Starting phenix.real_space_refine
on Wed Oct  9 23:35:51 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/10_2024/9czi_46417_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/10_2024/9czi_46417.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/10_2024/9czi_46417.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/10_2024/9czi_46417.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/10_2024/9czi_46417_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/10_2024/9czi_46417_neut.cif"
  }
  resolution = 3.0
  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    3510      2.51       5
     N    1010      2.21       5
     O    1040      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib"
  Total number of atoms: 5570
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 2.43, per 1000 atoms: 0.44
  Number of scatterers: 5570
  At special positions: 0
  Unit cell: (77.996, 144.398, 44.268, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O    1040      8.00
     N    1010      7.00
     C    3510      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 676.9 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 61.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310
    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 330
      removed outlier: 6.970A  pdb=" N   VAL C 318 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   THR A 319 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   SER C 320 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS A 321 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   CYS C 322 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLY A 323 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ILE C 328 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   HIS A 329 " --> pdb=" O   ILE C 328 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   HIS C 330 " --> pdb=" O   HIS A 329 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   VAL E 318 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR C 319 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   SER E 320 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LYS C 321 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   CYS E 322 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLY C 323 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE E 328 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   HIS C 329 " --> pdb=" O   ILE E 328 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   HIS E 330 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL G 318 " --> pdb=" O   LYS E 317 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR E 319 " --> pdb=" O   VAL G 318 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   SER G 320 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LYS E 321 " --> pdb=" O   SER G 320 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   CYS G 322 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLY E 323 " --> pdb=" O   CYS G 322 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE G 328 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   HIS E 329 " --> pdb=" O   ILE G 328 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   HIS G 330 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL I 318 " --> pdb=" O   LYS G 317 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   THR G 319 " --> pdb=" O   VAL I 318 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   SER I 320 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS G 321 " --> pdb=" O   SER I 320 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   CYS I 322 " --> pdb=" O   LYS G 321 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLY G 323 " --> pdb=" O   CYS I 322 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ILE I 328 " --> pdb=" O   ASN G 327 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   HIS G 329 " --> pdb=" O   ILE I 328 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   HIS I 330 " --> pdb=" O   HIS G 329 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.503A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL C 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS E 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL C 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL E 337 " --> pdb=" O   GLU G 338 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS G 340 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL E 339 " --> pdb=" O   LYS G 340 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL G 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS I 340 " --> pdb=" O   VAL G 337 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL G 339 " --> pdb=" O   LYS I 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 356
      removed outlier: 6.431A  pdb=" N   LEU A 344 " --> pdb=" O   ASP C 345 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LYS C 347 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   PHE A 346 " --> pdb=" O   LYS C 347 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ARG C 349 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ASP A 348 " --> pdb=" O   ARG C 349 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   GLN C 351 " --> pdb=" O   ASP A 348 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL A 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   LYS C 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER A 352 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLY C 355 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ILE A 354 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU C 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LYS E 347 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   PHE C 346 " --> pdb=" O   LYS E 347 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ARG E 349 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   ASP C 348 " --> pdb=" O   ARG E 349 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   GLN E 351 " --> pdb=" O   ASP C 348 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL C 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   LYS E 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER C 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLY E 355 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ILE C 354 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU E 344 " --> pdb=" O   ASP G 345 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LYS G 347 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   PHE E 346 " --> pdb=" O   LYS G 347 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ARG G 349 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   ASP E 348 " --> pdb=" O   ARG G 349 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   GLN G 351 " --> pdb=" O   ASP E 348 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL E 350 " --> pdb=" O   GLN G 351 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   LYS G 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER E 352 " --> pdb=" O   LYS G 353 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   GLY G 355 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ILE E 354 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU G 344 " --> pdb=" O   ASP I 345 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LYS I 347 " --> pdb=" O   LEU G 344 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   PHE G 346 " --> pdb=" O   LYS I 347 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ARG I 349 " --> pdb=" O   PHE G 346 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   ASP G 348 " --> pdb=" O   ARG I 349 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   GLN I 351 " --> pdb=" O   ASP G 348 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL G 350 " --> pdb=" O   GLN I 351 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   LYS I 353 " --> pdb=" O   VAL G 350 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER G 352 " --> pdb=" O   LYS I 353 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   GLY I 355 " --> pdb=" O   SER G 352 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ILE G 354 " --> pdb=" O   GLY I 355 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 359 through 362
      removed outlier: 6.510A  pdb=" N   ASN A 359 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   HIS C 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   THR A 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASN C 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   HIS E 362 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   THR C 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASN E 359 " --> pdb=" O   ILE G 360 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   HIS G 362 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR E 361 " --> pdb=" O   HIS G 362 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASN G 359 " --> pdb=" O   ILE I 360 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   HIS I 362 " --> pdb=" O   ASN G 359 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   THR G 361 " --> pdb=" O   HIS I 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 377
    Processing sheet with id=AA8, first strand: chain 'B' and resid 307 through 310
    Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 330
      removed outlier: 6.970A  pdb=" N   VAL D 318 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR B 319 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   SER D 320 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS B 321 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   CYS D 322 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLY B 323 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE D 328 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   HIS B 329 " --> pdb=" O   ILE D 328 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   HIS D 330 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   VAL F 318 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   THR D 319 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   SER F 320 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LYS D 321 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   CYS F 322 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLY D 323 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE F 328 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   HIS D 329 " --> pdb=" O   ILE F 328 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   HIS F 330 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL H 318 " --> pdb=" O   LYS F 317 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   THR F 319 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   SER H 320 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LYS F 321 " --> pdb=" O   SER H 320 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   CYS H 322 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLY F 323 " --> pdb=" O   CYS H 322 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE H 328 " --> pdb=" O   ASN F 327 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   HIS F 329 " --> pdb=" O   ILE H 328 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   HIS H 330 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL J 318 " --> pdb=" O   LYS H 317 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR H 319 " --> pdb=" O   VAL J 318 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   SER J 320 " --> pdb=" O   THR H 319 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LYS H 321 " --> pdb=" O   SER J 320 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   CYS J 322 " --> pdb=" O   LYS H 321 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLY H 323 " --> pdb=" O   CYS J 322 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ILE J 328 " --> pdb=" O   ASN H 327 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   HIS H 329 " --> pdb=" O   ILE J 328 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   HIS J 330 " --> pdb=" O   HIS H 329 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.504A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL D 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   LYS F 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL D 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL F 337 " --> pdb=" O   GLU H 338 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS H 340 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL F 339 " --> pdb=" O   LYS H 340 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL H 337 " --> pdb=" O   GLU J 338 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS J 340 " --> pdb=" O   VAL H 337 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL H 339 " --> pdb=" O   LYS J 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 356
      removed outlier: 6.431A  pdb=" N   LEU B 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LYS D 347 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   PHE B 346 " --> pdb=" O   LYS D 347 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ARG D 349 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ASP B 348 " --> pdb=" O   ARG D 349 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   GLN D 351 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL B 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   LYS D 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER B 352 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLY D 355 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ILE B 354 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU D 344 " --> pdb=" O   ASP F 345 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LYS F 347 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   PHE D 346 " --> pdb=" O   LYS F 347 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ARG F 349 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ASP D 348 " --> pdb=" O   ARG F 349 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   GLN F 351 " --> pdb=" O   ASP D 348 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL D 350 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   LYS F 353 " --> pdb=" O   VAL D 350 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER D 352 " --> pdb=" O   LYS F 353 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   GLY F 355 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ILE D 354 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU F 344 " --> pdb=" O   ASP H 345 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LYS H 347 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   PHE F 346 " --> pdb=" O   LYS H 347 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ARG H 349 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ASP F 348 " --> pdb=" O   ARG H 349 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   GLN H 351 " --> pdb=" O   ASP F 348 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL F 350 " --> pdb=" O   GLN H 351 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   LYS H 353 " --> pdb=" O   VAL F 350 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER F 352 " --> pdb=" O   LYS H 353 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLY H 355 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   ILE F 354 " --> pdb=" O   GLY H 355 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU H 344 " --> pdb=" O   ASP J 345 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LYS J 347 " --> pdb=" O   LEU H 344 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   PHE H 346 " --> pdb=" O   LYS J 347 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ARG J 349 " --> pdb=" O   PHE H 346 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   ASP H 348 " --> pdb=" O   ARG J 349 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   GLN J 351 " --> pdb=" O   ASP H 348 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL H 350 " --> pdb=" O   GLN J 351 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   LYS J 353 " --> pdb=" O   VAL H 350 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER H 352 " --> pdb=" O   LYS J 353 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   GLY J 355 " --> pdb=" O   SER H 352 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ILE H 354 " --> pdb=" O   GLY J 355 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 359 through 362
      removed outlier: 6.509A  pdb=" N   ASN B 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   HIS D 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ASN D 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   HIS F 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR D 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASN F 359 " --> pdb=" O   ILE H 360 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   HIS H 362 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR F 361 " --> pdb=" O   HIS H 362 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASN H 359 " --> pdb=" O   ILE J 360 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   HIS J 362 " --> pdb=" O   ASN H 359 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   THR H 361 " --> pdb=" O   HIS J 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 369 through 377

    128 hydrogen bonds defined for protein.
