Starting phenix.real_space_refine
on Fri Aug 22 13:40:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eoh_19855/08_2025/9eoh_19855.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eoh_19855/08_2025/9eoh_19855.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eoh_19855/08_2025/9eoh_19855.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eoh_19855/08_2025/9eoh_19855.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eoh_19855/08_2025/9eoh_19855.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eoh_19855/08_2025/9eoh_19855.map"
  }
  resolution = 2.8
  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=   0.001
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      12      5.16       5
     C    2142      2.51       5
     N     630      2.21       5
     O     630      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  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: 3414
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 569
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.55, per 1000 atoms: 0.16
  Number of scatterers: 3414
  At special positions: 0
  Unit cell: (144.673, 80.697, 36.35, 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      12     16.00
     O     630      8.00
     N     630      7.00
     C    2142      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: 0.24
  Conformation dependent library (CDL) restraints added in 97.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 62.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 307 through 310
      removed outlier: 6.609A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.874A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322
      removed outlier: 6.330A  pdb=" N   VAL A 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 8.255A  pdb=" N   LYS D 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   SER A 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330
      removed outlier: 6.899A  pdb=" N   GLY B 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ASN A 327 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLY A 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.464A  pdb=" N   HIS D 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 356
      removed outlier: 6.416A  pdb=" N   GLN A 336 " --> pdb=" O   MET B 337 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL B 339 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLU A 338 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   SER B 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LYS A 340 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   LYS B 343 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   GLU A 342 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 9.923A  pdb=" N   ASP B 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   LEU A 344 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 9.596A  pdb=" N   LYS B 347 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   PHE A 346 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 9.405A  pdb=" N   ARG B 349 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 8.869A  pdb=" N   ASP A 348 " --> pdb=" O   ARG B 349 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   GLN B 351 " --> pdb=" O   ASP A 348 " (cutoff:3.500A)
      removed outlier: 8.954A  pdb=" N   VAL A 350 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 9.957A  pdb=" N   LYS B 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 8.708A  pdb=" N   SER A 352 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 10.181A  pdb=" N   GLY B 355 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   ILE A 354 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LYS A 343 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LEU D 344 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   ASP A 345 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE D 346 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LYS A 347 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL D 350 " --> pdb=" O   ARG A 349 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   GLN A 351 " --> pdb=" O   VAL D 350 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   SER D 352 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LYS A 353 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   ILE D 354 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLY A 355 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 359 through 362
      removed outlier: 6.507A  pdb=" N   ASN A 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   HIS D 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   THR A 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 378
      removed outlier: 6.522A  pdb=" N   LYS A 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   GLU B 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ILE A 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   HIS B 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   THR A 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   LEU B 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LYS A 375 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   PHE B 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 307 through 310
      removed outlier: 6.610A  pdb=" N   GLN C 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   TYR E 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL C 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   GLN E 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   TYR F 310 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL E 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.874A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL E 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 322
    Processing sheet with id=AB2, first strand: chain 'C' and resid 325 through 330
      removed outlier: 6.899A  pdb=" N   GLY E 326 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ASN C 327 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   GLY F 326 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ASN E 327 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 356
      removed outlier: 6.416A  pdb=" N   GLN C 336 " --> pdb=" O   MET E 337 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL E 339 " --> pdb=" O   GLN C 336 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLU C 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   SER E 341 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LYS C 340 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   LYS E 343 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   GLU C 342 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
      removed outlier: 9.923A  pdb=" N   ASP E 345 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   LEU C 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
      removed outlier: 9.596A  pdb=" N   LYS E 347 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   PHE C 346 " --> pdb=" O   LYS E 347 " (cutoff:3.500A)
      removed outlier: 9.405A  pdb=" N   ARG E 349 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 8.870A  pdb=" N   ASP C 348 " --> pdb=" O   ARG E 349 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   GLN E 351 " --> pdb=" O   ASP C 348 " (cutoff:3.500A)
      removed outlier: 8.954A  pdb=" N   VAL C 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 9.957A  pdb=" N   LYS E 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
      removed outlier: 8.709A  pdb=" N   SER C 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 10.181A  pdb=" N   GLY E 355 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   ILE C 354 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   GLN E 336 " --> pdb=" O   MET F 337 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL F 339 " --> pdb=" O   GLN E 336 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLU E 338 " --> pdb=" O   VAL F 339 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   SER F 341 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LYS E 340 " --> pdb=" O   SER F 341 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   LYS F 343 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   GLU E 342 " --> pdb=" O   LYS F 343 " (cutoff:3.500A)
      removed outlier: 9.923A  pdb=" N   ASP F 345 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
      removed outlier: 9.213A  pdb=" N   LEU E 344 " --> pdb=" O   ASP F 345 " (cutoff:3.500A)
      removed outlier: 9.596A  pdb=" N   LYS F 347 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   PHE E 346 " --> pdb=" O   LYS F 347 " (cutoff:3.500A)
      removed outlier: 9.406A  pdb=" N   ARG F 349 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
      removed outlier: 8.870A  pdb=" N   ASP E 348 " --> pdb=" O   ARG F 349 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   GLN F 351 " --> pdb=" O   ASP E 348 " (cutoff:3.500A)
      removed outlier: 8.955A  pdb=" N   VAL E 350 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 9.957A  pdb=" N   LYS F 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
      removed outlier: 8.709A  pdb=" N   SER E 352 " --> pdb=" O   LYS F 353 " (cutoff:3.500A)
      removed outlier: 10.181A  pdb=" N   GLY F 355 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   ILE E 354 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 359 through 362
    Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.523A  pdb=" N   LYS C 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   GLU E 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ILE C 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   HIS E 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   THR C 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   LEU E 376 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LYS C 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   PHE E 378 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   THR C 377 " --> pdb=" O   PHE E 378 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LYS E 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   GLU F 372 " --> pdb=" O   LYS E 369 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ILE E 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   HIS F 374 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   THR E 373 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   LEU F 376 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LYS E 375 " --> pdb=" O   LEU F 376 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   PHE F 378 " --> pdb=" O   LYS E 375 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR E 377 " --> pdb=" O   PHE F 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    55 hydrogen bonds defined for protein.
