REVERT: G  379 ARG cc_start: 0.7381 (mmt90) cc_final: 0.6707 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9309 (mp) cc_final: 0.8907 (tt)
REVERT: H  343 LYS cc_start: 0.8241 (tppt) cc_final: 0.7955 (mmmm)
REVERT: H  345 ASP cc_start: 0.8711 (m-30) cc_final: 0.8091 (t0)
REVERT: H  379 ARG cc_start: 0.7396 (mmt90) cc_final: 0.7030 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9345 (mp) cc_final: 0.8820 (tt)
REVERT: I  342 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7140 (mm-30)
REVERT: I  358 ASP cc_start: 0.7878 (m-30) cc_final: 0.7519 (m-30)
REVERT: I  375 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8464 (ttmm)
REVERT: I  379 ARG cc_start: 0.7292 (mmt90) cc_final: 0.6461 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8821 (mmtt)
REVERT: J  315 LEU cc_start: 0.9323 (mp) cc_final: 0.8692 (tt)
REVERT: J  379 ARG cc_start: 0.7218 (mmt90) cc_final: 0.6666 (mmp-170)
  outliers start: 22
  outliers final: 18
  residues processed: 292
  average time/residue: 0.2542
  time to fit residues: 88.2870
Evaluate side-chains
  292 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 273
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
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  318 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  352 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    2.9990
   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:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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
G 327 ASN
** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.144220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.122574 restraints weight = 9882.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.125473 restraints weight = 4804.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.127345 restraints weight = 2974.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   5960  Z= 0.256
  Angle     :  0.753   6.391   7970  Z= 0.398
  Chirality :  0.049   0.149    890
  Planarity :  0.004   0.039   1020
  Dihedral  :  6.221  20.211    790
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.60 %
    Favored  : 88.40 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.99 %
    Favored  : 73.73 %
  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   0.016   0.003   PHE A 378 
 TYR   0.018   0.003   TYR J 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07630 (   65)
  hydrogen bonds       : angle       6.61345 (  195)
  covalent geometry    : bond        0.00633 ( 5960)
  covalent geometry    : angle       0.75337 ( 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
  288 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 266
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9132 (mp) cc_final: 0.8734 (tt)
REVERT: A  340 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8112 (mtpt)
REVERT: A  343 LYS cc_start: 0.8651 (tppt) cc_final: 0.7559 (pttp)
REVERT: A  379 ARG cc_start: 0.7566 (mmt90) cc_final: 0.6930 (pmt-80)
REVERT: B  315 LEU cc_start: 0.9259 (mp) cc_final: 0.8891 (tt)
REVERT: B  340 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8313 (tttt)
REVERT: B  343 LYS cc_start: 0.8393 (mmmm) cc_final: 0.8039 (mmmm)
REVERT: B  345 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8478 (t0)
REVERT: C  311 LYS cc_start: 0.8981 (mttt) cc_final: 0.8485 (mtmm)
REVERT: C  314 ASP cc_start: 0.8408 (t0) cc_final: 0.8145 (t0)
REVERT: C  315 LEU cc_start: 0.9271 (mp) cc_final: 0.8816 (tt)
REVERT: C  343 LYS cc_start: 0.8471 (tppt) cc_final: 0.8144 (mmmm)
REVERT: C  379 ARG cc_start: 0.7571 (mmt90) cc_final: 0.6940 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9408 (mp) cc_final: 0.8869 (tt)
REVERT: D  343 LYS cc_start: 0.8138 (tppt) cc_final: 0.7833 (mmmm)
REVERT: D  345 ASP cc_start: 0.8740 (m-30) cc_final: 0.8430 (t0)
