Starting phenix.real_space_refine
on Wed Mar  5 19:49:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eoh_19855/03_2025/9eoh_19855.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eoh_19855/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eoh_19855/03_2025/9eoh_19855.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eoh_19855/03_2025/9eoh_19855.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eoh_19855/03_2025/9eoh_19855.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eoh_19855/03_2025/9eoh_19855.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:
    C, B, E, D, F
  Time building chain proxies: 2.52, per 1000 atoms: 0.74
  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: 0.81
  Conformation dependent library (CDL) restraints added in 499.5 milliseconds
  

  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: 0.55
  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: 0.97

  Time building geometry restraints manager: 0.97 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  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:             6.410
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.150
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.230
-------------------------------------------------------------------------------
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= 0.609
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.95 (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
 HIS   0.014   0.005   HIS F 362 
 PHE   0.017   0.004   PHE B 346 
 TYR   0.034   0.010   TYR F 310 
 ARG   0.004   0.001   ARG B 349 

*********************** 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  : 0.380 
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: 1.1617
  time to fit residues: 221.5450
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  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.143655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.121531 restraints weight = 4291.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 2.45
r_work: 0.3809 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3706 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3468  Z= 0.286
  Angle     :  0.722   6.356   4632  Z= 0.369
  Chirality :  0.052   0.187    516
  Planarity :  0.003   0.019    588
  Dihedral  :  5.729  14.898    456
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 19.74 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (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
 HIS   0.004   0.001   HIS B 362 
 PHE   0.010   0.001   PHE A 378 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.001   0.000   ARG F 349 

*********************** 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: 18
    poor density    : 170
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8579 (mmmt)
REVERT: A  349 ARG cc_start: 0.7321 (mtm180) cc_final: 0.7090 (mtm180)
REVERT: B  311 LYS cc_start: 0.8824 (tttt) cc_final: 0.8544 (pptt)
REVERT: B  317 LYS cc_start: 0.8970 (ptmm) cc_final: 0.8542 (ptpp)
REVERT: B  375 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8697 (mttm)
REVERT: C  307 GLN cc_start: 0.8750 (tt0) cc_final: 0.8248 (tp40)
REVERT: C  313 VAL cc_start: 0.9184 (t) cc_final: 0.8817 (p)
REVERT: C  317 LYS cc_start: 0.8414 (ptmt) cc_final: 0.8171 (ptpp)
REVERT: C  331 LYS cc_start: 0.9066 (mttm) cc_final: 0.7179 (tmtt)
REVERT: C  349 ARG cc_start: 0.7836 (mtm180) cc_final: 0.5846 (mmt-90)
REVERT: C  378 PHE cc_start: 0.8619 (t80) cc_final: 0.7304 (p90)
REVERT: E  319 THR cc_start: 0.8417 (m) cc_final: 0.7827 (p)
REVERT: E  331 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8880 (mttt)
REVERT: F  311 LYS cc_start: 0.8834 (tttt) cc_final: 0.8508 (pptt)
REVERT: F  375 LYS cc_start: 0.8661 (mptm) cc_final: 0.8443 (mptm)
  outliers start: 18
  outliers final: 9
  residues processed: 173
  average time/residue: 1.2351
  time to fit residues: 219.0724
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  : 0.442 
-------------------------------------------------------------------------------
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 27 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 336 GLN ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.141468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.119129 restraints weight = 4240.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 2.51
r_work: 0.3853 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3743 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3468  Z= 0.205
  Angle     :  0.641   6.499   4632  Z= 0.319
  Chirality :  0.050   0.157    516
  Planarity :  0.002   0.015    588
  Dihedral  :  5.290  15.035    456
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.59 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.23), residues: 432