    165 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: 0.35

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 833
        1.34 -     1.46: 811
        1.46 -     1.57: 1806
        1.57 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 3468
  Sorted by residual:
  bond pdb=" CG  HIS F 362 "
       pdb=" CD2 HIS F 362 "
    ideal  model  delta    sigma   weight residual
    1.354  1.303  0.051 1.10e-02 8.26e+03 2.16e+01
  bond pdb=" CG  HIS B 362 "
       pdb=" CD2 HIS B 362 "
    ideal  model  delta    sigma   weight residual
    1.354  1.303  0.051 1.10e-02 8.26e+03 2.15e+01
  bond pdb=" CG  HIS E 362 "
       pdb=" CD2 HIS E 362 "
    ideal  model  delta    sigma   weight residual
    1.354  1.303  0.051 1.10e-02 8.26e+03 2.14e+01
  bond pdb=" CG  HIS C 362 "
       pdb=" CD2 HIS C 362 "
    ideal  model  delta    sigma   weight residual
    1.354  1.303  0.051 1.10e-02 8.26e+03 2.13e+01
  bond pdb=" CG  HIS A 362 "
       pdb=" CD2 HIS A 362 "
    ideal  model  delta    sigma   weight residual
    1.354  1.303  0.051 1.10e-02 8.26e+03 2.11e+01
  ... (remaining 3463 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 3332
        1.29 -     2.58: 936
        2.58 -     3.87: 251
        3.87 -     5.16: 77
        5.16 -     6.44: 36
  Bond angle restraints: 4632
  Sorted by residual:
  angle pdb=" N   GLY C 326 "
        pdb=" CA  GLY C 326 "
        pdb=" C   GLY C 326 "
      ideal   model   delta    sigma   weight residual
     110.80  117.24   -6.44 1.41e+00 5.03e-01 2.09e+01
  angle pdb=" N   GLY A 326 "
        pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     110.80  117.24   -6.44 1.41e+00 5.03e-01 2.08e+01
  angle pdb=" N   GLY B 326 "
        pdb=" CA  GLY B 326 "
        pdb=" C   GLY B 326 "
      ideal   model   delta    sigma   weight residual
     110.80  117.23   -6.43 1.41e+00 5.03e-01 2.08e+01
  angle pdb=" N   GLY D 326 "
        pdb=" CA  GLY D 326 "
        pdb=" C   GLY D 326 "
      ideal   model   delta    sigma   weight residual
     110.80  117.23   -6.43 1.41e+00 5.03e-01 2.08e+01
  angle pdb=" N   GLY E 326 "
        pdb=" CA  GLY E 326 "
        pdb=" C   GLY E 326 "
      ideal   model   delta    sigma   weight residual
     110.80  117.23   -6.43 1.41e+00 5.03e-01 2.08e+01
  ... (remaining 4627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.55: 1902
       13.55 -    27.11: 174
       27.11 -    40.66: 42
       40.66 -    54.21: 0
       54.21 -    67.76: 6
  Dihedral angle restraints: 2124
    sinusoidal: 900
      harmonic: 1224
  Sorted by residual:
  dihedral pdb=" C   LYS C 347 "
           pdb=" N   LYS C 347 "
           pdb=" CA  LYS C 347 "
           pdb=" CB  LYS C 347 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.49   13.89     0      2.50e+00 1.60e-01 3.08e+01
  dihedral pdb=" C   LYS A 347 "
           pdb=" N   LYS A 347 "
           pdb=" CA  LYS A 347 "
           pdb=" CB  LYS A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.47   13.87     0      2.50e+00 1.60e-01 3.08e+01
  dihedral pdb=" C   LYS D 347 "
           pdb=" N   LYS D 347 "
           pdb=" CA  LYS D 347 "
           pdb=" CB  LYS D 347 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.47   13.87     0      2.50e+00 1.60e-01 3.08e+01
  ... (remaining 2121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.105: 428
       0.105 -    0.210: 82
       0.210 -    0.315: 0
       0.315 -    0.420: 0
       0.420 -    0.525: 6
  Chirality restraints: 516
  Sorted by residual:
  chirality pdb=" CA  LYS C 347 "
            pdb=" N   LYS C 347 "
            pdb=" C   LYS C 347 "
            pdb=" CB  LYS C 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.88e+00
  chirality pdb=" CA  LYS B 347 "
            pdb=" N   LYS B 347 "
            pdb=" C   LYS B 347 "
            pdb=" CB  LYS B 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.85e+00
  chirality pdb=" CA  LYS A 347 "
            pdb=" N   LYS A 347 "
            pdb=" C   LYS A 347 "
            pdb=" CB  LYS A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.85e+00
  ... (remaining 513 not shown)

  Planarity restraints: 588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.026 2.00e-02 2.50e+03   1.53e-02 4.66e+00
        pdb=" CG  TYR F 310 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "    0.026 2.00e-02 2.50e+03   1.52e-02 4.62e+00
        pdb=" CG  TYR C 310 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "   -0.026 2.00e-02 2.50e+03   1.52e-02 4.60e+00
        pdb=" CG  TYR A 310 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 585 not shown)

  Histogram of nonbonded interaction distances:
        2.47 -     2.95: 1412
        2.95 -     3.44: 2902