    384 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: 1.81

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1512
        1.32 -     1.45: 1072
        1.45 -     1.58: 3006
        1.58 -     1.70: 60
        1.70 -     1.83: 10
  Bond restraints: 5660
  Sorted by residual:
  bond pdb=" CB  HIS D 374 "
       pdb=" CG  HIS D 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.434  0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" CB  HIS J 374 "
       pdb=" CG  HIS J 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.434  0.063 1.40e-02 5.10e+03 2.01e+01
  bond pdb=" CB  HIS F 374 "
       pdb=" CG  HIS F 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.435  0.062 1.40e-02 5.10e+03 1.99e+01
  bond pdb=" CB  HIS G 374 "
       pdb=" CG  HIS G 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.435  0.062 1.40e-02 5.10e+03 1.99e+01
  bond pdb=" CB  HIS A 374 "
       pdb=" CG  HIS A 374 "
    ideal  model  delta    sigma   weight residual
    1.497  1.435  0.062 1.40e-02 5.10e+03 1.98e+01
  ... (remaining 5655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 5391
        1.61 -     3.21: 1419
        3.21 -     4.81: 511
        4.81 -     6.42: 169
        6.42 -     8.02: 90
  Bond angle restraints: 7580
  Sorted by residual:
  angle pdb=" C   LYS H 331 "
        pdb=" N   PRO H 332 "
        pdb=" CA  PRO H 332 "
      ideal   model   delta    sigma   weight residual
     119.83  125.80   -5.97 1.08e+00 8.57e-01 3.05e+01
  angle pdb=" C   LYS B 331 "
        pdb=" N   PRO B 332 "
        pdb=" CA  PRO B 332 "
      ideal   model   delta    sigma   weight residual
     119.83  125.78   -5.95 1.08e+00 8.57e-01 3.04e+01
  angle pdb=" C   LYS G 331 "
        pdb=" N   PRO G 332 "
        pdb=" CA  PRO G 332 "
      ideal   model   delta    sigma   weight residual
     119.83  125.77   -5.94 1.08e+00 8.57e-01 3.02e+01
  angle pdb=" C   LYS E 331 "
        pdb=" N   PRO E 332 "
        pdb=" CA  PRO E 332 "
      ideal   model   delta    sigma   weight residual
     119.83  125.76   -5.93 1.08e+00 8.57e-01 3.02e+01
  angle pdb=" C   LYS I 331 "
        pdb=" N   PRO I 332 "
        pdb=" CA  PRO I 332 "
      ideal   model   delta    sigma   weight residual
     119.83  125.76   -5.93 1.08e+00 8.57e-01 3.01e+01
  ... (remaining 7575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.54: 3280
       12.54 -    25.09: 110
       25.09 -    37.63: 30
       37.63 -    50.17: 0
       50.17 -    62.71: 20
  Dihedral angle restraints: 3440
    sinusoidal: 1430
      harmonic: 2010
  Sorted by residual:
  dihedral pdb=" C   GLN H 336 "
           pdb=" N   GLN H 336 "
           pdb=" CA  GLN H 336 "
           pdb=" CB  GLN H 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.50   -9.10     0      2.50e+00 1.60e-01 1.33e+01
  dihedral pdb=" C   GLN F 336 "
           pdb=" N   GLN F 336 "
           pdb=" CA  GLN F 336 "
           pdb=" CB  GLN F 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.50   -9.10     0      2.50e+00 1.60e-01 1.32e+01
  dihedral pdb=" C   GLN J 336 "
           pdb=" N   GLN J 336 "
           pdb=" CA  GLN J 336 "
           pdb=" CB  GLN J 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.50   -9.10     0      2.50e+00 1.60e-01 1.32e+01
  ... (remaining 3437 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.085: 588
       0.085 -    0.169: 192
       0.169 -    0.252: 70
       0.252 -    0.336: 0
       0.336 -    0.419: 10
  Chirality restraints: 860
  Sorted by residual:
  chirality pdb=" CB  VAL J 306 "
            pdb=" CA  VAL J 306 "
            pdb=" CG1 VAL J 306 "
            pdb=" CG2 VAL J 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.05    0.42 2.00e-01 2.50e+01 4.39e+00
  chirality pdb=" CB  VAL E 306 "
            pdb=" CA  VAL E 306 "
            pdb=" CG1 VAL E 306 "
            pdb=" CG2 VAL E 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.04    0.42 2.00e-01 2.50e+01 4.32e+00
  chirality pdb=" CB  VAL A 306 "
            pdb=" CA  VAL A 306 "
            pdb=" CG1 VAL A 306 "
            pdb=" CG2 VAL A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.04    0.42 2.00e-01 2.50e+01 4.32e+00
  ... (remaining 857 not shown)

  Planarity restraints: 960
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO I 332 "   -0.015 2.00e-02 2.50e+03   2.91e-02 8.50e+00
        pdb=" C   PRO I 332 "    0.050 2.00e-02 2.50e+03
        pdb=" O   PRO I 332 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLY I 333 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO E 332 "   -0.015 2.00e-02 2.50e+03   2.90e-02 8.40e+00
        pdb=" C   PRO E 332 "    0.050 2.00e-02 2.50e+03
        pdb=" O   PRO E 332 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLY E 333 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO G 332 "   -0.015 2.00e-02 2.50e+03   2.90e-02 8.38e+00
        pdb=" C   PRO G 332 "    0.050 2.00e-02 2.50e+03
        pdb=" O   PRO G 332 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLY G 333 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 957 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 2342
        2.93 -     3.42: 4551
        3.42 -     3.91: 9620
        3.91 -     4.41: 10462
        4.41 -     4.90: 20321
  Nonbonded interactions: 47296
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 331 "
            pdb=" OE1 GLU D 338 "
     model   vdw
     2.435 3.120
  nonbonded pdb=" NZ  LYS B 331 "
            pdb=" OE1 GLU C 338 "
     model   vdw
     2.435 3.120
  nonbonded pdb=" NZ  LYS D 331 "
            pdb=" OE1 GLU E 338 "
     model   vdw
     2.435 3.120
  nonbonded pdb=" NZ  LYS I 331 "
            pdb=" OE1 GLU J 338 "
     model   vdw
     2.435 3.120
  nonbonded pdb=" NZ  LYS E 331 "
            pdb=" OE1 GLU F 338 "
     model   vdw
     2.435 3.120
  ... (remaining 47291 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.720
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   32.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
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      :  0.021   0.128   5660  Z= 1.402
  Angle     :  1.918   8.024   7580  Z= 1.231
  Chirality :  0.101   0.419    860
  Planarity :  0.009   0.029    960
  Dihedral  :  9.104  62.709   2160
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.72 (0.27), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.21), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS C 362 
 PHE   0.018   0.006   PHE I 346 
 TYR   0.016   0.007   TYR J 310 
 ARG   0.002   0.001   ARG F 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8157 (tttt) cc_final: 0.7477 (tmtt)
REVERT: A  342 GLU cc_start: 0.8292 (mt-10) cc_final: 0.6861 (pm20)
REVERT: A  343 LYS cc_start: 0.8179 (tttt) cc_final: 0.7588 (mmtt)
REVERT: A  349 ARG cc_start: 0.7701 (mtm180) cc_final: 0.7427 (mtm180)
REVERT: A  356 SER cc_start: 0.8777 (p) cc_final: 0.8535 (p)
REVERT: A  360 ILE cc_start: 0.8927 (mt) cc_final: 0.8716 (mp)
REVERT: A  369 LYS cc_start: 0.8744 (mttt) cc_final: 0.8194 (mttm)
REVERT: A  370 LYS cc_start: 0.9112 (tttm) cc_final: 0.8840 (tttm)
REVERT: B  316 SER cc_start: 0.8649 (p) cc_final: 0.8440 (p)
REVERT: B  321 LYS cc_start: 0.8208 (tttt) cc_final: 0.7453 (tmtt)
REVERT: B  343 LYS cc_start: 0.8415 (tttt) cc_final: 0.7874 (mmtt)
REVERT: B  360 ILE cc_start: 0.9020 (mt) cc_final: 0.8709 (mp)
REVERT: B  369 LYS cc_start: 0.8685 (mttt) cc_final: 0.7884 (mttp)
REVERT: B  370 LYS cc_start: 0.9044 (tttm) cc_final: 0.8791 (tttm)
REVERT: C  321 LYS cc_start: 0.7936 (tttt) cc_final: 0.7413 (mttp)
REVERT: C  343 LYS cc_start: 0.8057 (tttt) cc_final: 0.7592 (mmtp)
REVERT: C  360 ILE cc_start: 0.9001 (mt) cc_final: 0.8744 (mp)
REVERT: D  321 LYS cc_start: 0.7958 (tttt) cc_final: 0.7371 (tttm)
REVERT: D  360 ILE cc_start: 0.9092 (mt) cc_final: 0.8819 (mp)
REVERT: E  311 LYS cc_start: 0.8219 (mttt) cc_final: 0.7575 (pttt)