REVERT: D  375 LYS cc_start: 0.9092 (tttt) cc_final: 0.8755 (tttp)
REVERT: E  315 LEU cc_start: 0.9208 (mp) cc_final: 0.8792 (tt)
REVERT: E  343 LYS cc_start: 0.8151 (tppt) cc_final: 0.7842 (mmmm)
REVERT: E  345 ASP cc_start: 0.8591 (m-30) cc_final: 0.8128 (t0)
REVERT: E  370 LYS cc_start: 0.8890 (tttm) cc_final: 0.8441 (tttm)
REVERT: E  372 GLU cc_start: 0.8718 (tt0) cc_final: 0.8445 (mt-10)
REVERT: E  379 ARG cc_start: 0.7406 (mmt90) cc_final: 0.6850 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9283 (mp) cc_final: 0.8806 (tt)
REVERT: F  345 ASP cc_start: 0.8702 (m-30) cc_final: 0.8350 (t0)
REVERT: F  379 ARG cc_start: 0.7502 (mmt90) cc_final: 0.7036 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8945 (mttt) cc_final: 0.8441 (mtmt)
REVERT: G  315 LEU cc_start: 0.9415 (mp) cc_final: 0.8899 (tt)
REVERT: G  340 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8313 (tttt)
REVERT: G  345 ASP cc_start: 0.8681 (m-30) cc_final: 0.8195 (t0)
REVERT: G  379 ARG cc_start: 0.7436 (mmt90) cc_final: 0.6723 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9343 (mp) cc_final: 0.8879 (tt)
REVERT: H  343 LYS cc_start: 0.8341 (tppt) cc_final: 0.8052 (mmmm)
REVERT: H  345 ASP cc_start: 0.8740 (m-30) cc_final: 0.8103 (t0)
REVERT: H  379 ARG cc_start: 0.7481 (mmt90) cc_final: 0.7086 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9327 (mp) cc_final: 0.8784 (tt)
REVERT: I  343 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8138 (mmmt)
REVERT: I  358 ASP cc_start: 0.8077 (m-30) cc_final: 0.7690 (m-30)
REVERT: I  379 ARG cc_start: 0.7334 (mmt90) cc_final: 0.6534 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8834 (mmtt)
REVERT: J  315 LEU cc_start: 0.9377 (mp) cc_final: 0.8743 (tt)
REVERT: J  379 ARG cc_start: 0.7271 (mmt90) cc_final: 0.6807 (mmp-170)
  outliers start: 22
  outliers final: 16
  residues processed: 275
  average time/residue: 0.2795
  time to fit residues: 90.8933
Evaluate side-chains
  281 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 264
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  310 TYR
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  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:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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**
E 336 GLN
G 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.148836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.127051 restraints weight = 9859.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.130064 restraints weight = 4809.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.132038 restraints weight = 2942.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.3535

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= 0.140
  Angle     :  0.662   6.036   7970  Z= 0.350
  Chirality :  0.049   0.131    890
  Planarity :  0.004   0.035   1020
  Dihedral  :  5.553  20.796    790
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 23.73 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.23), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.56 (0.17), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.016   0.003   PHE A 378 
 TYR   0.012   0.002   TYR F 310 
 ARG   0.001   0.000   ARG H 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05258 (   65)
  hydrogen bonds       : angle       6.21199 (  195)
  covalent geometry    : bond        0.00367 ( 5960)
  covalent geometry    : angle       0.66177 ( 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
  304 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 286
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9075 (mp) cc_final: 0.8741 (tt)
REVERT: A  340 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7982 (mtpt)
REVERT: A  347 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8255 (ptpp)