        3.44 -     3.93: 5653
        3.93 -     4.41: 5488
        4.41 -     4.90: 10833
  Nonbonded interactions: 26288
  Sorted by model distance:
  nonbonded pdb=" O   ASP E 348 "
            pdb=" O   LYS F 347 "
     model   vdw
     2.465 3.040
  nonbonded pdb=" O   ASP C 348 "
            pdb=" O   LYS E 347 "
     model   vdw
     2.466 3.040
  nonbonded pdb=" O   ASP A 348 "
            pdb=" O   LYS B 347 "
     model   vdw
     2.466 3.040
  nonbonded pdb=" O   LYS A 347 "
            pdb=" O   ASP D 348 "
     model   vdw
     2.466 3.040
  nonbonded pdb=" OG  SER E 320 "
            pdb=" ND2 ASN F 368 "
     model   vdw
     2.585 3.120
  ... (remaining 26283 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             3.170
  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:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.830
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:5.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
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      :  0.009   0.060   3468  Z= 0.621
  Angle     :  1.450   6.444   4632  Z= 0.954
  Chirality :  0.093   0.525    516
  Planarity :  0.008   0.032    588
  Dihedral  : 11.762  67.764   1344
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.72 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Cbeta Deviations :  1.54 %
  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: -3.95 (0.27), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.20), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 349 
 TYR   0.034   0.010   TYR F 310 
 PHE   0.017   0.004   PHE B 346 
 HIS   0.014   0.005   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00895 ( 3468)
  covalent geometry    : angle       1.44998 ( 4632)
  hydrogen bonds       : bond        0.17229 (   55)
  hydrogen bonds       : angle       8.49489 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: B  307 GLN cc_start: 0.8127 (tt0) cc_final: 0.7783 (pm20)
REVERT: B  375 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8508 (pmtt)
REVERT: C  307 GLN cc_start: 0.8944 (tt0) cc_final: 0.8483 (tp40)
REVERT: C  313 VAL cc_start: 0.9155 (t) cc_final: 0.8892 (p)
REVERT: C  331 LYS cc_start: 0.8757 (mttm) cc_final: 0.7679 (tmtt)
REVERT: C  378 PHE cc_start: 0.8385 (t80) cc_final: 0.7265 (p90)
REVERT: F  311 LYS cc_start: 0.8945 (tttt) cc_final: 0.8711 (pptt)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.4917
  time to fit residues: 93.7151
Evaluate side-chains
  164 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
C 330 HIS
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 330 HIS
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 330 HIS
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 368 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.142482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.119103 restraints weight = 4217.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 2.47
r_work: 0.3823 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3721 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3468  Z= 0.183
  Angle     :  0.706   6.000   4632  Z= 0.362
  Chirality :  0.051   0.183    516
  Planarity :  0.003   0.018    588
  Dihedral  :  5.694  14.902    456
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 20.26 %
    Favored  : 75.38 %
  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: -3.44 (0.29), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.22), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 379 
 TYR   0.011   0.002   TYR A 310 
 PHE   0.010   0.001   PHE A 378 
 HIS   0.005   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 3468)
  covalent geometry    : angle       0.70610 ( 4632)
  hydrogen bonds       : bond        0.03337 (   55)
  hydrogen bonds       : angle       5.83175 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8574 (mmmt)
REVERT: A  349 ARG cc_start: 0.7342 (mtm180) cc_final: 0.7126 (mtm180)
REVERT: B  311 LYS cc_start: 0.8818 (tttt) cc_final: 0.8549 (pptt)
REVERT: B  317 LYS cc_start: 0.9006 (ptmm) cc_final: 0.8586 (ptpp)
REVERT: B  375 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8715 (mttm)
REVERT: C  307 GLN cc_start: 0.8748 (tt0) cc_final: 0.8271 (tp40)
REVERT: C  313 VAL cc_start: 0.9199 (t) cc_final: 0.8844 (p)
REVERT: C  317 LYS cc_start: 0.8439 (ptmt) cc_final: 0.8221 (ptpp)
REVERT: C  331 LYS cc_start: 0.9102 (mttm) cc_final: 0.7212 (tmtt)
REVERT: C  349 ARG cc_start: 0.7870 (mtm180) cc_final: 0.5887 (mmt-90)
REVERT: C  378 PHE cc_start: 0.8617 (t80) cc_final: 0.7289 (p90)
REVERT: E  319 THR cc_start: 0.8452 (m) cc_final: 0.7892 (p)
REVERT: E  331 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8873 (mttt)