REVERT: E  321 LYS cc_start: 0.7769 (tttt) cc_final: 0.7099 (tttt)
REVERT: E  360 ILE cc_start: 0.9057 (mt) cc_final: 0.8742 (mp)
REVERT: E  369 LYS cc_start: 0.8586 (mttt) cc_final: 0.7852 (mttp)
REVERT: E  370 LYS cc_start: 0.8949 (tttm) cc_final: 0.8684 (tttm)
REVERT: F  311 LYS cc_start: 0.8191 (mttt) cc_final: 0.7510 (pttt)
REVERT: F  321 LYS cc_start: 0.7992 (tttt) cc_final: 0.7288 (mttp)
REVERT: F  342 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7921 (mm-30)
REVERT: F  343 LYS cc_start: 0.7885 (tttt) cc_final: 0.7257 (mmtt)
REVERT: F  360 ILE cc_start: 0.9045 (mt) cc_final: 0.8685 (mp)
REVERT: G  311 LYS cc_start: 0.8366 (mttt) cc_final: 0.7947 (tttt)
REVERT: G  321 LYS cc_start: 0.7939 (tttt) cc_final: 0.7291 (mttp)
REVERT: G  343 LYS cc_start: 0.7768 (tttt) cc_final: 0.7342 (mmtt)
REVERT: G  358 ASP cc_start: 0.8478 (m-30) cc_final: 0.8250 (m-30)
REVERT: G  360 ILE cc_start: 0.8955 (mt) cc_final: 0.8705 (mp)
REVERT: G  369 LYS cc_start: 0.8743 (mttt) cc_final: 0.8540 (mttt)
REVERT: G  375 LYS cc_start: 0.8287 (tttt) cc_final: 0.7985 (ttpt)
REVERT: H  311 LYS cc_start: 0.8061 (mttt) cc_final: 0.7544 (tttt)
REVERT: H  321 LYS cc_start: 0.7949 (tttt) cc_final: 0.7323 (mttp)
REVERT: H  343 LYS cc_start: 0.7771 (tttt) cc_final: 0.7304 (mptt)
REVERT: H  358 ASP cc_start: 0.8501 (m-30) cc_final: 0.8242 (m-30)
REVERT: H  360 ILE cc_start: 0.9173 (mt) cc_final: 0.8905 (mp)
REVERT: H  369 LYS cc_start: 0.8658 (mttt) cc_final: 0.8415 (mttp)
REVERT: I  311 LYS cc_start: 0.8282 (mttt) cc_final: 0.7674 (tttt)
REVERT: I  316 SER cc_start: 0.8847 (p) cc_final: 0.8530 (p)
REVERT: I  321 LYS cc_start: 0.7752 (tttt) cc_final: 0.7334 (mttm)
REVERT: I  331 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8578 (mtmt)
REVERT: I  338 GLU cc_start: 0.8724 (tt0) cc_final: 0.8471 (tt0)
REVERT: I  343 LYS cc_start: 0.7700 (tttt) cc_final: 0.7190 (mptp)
REVERT: I  349 ARG cc_start: 0.7568 (mtm180) cc_final: 0.7293 (mtm180)
REVERT: I  358 ASP cc_start: 0.8449 (m-30) cc_final: 0.8182 (m-30)
REVERT: I  360 ILE cc_start: 0.9106 (mt) cc_final: 0.8820 (mp)
REVERT: I  369 LYS cc_start: 0.8671 (mttt) cc_final: 0.7944 (mttp)
REVERT: I  370 LYS cc_start: 0.9060 (tttm) cc_final: 0.8598 (tttm)
REVERT: J  311 LYS cc_start: 0.8317 (mttt) cc_final: 0.7634 (tttt)
REVERT: J  321 LYS cc_start: 0.7930 (tttt) cc_final: 0.7565 (mttm)
REVERT: J  358 ASP cc_start: 0.8422 (m-30) cc_final: 0.8067 (m-30)
REVERT: J  360 ILE cc_start: 0.9110 (mt) cc_final: 0.8780 (mp)
REVERT: J  369 LYS cc_start: 0.8751 (mttt) cc_final: 0.8494 (mppt)
REVERT: J  370 LYS cc_start: 0.8884 (tttm) cc_final: 0.8646 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 1.5185
  time to fit residues: 409.7666
Evaluate side-chains
  211 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    0.4980
   chunk 35 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    1.2988

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   5660  Z= 0.186
  Angle     :  0.592   5.150   7580  Z= 0.318
  Chirality :  0.050   0.150    860
  Planarity :  0.003   0.021    960
  Dihedral  :  4.990  16.563    740
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.03 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.27 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 374 
 PHE   0.004   0.001   PHE H 346 
 TYR   0.011   0.002   TYR D 310 
 ARG   0.001   0.000   ARG I 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 219
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8280 (tttt) cc_final: 0.7546 (tmtt)
REVERT: A  343 LYS cc_start: 0.8296 (tttt) cc_final: 0.7785 (mmtt)
REVERT: A  360 ILE cc_start: 0.8952 (mt) cc_final: 0.8684 (mp)
REVERT: B  321 LYS cc_start: 0.8239 (tttt) cc_final: 0.7404 (tmtt)
REVERT: B  325 LEU cc_start: 0.8806 (tp) cc_final: 0.8574 (tp)
REVERT: B  342 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.6856 (mp0)
REVERT: B  343 LYS cc_start: 0.8437 (tttt) cc_final: 0.7844 (mmtt)
REVERT: B  360 ILE cc_start: 0.9022 (mt) cc_final: 0.8713 (mp)
REVERT: B  369 LYS cc_start: 0.8533 (mttt) cc_final: 0.7839 (mttp)
REVERT: C  321 LYS cc_start: 0.7970 (tttt) cc_final: 0.7452 (mttm)
REVERT: C  338 GLU cc_start: 0.9012 (tt0) cc_final: 0.8589 (tt0)
REVERT: C  343 LYS cc_start: 0.8016 (tttt) cc_final: 0.7321 (mmtt)
REVERT: C  360 ILE cc_start: 0.9085 (mt) cc_final: 0.8857 (mp)
REVERT: D  321 LYS cc_start: 0.7942 (tttt) cc_final: 0.7314 (tttm)
REVERT: D  342 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7863 (mt-10)
REVERT: D  343 LYS cc_start: 0.7948 (tttt) cc_final: 0.7339 (mmtt)
REVERT: D  356 SER cc_start: 0.9215 (p) cc_final: 0.8385 (m)
REVERT: D  360 ILE cc_start: 0.9254 (mt) cc_final: 0.9000 (mp)
REVERT: D  370 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8744 (tttp)
REVERT: E  321 LYS cc_start: 0.7842 (tttt) cc_final: 0.7128 (ttpt)
REVERT: E  360 ILE cc_start: 0.9103 (mt) cc_final: 0.8854 (mp)
REVERT: E  369 LYS cc_start: 0.8428 (mttt) cc_final: 0.7720 (mttp)
REVERT: E  370 LYS cc_start: 0.8998 (tttm) cc_final: 0.8761 (tttm)
REVERT: F  321 LYS cc_start: 0.8086 (tttt) cc_final: 0.7447 (mttp)
REVERT: F  342 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7936 (mm-30)
REVERT: F  343 LYS cc_start: 0.7993 (tttt) cc_final: 0.7141 (mmtt)
REVERT: F  360 ILE cc_start: 0.9047 (mt) cc_final: 0.8790 (mp)
REVERT: F  369 LYS cc_start: 0.8838 (mppt) cc_final: 0.8038 (mttp)
REVERT: G  321 LYS cc_start: 0.7992 (tttt) cc_final: 0.7358 (mttp)
REVERT: G  342 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7281 (mm-30)
REVERT: G  343 LYS cc_start: 0.7942 (tttt) cc_final: 0.7370 (mmtt)
REVERT: G  360 ILE cc_start: 0.9001 (mt) cc_final: 0.8770 (mp)
REVERT: G  375 LYS cc_start: 0.8111 (tttt) cc_final: 0.7768 (ttpt)
REVERT: H  321 LYS cc_start: 0.7969 (tttt) cc_final: 0.7328 (mttp)
REVERT: H  358 ASP cc_start: 0.8755 (m-30) cc_final: 0.8337 (m-30)
REVERT: H  360 ILE cc_start: 0.9156 (mt) cc_final: 0.8913 (mp)
REVERT: H  369 LYS cc_start: 0.8632 (mttt) cc_final: 0.8361 (mttp)
REVERT: I  316 SER cc_start: 0.8839 (p) cc_final: 0.8620 (p)
REVERT: I  321 LYS cc_start: 0.7781 (tttt) cc_final: 0.7349 (mttm)
REVERT: I  331 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8653 (mtmt)
REVERT: I  343 LYS cc_start: 0.7600 (tttt) cc_final: 0.7063 (mptp)
REVERT: I  345 ASP cc_start: 0.7584 (t0) cc_final: 0.7086 (t0)
REVERT: I  349 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7256 (mtm180)
REVERT: I  360 ILE cc_start: 0.9152 (mt) cc_final: 0.8893 (mp)
REVERT: I  369 LYS cc_start: 0.8667 (mttt) cc_final: 0.7916 (mttp)
REVERT: I  370 LYS cc_start: 0.8765 (tttm) cc_final: 0.8343 (tmtm)
REVERT: J  321 LYS cc_start: 0.7979 (tttt) cc_final: 0.7582 (mttp)
REVERT: J  343 LYS cc_start: 0.7807 (tttt) cc_final: 0.7353 (mmtt)
REVERT: J  360 ILE cc_start: 0.9162 (mt) cc_final: 0.8846 (mp)
REVERT: J  370 LYS cc_start: 0.8895 (tttm) cc_final: 0.8366 (tptt)
  outliers start: 16
  outliers final: 2
  residues processed: 223
  average time/residue: 1.2944
  time to fit residues: 299.3467
Evaluate side-chains
  216 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 210
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  342 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 52 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    4.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
D 336 GLN
E 327 ASN
F 327 ASN
H 336 GLN
I 351 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   5660  Z= 0.455
  Angle     :  0.722   6.547   7580  Z= 0.370
  Chirality :  0.050   0.136    860
  Planarity :  0.004   0.038    960
  Dihedral  :  5.492  19.036    740
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 13.44 %
    Favored  : 82.50 %
  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: -1.83 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.39 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS I 330 
 PHE   0.011   0.002   PHE A 378 
 TYR   0.013   0.003   TYR D 310 
