Starting phenix.real_space_refine
on Fri Aug 22 16:03:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9czi_46417/08_2025/9czi_46417_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9czi_46417/08_2025/9czi_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/cci-nas-00/data/ceres_data/9czi_46417/08_2025/9czi_46417.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9czi_46417/08_2025/9czi_46417.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9czi_46417/08_2025/9czi_46417_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9czi_46417/08_2025/9czi_46417_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.86, per 1000 atoms: 0.15
  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: 0.45
  Conformation dependent library (CDL) restraints added in 220.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.24
  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: 0.83

  Time building geometry restraints manager: 0.58 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: 0.02
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:             1.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.620
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.120
-------------------------------------------------------------------------------
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= 1.028
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.001   ARG F 349 
 TYR   0.016   0.007   TYR J 310 
 PHE   0.018   0.006   PHE I 346 
 HIS   0.006   0.003   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.02059 ( 5660)
  covalent geometry    : angle       1.91760 ( 7580)
  hydrogen bonds       : bond        0.10127 (  128)
  hydrogen bonds       : angle      10.68602 (  384)

*********************** 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 to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.242 
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: 0.7071
  time to fit residues: 190.5318
Evaluate side-chains
  211 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.158376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.128253 restraints weight = 5555.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 1.80
r_work: 0.3502 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5660  Z= 0.114
  Angle     :  0.579   5.194   7580  Z= 0.313
  Chirality :  0.050   0.151    860
  Planarity :  0.003   0.020    960
  Dihedral  :  4.862  15.707    740
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.81 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG I 349 
 TYR   0.010   0.002   TYR D 310 
 PHE   0.004   0.001   PHE H 346 
 HIS   0.004   0.001   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5660)
  covalent geometry    : angle       0.57920 ( 7580)
  hydrogen bonds       : bond        0.04203 (  128)
  hydrogen bonds       : angle       7.21231 (  384)

*********************** 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
  233 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 220
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8359 (tttt) cc_final: 0.8115 (tmtt)
REVERT: A  343 LYS cc_start: 0.8407 (tttt) cc_final: 0.8187 (mmtt)
REVERT: A  356 SER cc_start: 0.9137 (p) cc_final: 0.8573 (m)
REVERT: A  360 ILE cc_start: 0.9151 (mt) cc_final: 0.8902 (mp)
REVERT: B  321 LYS cc_start: 0.8297 (tttt) cc_final: 0.7928 (tmtt)
REVERT: B  342 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7367 (mp0)
REVERT: B  343 LYS cc_start: 0.8537 (tttt) cc_final: 0.8204 (mmtt)
REVERT: B  360 ILE cc_start: 0.9238 (mt) cc_final: 0.8953 (mp)
REVERT: B  369 LYS cc_start: 0.8864 (mttt) cc_final: 0.8249 (mttp)
REVERT: C  338 GLU cc_start: 0.9127 (tt0) cc_final: 0.8838 (tt0)
REVERT: C  343 LYS cc_start: 0.8321 (tttt) cc_final: 0.7908 (mmtt)
REVERT: D  321 LYS cc_start: 0.8302 (tttt) cc_final: 0.7993 (tttm)
REVERT: D  343 LYS cc_start: 0.8302 (tttt) cc_final: 0.7877 (mmtt)
REVERT: D  356 SER cc_start: 0.9348 (p) cc_final: 0.8690 (m)
REVERT: D  370 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9015 (tttp)
REVERT: E  321 LYS cc_start: 0.8228 (tttt) cc_final: 0.7915 (tttt)
REVERT: E  360 ILE cc_start: 0.9470 (mt) cc_final: 0.9237 (mp)
REVERT: E  369 LYS cc_start: 0.8831 (mttt) cc_final: 0.8285 (mttp)
REVERT: F  343 LYS cc_start: 0.8230 (tttt) cc_final: 0.7578 (mmtt)
REVERT: F  360 ILE cc_start: 0.9453 (mt) cc_final: 0.9227 (mp)
REVERT: F  369 LYS cc_start: 0.9158 (mppt) cc_final: 0.8573 (mttp)
REVERT: G  342 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7453 (mm-30)
REVERT: G  343 LYS cc_start: 0.8087 (tttt) cc_final: 0.7713 (mmtt)
REVERT: G  375 LYS cc_start: 0.8307 (tttt) cc_final: 0.8012 (ttpt)
REVERT: H  358 ASP cc_start: 0.9094 (m-30) cc_final: 0.8792 (m-30)
REVERT: H  369 LYS cc_start: 0.8985 (mttt) cc_final: 0.8768 (mttp)
REVERT: I  331 LYS cc_start: 0.9317 (mtpt) cc_final: 0.9086 (mtmt)
REVERT: I  345 ASP cc_start: 0.8187 (t0) cc_final: 0.7830 (t0)
REVERT: I  349 ARG cc_start: 0.8015 (mtm180) cc_final: 0.7673 (mtm180)
REVERT: I  356 SER cc_start: 0.9260 (p) cc_final: 0.8935 (p)
REVERT: I  360 ILE cc_start: 0.9482 (mt) cc_final: 0.9162 (mp)
REVERT: I  369 LYS cc_start: 0.8983 (mttt) cc_final: 0.8439 (mttp)
REVERT: I  370 LYS cc_start: 0.8976 (tttm) cc_final: 0.8687 (tmtm)
REVERT: J  360 ILE cc_start: 0.9494 (mt) cc_final: 0.9172 (mp)
REVERT: J  370 LYS cc_start: 0.9099 (tttm) cc_final: 0.8684 (tptt)
  outliers start: 13
  outliers final: 2
  residues processed: 225
  average time/residue: 0.6380
  time to fit residues: 148.7965
Evaluate side-chains
  208 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 203
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B 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 55 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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
H 336 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.156393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.126061 restraints weight = 5443.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 1.73
r_work: 0.3437 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   5660  Z= 0.226
  Angle     :  0.681   5.890   7580  Z= 0.349
  Chirality :  0.050   0.133    860
  Planarity :  0.004   0.032    960
  Dihedral  :  5.324  18.010    740
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 14.38 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 349 
 TYR   0.013   0.003   TYR D 310 
 PHE   0.008   0.002   PHE B 378 
 HIS   0.005   0.002   HIS I 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 5660)
  covalent geometry    : angle       0.68137 ( 7580)
  hydrogen bonds       : bond        0.04300 (  128)
  hydrogen bonds       : angle       6.97245 (  384)