REVERT: E  351 GLN cc_start: 0.8156 (mp10) cc_final: 0.7927 (mp10)
REVERT: F  311 LYS cc_start: 0.8832 (tttt) cc_final: 0.8535 (pptt)
REVERT: F  375 LYS cc_start: 0.8672 (mptm) cc_final: 0.8470 (mptm)
  outliers start: 17
  outliers final: 9
  residues processed: 173
  average time/residue: 0.4865
  time to fit residues: 86.2976
Evaluate side-chains
  172 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 162
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  309 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.137847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.116695 restraints weight = 4274.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 2.41
r_work: 0.3808 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3699 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3468  Z= 0.177
  Angle     :  0.670   6.726   4632  Z= 0.339
  Chirality :  0.050   0.174    516
  Planarity :  0.002   0.015    588
  Dihedral  :  5.438  14.869    456
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.59 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.15 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 379 
 TYR   0.010   0.002   TYR A 310 
 PHE   0.007   0.001   PHE E 378 
 HIS   0.006   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 3468)
  covalent geometry    : angle       0.67046 ( 4632)
  hydrogen bonds       : bond        0.02519 (   55)
  hydrogen bonds       : angle       5.25289 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8956 (mttt) cc_final: 0.8685 (mtpt)
REVERT: A  349 ARG cc_start: 0.7230 (mtm180) cc_final: 0.6999 (mtm180)
REVERT: B  311 LYS cc_start: 0.8825 (tttt) cc_final: 0.8604 (pptt)
REVERT: B  317 LYS cc_start: 0.9039 (ptmm) cc_final: 0.8619 (ptpp)
REVERT: B  349 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7475 (ttp80)
REVERT: B  375 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8728 (mttm)
REVERT: B  378 PHE cc_start: 0.9138 (t80) cc_final: 0.8880 (t80)
REVERT: C  307 GLN cc_start: 0.8620 (tt0) cc_final: 0.8148 (tp-100)
REVERT: C  313 VAL cc_start: 0.9291 (t) cc_final: 0.8992 (p)
REVERT: C  317 LYS cc_start: 0.8534 (ptmt) cc_final: 0.8266 (ptpp)
REVERT: C  331 LYS cc_start: 0.9074 (mttm) cc_final: 0.7190 (tmtt)
REVERT: C  378 PHE cc_start: 0.8757 (t80) cc_final: 0.7214 (p90)
REVERT: D  375 LYS cc_start: 0.8470 (tptp) cc_final: 0.8095 (tptm)
REVERT: D  379 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7638 (mmp-170)
REVERT: E  353 LYS cc_start: 0.8708 (mttm) cc_final: 0.8279 (mtpm)
REVERT: F  311 LYS cc_start: 0.8785 (tttt) cc_final: 0.8537 (pptt)
REVERT: F  317 LYS cc_start: 0.9141 (ptmm) cc_final: 0.8873 (ptmm)
REVERT: F  349 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7699 (mtm180)
REVERT: F  375 LYS cc_start: 0.8698 (mptm) cc_final: 0.8419 (mptm)
  outliers start: 15
  outliers final: 7
  residues processed: 174
  average time/residue: 0.5416
  time to fit residues: 96.5327
Evaluate side-chains
  174 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 166
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain F residue  309 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.138490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.116198 restraints weight = 4309.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 2.51
r_work: 0.3820 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3468  Z= 0.157
  Angle     :  0.644   7.291   4632  Z= 0.321
  Chirality :  0.049   0.159    516
  Planarity :  0.002   0.013    588
  Dihedral  :  5.230  14.656    456
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 23.33 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.01 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 379 
 TYR   0.009   0.002   TYR A 310 
 PHE   0.006   0.001   PHE E 378 
 HIS   0.005   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3468)
  covalent geometry    : angle       0.64419 ( 4632)
  hydrogen bonds       : bond        0.02023 (   55)
  hydrogen bonds       : angle       5.00978 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 172
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8996 (mttt) cc_final: 0.8698 (mtpt)
REVERT: A  349 ARG cc_start: 0.7108 (mtm180) cc_final: 0.6896 (mtm180)
REVERT: A  379 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7857 (mtm-85)
REVERT: B  311 LYS cc_start: 0.8815 (tttt) cc_final: 0.8580 (pptt)
REVERT: B  317 LYS cc_start: 0.9032 (ptmm) cc_final: 0.8626 (ptpp)
REVERT: B  375 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8701 (mttm)
REVERT: B  378 PHE cc_start: 0.9137 (t80) cc_final: 0.8746 (t80)
REVERT: C  307 GLN cc_start: 0.8623 (tt0) cc_final: 0.8151 (tp-100)
REVERT: C  311 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5848 (mmpt)