 ARG   0.002   0.000   ARG I 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 241
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.8164 (tttt) cc_final: 0.7451 (tmtt)
REVERT: A  343 LYS cc_start: 0.8303 (tttt) cc_final: 0.7797 (mmtt)
REVERT: A  360 ILE cc_start: 0.9051 (mt) cc_final: 0.8809 (mp)
REVERT: B  321 LYS cc_start: 0.8197 (tttt) cc_final: 0.7267 (ttpt)
REVERT: B  342 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.6862 (mp0)
REVERT: B  343 LYS cc_start: 0.8424 (tttt) cc_final: 0.7904 (mmtt)
REVERT: B  347 LYS cc_start: 0.7126 (mttp) cc_final: 0.5918 (mtmt)
REVERT: B  360 ILE cc_start: 0.9055 (mt) cc_final: 0.8741 (mp)
REVERT: B  369 LYS cc_start: 0.8551 (mttt) cc_final: 0.7903 (mttp)
REVERT: C  321 LYS cc_start: 0.7824 (tttt) cc_final: 0.7314 (mttp)
REVERT: C  327 ASN cc_start: 0.8160 (m-40) cc_final: 0.7724 (t0)
REVERT: C  343 LYS cc_start: 0.8036 (tttt) cc_final: 0.7290 (mmtt)
REVERT: C  349 ARG cc_start: 0.7764 (mtm180) cc_final: 0.7343 (mtp-110)
REVERT: D  321 LYS cc_start: 0.7835 (tttt) cc_final: 0.7084 (ttpt)
REVERT: D  327 ASN cc_start: 0.8292 (m-40) cc_final: 0.7752 (t0)
REVERT: D  342 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7351 (mm-30)
REVERT: D  343 LYS cc_start: 0.8025 (tttt) cc_final: 0.7379 (mmtt)
REVERT: D  349 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7141 (mtm180)
REVERT: D  356 SER cc_start: 0.9160 (p) cc_final: 0.8439 (m)
REVERT: D  360 ILE cc_start: 0.9227 (mt) cc_final: 0.9024 (mp)
REVERT: D  370 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8894 (tttp)
REVERT: E  311 LYS cc_start: 0.8249 (mttt) cc_final: 0.7290 (pttt)
REVERT: E  321 LYS cc_start: 0.7765 (tttt) cc_final: 0.7104 (ttpt)
REVERT: E  342 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7739 (mt-10)
REVERT: E  343 LYS cc_start: 0.8033 (tttt) cc_final: 0.7165 (mmtt)
REVERT: E  356 SER cc_start: 0.9108 (p) cc_final: 0.8309 (m)
REVERT: E  360 ILE cc_start: 0.9135 (mt) cc_final: 0.8873 (mp)
REVERT: E  369 LYS cc_start: 0.8594 (mttt) cc_final: 0.7682 (mttp)
REVERT: E  370 LYS cc_start: 0.9036 (tttm) cc_final: 0.8824 (tttm)
REVERT: F  321 LYS cc_start: 0.8109 (tttt) cc_final: 0.7162 (tmtt)
REVERT: F  343 LYS cc_start: 0.8151 (tttt) cc_final: 0.7177 (mmtt)
REVERT: F  360 ILE cc_start: 0.9057 (mt) cc_final: 0.8810 (mp)
REVERT: F  369 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8072 (mttp)
REVERT: G  321 LYS cc_start: 0.7963 (tttt) cc_final: 0.7334 (mttp)
REVERT: G  343 LYS cc_start: 0.7899 (tttt) cc_final: 0.7312 (mmtt)
REVERT: G  360 ILE cc_start: 0.9027 (mt) cc_final: 0.8762 (mp)
REVERT: G  370 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8917 (tttp)
REVERT: H  321 LYS cc_start: 0.7776 (tttt) cc_final: 0.7177 (mttp)
REVERT: H  342 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7974 (mm-30)
REVERT: H  358 ASP cc_start: 0.8677 (m-30) cc_final: 0.8363 (m-30)
REVERT: H  360 ILE cc_start: 0.9141 (mt) cc_final: 0.8882 (mp)
REVERT: H  369 LYS cc_start: 0.8790 (mttt) cc_final: 0.8571 (mttp)
REVERT: I  321 LYS cc_start: 0.7823 (tttt) cc_final: 0.7346 (mttm)
REVERT: I  331 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8779 (mtmt)
REVERT: I  343 LYS cc_start: 0.7860 (tttt) cc_final: 0.7195 (mptp)
REVERT: I  345 ASP cc_start: 0.7445 (t0) cc_final: 0.6867 (t0)
REVERT: I  349 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7452 (mtm180)
REVERT: I  360 ILE cc_start: 0.9198 (mt) cc_final: 0.8968 (mp)
REVERT: I  369 LYS cc_start: 0.8709 (mttt) cc_final: 0.7915 (mttp)
REVERT: J  317 LYS cc_start: 0.8264 (tttt) cc_final: 0.7853 (ttmm)
REVERT: J  321 LYS cc_start: 0.8046 (tttt) cc_final: 0.7606 (mttp)
REVERT: J  325 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8535 (tt)
REVERT: J  343 LYS cc_start: 0.7959 (tttt) cc_final: 0.7432 (mmtt)
REVERT: J  358 ASP cc_start: 0.8632 (m-30) cc_final: 0.8292 (m-30)
  outliers start: 26
  outliers final: 8
  residues processed: 247
  average time/residue: 1.3156
  time to fit residues: 336.9650
Evaluate side-chains
  249 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 233
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  370 LYS
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  317 LYS
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 67 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
E 327 ASN
F 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5660  Z= 0.161
  Angle     :  0.558   6.230   7580  Z= 0.289
  Chirality :  0.049   0.121    860
  Planarity :  0.003   0.034    960
  Dihedral  :  4.893  15.610    740
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.50 %
    Favored  : 78.91 %
  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: -1.86 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.41 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS G 374 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.008   0.001   TYR C 310 
 ARG   0.001   0.000   ARG I 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 216
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8232 (tttt) cc_final: 0.7473 (tmtt)
REVERT: A  342 GLU cc_start: 0.8109 (mt-10) cc_final: 0.6516 (pm20)
REVERT: A  343 LYS cc_start: 0.8188 (tttt) cc_final: 0.7711 (mmtt)
REVERT: A  347 LYS cc_start: 0.7083 (mttp) cc_final: 0.5958 (mtmt)
REVERT: A  360 ILE cc_start: 0.8982 (mt) cc_final: 0.8693 (mp)
REVERT: B  321 LYS cc_start: 0.8280 (tttt) cc_final: 0.7446 (tmtt)
REVERT: B  342 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.6706 (mp0)
REVERT: B  343 LYS cc_start: 0.8483 (tttt) cc_final: 0.7845 (mmtt)
REVERT: B  347 LYS cc_start: 0.6997 (mttp) cc_final: 0.5759 (mtmt)
REVERT: B  360 ILE cc_start: 0.9030 (mt) cc_final: 0.8752 (mp)
REVERT: B  369 LYS cc_start: 0.8525 (mttt) cc_final: 0.7802 (mttp)
REVERT: C  321 LYS cc_start: 0.7874 (tttt) cc_final: 0.7361 (mttm)
REVERT: C  327 ASN cc_start: 0.7887 (m-40) cc_final: 0.7483 (t0)
REVERT: C  338 GLU cc_start: 0.9076 (tt0) cc_final: 0.8705 (tt0)
REVERT: C  342 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8295 (mm-30)
REVERT: C  343 LYS cc_start: 0.8124 (tttt) cc_final: 0.7269 (mmtt)
REVERT: C  349 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7296 (mtp-110)
REVERT: C  356 SER cc_start: 0.9142 (p) cc_final: 0.8316 (m)
REVERT: D  321 LYS cc_start: 0.7898 (tttt) cc_final: 0.7283 (tttm)
REVERT: D  327 ASN cc_start: 0.8040 (m-40) cc_final: 0.7544 (t0)
REVERT: D  342 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7407 (mm-30)
REVERT: D  343 LYS cc_start: 0.8022 (tttt) cc_final: 0.7276 (mmtt)
REVERT: D  349 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7231 (mtm180)
REVERT: D  356 SER cc_start: 0.9165 (p) cc_final: 0.8432 (m)
REVERT: D  360 ILE cc_start: 0.9247 (mt) cc_final: 0.9004 (mp)
REVERT: D  370 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8809 (tttm)
REVERT: E  321 LYS cc_start: 0.7744 (tttt) cc_final: 0.7087 (ttpt)
REVERT: E  342 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7954 (mm-30)
REVERT: E  360 ILE cc_start: 0.9119 (mt) cc_final: 0.8855 (mp)
REVERT: E  369 LYS cc_start: 0.8615 (mttt) cc_final: 0.7824 (mttp)
REVERT: F  321 LYS cc_start: 0.8071 (tttt) cc_final: 0.7401 (mttp)
REVERT: F  343 LYS cc_start: 0.8029 (tttt) cc_final: 0.7031 (mmtt)
REVERT: F  360 ILE cc_start: 0.9063 (mt) cc_final: 0.8819 (mp)
REVERT: F  369 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8097 (mttp)
REVERT: G  321 LYS cc_start: 0.7988 (tttt) cc_final: 0.7387 (mttp)
REVERT: G  342 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8287 (mm-30)
REVERT: G  343 LYS cc_start: 0.7876 (tttt) cc_final: 0.7398 (mmtt)
REVERT: G  358 ASP cc_start: 0.8599 (m-30) cc_final: 0.8291 (m-30)
REVERT: G  360 ILE cc_start: 0.9051 (mt) cc_final: 0.8816 (mp)
REVERT: H  321 LYS cc_start: 0.7778 (tttt) cc_final: 0.7267 (mttp)
REVERT: H  342 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7524 (mm-30)
REVERT: H  358 ASP cc_start: 0.8661 (m-30) cc_final: 0.8270 (m-30)
REVERT: H  360 ILE cc_start: 0.9138 (mt) cc_final: 0.8906 (mp)