*********************** 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
  266 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 237
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8377 (tttt) cc_final: 0.8061 (tmtt)
REVERT: A  347 LYS cc_start: 0.7644 (mttp) cc_final: 0.6867 (mppt)
REVERT: B  321 LYS cc_start: 0.8384 (tttt) cc_final: 0.7992 (tttt)
REVERT: B  342 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7316 (mp0)
REVERT: B  343 LYS cc_start: 0.8595 (tttt) cc_final: 0.8268 (mmtt)
REVERT: B  347 LYS cc_start: 0.7431 (mttp) cc_final: 0.6533 (mtmt)
REVERT: B  360 ILE cc_start: 0.9356 (mt) cc_final: 0.9075 (mp)
REVERT: B  369 LYS cc_start: 0.8906 (mttt) cc_final: 0.8414 (mttp)
REVERT: C  327 ASN cc_start: 0.8453 (m-40) cc_final: 0.8178 (t0)
REVERT: C  343 LYS cc_start: 0.8294 (tttt) cc_final: 0.7874 (mmtt)
REVERT: C  349 ARG cc_start: 0.8342 (mtm180) cc_final: 0.8024 (mtp-110)
REVERT: D  321 LYS cc_start: 0.8136 (tttt) cc_final: 0.7823 (ttpt)
REVERT: D  327 ASN cc_start: 0.8482 (m-40) cc_final: 0.8170 (t0)
REVERT: D  342 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7731 (mm-30)
REVERT: D  343 LYS cc_start: 0.8296 (tttt) cc_final: 0.7927 (mptt)
REVERT: D  349 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7757 (mtm180)
REVERT: D  356 SER cc_start: 0.9384 (p) cc_final: 0.8732 (m)
REVERT: D  370 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9072 (tttp)
REVERT: E  311 LYS cc_start: 0.8339 (mttt) cc_final: 0.7642 (pttt)
REVERT: E  321 LYS cc_start: 0.8209 (tttt) cc_final: 0.7890 (ttpt)
REVERT: E  342 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8072 (mt-10)
REVERT: E  343 LYS cc_start: 0.8285 (tttt) cc_final: 0.7742 (mmtt)
REVERT: E  356 SER cc_start: 0.9297 (p) cc_final: 0.8690 (m)
REVERT: E  369 LYS cc_start: 0.8982 (mttt) cc_final: 0.8280 (mttp)
REVERT: F  342 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8347 (mm-30)
REVERT: F  343 LYS cc_start: 0.8348 (tttt) cc_final: 0.7593 (mmtt)
REVERT: F  369 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8545 (mttp)
REVERT: G  343 LYS cc_start: 0.8118 (tttt) cc_final: 0.7719 (mmtt)
REVERT: G  372 GLU cc_start: 0.8618 (tt0) cc_final: 0.8396 (tp30)
REVERT: H  342 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7943 (mm-30)
REVERT: H  358 ASP cc_start: 0.9060 (m-30) cc_final: 0.8789 (m-30)
REVERT: I  331 LYS cc_start: 0.9330 (mtpt) cc_final: 0.9122 (mtmt)
REVERT: I  345 ASP cc_start: 0.8079 (t0) cc_final: 0.7729 (t0)
REVERT: I  349 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7811 (mtm180)
REVERT: I  369 LYS cc_start: 0.9072 (mttt) cc_final: 0.8448 (mttp)
REVERT: I  370 LYS cc_start: 0.9183 (tttm) cc_final: 0.8809 (tmtm)
REVERT: J  317 LYS cc_start: 0.8551 (tttt) cc_final: 0.8287 (ttmm)
REVERT: J  358 ASP cc_start: 0.8864 (m-30) cc_final: 0.8572 (m-30)
  outliers start: 29
  outliers final: 7
  residues processed: 242
  average time/residue: 0.6813
  time to fit residues: 170.6182
Evaluate side-chains
  236 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 223
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
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  321 LYS
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  317 LYS
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 9 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   overall best weight:    5.3990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.151459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.121566 restraints weight = 5523.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.75
r_work: 0.3378 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049   5660  Z= 0.337
  Angle     :  0.773   7.155   7580  Z= 0.391
  Chirality :  0.051   0.126    860
  Planarity :  0.005   0.047    960
  Dihedral  :  5.662  20.930    740
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 15.16 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.04 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 349 
 TYR   0.015   0.003   TYR H 310 
 PHE   0.010   0.002   PHE G 378 
 HIS   0.005   0.002   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00814 ( 5660)
  covalent geometry    : angle       0.77282 ( 7580)
  hydrogen bonds       : bond        0.04764 (  128)
  hydrogen bonds       : angle       6.94005 (  384)