REVERT: C  313 VAL cc_start: 0.9293 (t) cc_final: 0.8992 (p)
REVERT: C  317 LYS cc_start: 0.8509 (ptmt) cc_final: 0.8208 (ptpp)
REVERT: C  331 LYS cc_start: 0.8978 (mttm) cc_final: 0.7097 (tmtt)
REVERT: C  378 PHE cc_start: 0.8661 (t80) cc_final: 0.7159 (p90)
REVERT: D  375 LYS cc_start: 0.8392 (tptp) cc_final: 0.7949 (tptm)
REVERT: D  379 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7491 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8865 (mttt)
REVERT: E  351 GLN cc_start: 0.8191 (mp10) cc_final: 0.7985 (mp10)
REVERT: F  311 LYS cc_start: 0.8834 (tttt) cc_final: 0.8565 (pptt)
REVERT: F  317 LYS cc_start: 0.9137 (ptmm) cc_final: 0.8888 (ptmm)
REVERT: F  321 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8301 (tmmt)
REVERT: F  375 LYS cc_start: 0.8625 (mptm) cc_final: 0.8294 (mptm)
  outliers start: 17
  outliers final: 13
  residues processed: 174
  average time/residue: 0.5421
  time to fit residues: 96.4987
Evaluate side-chains
  182 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  320 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0170
   chunk 20 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    3.2026

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.136333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.115513 restraints weight = 4346.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 2.37
r_work: 0.3797 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3687 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3468  Z= 0.194
  Angle     :  0.662   8.119   4632  Z= 0.331
  Chirality :  0.049   0.164    516
  Planarity :  0.002   0.011    588
  Dihedral  :  5.283  14.607    456
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 23.85 %
    Favored  : 70.77 %
  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: -2.92 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 379 
 TYR   0.010   0.002   TYR A 310 
 PHE   0.006   0.001   PHE E 378 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 3468)
  covalent geometry    : angle       0.66206 ( 4632)
  hydrogen bonds       : bond        0.02016 (   55)
  hydrogen bonds       : angle       4.99389 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9052 (mttt) cc_final: 0.8723 (mtpt)
REVERT: A  379 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7830 (mtp-110)
REVERT: B  317 LYS cc_start: 0.9049 (ptmm) cc_final: 0.8655 (ptpp)
REVERT: B  375 LYS cc_start: 0.9052 (ttmt) cc_final: 0.8698 (mttm)
REVERT: B  378 PHE cc_start: 0.9151 (t80) cc_final: 0.8834 (t80)
REVERT: C  307 GLN cc_start: 0.8614 (tt0) cc_final: 0.8215 (tp-100)
REVERT: C  313 VAL cc_start: 0.9314 (t) cc_final: 0.9023 (p)
REVERT: C  317 LYS cc_start: 0.8615 (ptmt) cc_final: 0.8292 (ptpp)
REVERT: C  331 LYS cc_start: 0.9033 (mttm) cc_final: 0.7197 (tmtt)
REVERT: C  378 PHE cc_start: 0.8745 (t80) cc_final: 0.7191 (p90)
REVERT: D  375 LYS cc_start: 0.8393 (tptp) cc_final: 0.7963 (tptm)
REVERT: D  379 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7502 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8938 (mttt)
REVERT: F  311 LYS cc_start: 0.8799 (tttt) cc_final: 0.8583 (pptt)
REVERT: F  317 LYS cc_start: 0.9158 (ptmm) cc_final: 0.8925 (ptmm)
REVERT: F  349 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7714 (mtm180)
REVERT: F  375 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8368 (mptm)
  outliers start: 21
  outliers final: 17
  residues processed: 174
  average time/residue: 0.4894
  time to fit residues: 87.1312
Evaluate side-chains
  189 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  353 LYS
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain F residue  375 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.133479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.111782 restraints weight = 4466.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.47
r_work: 0.3766 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3468  Z= 0.236
  Angle     :  0.719   8.766   4632  Z= 0.360
  Chirality :  0.050   0.171    516
  Planarity :  0.002   0.016    588
  Dihedral  :  5.419  15.127    456
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 23.59 %
    Favored  : 70.00 %
  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: -2.83 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 379 
 TYR   0.011   0.003   TYR B 310 
 PHE   0.008   0.001   PHE E 378 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 3468)
  covalent geometry    : angle       0.71869 ( 4632)
  hydrogen bonds       : bond        0.02151 (   55)
  hydrogen bonds       : angle       4.92287 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9116 (mttt) cc_final: 0.8507 (pttm)
REVERT: A  379 ARG cc_start: 0.8210 (mtm110) cc_final: 0.7740 (mtm-85)