REVERT: H  369 LYS cc_start: 0.8743 (mttt) cc_final: 0.8491 (mttt)
REVERT: I  321 LYS cc_start: 0.7816 (tttt) cc_final: 0.7381 (mttp)
REVERT: I  331 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8792 (mtmt)
REVERT: I  343 LYS cc_start: 0.7745 (tttt) cc_final: 0.7120 (mptp)
REVERT: I  345 ASP cc_start: 0.7404 (t0) cc_final: 0.6802 (t0)
REVERT: I  349 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7462 (mtm180)
REVERT: I  358 ASP cc_start: 0.8477 (m-30) cc_final: 0.8258 (m-30)
REVERT: I  360 ILE cc_start: 0.9164 (mt) cc_final: 0.8922 (mp)
REVERT: I  369 LYS cc_start: 0.8719 (mttt) cc_final: 0.7915 (mttp)
REVERT: I  370 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8628 (tmtm)
REVERT: J  317 LYS cc_start: 0.8194 (tttt) cc_final: 0.7770 (ttmm)
REVERT: J  321 LYS cc_start: 0.8006 (tttt) cc_final: 0.7626 (mttp)
REVERT: J  343 LYS cc_start: 0.7948 (tttt) cc_final: 0.7438 (mmtt)
REVERT: J  345 ASP cc_start: 0.7230 (t0) cc_final: 0.6632 (t0)
REVERT: J  356 SER cc_start: 0.9030 (p) cc_final: 0.8669 (p)
REVERT: J  357 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8548 (tp)
REVERT: J  358 ASP cc_start: 0.8452 (m-30) cc_final: 0.7839 (m-30)
  outliers start: 23
  outliers final: 5
  residues processed: 222
  average time/residue: 1.3136
  time to fit residues: 302.4598
Evaluate side-chains
  223 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 211
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 327 ASN
F 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.052   5660  Z= 0.623
  Angle     :  0.780   7.763   7580  Z= 0.394
  Chirality :  0.051   0.124    860
  Planarity :  0.005   0.049    960
  Dihedral  :  5.615  20.312    740
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 16.56 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS D 374 
 PHE   0.007   0.002   PHE G 378 
 TYR   0.011   0.002   TYR C 310 
 ARG   0.002   0.001   ARG J 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 228
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8119 (tttt) cc_final: 0.7467 (tmtt)
REVERT: A  342 GLU cc_start: 0.8476 (mt-10) cc_final: 0.6819 (pm20)
REVERT: A  343 LYS cc_start: 0.8250 (tttt) cc_final: 0.7673 (mmtt)
REVERT: A  347 LYS cc_start: 0.7204 (mttp) cc_final: 0.6489 (mtpt)
REVERT: A  360 ILE cc_start: 0.9077 (mt) cc_final: 0.8821 (mp)
REVERT: B  317 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7513 (ttpp)
REVERT: B  321 LYS cc_start: 0.8229 (tttt) cc_final: 0.7604 (mttp)
REVERT: B  342 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.6665 (mp0)
REVERT: B  343 LYS cc_start: 0.8400 (tttt) cc_final: 0.7930 (mmtt)
REVERT: B  347 LYS cc_start: 0.7061 (mttp) cc_final: 0.5700 (mtmt)
REVERT: B  360 ILE cc_start: 0.9082 (mt) cc_final: 0.8773 (mp)
REVERT: B  369 LYS cc_start: 0.8641 (mttt) cc_final: 0.7923 (mttp)
REVERT: C  321 LYS cc_start: 0.7885 (tttt) cc_final: 0.7352 (mttp)
REVERT: C  327 ASN cc_start: 0.8163 (m-40) cc_final: 0.7756 (t0)
REVERT: C  343 LYS cc_start: 0.8138 (tttt) cc_final: 0.7230 (mmtt)
REVERT: C  349 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7584 (mtm180)
REVERT: D  321 LYS cc_start: 0.7724 (tttt) cc_final: 0.7088 (ttpt)
REVERT: D  327 ASN cc_start: 0.8326 (m-40) cc_final: 0.7824 (t0)
REVERT: D  342 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7296 (mm-30)
REVERT: D  343 LYS cc_start: 0.8051 (tttt) cc_final: 0.7384 (mmtt)
REVERT: D  349 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7232 (mtm180)
REVERT: D  356 SER cc_start: 0.9175 (p) cc_final: 0.8434 (m)
REVERT: D  360 ILE cc_start: 0.9139 (mt) cc_final: 0.8936 (mp)
REVERT: D  370 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8808 (tttp)
REVERT: E  311 LYS cc_start: 0.8226 (mttt) cc_final: 0.7293 (pttt)
REVERT: E  321 LYS cc_start: 0.7829 (tttt) cc_final: 0.7113 (ttpt)
REVERT: E  342 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7693 (mt-10)
REVERT: E  343 LYS cc_start: 0.8066 (tttt) cc_final: 0.7236 (mmtt)
REVERT: E  347 LYS cc_start: 0.6810 (mttp) cc_final: 0.6278 (mmtp)
REVERT: E  356 SER cc_start: 0.9141 (p) cc_final: 0.8286 (m)
REVERT: E  360 ILE cc_start: 0.9109 (mt) cc_final: 0.8837 (mp)
REVERT: E  369 LYS cc_start: 0.8723 (mttt) cc_final: 0.7845 (mttp)
REVERT: F  321 LYS cc_start: 0.8091 (tttt) cc_final: 0.7220 (tmtt)
REVERT: F  343 LYS cc_start: 0.8062 (tttt) cc_final: 0.7075 (mmtt)
REVERT: F  369 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8099 (mttp)
REVERT: G  321 LYS cc_start: 0.7879 (tttt) cc_final: 0.7282 (mttp)
REVERT: G  342 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7477 (mm-30)
REVERT: G  343 LYS cc_start: 0.7853 (tttt) cc_final: 0.7291 (mmtt)
REVERT: G  360 ILE cc_start: 0.9053 (mt) cc_final: 0.8774 (mp)
REVERT: H  321 LYS cc_start: 0.7838 (tttt) cc_final: 0.7213 (mttp)
REVERT: H  342 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7739 (mm-30)
REVERT: H  358 ASP cc_start: 0.8664 (m-30) cc_final: 0.8401 (m-30)
REVERT: H  360 ILE cc_start: 0.9148 (mt) cc_final: 0.8900 (mp)
REVERT: H  369 LYS cc_start: 0.8785 (mttt) cc_final: 0.8572 (mttp)
REVERT: I  321 LYS cc_start: 0.7901 (tttt) cc_final: 0.7405 (mttm)
REVERT: I  331 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8795 (mtmt)
REVERT: I  342 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.6922 (mt-10)
REVERT: I  343 LYS cc_start: 0.7890 (tttt) cc_final: 0.7140 (mptp)
REVERT: I  345 ASP cc_start: 0.7447 (t0) cc_final: 0.6796 (t0)
REVERT: I  349 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7709 (mtm180)
REVERT: I  360 ILE cc_start: 0.9268 (mt) cc_final: 0.8963 (mp)
REVERT: I  369 LYS cc_start: 0.8778 (mttt) cc_final: 0.8016 (mttp)
REVERT: J  317 LYS cc_start: 0.8200 (tttt) cc_final: 0.7787 (ttmm)
REVERT: J  321 LYS cc_start: 0.8017 (tttt) cc_final: 0.7580 (mttp)
REVERT: J  343 LYS cc_start: 0.7992 (tttt) cc_final: 0.7365 (mmtt)
REVERT: J  357 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8791 (tp)
REVERT: J  358 ASP cc_start: 0.8646 (m-30) cc_final: 0.8281 (m-30)
  outliers start: 35
  outliers final: 10
  residues processed: 240
  average time/residue: 1.3418
  time to fit residues: 333.7779
Evaluate side-chains
  247 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 226
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  369 LYS
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain H residue  370 LYS
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain I residue  370 LYS
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  357 LEU
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 16 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
E 327 ASN
F 327 ASN
I 327 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5660  Z= 0.181
  Angle     :  0.563   5.812   7580  Z= 0.293
  Chirality :  0.049   0.123    860
  Planarity :  0.003   0.042    960
  Dihedral  :  4.984  15.647    740
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.22 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS G 374 
 PHE   0.005   0.001   PHE G 378 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.001   0.000   ARG I 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 209
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8255 (tttt) cc_final: 0.7503 (tmtt)
REVERT: A  342 GLU cc_start: 0.8143 (mt-10) cc_final: 0.6537 (pm20)
REVERT: A  343 LYS cc_start: 0.8187 (tttt) cc_final: 0.7634 (mmtt)
REVERT: A  347 LYS cc_start: 0.7099 (mttp) cc_final: 0.6481 (mtpt)
REVERT: A  360 ILE cc_start: 0.9018 (mt) cc_final: 0.8725 (mp)
REVERT: A  369 LYS cc_start: 0.8676 (mttt) cc_final: 0.8440 (mttt)
REVERT: B  321 LYS cc_start: 0.8259 (tttt) cc_final: 0.7396 (ttpt)
REVERT: B  342 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.6613 (mp0)
REVERT: B  343 LYS cc_start: 0.8468 (tttt) cc_final: 0.7837 (mmtt)
REVERT: B  347 LYS cc_start: 0.7182 (mttp) cc_final: 0.5685 (mtmt)
REVERT: B  360 ILE cc_start: 0.9045 (mt) cc_final: 0.8748 (mp)
REVERT: B  369 LYS cc_start: 0.8601 (mttt) cc_final: 0.7866 (mttp)