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

*********************** 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
  182 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8906 (mttt) cc_final: 0.8696 (mtpt)
REVERT: A  316 SER cc_start: 0.9406 (p) cc_final: 0.9160 (p)
REVERT: A  349 ARG cc_start: 0.7067 (mtm180) cc_final: 0.6852 (mtm180)
REVERT: B  311 LYS cc_start: 0.8841 (tttt) cc_final: 0.8552 (pptt)
REVERT: B  317 LYS cc_start: 0.9008 (ptmm) cc_final: 0.8575 (ptpp)
REVERT: B  375 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8680 (mttm)
REVERT: B  378 PHE cc_start: 0.9115 (t80) cc_final: 0.8913 (t80)
REVERT: C  307 GLN cc_start: 0.8622 (tt0) cc_final: 0.8099 (tp-100)
REVERT: C  313 VAL cc_start: 0.9251 (t) cc_final: 0.8946 (p)
REVERT: C  317 LYS cc_start: 0.8411 (ptmt) cc_final: 0.8152 (ptpp)
REVERT: C  331 LYS cc_start: 0.9088 (mttm) cc_final: 0.7165 (tmtt)
REVERT: C  349 ARG cc_start: 0.7799 (mtm180) cc_final: 0.5883 (mmt-90)
REVERT: C  378 PHE cc_start: 0.8702 (t80) cc_final: 0.7194 (p90)
REVERT: D  375 LYS cc_start: 0.8446 (tptp) cc_final: 0.7982 (tptm)
REVERT: E  331 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8764 (mttt)
REVERT: F  311 LYS cc_start: 0.8807 (tttt) cc_final: 0.8514 (pptt)
REVERT: F  317 LYS cc_start: 0.9114 (ptmm) cc_final: 0.8840 (ptmm)
REVERT: F  349 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7636 (mtm180)
REVERT: F  375 LYS cc_start: 0.8616 (mptm) cc_final: 0.8335 (mptm)
  outliers start: 13
  outliers final: 7
  residues processed: 171
  average time/residue: 1.2155
  time to fit residues: 212.9648
Evaluate side-chains
  171 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
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 C residue  353 LYS
Chi-restraints excluded: chain E residue  331 LYS
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 36 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 6 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 1 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 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 = 0.4130 r_free = 0.4130 target = 0.132198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.111500 restraints weight = 4425.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 2.36
r_work: 0.3746 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   3468  Z= 0.490
  Angle     :  0.754   7.714   4632  Z= 0.391
  Chirality :  0.052   0.201    516
  Planarity :  0.003   0.012    588
  Dihedral  :  5.691  16.941    456
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 22.82 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 330 
 PHE   0.011   0.002   PHE E 378 
 TYR   0.011   0.003   TYR A 310 
 ARG   0.003   0.000   ARG A 379 

*********************** 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
  192 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9043 (mttt) cc_final: 0.8748 (mtpt)
REVERT: A  349 ARG cc_start: 0.7375 (mtm180) cc_final: 0.7162 (mtm180)
REVERT: A  379 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7897 (mtm-85)
REVERT: B  311 LYS cc_start: 0.8825 (tttt) cc_final: 0.8625 (pptt)
REVERT: B  317 LYS cc_start: 0.9059 (ptmm) cc_final: 0.8649 (ptpp)
REVERT: B  349 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7525 (ttp80)
REVERT: B  375 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8745 (mttm)
REVERT: B  378 PHE cc_start: 0.9168 (t80) cc_final: 0.8955 (t80)
REVERT: C  307 GLN cc_start: 0.8656 (tt0) cc_final: 0.8224 (tp-100)
REVERT: C  317 LYS cc_start: 0.8661 (ptmt) cc_final: 0.8320 (ptpp)
REVERT: C  331 LYS cc_start: 0.9087 (mttm) cc_final: 0.7238 (tmtt)
REVERT: C  378 PHE cc_start: 0.8803 (t80) cc_final: 0.7238 (p90)
REVERT: D  340 LYS cc_start: 0.8162 (mtpm) cc_final: 0.7673 (mttp)
REVERT: D  375 LYS cc_start: 0.8483 (tptp) cc_final: 0.8091 (tptm)
REVERT: D  379 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7500 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8943 (mttt)
REVERT: E  353 LYS cc_start: 0.8678 (mttm) cc_final: 0.8256 (mtpm)
REVERT: F  311 LYS cc_start: 0.8808 (tttt) cc_final: 0.8589 (pptt)
REVERT: F  317 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8900 (ptmm)
REVERT: F  349 ARG cc_start: 0.8042 (mtm180) cc_final: 0.7742 (mtm180)
REVERT: F  373 THR cc_start: 0.9169 (m) cc_final: 0.8969 (p)
REVERT: F  375 LYS cc_start: 0.8729 (mptm) cc_final: 0.8524 (mptm)
  outliers start: 24
  outliers final: 15
  residues processed: 171
  average time/residue: 1.1863
  time to fit residues: 207.9914
Evaluate side-chains
  179 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  320 SER
Chi-restraints excluded: chain B residue  349 ARG
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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 336 GLN ** 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 = 0.4223 r_free = 0.4223 target = 0.139262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.118109 restraints weight = 4277.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 2.44
r_work: 0.3827 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3468  Z= 0.247
  Angle     :  0.656   7.707   4632  Z= 0.326
  Chirality :  0.049   0.155    516
  Planarity :  0.002   0.012    588
  Dihedral  :  5.290  14.790    456
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.90 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS A 330 
 PHE   0.007   0.001   PHE E 378 
 TYR   0.009   0.002   TYR A 310 
 ARG   0.002   0.000   ARG A 379 