REVERT: B  317 LYS cc_start: 0.9037 (ptmm) cc_final: 0.8631 (ptpp)
REVERT: B  349 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7428 (ttp80)
REVERT: B  375 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8664 (mttm)
REVERT: B  378 PHE cc_start: 0.9159 (t80) cc_final: 0.8834 (t80)
REVERT: C  307 GLN cc_start: 0.8597 (tt0) cc_final: 0.8212 (tp-100)
REVERT: C  311 LYS cc_start: 0.5122 (OUTLIER) cc_final: 0.4729 (mmtt)
REVERT: C  316 SER cc_start: 0.9414 (p) cc_final: 0.9135 (p)
REVERT: C  317 LYS cc_start: 0.8588 (ptmt) cc_final: 0.8183 (ptpp)
REVERT: C  331 LYS cc_start: 0.8992 (mttm) cc_final: 0.7079 (tmtt)
REVERT: C  378 PHE cc_start: 0.8776 (t80) cc_final: 0.7202 (p90)
REVERT: D  375 LYS cc_start: 0.8357 (tptp) cc_final: 0.7873 (tptm)
REVERT: D  379 ARG cc_start: 0.8018 (mtm180) cc_final: 0.7386 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8890 (mttt)
REVERT: E  349 ARG cc_start: 0.7425 (mtm180) cc_final: 0.7035 (mtp180)
REVERT: F  311 LYS cc_start: 0.8828 (tttt) cc_final: 0.8585 (pptt)
REVERT: F  317 LYS cc_start: 0.9147 (ptmm) cc_final: 0.8906 (ptmm)
REVERT: F  349 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7696 (mtm180)
REVERT: F  375 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8484 (mptm)
REVERT: F  377 THR cc_start: 0.8785 (m) cc_final: 0.8487 (p)
  outliers start: 25
  outliers final: 16
  residues processed: 174
  average time/residue: 0.5507
  time to fit residues: 97.9935
Evaluate side-chains
  189 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  375 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.136653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.114888 restraints weight = 4443.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 2.51
r_work: 0.3808 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3698 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.4420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3468  Z= 0.168
  Angle     :  0.685   9.186   4632  Z= 0.336
  Chirality :  0.049   0.146    516
  Planarity :  0.002   0.031    588
  Dihedral  :  5.241  14.817    456
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 25.13 %
    Favored  : 69.23 %
  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: -2.75 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 349 
 TYR   0.009   0.002   TYR A 310 
 PHE   0.007   0.001   PHE E 378 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 3468)
  covalent geometry    : angle       0.68493 ( 4632)
  hydrogen bonds       : bond        0.01807 (   55)
  hydrogen bonds       : angle       4.84713 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.9106 (mttt) cc_final: 0.8504 (pttm)
REVERT: A  379 ARG cc_start: 0.8213 (mtm110) cc_final: 0.7802 (mtp-110)
REVERT: B  311 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6388 (pptt)
REVERT: B  317 LYS cc_start: 0.9036 (ptmm) cc_final: 0.8649 (ptpp)
REVERT: B  349 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7372 (ttp80)
REVERT: B  375 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8727 (ttmm)
REVERT: B  377 THR cc_start: 0.8628 (m) cc_final: 0.8349 (p)
REVERT: B  378 PHE cc_start: 0.9021 (t80) cc_final: 0.8680 (t80)
REVERT: C  307 GLN cc_start: 0.8602 (tt0) cc_final: 0.8216 (tp-100)
REVERT: C  311 LYS cc_start: 0.5072 (OUTLIER) cc_final: 0.4592 (mmmt)
REVERT: C  313 VAL cc_start: 0.9277 (t) cc_final: 0.8989 (p)
REVERT: C  316 SER cc_start: 0.9422 (p) cc_final: 0.9145 (p)
REVERT: C  317 LYS cc_start: 0.8564 (ptmt) cc_final: 0.8186 (ptpp)
REVERT: C  331 LYS cc_start: 0.8995 (mttm) cc_final: 0.7108 (tmtt)
REVERT: C  378 PHE cc_start: 0.8678 (t80) cc_final: 0.7152 (p90)
REVERT: D  379 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7379 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8854 (mttt)
REVERT: F  311 LYS cc_start: 0.8792 (tttt) cc_final: 0.8578 (pptt)
REVERT: F  317 LYS cc_start: 0.9142 (ptmm) cc_final: 0.8922 (ptmm)
REVERT: F  375 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8411 (mptm)
REVERT: F  377 THR cc_start: 0.8676 (m) cc_final: 0.8437 (p)
  outliers start: 22
  outliers final: 15
  residues processed: 177
  average time/residue: 0.5200
  time to fit residues: 94.1648
Evaluate side-chains
  193 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  375 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0370
   chunk 6 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    5.0066

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.132530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.111599 restraints weight = 4564.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.43
r_work: 0.3753 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   3468  Z= 0.289
  Angle     :  0.774   9.422   4632  Z= 0.388