*********************** 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
  261 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 221
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8352 (tttt) cc_final: 0.8077 (tmtt)
REVERT: A  342 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7559 (pm20)
REVERT: A  347 LYS cc_start: 0.7771 (mttp) cc_final: 0.7334 (mtpt)
REVERT: B  342 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7279 (mp0)
REVERT: B  343 LYS cc_start: 0.8550 (tttt) cc_final: 0.8246 (mmtt)
REVERT: B  347 LYS cc_start: 0.7687 (mttp) cc_final: 0.6601 (mtmt)
REVERT: B  360 ILE cc_start: 0.9376 (mt) cc_final: 0.9108 (mp)
REVERT: B  369 LYS cc_start: 0.9004 (mttt) cc_final: 0.8460 (mttp)
REVERT: C  327 ASN cc_start: 0.8560 (m-40) cc_final: 0.8225 (t0)
REVERT: C  343 LYS cc_start: 0.8404 (tttt) cc_final: 0.7987 (mmtt)
REVERT: C  349 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8262 (mtm180)
REVERT: D  321 LYS cc_start: 0.8202 (tttt) cc_final: 0.7849 (ttpt)
REVERT: D  327 ASN cc_start: 0.8598 (m-40) cc_final: 0.8283 (t0)
REVERT: D  342 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7724 (mm-30)
REVERT: D  343 LYS cc_start: 0.8322 (tttt) cc_final: 0.7912 (mptt)
REVERT: D  349 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7835 (mtm180)
REVERT: D  356 SER cc_start: 0.9340 (p) cc_final: 0.8679 (m)
REVERT: D  370 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9125 (tttp)
REVERT: E  311 LYS cc_start: 0.8341 (mttt) cc_final: 0.7562 (pttt)
REVERT: E  321 LYS cc_start: 0.8271 (tttt) cc_final: 0.7897 (ttpt)
REVERT: E  342 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8129 (mt-10)
REVERT: E  343 LYS cc_start: 0.8298 (tttt) cc_final: 0.7741 (mmtt)
REVERT: E  347 LYS cc_start: 0.7587 (mttp) cc_final: 0.7122 (mmtp)
REVERT: E  356 SER cc_start: 0.9333 (p) cc_final: 0.8724 (m)
REVERT: E  369 LYS cc_start: 0.9085 (mttt) cc_final: 0.8436 (mttp)
REVERT: F  343 LYS cc_start: 0.8390 (tttt) cc_final: 0.7647 (mmtt)
REVERT: F  358 ASP cc_start: 0.9140 (m-30) cc_final: 0.8852 (m-30)
REVERT: F  369 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8603 (mttp)
REVERT: G  321 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8504 (mttp)
REVERT: G  342 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7795 (mm-30)
REVERT: G  343 LYS cc_start: 0.8104 (tttt) cc_final: 0.7732 (mmtt)
REVERT: H  342 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8028 (mm-30)
REVERT: H  358 ASP cc_start: 0.9035 (m-30) cc_final: 0.8749 (m-30)
REVERT: I  342 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7403 (mt-10)
REVERT: I  345 ASP cc_start: 0.8027 (t0) cc_final: 0.7592 (t0)
REVERT: I  349 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8028 (mtm180)
REVERT: I  369 LYS cc_start: 0.9060 (mttt) cc_final: 0.8413 (mttp)
REVERT: J  317 LYS cc_start: 0.8521 (tttt) cc_final: 0.8281 (ttmm)
REVERT: J  345 ASP cc_start: 0.7857 (t0) cc_final: 0.7368 (t0)
  outliers start: 40
  outliers final: 17
  residues processed: 233
  average time/residue: 0.7054
  time to fit residues: 169.8632
Evaluate side-chains
  248 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 221
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  357 LEU
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  321 LYS
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  321 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  317 LYS
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  340 LYS
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain J residue  357 LEU
Chi-restraints excluded: chain J residue  373 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 62 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.156896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.126965 restraints weight = 5596.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 1.78
r_work: 0.3463 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.3631

