Starting phenix.real_space_refine
on Mon Jan 13 17:42:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eoh_19855/01_2025/9eoh_19855.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eoh_19855/01_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_19855/01_2025/9eoh_19855.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eoh_19855/01_2025/9eoh_19855.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eoh_19855/01_2025/9eoh_19855.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eoh_19855/01_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-5571/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: 3.09, per 1000 atoms: 0.91
  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: 0.71
  Conformation dependent library (CDL) restraints added in 402.3 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: 0.47
  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: 0.80

  Time building geometry restraints manager: 0.86 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:             3.560
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.000
  Find NCS groups from input model:        0.070
  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:12.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.670
-------------------------------------------------------------------------------
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  : 0.395 
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: 1.3011
  time to fit residues: 248.0002
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  : 0.429 
-------------------------------------------------------------------------------
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 = 34)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.121582 restraints weight = 4291.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 2.43
r_work: 0.3819 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
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  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8587 (mmmt)
REVERT: A  349 ARG cc_start: 0.7354 (mtm180) cc_final: 0.7125 (mtm180)
REVERT: B  311 LYS cc_start: 0.8816 (tttt) cc_final: 0.8551 (pptt)
REVERT: B  317 LYS cc_start: 0.8977 (ptmm) cc_final: 0.8554 (ptpp)
REVERT: B  375 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8702 (mttm)
REVERT: C  307 GLN cc_start: 0.8747 (tt0) cc_final: 0.8253 (tp40)
REVERT: C  313 VAL cc_start: 0.9191 (t) cc_final: 0.8829 (p)
REVERT: C  317 LYS cc_start: 0.8438 (ptmt) cc_final: 0.8199 (ptpp)
REVERT: C  331 LYS cc_start: 0.9086 (mttm) cc_final: 0.7217 (tmtt)
REVERT: C  349 ARG cc_start: 0.7859 (mtm180) cc_final: 0.5881 (mmt-90)
REVERT: C  378 PHE cc_start: 0.8618 (t80) cc_final: 0.7307 (p90)
REVERT: E  319 THR cc_start: 0.8439 (m) cc_final: 0.7858 (p)
REVERT: E  331 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8903 (mttt)
REVERT: F  311 LYS cc_start: 0.8824 (tttt) cc_final: 0.8514 (pptt)
REVERT: F  375 LYS cc_start: 0.8663 (mptm) cc_final: 0.8449 (mptm)
  outliers start: 18
  outliers final: 9
  residues processed: 173
  average time/residue: 1.3146
  time to fit residues: 233.2919
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  : 0.453 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.2106

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.139794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.117430 restraints weight = 4268.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 2.50
r_work: 0.3830 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3468  Z= 0.236
  Angle     :  0.656   6.600   4632  Z= 0.329
  Chirality :  0.050   0.165    516
  Planarity :  0.002   0.015    588
  Dihedral  :  5.368  15.047    456
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 23.33 %
    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: -3.14 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E 330 
 PHE   0.007   0.001   PHE E 378 
 TYR   0.010   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: 14
    poor density    : 168
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8917 (mttt) cc_final: 0.8704 (mtpt)
REVERT: A  349 ARG cc_start: 0.7124 (mtm180) cc_final: 0.6894 (mtm180)
REVERT: B  311 LYS cc_start: 0.8836 (tttt) cc_final: 0.8560 (pptt)
REVERT: B  317 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8587 (ptpp)
REVERT: B  375 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8692 (mttm)
REVERT: C  307 GLN cc_start: 0.8656 (tt0) cc_final: 0.8129 (tp-100)
REVERT: C  313 VAL cc_start: 0.9260 (t) cc_final: 0.8957 (p)
REVERT: C  317 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8156 (ptpp)
REVERT: C  331 LYS cc_start: 0.9079 (mttm) cc_final: 0.7130 (tmtt)