  Chirality :  0.051   0.179    516
  Planarity :  0.003   0.037    588
  Dihedral  :  5.668  17.774    456
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 25.38 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.79 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F 379 
 TYR   0.012   0.003   TYR B 310 
 PHE   0.007   0.002   PHE E 378 
 HIS   0.005   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00663 ( 3468)
  covalent geometry    : angle       0.77372 ( 4632)
  hydrogen bonds       : bond        0.02248 (   55)
  hydrogen bonds       : angle       4.94905 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9133 (mttt) cc_final: 0.8555 (pttm)
REVERT: A  379 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7753 (mtp-110)
REVERT: B  311 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.5993 (pptt)
REVERT: B  317 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8645 (ptpp)
REVERT: B  349 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7501 (ttp80)
REVERT: B  375 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8725 (ttmm)
REVERT: B  377 THR cc_start: 0.8727 (m) cc_final: 0.8439 (p)
REVERT: C  307 GLN cc_start: 0.8542 (tt0) cc_final: 0.8186 (tp-100)
REVERT: C  311 LYS cc_start: 0.4725 (OUTLIER) cc_final: 0.4305 (mmtt)
REVERT: C  313 VAL cc_start: 0.9279 (t) cc_final: 0.8972 (p)
REVERT: C  317 LYS cc_start: 0.8601 (ptmt) cc_final: 0.8201 (ptpp)
REVERT: C  331 LYS cc_start: 0.9006 (mttm) cc_final: 0.7093 (tmtt)
REVERT: D  311 LYS cc_start: 0.4525 (OUTLIER) cc_final: 0.3099 (mmpt)
REVERT: D  375 LYS cc_start: 0.8341 (tptp) cc_final: 0.7858 (tptm)
REVERT: D  379 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7229 (mmp-170)
REVERT: E  311 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8272 (mptm)
REVERT: E  331 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8889 (mttt)
REVERT: E  349 ARG cc_start: 0.7442 (mtm180) cc_final: 0.7064 (mtp180)
REVERT: F  307 GLN cc_start: 0.6989 (tm-30) cc_final: 0.6760 (tm-30)
REVERT: F  317 LYS cc_start: 0.9132 (ptmm) cc_final: 0.8876 (ptmm)
REVERT: F  349 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7882 (mtm180)
REVERT: F  375 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8475 (mptm)
REVERT: F  377 THR cc_start: 0.8837 (m) cc_final: 0.8538 (p)
  outliers start: 22
  outliers final: 14
  residues processed: 170
  average time/residue: 0.5516
  time to fit residues: 95.8667
Evaluate side-chains
  187 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  375 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0970
   chunk 7 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.139100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.117474 restraints weight = 4390.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 2.55
r_work: 0.3838 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.4733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3468  Z= 0.146
  Angle     :  0.716   8.940   4632  Z= 0.345
  Chirality :  0.049   0.133    516
  Planarity :  0.003   0.037    588
  Dihedral  :  5.211  17.576    456
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 27.18 %
    Favored  : 67.95 %
  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: -2.75 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 379 
 TYR   0.009   0.002   TYR B 310 
 PHE   0.004   0.001   PHE A 378 
 HIS   0.006   0.002   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3468)
  covalent geometry    : angle       0.71606 ( 4632)
  hydrogen bonds       : bond        0.01682 (   55)
  hydrogen bonds       : angle       4.85807 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 174
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8066 (pp30)
REVERT: A  311 LYS cc_start: 0.9141 (mttt) cc_final: 0.8590 (pttm)
REVERT: A  379 ARG cc_start: 0.8189 (mtm110) cc_final: 0.7851 (mtp-110)
REVERT: B  317 LYS cc_start: 0.9027 (ptmm) cc_final: 0.8646 (ptpp)
REVERT: B  375 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8677 (ttmm)
REVERT: B  377 THR cc_start: 0.8565 (m) cc_final: 0.8305 (p)
REVERT: B  378 PHE cc_start: 0.8970 (t80) cc_final: 0.8538 (t80)
REVERT: C  307 GLN cc_start: 0.8555 (tt0) cc_final: 0.8181 (tp-100)
REVERT: C  311 LYS cc_start: 0.4835 (OUTLIER) cc_final: 0.4395 (mmmt)
REVERT: C  313 VAL cc_start: 0.9270 (t) cc_final: 0.8978 (p)
REVERT: C  316 SER cc_start: 0.9411 (p) cc_final: 0.9137 (p)
REVERT: C  317 LYS cc_start: 0.8568 (ptmt) cc_final: 0.8188 (ptpp)
REVERT: C  331 LYS cc_start: 0.9005 (mttm) cc_final: 0.7115 (tmtt)
REVERT: C  378 PHE cc_start: 0.8762 (t80) cc_final: 0.6972 (p90)
REVERT: D  375 LYS cc_start: 0.8285 (tptp) cc_final: 0.7770 (tptm)
REVERT: D  379 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7284 (mmp-170)