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= 0.126
  Angle     :  0.584   5.144   7580  Z= 0.302
  Chirality :  0.049   0.122    860
  Planarity :  0.004   0.039    960
  Dihedral  :  5.006  16.573    740
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 19.06 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.02 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 349 
 TYR   0.013   0.002   TYR H 310 
 PHE   0.006   0.001   PHE G 378 
 HIS   0.002   0.001   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5660)
  covalent geometry    : angle       0.58358 ( 7580)
  hydrogen bonds       : bond        0.03525 (  128)
  hydrogen bonds       : angle       6.59780 (  384)

*********************** 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
  232 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 206
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8445 (tttt) cc_final: 0.8103 (tmtt)
REVERT: A  342 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7567 (pm20)
REVERT: A  347 LYS cc_start: 0.7709 (mttp) cc_final: 0.6791 (mppt)
REVERT: B  321 LYS cc_start: 0.8858 (mttp) cc_final: 0.7967 (ttpt)
REVERT: B  342 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7171 (mp0)
REVERT: B  343 LYS cc_start: 0.8578 (tttt) cc_final: 0.8187 (mmtt)
REVERT: B  347 LYS cc_start: 0.7728 (mttp) cc_final: 0.6565 (mtmt)
REVERT: B  360 ILE cc_start: 0.9323 (mt) cc_final: 0.9079 (mp)
REVERT: B  369 LYS cc_start: 0.8979 (mttt) cc_final: 0.8413 (mttp)
REVERT: C  327 ASN cc_start: 0.8228 (m-40) cc_final: 0.8023 (t0)
REVERT: C  338 GLU cc_start: 0.9169 (tt0) cc_final: 0.8861 (tt0)
REVERT: C  343 LYS cc_start: 0.8349 (tttt) cc_final: 0.7827 (mmtt)
REVERT: C  349 ARG cc_start: 0.8413 (mtm180) cc_final: 0.8155 (mtm180)
REVERT: D  321 LYS cc_start: 0.8235 (tttt) cc_final: 0.7946 (tttm)
REVERT: D  327 ASN cc_start: 0.8344 (m-40) cc_final: 0.8050 (t0)
REVERT: D  342 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7850 (mm-30)
REVERT: D  343 LYS cc_start: 0.8313 (tttt) cc_final: 0.7768 (mmtt)
REVERT: D  356 SER cc_start: 0.9317 (p) cc_final: 0.8739 (m)
REVERT: E  321 LYS cc_start: 0.8171 (tttt) cc_final: 0.7874 (ttpt)
REVERT: E  342 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8317 (mm-30)
REVERT: E  356 SER cc_start: 0.9234 (p) cc_final: 0.8696 (m)
REVERT: E  369 LYS cc_start: 0.9069 (mttt) cc_final: 0.8490 (mttp)
REVERT: F  343 LYS cc_start: 0.8303 (tttt) cc_final: 0.7564 (mmtt)
REVERT: F  356 SER cc_start: 0.9278 (p) cc_final: 0.8709 (m)
REVERT: G  321 LYS cc_start: 0.8806 (mttp) cc_final: 0.8497 (mttp)
REVERT: G  343 LYS cc_start: 0.8054 (tttt) cc_final: 0.7775 (mmtt)
REVERT: G  349 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7791 (ttp-170)
REVERT: H  358 ASP cc_start: 0.8998 (m-30) cc_final: 0.8746 (m-30)
REVERT: I  342 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7909 (mt-10)
REVERT: I  345 ASP cc_start: 0.7979 (t0) cc_final: 0.7566 (t0)
REVERT: I  349 ARG cc_start: 0.8271 (mtm180) cc_final: 0.7990 (mtm180)
REVERT: I  369 LYS cc_start: 0.9044 (mttt) cc_final: 0.8392 (mttp)
REVERT: J  317 LYS cc_start: 0.8496 (tttt) cc_final: 0.8256 (ttmm)
REVERT: J  345 ASP cc_start: 0.7844 (t0) cc_final: 0.7399 (t0)
REVERT: J  360 ILE cc_start: 0.9465 (mt) cc_final: 0.9235 (mp)
  outliers start: 26
  outliers final: 8
  residues processed: 213
  average time/residue: 0.6946
  time to fit residues: 153.0032
Evaluate side-chains
  214 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 203
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  357 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 H residue  370 LYS
Chi-restraints excluded: chain I residue  317 LYS
Chi-restraints excluded: chain I residue  357 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0270
   chunk 9 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 58 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 69 optimal weight:    0.1980
   overall best weight:    0.8042

-------------------------------------------------------------------------------
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
F 374 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.161014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.131222 restraints weight = 5537.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.77
r_work: 0.3531 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   5660  Z= 0.086
  Angle     :  0.519   6.507   7580  Z= 0.269
  Chirality :  0.048   0.123    860
  Planarity :  0.003   0.031    960
  Dihedral  :  4.651  14.584    740
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 349 
 TYR   0.013   0.002   TYR H 310 
 PHE   0.006   0.001   PHE G 378 
 HIS   0.002   0.000   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 5660)
  covalent geometry    : angle       0.51912 ( 7580)
  hydrogen bonds       : bond        0.02893 (  128)
  hydrogen bonds       : angle       6.30629 (  384)