REVERT: A  379 ARG cc_start: 0.7549 (mmt90) cc_final: 0.6952 (pmt-80)
REVERT: B  311 LYS cc_start: 0.9089 (pttt) cc_final: 0.8786 (ptpp)
REVERT: B  315 LEU cc_start: 0.9234 (mp) cc_final: 0.8868 (tt)
REVERT: B  340 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8234 (tttt)
REVERT: B  343 LYS cc_start: 0.8350 (mmmm) cc_final: 0.8019 (mmmm)
REVERT: B  345 ASP cc_start: 0.8710 (m-30) cc_final: 0.8450 (t0)
REVERT: C  311 LYS cc_start: 0.8922 (mttt) cc_final: 0.8691 (mttp)
REVERT: C  314 ASP cc_start: 0.8378 (t0) cc_final: 0.8105 (t0)
REVERT: C  315 LEU cc_start: 0.9242 (mp) cc_final: 0.8813 (tt)
REVERT: C  375 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8821 (tttm)
REVERT: C  379 ARG cc_start: 0.7461 (mmt90) cc_final: 0.6862 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9406 (mp) cc_final: 0.8836 (tt)
REVERT: D  345 ASP cc_start: 0.8737 (m-30) cc_final: 0.8348 (t0)
REVERT: D  375 LYS cc_start: 0.9090 (tttt) cc_final: 0.8761 (tttp)
REVERT: E  315 LEU cc_start: 0.9207 (mp) cc_final: 0.8795 (tt)
REVERT: E  343 LYS cc_start: 0.8062 (tppt) cc_final: 0.7752 (mmmm)
REVERT: E  345 ASP cc_start: 0.8491 (m-30) cc_final: 0.8055 (t0)
REVERT: E  370 LYS cc_start: 0.8856 (tttm) cc_final: 0.8571 (tttm)
REVERT: E  372 GLU cc_start: 0.8667 (tt0) cc_final: 0.8375 (mt-10)
REVERT: E  375 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8600 (ttmm)
REVERT: E  379 ARG cc_start: 0.7372 (mmt90) cc_final: 0.6725 (mmm-85)
REVERT: F  315 LEU cc_start: 0.9265 (mp) cc_final: 0.8794 (tt)
REVERT: F  336 GLN cc_start: 0.8847 (tp40) cc_final: 0.8347 (tp40)
REVERT: F  345 ASP cc_start: 0.8625 (m-30) cc_final: 0.8355 (t0)
REVERT: F  379 ARG cc_start: 0.7490 (mmt90) cc_final: 0.6995 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8906 (mttt) cc_final: 0.8382 (mtmt)
REVERT: G  315 LEU cc_start: 0.9376 (mp) cc_final: 0.8904 (tt)
REVERT: G  340 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8209 (tttt)
REVERT: G  342 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7494 (mm-30)
REVERT: G  345 ASP cc_start: 0.8681 (m-30) cc_final: 0.8175 (t0)
REVERT: G  379 ARG cc_start: 0.7331 (mmt90) cc_final: 0.6626 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9306 (mp) cc_final: 0.8900 (tt)
REVERT: H  343 LYS cc_start: 0.8247 (tppt) cc_final: 0.7983 (mmmm)
REVERT: H  345 ASP cc_start: 0.8693 (m-30) cc_final: 0.8099 (t0)
REVERT: H  379 ARG cc_start: 0.7498 (mmt90) cc_final: 0.7087 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9357 (mp) cc_final: 0.8852 (tt)
REVERT: I  358 ASP cc_start: 0.7886 (m-30) cc_final: 0.7551 (m-30)
REVERT: I  379 ARG cc_start: 0.7270 (mmt90) cc_final: 0.6484 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8771 (mmtt)
REVERT: J  315 LEU cc_start: 0.9278 (mp) cc_final: 0.8653 (tt)
REVERT: J  349 ARG cc_start: 0.7503 (mtm180) cc_final: 0.6812 (mmm160)
REVERT: J  379 ARG cc_start: 0.7324 (mmt90) cc_final: 0.6800 (mmp-170)
  outliers start: 18
  outliers final: 13
  residues processed: 293
  average time/residue: 0.2611
  time to fit residues: 90.5362
Evaluate side-chains
  288 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 274
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 LYS
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 H residue  339 VAL
Chi-restraints excluded: chain H residue  352 SER
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  358 ASP
Chi-restraints excluded: chain J residue  373 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0670
   chunk 35 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0170
   chunk 69 optimal weight:    5.9990
   overall best weight:    1.0160

-------------------------------------------------------------------------------
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