*********************** 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
  190 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 171
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9064 (mttt) cc_final: 0.8738 (mtpt)
REVERT: A  379 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7936 (mtm-85)
REVERT: B  317 LYS cc_start: 0.9047 (ptmm) cc_final: 0.8672 (ptpp)
REVERT: B  375 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8701 (mttm)
REVERT: B  377 THR cc_start: 0.8652 (m) cc_final: 0.8339 (p)
REVERT: B  378 PHE cc_start: 0.9073 (t80) cc_final: 0.8662 (t80)
REVERT: C  307 GLN cc_start: 0.8622 (tt0) cc_final: 0.8216 (tp-100)
REVERT: C  313 VAL cc_start: 0.9270 (t) cc_final: 0.9000 (p)
REVERT: C  316 SER cc_start: 0.9393 (p) cc_final: 0.9127 (p)
REVERT: C  317 LYS cc_start: 0.8589 (ptmt) cc_final: 0.8264 (ptpp)
REVERT: C  331 LYS cc_start: 0.9067 (mttm) cc_final: 0.7096 (tmtt)
REVERT: C  378 PHE cc_start: 0.8736 (t80) cc_final: 0.7197 (p90)
REVERT: D  316 SER cc_start: 0.9355 (p) cc_final: 0.9137 (p)
REVERT: D  336 GLN cc_start: 0.8548 (tp40) cc_final: 0.7982 (tt0)
REVERT: D  375 LYS cc_start: 0.8417 (tptp) cc_final: 0.7987 (tptm)
REVERT: D  379 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7504 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8801 (mttt)
REVERT: F  311 LYS cc_start: 0.8805 (tttt) cc_final: 0.8582 (pptt)
REVERT: F  317 LYS cc_start: 0.9150 (ptmm) cc_final: 0.8901 (ptmm)
REVERT: F  375 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8387 (mptm)
  outliers start: 19
  outliers final: 13
  residues processed: 172
  average time/residue: 1.2326
  time to fit residues: 217.2427
Evaluate side-chains
  183 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
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  320 SER
Chi-restraints excluded: chain C residue  353 LYS
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  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  375 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0470
   chunk 7 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.1884

-------------------------------------------------------------------------------
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 336 GLN ** 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 = 0.4216 r_free = 0.4216 target = 0.138813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.118131 restraints weight = 4349.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.40
r_work: 0.3837 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.4392

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= 0.241
  Angle     :  0.662   8.467   4632  Z= 0.324
  Chirality :  0.049   0.145    516
  Planarity :  0.002   0.015    588
  Dihedral  :  5.162  13.944    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 :  4.87 %
    Allowed  : 25.64 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 330 
 PHE   0.006   0.001   PHE E 378 
 TYR   0.009   0.002   TYR A 310 
 ARG   0.003   0.000   ARG F 379 