*********************** 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
  217 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8380 (tttt) cc_final: 0.8067 (tmtt)
REVERT: A  342 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7342 (pm20)
REVERT: A  347 LYS cc_start: 0.7703 (mttp) cc_final: 0.6781 (mppt)
REVERT: A  369 LYS cc_start: 0.8980 (mttt) cc_final: 0.8730 (mttt)
REVERT: B  321 LYS cc_start: 0.8858 (mttp) cc_final: 0.7960 (ttpt)
REVERT: B  342 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7038 (mp0)
REVERT: B  343 LYS cc_start: 0.8524 (tttt) cc_final: 0.8144 (mmtt)
REVERT: B  347 LYS cc_start: 0.7715 (mttp) cc_final: 0.6511 (mtmt)
REVERT: B  360 ILE cc_start: 0.9289 (mt) cc_final: 0.9058 (mp)
REVERT: B  369 LYS cc_start: 0.8921 (mttt) cc_final: 0.8364 (mttp)
REVERT: C  338 GLU cc_start: 0.9105 (tt0) cc_final: 0.8829 (tt0)
REVERT: C  343 LYS cc_start: 0.8320 (tttt) cc_final: 0.7891 (mmtt)
REVERT: C  349 ARG cc_start: 0.8313 (mtm180) cc_final: 0.7896 (mtp-110)
REVERT: C  356 SER cc_start: 0.9323 (p) cc_final: 0.8813 (m)
REVERT: D  311 LYS cc_start: 0.8609 (pttp) cc_final: 0.7646 (tttt)
REVERT: D  321 LYS cc_start: 0.8298 (tttt) cc_final: 0.8020 (tttm)
REVERT: D  342 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7826 (mm-30)
REVERT: D  343 LYS cc_start: 0.8227 (tttt) cc_final: 0.7713 (mmtt)
REVERT: D  349 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7965 (mtm180)
REVERT: D  356 SER cc_start: 0.9292 (p) cc_final: 0.8728 (m)
REVERT: E  342 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8242 (mm-30)
REVERT: E  343 LYS cc_start: 0.8199 (tttt) cc_final: 0.7813 (mptt)
REVERT: E  369 LYS cc_start: 0.9047 (mttt) cc_final: 0.8431 (mttp)
REVERT: F  343 LYS cc_start: 0.8267 (tttt) cc_final: 0.7535 (mmtt)
REVERT: G  343 LYS cc_start: 0.7992 (tttt) cc_final: 0.7739 (mmtt)
REVERT: G  349 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7705 (mtm-85)
REVERT: H  342 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7688 (mm-30)
REVERT: I  342 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7802 (mt-10)
REVERT: I  345 ASP cc_start: 0.7959 (t0) cc_final: 0.7632 (t0)
REVERT: I  349 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7851 (mtm180)
REVERT: I  369 LYS cc_start: 0.9017 (mttt) cc_final: 0.8351 (mttp)
REVERT: J  345 ASP cc_start: 0.7861 (t0) cc_final: 0.7445 (t0)
REVERT: J  360 ILE cc_start: 0.9412 (mt) cc_final: 0.9171 (mp)
  outliers start: 18
  outliers final: 4
  residues processed: 205
  average time/residue: 0.6977
  time to fit residues: 147.9380
Evaluate side-chains
  203 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 195
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  349 ARG
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  349 ARG
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain H residue  357 LEU
Chi-restraints excluded: chain I residue  340 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 62 optimal weight:    8.9990
   chunk 49 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 39 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 59 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    7.7990

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.149390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.119547 restraints weight = 5667.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.76
r_work: 0.3364 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.065   5660  Z= 0.471
  Angle     :  0.847   8.854   7580  Z= 0.425
  Chirality :  0.052   0.171    860
  Planarity :  0.005   0.048    960
  Dihedral  :  5.686  19.957    740
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 17.81 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (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
 ARG   0.004   0.001   ARG I 349 
 TYR   0.012   0.003   TYR B 310 
 PHE   0.009   0.002   PHE G 378 
 HIS   0.006   0.002   HIS C 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.01146 ( 5660)
  covalent geometry    : angle       0.84696 ( 7580)
  hydrogen bonds       : bond        0.05152 (  128)
  hydrogen bonds       : angle       6.78810 (  384)