REVERT: E  311 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8180 (mptm)
REVERT: E  331 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8802 (mttt)
REVERT: F  307 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6704 (tm-30)
REVERT: F  317 LYS cc_start: 0.9137 (ptmm) cc_final: 0.8919 (ptmm)
REVERT: F  375 LYS cc_start: 0.8600 (mptm) cc_final: 0.8352 (mptm)
REVERT: F  377 THR cc_start: 0.8646 (m) cc_final: 0.8432 (p)
  outliers start: 19
  outliers final: 13
  residues processed: 176
  average time/residue: 0.5125
  time to fit residues: 92.3537
Evaluate side-chains
  187 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 171
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  353 LYS
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 23 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    3.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.134770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.113263 restraints weight = 4528.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.48
r_work: 0.3783 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3672 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3468  Z= 0.221
  Angle     :  0.779   9.521   4632  Z= 0.377
  Chirality :  0.050   0.152    516
  Planarity :  0.003   0.040    588
  Dihedral  :  5.435  19.873    456
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 28.21 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.77 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 379 
 TYR   0.009   0.002   TYR B 310 
 PHE   0.006   0.001   PHE A 378 
 HIS   0.005   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 3468)
  covalent geometry    : angle       0.77879 ( 4632)
  hydrogen bonds       : bond        0.02086 (   55)
  hydrogen bonds       : angle       4.82186 (  165)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9145 (mttt) cc_final: 0.8594 (pttm)
REVERT: A  379 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7843 (mtp-110)
REVERT: B  317 LYS cc_start: 0.9033 (ptmm) cc_final: 0.8641 (ptpp)
REVERT: B  375 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8315 (pmtt)
REVERT: B  377 THR cc_start: 0.8677 (m) cc_final: 0.8396 (p)
REVERT: B  378 PHE cc_start: 0.9000 (t80) cc_final: 0.8572 (t80)
REVERT: C  307 GLN cc_start: 0.8567 (tt0) cc_final: 0.8203 (tp-100)
REVERT: C  311 LYS cc_start: 0.4780 (OUTLIER) cc_final: 0.4439 (mmmt)
REVERT: C  313 VAL cc_start: 0.9271 (t) cc_final: 0.8970 (p)
REVERT: C  316 SER cc_start: 0.9422 (p) cc_final: 0.9162 (p)
REVERT: C  317 LYS cc_start: 0.8593 (ptmt) cc_final: 0.8166 (ptpp)
REVERT: C  331 LYS cc_start: 0.8981 (mttm) cc_final: 0.7089 (tmtt)
REVERT: C  378 PHE cc_start: 0.8775 (t80) cc_final: 0.6989 (p90)
REVERT: D  311 LYS cc_start: 0.4674 (OUTLIER) cc_final: 0.3919 (mmpt)
REVERT: D  375 LYS cc_start: 0.8304 (tptp) cc_final: 0.7826 (tptm)
REVERT: D  379 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7269 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8830 (mttt)
REVERT: E  349 ARG cc_start: 0.7434 (mtm180) cc_final: 0.7025 (mtp180)
REVERT: F  307 GLN cc_start: 0.6972 (tm-30) cc_final: 0.6747 (tm-30)
REVERT: F  317 LYS cc_start: 0.9137 (ptmm) cc_final: 0.8911 (ptmm)
REVERT: F  375 LYS cc_start: 0.8638 (mptm) cc_final: 0.8395 (mptm)
REVERT: F  377 THR cc_start: 0.8811 (m) cc_final: 0.8569 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 173
  average time/residue: 0.5490
  time to fit residues: 97.2881
Evaluate side-chains
  185 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  353 LYS
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0020
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    3.1996

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.135405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.113988 restraints weight = 4536.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.51
r_work: 0.3794 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3468  Z= 0.206
  Angle     :  0.774   9.323   4632  Z= 0.372
  Chirality :  0.050   0.142    516
  Planarity :  0.003   0.041    588
  Dihedral  :  5.403  20.299    456
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 27.95 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.76 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 379 
 TYR   0.010   0.002   TYR B 310 
 PHE   0.006   0.001   PHE A 378 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 3468)
  covalent geometry    : angle       0.77381 ( 4632)
  hydrogen bonds       : bond        0.02008 (   55)
  hydrogen bonds       : angle       4.82344 (  165)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1961.64 seconds
wall clock time: 34 minutes 1.84 seconds (2041.84 seconds total)