REVERT: C  349 ARG cc_start: 0.7835 (mtm180) cc_final: 0.5918 (mmt-90)
REVERT: C  378 PHE cc_start: 0.8748 (t80) cc_final: 0.7208 (p90)
REVERT: D  375 LYS cc_start: 0.8445 (tptp) cc_final: 0.7984 (tptm)
REVERT: E  331 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8764 (mttt)
REVERT: E  353 LYS cc_start: 0.8690 (mttm) cc_final: 0.8219 (mtpm)
REVERT: F  311 LYS cc_start: 0.8805 (tttt) cc_final: 0.8517 (pptt)
REVERT: F  317 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8846 (ptmm)
REVERT: F  349 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7667 (mtm180)
REVERT: F  375 LYS cc_start: 0.8625 (mptm) cc_final: 0.8348 (mptm)
  outliers start: 14
  outliers final: 8
  residues processed: 171
  average time/residue: 1.2846
  time to fit residues: 225.0749
Evaluate side-chains
  170 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
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 D residue  320 SER
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:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 6 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    5.1588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.132948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.112189 restraints weight = 4420.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.37
r_work: 0.3754 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   3468  Z= 0.451
  Angle     :  0.738   7.697   4632  Z= 0.381
  Chirality :  0.052   0.197    516
  Planarity :  0.003   0.014    588
  Dihedral  :  5.648  16.676    456
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 22.56 %
    Favored  : 71.54 %
  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: -3.02 (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   0.005   0.001   HIS C 330 
 PHE   0.010   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
  193 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.9056 (mttt) cc_final: 0.8758 (mtpt)
REVERT: A  349 ARG cc_start: 0.7346 (mtm180) cc_final: 0.7136 (mtm180)
REVERT: A  379 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7896 (mtm-85)
REVERT: B  311 LYS cc_start: 0.8830 (tttt) cc_final: 0.8626 (pptt)
REVERT: B  317 LYS cc_start: 0.9059 (ptmm) cc_final: 0.8650 (ptpp)
REVERT: B  349 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7518 (ttp80)
REVERT: B  375 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8741 (mttm)
REVERT: C  307 GLN cc_start: 0.8655 (tt0) cc_final: 0.8216 (tp-100)
REVERT: C  317 LYS cc_start: 0.8650 (ptmt) cc_final: 0.8312 (ptpp)
REVERT: C  331 LYS cc_start: 0.9071 (mttm) cc_final: 0.7211 (tmtt)
REVERT: C  378 PHE cc_start: 0.8796 (t80) cc_final: 0.7183 (p90)
REVERT: D  375 LYS cc_start: 0.8431 (tptp) cc_final: 0.8011 (tptm)
REVERT: D  379 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7497 (mmp-170)
REVERT: E  353 LYS cc_start: 0.8669 (mttm) cc_final: 0.8260 (mtpm)
REVERT: F  311 LYS cc_start: 0.8807 (tttt) cc_final: 0.8588 (pptt)
REVERT: F  317 LYS cc_start: 0.9148 (ptmm) cc_final: 0.8885 (ptmm)
REVERT: F  349 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7731 (mtm180)
REVERT: F  375 LYS cc_start: 0.8740 (mptm) cc_final: 0.8537 (mptm)
  outliers start: 23
  outliers final: 15
  residues processed: 173
  average time/residue: 1.3406
  time to fit residues: 237.5396
Evaluate side-chains
  181 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
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 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:    4.9990
   chunk 35 optimal weight:    0.0370
   chunk 19 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.4064

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.138219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.115929 restraints weight = 4342.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 2.53
r_work: 0.3819 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3468  Z= 0.250
  Angle     :  0.653   7.698   4632  Z= 0.326
  Chirality :  0.049   0.158    516
  Planarity :  0.002   0.013    588
  Dihedral  :  5.288  14.602    456
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.38 %
    Favored  : 69.74 %
  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: -2.92 (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   0.005   0.001   HIS C 330 
 PHE   0.008   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
  189 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9043 (mttt) cc_final: 0.8711 (mtpt)
REVERT: A  379 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7700 (mtm-85)
REVERT: B  311 LYS cc_start: 0.8829 (tttt) cc_final: 0.8596 (pptt)
REVERT: B  317 LYS cc_start: 0.9039 (ptmm) cc_final: 0.8648 (ptpp)
REVERT: B  375 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8691 (mttm)