REVERT: C  321 LYS cc_start: 0.7890 (tttt) cc_final: 0.7360 (mttp)
REVERT: C  327 ASN cc_start: 0.7872 (m-40) cc_final: 0.7486 (t0)
REVERT: C  338 GLU cc_start: 0.9094 (tt0) cc_final: 0.8706 (tt0)
REVERT: C  342 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8251 (mm-30)
REVERT: C  343 LYS cc_start: 0.8113 (tttt) cc_final: 0.7256 (mmtt)
REVERT: C  349 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7449 (mtm180)
REVERT: C  356 SER cc_start: 0.9144 (p) cc_final: 0.8340 (m)
REVERT: D  311 LYS cc_start: 0.8541 (pttp) cc_final: 0.7391 (tttt)
REVERT: D  321 LYS cc_start: 0.7905 (tttt) cc_final: 0.7269 (tttm)
REVERT: D  327 ASN cc_start: 0.8099 (m-40) cc_final: 0.7567 (t0)
REVERT: D  342 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7412 (mm-30)
REVERT: D  343 LYS cc_start: 0.8022 (tttt) cc_final: 0.7265 (mmtt)
REVERT: D  356 SER cc_start: 0.9170 (p) cc_final: 0.8473 (m)
REVERT: D  370 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8818 (tttp)
REVERT: E  321 LYS cc_start: 0.7738 (tttt) cc_final: 0.7083 (ttpt)
REVERT: E  342 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7985 (mm-30)
REVERT: E  360 ILE cc_start: 0.9112 (mt) cc_final: 0.8820 (mp)
REVERT: E  369 LYS cc_start: 0.8721 (mttt) cc_final: 0.7912 (mttp)
REVERT: F  321 LYS cc_start: 0.8048 (tttt) cc_final: 0.7383 (mttp)
REVERT: F  343 LYS cc_start: 0.8050 (tttt) cc_final: 0.7049 (mmtt)
REVERT: F  360 ILE cc_start: 0.9163 (mt) cc_final: 0.8957 (mp)
REVERT: G  321 LYS cc_start: 0.7949 (tttt) cc_final: 0.7335 (mttp)
REVERT: G  342 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8357 (mm-30)
REVERT: G  343 LYS cc_start: 0.7866 (tttt) cc_final: 0.7379 (mmtt)
REVERT: G  360 ILE cc_start: 0.9058 (mt) cc_final: 0.8809 (mp)
REVERT: H  321 LYS cc_start: 0.7864 (tttt) cc_final: 0.7284 (mttp)
REVERT: H  342 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7478 (mm-30)
REVERT: H  358 ASP cc_start: 0.8657 (m-30) cc_final: 0.8269 (m-30)
REVERT: H  369 LYS cc_start: 0.8744 (mttt) cc_final: 0.8499 (mttt)
REVERT: I  321 LYS cc_start: 0.7819 (tttt) cc_final: 0.7325 (mttp)
REVERT: I  343 LYS cc_start: 0.7837 (tttt) cc_final: 0.7134 (mptp)
REVERT: I  345 ASP cc_start: 0.7406 (t0) cc_final: 0.6775 (t0)
REVERT: I  349 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7519 (mtm180)
REVERT: I  360 ILE cc_start: 0.9205 (mt) cc_final: 0.8955 (mp)
REVERT: I  369 LYS cc_start: 0.8754 (mttt) cc_final: 0.7964 (mttp)
REVERT: J  317 LYS cc_start: 0.8218 (tttt) cc_final: 0.7827 (ttmm)
REVERT: J  321 LYS cc_start: 0.7981 (tttt) cc_final: 0.7621 (mttp)
REVERT: J  343 LYS cc_start: 0.7942 (tttt) cc_final: 0.7354 (mmtt)
REVERT: J  345 ASP cc_start: 0.7252 (t0) cc_final: 0.6641 (t0)
REVERT: J  356 SER cc_start: 0.9024 (p) cc_final: 0.8665 (p)
REVERT: J  357 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8563 (tp)
REVERT: J  358 ASP cc_start: 0.8420 (m-30) cc_final: 0.7758 (m-30)
REVERT: J  360 ILE cc_start: 0.9169 (mt) cc_final: 0.8909 (mp)
  outliers start: 19
  outliers final: 5
  residues processed: 217
  average time/residue: 1.3262
  time to fit residues: 298.3287
Evaluate side-chains
  216 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 204
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  357 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 67 optimal weight:    7.9990
   chunk 42 optimal weight:    0.3980
   chunk 41 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    4.6788

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

Flipped N/Q/H residues before XYZ refinement:
E 327 ASN
F 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   5660  Z= 0.478
  Angle     :  0.698   7.007   7580  Z= 0.355
  Chirality :  0.049   0.123    860
  Planarity :  0.004   0.050    960
  Dihedral  :  5.421  18.556    740
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.44 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 374 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.011   0.002   TYR C 310 
 ARG   0.002   0.000   ARG I 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 221
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8123 (tttt) cc_final: 0.7465 (ttpt)
REVERT: A  342 GLU cc_start: 0.8394 (mt-10) cc_final: 0.6804 (pm20)
REVERT: A  343 LYS cc_start: 0.8258 (tttt) cc_final: 0.7699 (mmtt)
REVERT: A  347 LYS cc_start: 0.7270 (mttp) cc_final: 0.6498 (mtpt)
REVERT: A  360 ILE cc_start: 0.9088 (mt) cc_final: 0.8807 (mp)
REVERT: A  369 LYS cc_start: 0.8757 (mttt) cc_final: 0.8509 (mttt)
REVERT: B  321 LYS cc_start: 0.8213 (tttt) cc_final: 0.7304 (ttpt)
REVERT: B  342 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.6684 (mp0)
REVERT: B  343 LYS cc_start: 0.8395 (tttt) cc_final: 0.7880 (mmtt)
REVERT: B  347 LYS cc_start: 0.7159 (mttp) cc_final: 0.5756 (mtmt)
REVERT: B  360 ILE cc_start: 0.9083 (mt) cc_final: 0.8758 (mp)
REVERT: B  369 LYS cc_start: 0.8650 (mttt) cc_final: 0.7910 (mttp)
REVERT: C  321 LYS cc_start: 0.7907 (tttt) cc_final: 0.7355 (mttm)
REVERT: C  327 ASN cc_start: 0.8062 (m-40) cc_final: 0.7744 (t0)
REVERT: C  338 GLU cc_start: 0.9086 (tt0) cc_final: 0.8885 (tt0)
REVERT: C  343 LYS cc_start: 0.8130 (tttt) cc_final: 0.7271 (mmtt)
REVERT: C  349 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7367 (mtm180)
REVERT: D  321 LYS cc_start: 0.7875 (tttt) cc_final: 0.7192 (ttpt)
REVERT: D  327 ASN cc_start: 0.8273 (m-40) cc_final: 0.7781 (t0)
REVERT: D  342 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7305 (mm-30)
REVERT: D  343 LYS cc_start: 0.7995 (tttt) cc_final: 0.7269 (mmtt)
REVERT: D  349 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7229 (mtm180)
REVERT: D  356 SER cc_start: 0.9161 (p) cc_final: 0.8481 (m)
REVERT: D  370 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8869 (tttp)
REVERT: E  311 LYS cc_start: 0.8174 (mttt) cc_final: 0.7221 (pttt)
REVERT: E  321 LYS cc_start: 0.7811 (tttt) cc_final: 0.7108 (ttpt)
REVERT: E  342 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7852 (mm-30)
REVERT: E  343 LYS cc_start: 0.8123 (tttt) cc_final: 0.7223 (mmtt)
REVERT: E  347 LYS cc_start: 0.6790 (mttp) cc_final: 0.6222 (mmtp)
REVERT: E  356 SER cc_start: 0.9146 (p) cc_final: 0.8289 (m)
REVERT: E  360 ILE cc_start: 0.9129 (mt) cc_final: 0.8840 (mp)
REVERT: E  369 LYS cc_start: 0.8761 (mttt) cc_final: 0.7895 (mttp)
REVERT: F  321 LYS cc_start: 0.8089 (tttt) cc_final: 0.7213 (tmtt)
REVERT: F  343 LYS cc_start: 0.8091 (tttt) cc_final: 0.7095 (mmtt)
REVERT: F  356 SER cc_start: 0.9124 (p) cc_final: 0.8524 (m)
REVERT: G  321 LYS cc_start: 0.7982 (tttt) cc_final: 0.7368 (mttp)
REVERT: G  342 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7549 (mm-30)
REVERT: G  343 LYS cc_start: 0.7883 (tttt) cc_final: 0.7268 (mmtt)
REVERT: G  360 ILE cc_start: 0.9071 (mt) cc_final: 0.8844 (mp)
REVERT: H  321 LYS cc_start: 0.7995 (tttt) cc_final: 0.7328 (mttp)
REVERT: H  342 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7695 (mm-30)
REVERT: H  358 ASP cc_start: 0.8627 (m-30) cc_final: 0.8361 (m-30)
REVERT: H  369 LYS cc_start: 0.8795 (mttt) cc_final: 0.7374 (mptt)
REVERT: I  321 LYS cc_start: 0.7831 (tttt) cc_final: 0.7320 (mttm)
REVERT: I  342 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7036 (mt-10)
REVERT: I  343 LYS cc_start: 0.7903 (tttt) cc_final: 0.7144 (mptp)
REVERT: I  345 ASP cc_start: 0.7479 (t0) cc_final: 0.6866 (t0)
REVERT: I  349 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7594 (mtm180)
REVERT: I  360 ILE cc_start: 0.9272 (mt) cc_final: 0.8972 (mp)
REVERT: I  369 LYS cc_start: 0.8759 (mttt) cc_final: 0.7998 (mttp)
REVERT: J  317 LYS cc_start: 0.8218 (tttt) cc_final: 0.7809 (ttmm)
REVERT: J  321 LYS cc_start: 0.8008 (tttt) cc_final: 0.7571 (mttp)
REVERT: J  343 LYS cc_start: 0.7961 (tttt) cc_final: 0.7340 (mmtt)
REVERT: J  358 ASP cc_start: 0.8590 (m-30) cc_final: 0.8151 (m-30)
  outliers start: 25
  outliers final: 9
  residues processed: 231
  average time/residue: 1.4262