*********************** 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
  245 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 211
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8370 (tttt) cc_final: 0.8079 (ttpt)
REVERT: A  342 GLU cc_start: 0.8667 (mt-10) cc_final: 0.7519 (pm20)
REVERT: A  347 LYS cc_start: 0.7858 (mttp) cc_final: 0.7389 (mtpt)
REVERT: B  321 LYS cc_start: 0.8909 (mttp) cc_final: 0.8019 (tttt)
REVERT: B  342 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7255 (mp0)
REVERT: B  343 LYS cc_start: 0.8525 (tttt) cc_final: 0.8292 (mmtt)
REVERT: B  347 LYS cc_start: 0.7671 (mttp) cc_final: 0.6523 (mtmt)
REVERT: B  360 ILE cc_start: 0.9404 (mt) cc_final: 0.9135 (mp)
REVERT: B  369 LYS cc_start: 0.8989 (mttt) cc_final: 0.8348 (mttp)
REVERT: C  338 GLU cc_start: 0.9154 (tt0) cc_final: 0.8853 (tt0)
REVERT: C  343 LYS cc_start: 0.8444 (tttt) cc_final: 0.7988 (mmtt)
REVERT: C  349 ARG cc_start: 0.8469 (mtm180) cc_final: 0.8186 (mtm180)
REVERT: D  321 LYS cc_start: 0.8207 (tttt) cc_final: 0.7889 (ttpt)
REVERT: D  342 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7805 (mm-30)
REVERT: D  343 LYS cc_start: 0.8289 (tttt) cc_final: 0.7856 (mmtt)
REVERT: D  349 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7930 (mtm180)
REVERT: E  311 LYS cc_start: 0.8212 (mttt) cc_final: 0.7467 (pttt)
REVERT: E  342 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8165 (mt-10)
REVERT: E  343 LYS cc_start: 0.8361 (tttt) cc_final: 0.7749 (mmtt)
REVERT: E  347 LYS cc_start: 0.7612 (mttp) cc_final: 0.7120 (mmtp)
REVERT: E  369 LYS cc_start: 0.9135 (mttt) cc_final: 0.8480 (mttp)
REVERT: F  311 LYS cc_start: 0.8285 (mttt) cc_final: 0.7688 (pttp)
REVERT: F  343 LYS cc_start: 0.8342 (tttt) cc_final: 0.7658 (mmtt)
REVERT: G  343 LYS cc_start: 0.8177 (tttt) cc_final: 0.7733 (mmtt)
REVERT: G  349 ARG cc_start: 0.8257 (mtm180) cc_final: 0.7890 (ttp-170)
REVERT: H  342 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7993 (mm-30)
REVERT: H  369 LYS cc_start: 0.9136 (mttt) cc_final: 0.8637 (mttp)
REVERT: I  342 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8094 (mt-10)
REVERT: I  345 ASP cc_start: 0.8052 (t0) cc_final: 0.7654 (t0)
REVERT: I  369 LYS cc_start: 0.9130 (mttt) cc_final: 0.8484 (mttp)
REVERT: J  317 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8206 (ttmm)
REVERT: J  345 ASP cc_start: 0.7925 (t0) cc_final: 0.7476 (t0)
  outliers start: 34
  outliers final: 9
  residues processed: 225
  average time/residue: 0.7190
  time to fit residues: 167.1029
Evaluate side-chains
  227 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 212
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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 E residue  325 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain F residue  370 LYS
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  340 LYS
Chi-restraints excluded: chain I residue  342 GLU
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 49 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
C 327 ASN
C 374 HIS
D 327 ASN
E 327 ASN
F 327 ASN
I 327 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.155727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125781 restraints weight = 5548.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.77
r_work: 0.3452 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.3829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5660  Z= 0.135
  Angle     :  0.594   6.091   7580  Z= 0.305
  Chirality :  0.049   0.124    860
  Planarity :  0.004   0.043    960
  Dihedral  :  5.126  16.484    740
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.53 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.009   0.002   TYR C 310 
 PHE   0.007   0.001   PHE G 378 
 HIS   0.002   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5660)
  covalent geometry    : angle       0.59435 ( 7580)
  hydrogen bonds       : bond        0.03556 (  128)
  hydrogen bonds       : angle       6.44301 (  384)