** 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 = 0.4328 r_free = 0.4328 target = 0.151388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.129454 restraints weight = 9772.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.132466 restraints weight = 4773.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.134435 restraints weight = 2933.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3861

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     :  0.652   5.923   7970  Z= 0.345
  Chirality :  0.049   0.130    890
  Planarity :  0.004   0.035   1020
  Dihedral  :  5.419  21.356    790
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 24.93 %
    Favored  : 72.99 %
  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: -3.27 (0.23), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS I 362 
 PHE   0.015   0.003   PHE A 378 
 TYR   0.008   0.002   TYR J 310 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04787 (   65)
  hydrogen bonds       : angle       6.06928 (  195)
  covalent geometry    : bond        0.00349 ( 5960)
  covalent geometry    : angle       0.65223 ( 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
  303 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 289
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9051 (mp) cc_final: 0.8710 (tt)
REVERT: A  340 LYS cc_start: 0.8317 (ttmm) cc_final: 0.8029 (mtpt)
REVERT: A  347 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8221 (ptpp)
REVERT: A  379 ARG cc_start: 0.7520 (mmt90) cc_final: 0.6908 (pmt-80)
REVERT: B  311 LYS cc_start: 0.9080 (pttt) cc_final: 0.8783 (ptpp)
REVERT: B  315 LEU cc_start: 0.9213 (mp) cc_final: 0.8849 (tt)
REVERT: B  343 LYS cc_start: 0.8361 (mmmm) cc_final: 0.8068 (mmmm)
REVERT: B  345 ASP cc_start: 0.8719 (m-30) cc_final: 0.8476 (t0)
REVERT: B  379 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7312 (mmm-85)
REVERT: C  311 LYS cc_start: 0.8908 (mttt) cc_final: 0.8471 (mtmm)
REVERT: C  314 ASP cc_start: 0.8379 (t0) cc_final: 0.8108 (t0)
REVERT: C  315 LEU cc_start: 0.9242 (mp) cc_final: 0.8817 (tt)
REVERT: C  375 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8796 (tttm)
REVERT: C  379 ARG cc_start: 0.7478 (mmt90) cc_final: 0.6827 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9391 (mp) cc_final: 0.8855 (tt)
REVERT: D  345 ASP cc_start: 0.8726 (m-30) cc_final: 0.8335 (t0)
REVERT: D  375 LYS cc_start: 0.9014 (tttt) cc_final: 0.8687 (tttp)
REVERT: E  311 LYS cc_start: 0.8801 (mttt) cc_final: 0.8591 (mtmm)
REVERT: E  315 LEU cc_start: 0.9211 (mp) cc_final: 0.8800 (tt)
REVERT: E  345 ASP cc_start: 0.8448 (m-30) cc_final: 0.7975 (t0)
REVERT: E  370 LYS cc_start: 0.8856 (tttm) cc_final: 0.8390 (tttm)
REVERT: E  379 ARG cc_start: 0.7391 (mmt90) cc_final: 0.6758 (mmm-85)
REVERT: F  314 ASP cc_start: 0.8197 (t0) cc_final: 0.7995 (t0)
REVERT: F  315 LEU cc_start: 0.9258 (mp) cc_final: 0.8788 (tt)
REVERT: F  336 GLN cc_start: 0.8831 (tp40) cc_final: 0.8380 (tp40)
REVERT: F  345 ASP cc_start: 0.8562 (m-30) cc_final: 0.8314 (t0)
REVERT: F  379 ARG cc_start: 0.7499 (mmt90) cc_final: 0.6988 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8877 (mttt) cc_final: 0.8539 (mtmt)
REVERT: G  315 LEU cc_start: 0.9345 (mp) cc_final: 0.8902 (tt)
REVERT: G  340 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8186 (tttt)
REVERT: G  345 ASP cc_start: 0.8593 (m-30) cc_final: 0.8126 (t0)
REVERT: G  379 ARG cc_start: 0.7331 (mmt90) cc_final: 0.6673 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9292 (mp) cc_final: 0.8921 (tt)
REVERT: H  343 LYS cc_start: 0.8157 (tppt) cc_final: 0.7912 (mmmm)
REVERT: H  345 ASP cc_start: 0.8640 (m-30) cc_final: 0.8077 (t0)
REVERT: H  351 GLN cc_start: 0.9333 (tt0) cc_final: 0.9091 (mt0)
REVERT: H  379 ARG cc_start: 0.7491 (mmt90) cc_final: 0.7066 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9350 (mp) cc_final: 0.8843 (tt)