*********************** 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
  187 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9132 (mttt) cc_final: 0.8555 (pttm)
REVERT: A  379 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7845 (mtp-110)
REVERT: B  317 LYS cc_start: 0.9051 (ptmm) cc_final: 0.8685 (ptpp)
REVERT: B  321 LYS cc_start: 0.8877 (ttmm) cc_final: 0.7636 (pmtt)
REVERT: B  375 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8666 (mttm)
REVERT: B  377 THR cc_start: 0.8649 (m) cc_final: 0.8347 (p)
REVERT: B  378 PHE cc_start: 0.9014 (t80) cc_final: 0.8616 (t80)
REVERT: C  307 GLN cc_start: 0.8585 (tt0) cc_final: 0.8192 (tp-100)
REVERT: C  313 VAL cc_start: 0.9264 (t) cc_final: 0.8994 (p)
REVERT: C  316 SER cc_start: 0.9402 (p) cc_final: 0.9136 (p)
REVERT: C  317 LYS cc_start: 0.8622 (ptmt) cc_final: 0.8286 (ptpp)
REVERT: C  331 LYS cc_start: 0.9082 (mttm) cc_final: 0.7104 (tmtt)
REVERT: C  378 PHE cc_start: 0.8661 (t80) cc_final: 0.7183 (p90)
REVERT: D  316 SER cc_start: 0.9355 (p) cc_final: 0.9135 (p)
REVERT: D  336 GLN cc_start: 0.8542 (tp40) cc_final: 0.7975 (tp40)
REVERT: D  340 LYS cc_start: 0.8162 (mtpm) cc_final: 0.7676 (mttp)
REVERT: D  375 LYS cc_start: 0.8405 (tptp) cc_final: 0.7958 (tptm)
REVERT: D  379 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7447 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8801 (mttt)
REVERT: F  375 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8377 (mptm)
REVERT: F  377 THR cc_start: 0.8723 (m) cc_final: 0.8425 (p)
  outliers start: 19
  outliers final: 15
  residues processed: 170
  average time/residue: 1.2163
  time to fit residues: 211.8827
Evaluate side-chains
  184 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    2.2788

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.139354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.118316 restraints weight = 4355.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 2.52
r_work: 0.3830 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3468  Z= 0.249
  Angle     :  0.686   9.105   4632  Z= 0.333
  Chirality :  0.049   0.140    516
  Planarity :  0.003   0.027    588
  Dihedral  :  5.132  14.377    456
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 25.64 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (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
 HIS   0.005   0.001   HIS A 330 
 PHE   0.008   0.001   PHE E 378 
 TYR   0.010   0.002   TYR F 310 
 ARG   0.001   0.000   ARG E 349 

*********************** 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
  193 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.9103 (mttt) cc_final: 0.8491 (pttm)
REVERT: A  379 ARG cc_start: 0.8214 (mtm110) cc_final: 0.7800 (mtp-110)
REVERT: B  317 LYS cc_start: 0.9031 (ptmm) cc_final: 0.8647 (ptpp)
REVERT: B  349 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7358 (ttp80)
REVERT: B  375 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8680 (mptm)
REVERT: B  377 THR cc_start: 0.8615 (m) cc_final: 0.8339 (p)
REVERT: B  378 PHE cc_start: 0.9013 (t80) cc_final: 0.8556 (t80)
REVERT: C  307 GLN cc_start: 0.8575 (tt0) cc_final: 0.8188 (tp-100)
REVERT: C  311 LYS cc_start: 0.5135 (OUTLIER) cc_final: 0.4592 (mmmt)
REVERT: C  313 VAL cc_start: 0.9252 (t) cc_final: 0.8940 (p)
REVERT: C  316 SER cc_start: 0.9407 (p) cc_final: 0.9130 (p)
REVERT: C  317 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8198 (ptpp)
REVERT: C  331 LYS cc_start: 0.9020 (mttm) cc_final: 0.6980 (tmtt)
REVERT: C  378 PHE cc_start: 0.8659 (t80) cc_final: 0.7065 (p90)
REVERT: D  336 GLN cc_start: 0.8517 (tp40) cc_final: 0.7921 (tp40)
REVERT: D  340 LYS cc_start: 0.8146 (mtpm) cc_final: 0.7635 (mttp)
REVERT: D  379 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7409 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8715 (mttt)
REVERT: F  375 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8399 (mptm)
REVERT: F  377 THR cc_start: 0.8650 (m) cc_final: 0.8414 (p)
  outliers start: 23
  outliers final: 15
  residues processed: 171
  average time/residue: 1.2490
  time to fit residues: 218.7946
Evaluate side-chains
  188 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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  349 ARG
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    0.3980
   chunk 28 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.0186