*********************** 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
  222 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8417 (tttt) cc_final: 0.8093 (tmtt)
REVERT: A  342 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7457 (pm20)
REVERT: A  347 LYS cc_start: 0.7769 (mttp) cc_final: 0.7261 (mtpt)
REVERT: B  321 LYS cc_start: 0.8870 (mttp) cc_final: 0.8012 (tmmt)
REVERT: B  342 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7141 (mp0)
REVERT: B  343 LYS cc_start: 0.8574 (tttt) cc_final: 0.8242 (mmtt)
REVERT: B  347 LYS cc_start: 0.7682 (mttp) cc_final: 0.6519 (mtmt)
REVERT: B  360 ILE cc_start: 0.9347 (mt) cc_final: 0.9082 (mp)
REVERT: B  369 LYS cc_start: 0.9022 (mttt) cc_final: 0.8457 (mttp)
REVERT: C  343 LYS cc_start: 0.8384 (tttt) cc_final: 0.7941 (mmtt)
REVERT: C  349 ARG cc_start: 0.8372 (mtm180) cc_final: 0.8155 (mtm180)
REVERT: C  356 SER cc_start: 0.9359 (p) cc_final: 0.8767 (m)
REVERT: D  311 LYS cc_start: 0.8695 (pttp) cc_final: 0.7661 (tttt)
REVERT: D  321 LYS cc_start: 0.8196 (tttt) cc_final: 0.7983 (tttm)
REVERT: D  342 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7906 (mm-30)
REVERT: D  343 LYS cc_start: 0.8340 (tttt) cc_final: 0.7783 (mmtt)
REVERT: D  349 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7793 (mtm180)
REVERT: D  356 SER cc_start: 0.9349 (p) cc_final: 0.8794 (m)
REVERT: E  342 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8273 (mm-30)
REVERT: E  369 LYS cc_start: 0.9112 (mttt) cc_final: 0.8464 (mttp)
REVERT: F  343 LYS cc_start: 0.8275 (tttt) cc_final: 0.7601 (mmtt)
REVERT: F  356 SER cc_start: 0.9245 (p) cc_final: 0.8717 (m)
REVERT: F  369 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8607 (mttp)
REVERT: G  342 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8305 (mm-30)
REVERT: G  343 LYS cc_start: 0.8011 (tttt) cc_final: 0.7742 (mmtt)
REVERT: G  349 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7720 (ttp-170)
REVERT: H  342 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7686 (mm-30)
REVERT: H  349 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7569 (mtm180)
REVERT: I  342 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7931 (mt-10)
REVERT: I  345 ASP cc_start: 0.8039 (t0) cc_final: 0.7641 (t0)
REVERT: I  369 LYS cc_start: 0.9064 (mttt) cc_final: 0.8399 (mttp)
REVERT: J  317 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8194 (ttmm)
REVERT: J  345 ASP cc_start: 0.7895 (t0) cc_final: 0.7474 (t0)
  outliers start: 22
  outliers final: 8
  residues processed: 208
  average time/residue: 0.6670
  time to fit residues: 143.4897
Evaluate side-chains
  214 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 200
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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 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  369 LYS
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  357 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 51 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0070
   chunk 31 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    3.7004

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.152308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.122140 restraints weight = 5612.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.78
r_work: 0.3383 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5660  Z= 0.240
  Angle     :  0.668   6.229   7580  Z= 0.338
  Chirality :  0.050   0.136    860
  Planarity :  0.004   0.049    960
  Dihedral  :  5.370  17.885    740
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.94 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.28), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.015   0.002   TYR H 310 
 PHE   0.008   0.001   PHE G 378 
 HIS   0.004   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 5660)
  covalent geometry    : angle       0.66772 ( 7580)
  hydrogen bonds       : bond        0.04090 (  128)
  hydrogen bonds       : angle       6.52062 (  384)

*********************** 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
  224 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 206
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8398 (tttt) cc_final: 0.8100 (ttpt)
REVERT: A  342 GLU cc_start: 0.8665 (mt-10) cc_final: 0.7595 (pm20)
REVERT: A  347 LYS cc_start: 0.7819 (mttp) cc_final: 0.7294 (mtpt)
REVERT: B  321 LYS cc_start: 0.8876 (mttp) cc_final: 0.7999 (tttt)
REVERT: B  342 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7252 (mp0)
REVERT: B  343 LYS cc_start: 0.8494 (tttt) cc_final: 0.8254 (mmtt)
REVERT: B  347 LYS cc_start: 0.7764 (mttp) cc_final: 0.6586 (mtmt)
REVERT: B  360 ILE cc_start: 0.9383 (mt) cc_final: 0.9103 (mp)
REVERT: B  369 LYS cc_start: 0.9037 (mttt) cc_final: 0.8477 (mttp)
REVERT: C  343 LYS cc_start: 0.8402 (tttt) cc_final: 0.7975 (mmtt)
REVERT: C  349 ARG cc_start: 0.8415 (mtm180) cc_final: 0.8171 (mtm180)
REVERT: D  321 LYS cc_start: 0.8261 (tttt) cc_final: 0.8022 (tttm)
REVERT: D  342 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7823 (mm-30)
REVERT: D  343 LYS cc_start: 0.8305 (tttt) cc_final: 0.7811 (mmtt)
REVERT: D  349 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7808 (mtm180)
REVERT: D  356 SER cc_start: 0.9369 (p) cc_final: 0.8764 (m)
REVERT: E  311 LYS cc_start: 0.8324 (mttt) cc_final: 0.7572 (pttt)
REVERT: E  342 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8239 (mm-30)
REVERT: E  343 LYS cc_start: 0.8266 (tttt) cc_final: 0.7614 (mmtt)
REVERT: E  369 LYS cc_start: 0.9112 (mttt) cc_final: 0.8501 (mttp)
REVERT: F  343 LYS cc_start: 0.8337 (tttt) cc_final: 0.7649 (mmtt)
REVERT: F  356 SER cc_start: 0.9277 (p) cc_final: 0.8726 (m)
REVERT: F  369 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8639 (mttp)
REVERT: G  343 LYS cc_start: 0.8086 (tttt) cc_final: 0.7713 (mmtt)
REVERT: G  349 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7789 (ttp-170)
REVERT: H  342 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7899 (mm-30)
REVERT: H  369 LYS cc_start: 0.9133 (mttt) cc_final: 0.8627 (mttp)
REVERT: I  345 ASP cc_start: 0.8032 (t0) cc_final: 0.7636 (t0)
REVERT: I  369 LYS cc_start: 0.9096 (mttt) cc_final: 0.8432 (mttp)
REVERT: J  317 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8137 (ttmm)
REVERT: J  345 ASP cc_start: 0.7948 (t0) cc_final: 0.7512 (t0)
  outliers start: 18
  outliers final: 7
  residues processed: 213
  average time/residue: 0.6388
  time to fit residues: 140.7351
Evaluate side-chains
  217 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 204
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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 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  369 LYS
Chi-restraints excluded: chain F residue  370 LYS
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 43 optimal weight:    9.9990
   chunk 50 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.7988