REVERT: I  358 ASP cc_start: 0.7960 (m-30) cc_final: 0.7702 (m-30)
REVERT: I  379 ARG cc_start: 0.7276 (mmt90) cc_final: 0.6484 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8758 (mmtt)
REVERT: J  315 LEU cc_start: 0.9270 (mp) cc_final: 0.8686 (tt)
REVERT: J  349 ARG cc_start: 0.7578 (mtm180) cc_final: 0.6776 (mmm160)
REVERT: J  379 ARG cc_start: 0.7347 (mmt90) cc_final: 0.6827 (mmp-170)
  outliers start: 14
  outliers final: 8
  residues processed: 295
  average time/residue: 0.2470
  time to fit residues: 86.7222
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  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 LYS
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 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  358 ASP
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:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0050
   overall best weight:    1.9600

-------------------------------------------------------------------------------
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 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 = 0.4294 r_free = 0.4294 target = 0.149102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.127021 restraints weight = 9871.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.129977 restraints weight = 4837.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.131970 restraints weight = 2984.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3811

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= 0.168
  Angle     :  0.699   5.808   7970  Z= 0.370
  Chirality :  0.048   0.151    890
  Planarity :  0.005   0.052   1020
  Dihedral  :  5.704  21.206    790
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 25.52 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.18), 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   0.012   0.002   TYR E 310 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05864 (   65)
  hydrogen bonds       : angle       6.18268 (  195)
  covalent geometry    : bond        0.00434 ( 5960)
  covalent geometry    : angle       0.69925 ( 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
  287 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 277
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9090 (mp) cc_final: 0.8743 (tt)
REVERT: A  340 LYS cc_start: 0.8254 (ttmm) cc_final: 0.8013 (mtpt)
REVERT: A  347 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8191 (ptpp)
REVERT: A  379 ARG cc_start: 0.7530 (mmt90) cc_final: 0.7052 (pmt-80)
REVERT: B  311 LYS cc_start: 0.9139 (pttt) cc_final: 0.8810 (ptpp)
REVERT: B  315 LEU cc_start: 0.9260 (mp) cc_final: 0.8875 (tt)
REVERT: B  345 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8378 (t0)
REVERT: B  379 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7304 (mmm-85)
REVERT: C  311 LYS cc_start: 0.8952 (mttt) cc_final: 0.8486 (mtmm)
REVERT: C  314 ASP cc_start: 0.8369 (t0) cc_final: 0.8085 (t0)
REVERT: C  315 LEU cc_start: 0.9253 (mp) cc_final: 0.8823 (tt)
REVERT: C  375 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8857 (tttm)
REVERT: C  379 ARG cc_start: 0.7493 (mmt90) cc_final: 0.6825 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9372 (mp) cc_final: 0.8820 (tt)
REVERT: D  345 ASP cc_start: 0.8754 (m-30) cc_final: 0.8422 (t0)
REVERT: D  375 LYS cc_start: 0.9035 (tttt) cc_final: 0.8757 (tttp)
REVERT: E  314 ASP cc_start: 0.8305 (t0) cc_final: 0.7975 (t0)
REVERT: E  315 LEU cc_start: 0.9192 (mp) cc_final: 0.8866 (tt)
REVERT: E  345 ASP cc_start: 0.8471 (m-30) cc_final: 0.8041 (t0)
REVERT: E  379 ARG cc_start: 0.7418 (mmt90) cc_final: 0.6746 (mmm-85)
REVERT: F  314 ASP cc_start: 0.8232 (t0) cc_final: 0.7998 (t0)
REVERT: F  315 LEU cc_start: 0.9279 (mp) cc_final: 0.8779 (tt)
REVERT: F  336 GLN cc_start: 0.8887 (tp40) cc_final: 0.8342 (tp40)