-------------------------------------------------------------------------------
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 336 GLN ** 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 = 0.4308 r_free = 0.4308 target = 0.144387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.122244 restraints weight = 4284.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 2.57
r_work: 0.3907 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3796 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3468  Z= 0.178
  Angle     :  0.663   8.764   4632  Z= 0.314
  Chirality :  0.048   0.133    516
  Planarity :  0.003   0.036    588
  Dihedral  :  4.838  14.404    456
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 27.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS E 330 
 PHE   0.005   0.001   PHE E 378 
 TYR   0.008   0.001   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

*********************** 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
  191 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.9122 (mttt) cc_final: 0.8564 (pttm)
REVERT: A  379 ARG cc_start: 0.8179 (mtm110) cc_final: 0.7776 (mtp-110)
REVERT: B  311 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6030 (pptt)
REVERT: B  317 LYS cc_start: 0.9000 (ptmm) cc_final: 0.8615 (ptpp)
REVERT: B  321 LYS cc_start: 0.8853 (ttmm) cc_final: 0.7583 (pmtt)
REVERT: B  375 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8567 (mptm)
REVERT: B  377 THR cc_start: 0.8554 (m) cc_final: 0.8304 (p)
REVERT: B  378 PHE cc_start: 0.8971 (t80) cc_final: 0.8557 (t80)
REVERT: C  307 GLN cc_start: 0.8547 (tt0) cc_final: 0.8177 (tp-100)
REVERT: C  311 LYS cc_start: 0.4998 (OUTLIER) cc_final: 0.4510 (mmmt)
REVERT: C  313 VAL cc_start: 0.9185 (t) cc_final: 0.8848 (p)
REVERT: C  316 SER cc_start: 0.9400 (p) cc_final: 0.9126 (p)
REVERT: C  317 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8206 (ptpp)
REVERT: C  331 LYS cc_start: 0.9038 (mttm) cc_final: 0.6987 (tmtt)
REVERT: C  378 PHE cc_start: 0.8524 (t80) cc_final: 0.6975 (p90)
REVERT: D  319 THR cc_start: 0.8483 (m) cc_final: 0.8009 (p)
REVERT: D  336 GLN cc_start: 0.8480 (tp40) cc_final: 0.7876 (tt0)
REVERT: D  375 LYS cc_start: 0.8358 (tptp) cc_final: 0.7888 (tptm)
REVERT: D  379 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7515 (mmp-170)
REVERT: F  375 LYS cc_start: 0.8599 (mptm) cc_final: 0.8333 (mptm)
  outliers start: 17
  outliers final: 10
  residues processed: 175
  average time/residue: 1.2483
  time to fit residues: 223.7930
Evaluate side-chains
  182 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
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 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  320 SER
Chi-restraints excluded: chain E residue  320 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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**
A 368 ASN
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.141343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.120381 restraints weight = 4238.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.41
r_work: 0.3865 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3757 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.4806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3468  Z= 0.232
  Angle     :  0.723   9.760   4632  Z= 0.339
  Chirality :  0.049   0.133    516
  Planarity :  0.003   0.039    588
  Dihedral  :  4.981  15.530    456
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 29.23 %
    Favored  : 66.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.007   0.001   PHE E 378 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 379 