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.155728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.125533 restraints weight = 5631.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.79
r_work: 0.3446 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5660  Z= 0.135
  Angle     :  0.585   6.060   7580  Z= 0.299
  Chirality :  0.049   0.125    860
  Planarity :  0.004   0.044    960
  Dihedral  :  5.108  16.082    740
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.09 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.015   0.002   TYR H 310 
 PHE   0.008   0.001   PHE G 378 
 HIS   0.002   0.001   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5660)
  covalent geometry    : angle       0.58459 ( 7580)
  hydrogen bonds       : bond        0.03376 (  128)
  hydrogen bonds       : angle       6.32155 (  384)

********************** 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
  220 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 204
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8451 (tttt) cc_final: 0.8116 (tmtt)
REVERT: A  342 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7391 (pm20)
REVERT: A  347 LYS cc_start: 0.7771 (mttp) cc_final: 0.7256 (mtpt)
REVERT: B  321 LYS cc_start: 0.8874 (mttp) cc_final: 0.8010 (tmmt)
REVERT: B  342 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7093 (mp0)
REVERT: B  343 LYS cc_start: 0.8550 (tttt) cc_final: 0.8232 (mmtt)
REVERT: B  347 LYS cc_start: 0.7747 (mttp) cc_final: 0.6530 (mtmt)
REVERT: B  360 ILE cc_start: 0.9343 (mt) cc_final: 0.9081 (mp)
REVERT: B  369 LYS cc_start: 0.9028 (mttt) cc_final: 0.8468 (mttp)
REVERT: C  343 LYS cc_start: 0.8383 (tttt) cc_final: 0.7992 (mmtt)
REVERT: C  356 SER cc_start: 0.9337 (p) cc_final: 0.8772 (m)
REVERT: D  321 LYS cc_start: 0.8240 (tttt) cc_final: 0.8025 (tttm)
REVERT: D  342 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7874 (mm-30)
REVERT: D  343 LYS cc_start: 0.8310 (tttt) cc_final: 0.7760 (mmtt)
REVERT: D  349 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7824 (mtm180)
REVERT: D  356 SER cc_start: 0.9371 (p) cc_final: 0.8820 (m)
REVERT: E  342 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8284 (mm-30)
REVERT: E  369 LYS cc_start: 0.9110 (mttt) cc_final: 0.8455 (mttp)
REVERT: F  343 LYS cc_start: 0.8271 (tttt) cc_final: 0.7608 (mmtt)
REVERT: F  356 SER cc_start: 0.9243 (p) cc_final: 0.8722 (m)
REVERT: F  369 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8620 (mttp)
REVERT: G  342 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: G  343 LYS cc_start: 0.8018 (tttt) cc_final: 0.7762 (mmtt)
REVERT: G  349 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7719 (ttp-170)
REVERT: H  342 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7737 (mm-30)
REVERT: H  349 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7505 (mtm180)
REVERT: I  342 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7749 (mt-10)
REVERT: I  345 ASP cc_start: 0.8003 (t0) cc_final: 0.7620 (t0)
REVERT: I  369 LYS cc_start: 0.9055 (mttt) cc_final: 0.8392 (mttp)
REVERT: J  317 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8119 (ttmm)
REVERT: J  345 ASP cc_start: 0.7974 (t0) cc_final: 0.7530 (t0)
  outliers start: 16
  outliers final: 8
  residues processed: 211
  average time/residue: 0.6328
  time to fit residues: 138.1825
Evaluate side-chains
  218 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 204
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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 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 H residue  342 GLU
Chi-restraints excluded: chain H residue  357 LEU
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.5990

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.156249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.126088 restraints weight = 5577.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.79
r_work: 0.3467 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.3932

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= 0.124
  Angle     :  0.570   6.321   7580  Z= 0.291
  Chirality :  0.049   0.125    860
  Planarity :  0.003   0.040    960
  Dihedral  :  5.003  15.804    740
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 22.03 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.03 (0.29), residues: 710
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 349 
 TYR   0.016   0.002   TYR H 310 
 PHE   0.009   0.001   PHE G 378 
 HIS   0.002   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5660)
  covalent geometry    : angle       0.56999 ( 7580)
  hydrogen bonds       : bond        0.03238 (  128)
  hydrogen bonds       : angle       6.21766 (  384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2942.59 seconds
wall clock time: 51 minutes 12.06 seconds (3072.06 seconds total)