REVERT: F  345 ASP cc_start: 0.8567 (m-30) cc_final: 0.8316 (t0)
REVERT: F  379 ARG cc_start: 0.7524 (mmt90) cc_final: 0.7004 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8874 (mttt) cc_final: 0.8356 (mtmt)
REVERT: G  315 LEU cc_start: 0.9366 (mp) cc_final: 0.8888 (tt)
REVERT: G  340 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8259 (tttt)
REVERT: G  345 ASP cc_start: 0.8612 (m-30) cc_final: 0.8151 (t0)
REVERT: G  379 ARG cc_start: 0.7308 (mmt90) cc_final: 0.6658 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9315 (mp) cc_final: 0.8924 (tt)
REVERT: H  343 LYS cc_start: 0.8199 (tppt) cc_final: 0.7953 (mmmm)
REVERT: H  345 ASP cc_start: 0.8697 (m-30) cc_final: 0.8104 (t0)
REVERT: H  379 ARG cc_start: 0.7524 (mmt90) cc_final: 0.7076 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9378 (mp) cc_final: 0.8853 (tt)
REVERT: I  358 ASP cc_start: 0.7920 (m-30) cc_final: 0.7607 (m-30)
REVERT: I  379 ARG cc_start: 0.7294 (mmt90) cc_final: 0.6497 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8767 (mmtt)
REVERT: J  315 LEU cc_start: 0.9309 (mp) cc_final: 0.8652 (tt)
REVERT: J  349 ARG cc_start: 0.7426 (mtm180) cc_final: 0.6748 (mmm160)
REVERT: J  379 ARG cc_start: 0.7363 (mmt90) cc_final: 0.6816 (mmp-170)
  outliers start: 10
  outliers final: 8
  residues processed: 284
  average time/residue: 0.2622
  time to fit residues: 88.2517
Evaluate side-chains
  282 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 272
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain B residue  345 ASP
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 50 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0670
   chunk 10 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6120

-------------------------------------------------------------------------------
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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.155737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.133613 restraints weight = 9755.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.136731 restraints weight = 4782.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.138748 restraints weight = 2941.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.4202

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= 0.126
  Angle     :  0.653   5.864   7970  Z= 0.346
  Chirality :  0.048   0.127    890
  Planarity :  0.005   0.048   1020
  Dihedral  :  5.275  22.002    790
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 27.01 %
    Favored  : 71.79 %
  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: -3.17 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F 362 
 PHE   0.015   0.003   PHE A 378 
 TYR   0.013   0.001   TYR I 310 
 ARG   0.009   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04127 (   65)
  hydrogen bonds       : angle       5.82968 (  195)
  covalent geometry    : bond        0.00339 ( 5960)
  covalent geometry    : angle       0.65334 ( 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
  298 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 290
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.9016 (mp) cc_final: 0.8677 (tt)
REVERT: A  347 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8075 (ptpp)
REVERT: A  379 ARG cc_start: 0.7594 (mmt90) cc_final: 0.6774 (pmt-80)
REVERT: B  311 LYS cc_start: 0.9059 (pttt) cc_final: 0.8715 (ptpp)
REVERT: B  315 LEU cc_start: 0.9196 (mp) cc_final: 0.8833 (tt)
REVERT: B  345 ASP cc_start: 0.8731 (m-30) cc_final: 0.8435 (t0)
REVERT: B  379 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7270 (mmm-85)
REVERT: C  311 LYS cc_start: 0.8957 (mttt) cc_final: 0.8488 (mtmm)
REVERT: C  314 ASP cc_start: 0.8312 (t0) cc_final: 0.8038 (t0)
REVERT: C  315 LEU cc_start: 0.9236 (mp) cc_final: 0.8827 (tt)