*********************** 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
  182 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.9135 (mttt) cc_final: 0.8612 (pttm)
REVERT: A  379 ARG cc_start: 0.8150 (mtm110) cc_final: 0.7752 (mtp-110)
REVERT: B  311 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.5886 (pptt)
REVERT: B  375 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8634 (mptm)
REVERT: B  377 THR cc_start: 0.8602 (m) cc_final: 0.8343 (p)
REVERT: B  378 PHE cc_start: 0.9011 (t80) cc_final: 0.8597 (t80)
REVERT: C  307 GLN cc_start: 0.8539 (tt0) cc_final: 0.8185 (tp-100)
REVERT: C  311 LYS cc_start: 0.5039 (OUTLIER) cc_final: 0.4514 (mmmt)
REVERT: C  313 VAL cc_start: 0.9303 (t) cc_final: 0.9010 (p)
REVERT: C  316 SER cc_start: 0.9338 (p) cc_final: 0.9100 (p)
REVERT: C  317 LYS cc_start: 0.8629 (ptmt) cc_final: 0.8216 (ptpp)
REVERT: C  331 LYS cc_start: 0.9051 (mttm) cc_final: 0.7082 (tmtt)
REVERT: C  378 PHE cc_start: 0.8579 (t80) cc_final: 0.7041 (p90)
REVERT: D  319 THR cc_start: 0.8525 (m) cc_final: 0.8069 (p)
REVERT: D  336 GLN cc_start: 0.8512 (tp40) cc_final: 0.7944 (tp40)
REVERT: D  379 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7357 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8810 (mttt)
REVERT: F  375 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8334 (mptm)
  outliers start: 15
  outliers final: 9
  residues processed: 168
  average time/residue: 1.2773
  time to fit residues: 219.6994
Evaluate side-chains
  179 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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  311 LYS
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  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  375 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 30 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.137393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.115394 restraints weight = 4437.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.51
r_work: 0.3824 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.4736

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= 0.287
  Angle     :  0.760  10.181   4632  Z= 0.358
  Chirality :  0.049   0.137    516
  Planarity :  0.003   0.042    588
  Dihedral  :  5.196  17.291    456
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 29.49 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 330 
 PHE   0.010   0.002   PHE E 378 
 TYR   0.009   0.002   TYR A 310 
 ARG   0.001   0.000   ARG F 349 

********************** 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
  182 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9114 (mttt) cc_final: 0.8564 (pttm)
REVERT: A  379 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7772 (mtp-110)
REVERT: B  311 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6122 (pptt)
REVERT: B  375 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8627 (mptm)
REVERT: B  377 THR cc_start: 0.8565 (m) cc_final: 0.8324 (p)
REVERT: B  378 PHE cc_start: 0.8972 (t80) cc_final: 0.8548 (t80)
REVERT: C  307 GLN cc_start: 0.8568 (tt0) cc_final: 0.8168 (tp-100)
REVERT: C  311 LYS cc_start: 0.4819 (OUTLIER) cc_final: 0.4374 (mmmt)
REVERT: C  316 SER cc_start: 0.9415 (p) cc_final: 0.9140 (p)
REVERT: C  317 LYS cc_start: 0.8570 (ptmt) cc_final: 0.8123 (ptpp)
REVERT: C  331 LYS cc_start: 0.8999 (mttm) cc_final: 0.6972 (tmtt)
REVERT: C  378 PHE cc_start: 0.8676 (t80) cc_final: 0.7092 (p90)
REVERT: D  336 GLN cc_start: 0.8530 (tp40) cc_final: 0.7924 (tp40)
REVERT: D  375 LYS cc_start: 0.8401 (tttt) cc_final: 0.7799 (tptm)
REVERT: D  379 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7323 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8760 (mttt)
REVERT: F  375 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8390 (mptm)
  outliers start: 13
  outliers final: 9
  residues processed: 170
  average time/residue: 1.2417
  time to fit residues: 216.3789
Evaluate side-chains
  180 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
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  311 LYS
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  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  375 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 = 0.4239 r_free = 0.4239 target = 0.138367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.116055 restraints weight = 4424.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.54
r_work: 0.3827 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.4797

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= 0.272
  Angle     :  0.760   9.722   4632  Z= 0.356
  Chirality :  0.049   0.132    516
  Planarity :  0.003   0.046    588
  Dihedral  :  5.225  17.974    456
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 29.49 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.006   0.001   PHE E 378 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.008   0.001   ARG E 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4502.50 seconds
wall clock time: 77 minutes 29.24 seconds (4649.24 seconds total)