  time to fit residues: 340.9073
Evaluate side-chains
  239 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 223
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  357 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain H residue  370 LYS
Chi-restraints excluded: chain I residue  370 LYS
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 362 HIS
E 327 ASN
F 327 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5660  Z= 0.263
  Angle     :  0.605   5.616   7580  Z= 0.312
  Chirality :  0.049   0.120    860
  Planarity :  0.004   0.048    960
  Dihedral  :  5.179  16.665    740
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 18.75 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 374 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.001   0.000   ARG I 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 213
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8189 (tttt) cc_final: 0.7497 (tmtt)
REVERT: A  342 GLU cc_start: 0.8308 (mt-10) cc_final: 0.6580 (pm20)
REVERT: A  343 LYS cc_start: 0.8281 (tttt) cc_final: 0.7689 (mmtt)
REVERT: A  347 LYS cc_start: 0.7059 (mttp) cc_final: 0.6393 (mtpt)
REVERT: A  360 ILE cc_start: 0.9056 (mt) cc_final: 0.8765 (mp)
REVERT: A  369 LYS cc_start: 0.8736 (mttt) cc_final: 0.8482 (mttt)
REVERT: B  321 LYS cc_start: 0.8285 (tttt) cc_final: 0.7414 (ttpt)
REVERT: B  342 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.6638 (mp0)
REVERT: B  343 LYS cc_start: 0.8442 (tttt) cc_final: 0.7864 (mmtt)
REVERT: B  347 LYS cc_start: 0.7153 (mttp) cc_final: 0.5696 (mtmt)
REVERT: B  360 ILE cc_start: 0.9067 (mt) cc_final: 0.8756 (mp)
REVERT: B  369 LYS cc_start: 0.8639 (mttt) cc_final: 0.7908 (mttp)
REVERT: C  321 LYS cc_start: 0.7893 (tttt) cc_final: 0.7349 (mttp)
REVERT: C  327 ASN cc_start: 0.7985 (m-40) cc_final: 0.7564 (t0)
REVERT: C  343 LYS cc_start: 0.8142 (tttt) cc_final: 0.7268 (mmtt)
REVERT: C  349 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7441 (mtm180)
REVERT: C  351 GLN cc_start: 0.8082 (tt0) cc_final: 0.7798 (tt0)
REVERT: D  321 LYS cc_start: 0.7840 (tttt) cc_final: 0.7304 (tttm)
REVERT: D  327 ASN cc_start: 0.8175 (m-40) cc_final: 0.7683 (t0)
REVERT: D  342 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7384 (mm-30)
REVERT: D  343 LYS cc_start: 0.8062 (tttt) cc_final: 0.7249 (mmtt)
REVERT: D  349 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7267 (mtm180)
REVERT: D  356 SER cc_start: 0.9166 (p) cc_final: 0.8505 (m)
REVERT: D  370 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8831 (tttp)
REVERT: E  321 LYS cc_start: 0.7790 (tttt) cc_final: 0.7094 (ttpt)
REVERT: E  342 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8019 (mm-30)
REVERT: E  356 SER cc_start: 0.8986 (p) cc_final: 0.8263 (m)
REVERT: E  360 ILE cc_start: 0.9127 (mt) cc_final: 0.8835 (mp)
REVERT: E  369 LYS cc_start: 0.8748 (mttt) cc_final: 0.7921 (mttp)
REVERT: F  321 LYS cc_start: 0.8075 (tttt) cc_final: 0.7412 (mttp)
REVERT: F  343 LYS cc_start: 0.8051 (tttt) cc_final: 0.7086 (mmtt)
REVERT: F  356 SER cc_start: 0.9020 (p) cc_final: 0.8500 (m)
REVERT: G  321 LYS cc_start: 0.7980 (tttt) cc_final: 0.7370 (mttp)
REVERT: G  342 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7633 (mm-30)
REVERT: G  343 LYS cc_start: 0.7870 (tttt) cc_final: 0.7383 (mmtt)
REVERT: G  360 ILE cc_start: 0.9055 (mt) cc_final: 0.8810 (mp)
REVERT: H  321 LYS cc_start: 0.7909 (tttt) cc_final: 0.7262 (mttp)
REVERT: H  342 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7493 (mm-30)
REVERT: H  358 ASP cc_start: 0.8614 (m-30) cc_final: 0.8331 (m-30)
REVERT: H  369 LYS cc_start: 0.8761 (mttt) cc_final: 0.7345 (mptt)
REVERT: I  321 LYS cc_start: 0.7825 (tttt) cc_final: 0.7324 (mttm)
REVERT: I  343 LYS cc_start: 0.7987 (tttt) cc_final: 0.7268 (mptp)
REVERT: I  345 ASP cc_start: 0.7418 (t0) cc_final: 0.6805 (t0)
REVERT: I  349 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7533 (mtm180)
REVERT: I  360 ILE cc_start: 0.9253 (mt) cc_final: 0.8993 (mp)
REVERT: I  369 LYS cc_start: 0.8757 (mttt) cc_final: 0.7970 (mttp)
REVERT: J  317 LYS cc_start: 0.8244 (tttt) cc_final: 0.7844 (ttmm)
REVERT: J  321 LYS cc_start: 0.7979 (tttt) cc_final: 0.7557 (mttp)
REVERT: J  343 LYS cc_start: 0.7983 (tttt) cc_final: 0.7385 (mmtt)
REVERT: J  345 ASP cc_start: 0.7332 (t0) cc_final: 0.6708 (t0)
REVERT: J  356 SER cc_start: 0.9053 (p) cc_final: 0.8676 (p)
REVERT: J  358 ASP cc_start: 0.8507 (m-30) cc_final: 0.7835 (m-30)
  outliers start: 22
  outliers final: 9
  residues processed: 218
  average time/residue: 1.3900
  time to fit residues: 313.8004
Evaluate side-chains
  226 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 210
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  357 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain H residue  370 LYS
Chi-restraints excluded: chain I residue  317 LYS
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 40 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    2.7524

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5660  Z= 0.299
  Angle     :  0.618   5.855   7580  Z= 0.316
  Chirality :  0.049   0.119    860
  Planarity :  0.004   0.049    960
  Dihedral  :  5.184  16.615    740
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.38 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 362 
 PHE   0.008   0.001   PHE G 378 
 TYR   0.010   0.002   TYR C 310 
 ARG   0.001   0.000   ARG I 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 210
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8216 (tttt) cc_final: 0.7516 (ttpt)
REVERT: A  342 GLU cc_start: 0.8217 (mt-10) cc_final: 0.6575 (pm20)
REVERT: A  343 LYS cc_start: 0.8280 (tttt) cc_final: 0.7740 (mmtt)
REVERT: A  347 LYS cc_start: 0.7038 (mttp) cc_final: 0.6379 (mtpt)
REVERT: A  360 ILE cc_start: 0.9063 (mt) cc_final: 0.8777 (mp)
REVERT: A  369 LYS cc_start: 0.8706 (mttt) cc_final: 0.8457 (mttt)
REVERT: B  321 LYS cc_start: 0.8299 (tttt) cc_final: 0.7424 (ttpt)
REVERT: B  342 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6625 (mp0)
REVERT: B  343 LYS cc_start: 0.8440 (tttt) cc_final: 0.7864 (mmtt)
REVERT: B  347 LYS cc_start: 0.7177 (mttp) cc_final: 0.5739 (mtmt)
REVERT: B  360 ILE cc_start: 0.9068 (mt) cc_final: 0.8732 (mp)
REVERT: B  369 LYS cc_start: 0.8637 (mttt) cc_final: 0.7905 (mttp)
REVERT: C  321 LYS cc_start: 0.7904 (tttt) cc_final: 0.7343 (mttp)
REVERT: C  327 ASN cc_start: 0.8001 (m-40) cc_final: 0.7562 (t0)
REVERT: C  342 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8257 (mm-30)
REVERT: C  343 LYS cc_start: 0.8149 (tttt) cc_final: 0.7273 (mmtt)
REVERT: C  349 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7443 (mtm180)
REVERT: D  321 LYS cc_start: 0.7875 (tttt) cc_final: 0.7336 (tttm)
REVERT: D  327 ASN cc_start: 0.8201 (m-40) cc_final: 0.7645 (t0)
REVERT: D  342 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7281 (mm-30)
REVERT: D  343 LYS cc_start: 0.8076 (tttt) cc_final: 0.7245 (mmtt)
REVERT: D  349 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7294 (mtm180)
REVERT: D  356 SER cc_start: 0.9123 (p) cc_final: 0.8457 (m)
REVERT: D  370 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8777 (tttp)
REVERT: E  321 LYS cc_start: 0.7794 (tttt) cc_final: 0.7116 (ttpt)
REVERT: E  342 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8019 (mm-30)
REVERT: E  356 SER cc_start: 0.9133 (p) cc_final: 0.8278 (m)
REVERT: E  360 ILE cc_start: 0.9117 (mt) cc_final: 0.8819 (mp)
REVERT: E  369 LYS cc_start: 0.8753 (mttt) cc_final: 0.7923 (mttp)
REVERT: F  321 LYS cc_start: 0.8079 (tttt) cc_final: 0.7410 (mttp)
REVERT: F  343 LYS cc_start: 0.8064 (tttt) cc_final: 0.7104 (mmtt)
REVERT: F  356 SER cc_start: 0.9005 (p) cc_final: 0.8514 (m)
REVERT: F  369 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8115 (mttp)
REVERT: G  321 LYS cc_start: 0.7981 (tttt) cc_final: 0.7374 (mttp)
REVERT: G  342 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7449 (mm-30)