REVERT: C  375 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8805 (tttm)
REVERT: C  379 ARG cc_start: 0.7383 (mmt90) cc_final: 0.6739 (pmt-80)
REVERT: D  315 LEU cc_start: 0.9376 (mp) cc_final: 0.8834 (tt)
REVERT: D  345 ASP cc_start: 0.8723 (m-30) cc_final: 0.8400 (t0)
REVERT: D  375 LYS cc_start: 0.8995 (tttt) cc_final: 0.8661 (tttp)
REVERT: E  311 LYS cc_start: 0.8789 (mttt) cc_final: 0.8535 (mtmm)
REVERT: E  314 ASP cc_start: 0.8589 (t0) cc_final: 0.8283 (t0)
REVERT: E  315 LEU cc_start: 0.9195 (mp) cc_final: 0.8891 (tt)
REVERT: E  345 ASP cc_start: 0.8426 (m-30) cc_final: 0.8000 (t0)
REVERT: E  375 LYS cc_start: 0.9105 (tttp) cc_final: 0.8725 (ttmm)
REVERT: E  379 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6682 (mmm-85)
REVERT: F  314 ASP cc_start: 0.8195 (t0) cc_final: 0.7968 (t0)
REVERT: F  315 LEU cc_start: 0.9252 (mp) cc_final: 0.8829 (tt)
REVERT: F  336 GLN cc_start: 0.8736 (tp40) cc_final: 0.8382 (tp40)
REVERT: F  379 ARG cc_start: 0.7448 (mmt90) cc_final: 0.6894 (mmm-85)
REVERT: G  311 LYS cc_start: 0.8796 (mttt) cc_final: 0.8438 (mtmt)
REVERT: G  315 LEU cc_start: 0.9329 (mp) cc_final: 0.8808 (tt)
REVERT: G  340 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8208 (tttt)
REVERT: G  345 ASP cc_start: 0.8533 (m-30) cc_final: 0.8110 (t0)
REVERT: G  375 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8859 (ttmm)
REVERT: G  379 ARG cc_start: 0.7278 (mmt90) cc_final: 0.6601 (mmm-85)
REVERT: H  315 LEU cc_start: 0.9240 (mp) cc_final: 0.8899 (tt)
REVERT: H  343 LYS cc_start: 0.8070 (tppt) cc_final: 0.7833 (mmmm)
REVERT: H  345 ASP cc_start: 0.8672 (m-30) cc_final: 0.8163 (t0)
REVERT: H  351 GLN cc_start: 0.9324 (tt0) cc_final: 0.9111 (mt0)
REVERT: H  379 ARG cc_start: 0.7544 (mmt90) cc_final: 0.7060 (mmm-85)
REVERT: I  315 LEU cc_start: 0.9335 (mp) cc_final: 0.8784 (tt)
REVERT: I  358 ASP cc_start: 0.7973 (m-30) cc_final: 0.7720 (m-30)
REVERT: I  379 ARG cc_start: 0.7266 (mmt90) cc_final: 0.6473 (mmp-170)
REVERT: J  311 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8771 (mmtt)
REVERT: J  315 LEU cc_start: 0.9167 (mp) cc_final: 0.8453 (tt)
REVERT: J  349 ARG cc_start: 0.7459 (mtm180) cc_final: 0.6684 (mmm160)
REVERT: J  379 ARG cc_start: 0.7367 (mmt90) cc_final: 0.6843 (mmp-170)
  outliers start: 8
  outliers final: 6
  residues processed: 294
  average time/residue: 0.2504
  time to fit residues: 87.8614
Evaluate side-chains
  286 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 279
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 LYS
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 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:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 68 optimal weight:    0.2980
   chunk 34 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.153358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.130995 restraints weight = 9789.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.134039 restraints weight = 4821.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.136065 restraints weight = 2979.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5960  Z= 0.140
  Angle     :  0.676   6.215   7970  Z= 0.357
  Chirality :  0.048   0.129    890
  Planarity :  0.005   0.053   1020
  Dihedral  :  5.433  22.253    790
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 27.46 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J 330 
 PHE   0.016   0.002   PHE A 378 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.008   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04940 (   65)
  hydrogen bonds       : angle       5.94358 (  195)
  covalent geometry    : bond        0.00371 ( 5960)
  covalent geometry    : angle       0.67550 ( 7970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2698.00 seconds
wall clock time: 48 minutes 32.05 seconds (2912.05 seconds total)