REVERT: G  343 LYS cc_start: 0.7883 (tttt) cc_final: 0.7396 (mmtt)
REVERT: G  360 ILE cc_start: 0.9074 (mt) cc_final: 0.8839 (mp)
REVERT: H  321 LYS cc_start: 0.7908 (tttt) cc_final: 0.7311 (mttp)
REVERT: H  342 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7437 (mm-30)
REVERT: H  358 ASP cc_start: 0.8614 (m-30) cc_final: 0.8341 (m-30)
REVERT: H  369 LYS cc_start: 0.8745 (mttt) cc_final: 0.7355 (mptt)
REVERT: I  321 LYS cc_start: 0.7831 (tttt) cc_final: 0.7323 (mttm)
REVERT: I  342 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6598 (mt-10)
REVERT: I  343 LYS cc_start: 0.7988 (tttt) cc_final: 0.7267 (mptp)
REVERT: I  345 ASP cc_start: 0.7428 (t0) cc_final: 0.6817 (t0)
REVERT: I  349 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7565 (mtm180)
REVERT: I  360 ILE cc_start: 0.9228 (mt) cc_final: 0.8978 (mp)
REVERT: I  369 LYS cc_start: 0.8757 (mttt) cc_final: 0.7971 (mttp)
REVERT: J  317 LYS cc_start: 0.8255 (tttt) cc_final: 0.7860 (ttmm)
REVERT: J  321 LYS cc_start: 0.7981 (tttt) cc_final: 0.7568 (mttp)
REVERT: J  343 LYS cc_start: 0.7986 (tttt) cc_final: 0.7386 (mmtt)
REVERT: J  358 ASP cc_start: 0.8555 (m-30) cc_final: 0.8166 (m-30)
  outliers start: 23
  outliers final: 8
  residues processed: 217
  average time/residue: 1.3787
  time to fit residues: 309.7334
Evaluate side-chains
  228 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 211
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  357 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  369 LYS
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain H residue  370 LYS
Chi-restraints excluded: chain I residue  317 LYS
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 59 optimal weight:    0.3980
   chunk 17 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.6586

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5660  Z= 0.290
  Angle     :  0.606   5.482   7580  Z= 0.313
  Chirality :  0.049   0.120    860
  Planarity :  0.004   0.049    960
  Dihedral  :  5.195  16.600    740
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.22 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 362 
 PHE   0.008   0.001   PHE G 378 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.001   0.000   ARG I 349 

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

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 210
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8241 (tttt) cc_final: 0.7550 (ttpt)
REVERT: A  342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.6543 (pm20)
REVERT: A  343 LYS cc_start: 0.8299 (tttt) cc_final: 0.7735 (mmtt)
REVERT: A  347 LYS cc_start: 0.7031 (mttp) cc_final: 0.6379 (mtpt)
REVERT: A  360 ILE cc_start: 0.9061 (mt) cc_final: 0.8773 (mp)
REVERT: A  369 LYS cc_start: 0.8706 (mttt) cc_final: 0.8457 (mttt)
REVERT: B  321 LYS cc_start: 0.8298 (tttt) cc_final: 0.7425 (ttpt)
REVERT: B  342 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6619 (mp0)
REVERT: B  343 LYS cc_start: 0.8438 (tttt) cc_final: 0.7851 (mmtt)
REVERT: B  347 LYS cc_start: 0.7155 (mttp) cc_final: 0.5692 (mtmt)
REVERT: B  360 ILE cc_start: 0.9067 (mt) cc_final: 0.8731 (mp)
REVERT: B  369 LYS cc_start: 0.8638 (mttt) cc_final: 0.7906 (mttp)
REVERT: C  321 LYS cc_start: 0.7901 (tttt) cc_final: 0.7352 (mttp)
REVERT: C  327 ASN cc_start: 0.7999 (m-40) cc_final: 0.7570 (t0)
REVERT: C  342 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: C  343 LYS cc_start: 0.8142 (tttt) cc_final: 0.7286 (mmtt)
REVERT: C  349 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7425 (mtm180)
REVERT: D  311 LYS cc_start: 0.8556 (pttp) cc_final: 0.7384 (tttt)
REVERT: D  321 LYS cc_start: 0.7865 (tttt) cc_final: 0.7334 (tttm)
REVERT: D  327 ASN cc_start: 0.8207 (m-40) cc_final: 0.7659 (t0)
REVERT: D  342 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7253 (mm-30)
REVERT: D  343 LYS cc_start: 0.8072 (tttt) cc_final: 0.7240 (mmtt)
REVERT: D  349 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7265 (mtm180)
REVERT: D  356 SER cc_start: 0.9153 (p) cc_final: 0.8515 (m)
REVERT: D  370 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8789 (tttp)
REVERT: E  321 LYS cc_start: 0.7789 (tttt) cc_final: 0.7091 (ttpt)
REVERT: E  342 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8025 (mm-30)
REVERT: E  356 SER cc_start: 0.9119 (p) cc_final: 0.8274 (m)
REVERT: E  360 ILE cc_start: 0.9116 (mt) cc_final: 0.8823 (mp)
REVERT: E  369 LYS cc_start: 0.8755 (mttt) cc_final: 0.7925 (mttp)
REVERT: F  321 LYS cc_start: 0.8077 (tttt) cc_final: 0.7410 (mttp)
REVERT: F  343 LYS cc_start: 0.8054 (tttt) cc_final: 0.7097 (mmtt)
REVERT: F  356 SER cc_start: 0.8996 (p) cc_final: 0.8513 (m)
REVERT: F  369 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8115 (mttp)
REVERT: G  321 LYS cc_start: 0.7982 (tttt) cc_final: 0.7377 (mttp)
REVERT: G  342 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7466 (mm-30)
REVERT: G  343 LYS cc_start: 0.7877 (tttt) cc_final: 0.7393 (mmtt)
REVERT: G  360 ILE cc_start: 0.9073 (mt) cc_final: 0.8841 (mp)
REVERT: H  321 LYS cc_start: 0.7919 (tttt) cc_final: 0.7319 (mttp)
REVERT: H  342 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7454 (mm-30)
REVERT: H  349 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.6938 (mtm180)
REVERT: H  358 ASP cc_start: 0.8621 (m-30) cc_final: 0.8348 (m-30)
REVERT: H  369 LYS cc_start: 0.8745 (mttt) cc_final: 0.7354 (mptt)
REVERT: I  321 LYS cc_start: 0.7826 (tttt) cc_final: 0.7320 (mttm)
REVERT: I  342 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6497 (mt-10)
REVERT: I  343 LYS cc_start: 0.8010 (tttt) cc_final: 0.7272 (mptp)
REVERT: I  345 ASP cc_start: 0.7426 (t0) cc_final: 0.6813 (t0)
REVERT: I  349 ARG cc_start: 0.7965 (mtm180) cc_final: 0.7552 (mtm180)
REVERT: I  360 ILE cc_start: 0.9227 (mt) cc_final: 0.8977 (mp)
REVERT: I  369 LYS cc_start: 0.8759 (mttt) cc_final: 0.7972 (mttp)
REVERT: J  317 LYS cc_start: 0.8262 (tttt) cc_final: 0.7864 (ttmm)
REVERT: J  321 LYS cc_start: 0.7982 (tttt) cc_final: 0.7567 (mttp)
REVERT: J  343 LYS cc_start: 0.7972 (tttt) cc_final: 0.7379 (mmtt)
REVERT: J  345 ASP cc_start: 0.7353 (t0) cc_final: 0.6726 (t0)
REVERT: J  358 ASP cc_start: 0.8526 (m-30) cc_final: 0.8178 (m-30)
  outliers start: 19
  outliers final: 9
  residues processed: 216
  average time/residue: 1.3890
  time to fit residues: 310.5782
Evaluate side-chains
  227 residues out of total 640 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 209
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain C residue  370 LYS
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  349 ARG
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  370 LYS
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  357 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  369 LYS
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain H residue  370 LYS
Chi-restraints excluded: chain I residue  317 LYS
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain I residue  370 LYS
Chi-restraints excluded: chain J residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    3.7988

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.152626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.122615 restraints weight = 5539.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.76
r_work: 0.3395 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   5660  Z= 0.395
  Angle     :  0.666   6.682   7580  Z= 0.339
  Chirality :  0.049   0.129    860
  Planarity :  0.004   0.052    960
  Dihedral  :  5.370  17.748    740
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.69 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.21), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 362 
 PHE   0.010   0.001   PHE G 378 
 TYR   0.010   0.002   TYR C 310 
 ARG   0.002   0.000   ARG I 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4299.88 seconds
wall clock time: 77 minutes 37.91 seconds (4657.91 seconds total)