REVERT: B  378 PHE cc_start: 0.8952 (t80) cc_final: 0.8582 (t80)
REVERT: C  307 GLN cc_start: 0.8612 (tt0) cc_final: 0.8172 (tp-100)
REVERT: C  313 VAL cc_start: 0.9269 (t) cc_final: 0.8992 (p)
REVERT: C  316 SER cc_start: 0.9403 (p) cc_final: 0.9127 (p)
REVERT: C  317 LYS cc_start: 0.8538 (ptmt) cc_final: 0.8196 (ptpp)
REVERT: C  331 LYS cc_start: 0.8979 (mttm) cc_final: 0.7109 (tmtt)
REVERT: C  378 PHE cc_start: 0.8736 (t80) cc_final: 0.7181 (p90)
REVERT: D  316 SER cc_start: 0.9349 (p) cc_final: 0.9123 (p)
REVERT: D  375 LYS cc_start: 0.8381 (tptp) cc_final: 0.7926 (tptm)
REVERT: D  379 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7472 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8853 (mttt)
REVERT: F  311 LYS cc_start: 0.8837 (tttt) cc_final: 0.8562 (pptt)
REVERT: F  317 LYS cc_start: 0.9146 (ptmm) cc_final: 0.8919 (ptmm)
REVERT: F  375 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8433 (mptm)
  outliers start: 19
  outliers final: 14
  residues processed: 172
  average time/residue: 1.2560
  time to fit residues: 221.2008
Evaluate side-chains
  184 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
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  375 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0980
   chunk 7 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    1.8188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.139303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.117423 restraints weight = 4361.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 2.50
r_work: 0.3846 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.4356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3468  Z= 0.212
  Angle     :  0.638   8.222   4632  Z= 0.313
  Chirality :  0.048   0.141    516
  Planarity :  0.002   0.012    588
  Dihedral  :  5.081  13.962    456
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 24.62 %
    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: -2.88 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 330 
 PHE   0.005   0.001   PHE A 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
  185 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9055 (mttt) cc_final: 0.8470 (pttm)
REVERT: A  379 ARG cc_start: 0.8185 (mtm110) cc_final: 0.7816 (mtp-110)
REVERT: B  317 LYS cc_start: 0.9036 (ptmm) cc_final: 0.8659 (ptpp)
REVERT: B  321 LYS cc_start: 0.8867 (ttmm) cc_final: 0.7552 (pmtt)
REVERT: B  349 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7340 (ttp80)
REVERT: B  375 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8652 (mttm)
REVERT: B  377 THR cc_start: 0.8519 (m) cc_final: 0.8240 (p)
REVERT: B  378 PHE cc_start: 0.8926 (t80) cc_final: 0.8494 (t80)
REVERT: C  307 GLN cc_start: 0.8592 (tt0) cc_final: 0.8158 (tp-100)
REVERT: C  313 VAL cc_start: 0.9250 (t) cc_final: 0.8964 (p)
REVERT: C  316 SER cc_start: 0.9407 (p) cc_final: 0.9133 (p)
REVERT: C  317 LYS cc_start: 0.8528 (ptmt) cc_final: 0.8178 (ptpp)
REVERT: C  331 LYS cc_start: 0.9004 (mttm) cc_final: 0.7118 (tmtt)
REVERT: C  378 PHE cc_start: 0.8666 (t80) cc_final: 0.7159 (p90)
REVERT: D  316 SER cc_start: 0.9349 (p) cc_final: 0.9118 (p)
REVERT: D  340 LYS cc_start: 0.8134 (mtpm) cc_final: 0.7613 (mttp)
REVERT: D  375 LYS cc_start: 0.8371 (tptp) cc_final: 0.7899 (tptm)
REVERT: D  379 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7443 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8839 (mttt)
REVERT: F  311 LYS cc_start: 0.8815 (tttt) cc_final: 0.8566 (pptt)
REVERT: F  317 LYS cc_start: 0.9134 (ptmm) cc_final: 0.8925 (ptmm)
REVERT: F  375 LYS cc_start: 0.8639 (mptm) cc_final: 0.8404 (mptm)
REVERT: F  377 THR cc_start: 0.8648 (m) cc_final: 0.8374 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 170
  average time/residue: 1.2731
  time to fit residues: 221.6933
Evaluate side-chains
  182 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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  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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    3.9990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.134433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.113652 restraints weight = 4422.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 2.39
r_work: 0.3775 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3667 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.4347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3468  Z= 0.371
  Angle     :  0.734   9.543   4632  Z= 0.365
  Chirality :  0.050   0.166    516
  Planarity :  0.002   0.018    588
  Dihedral  :  5.431  14.605    456
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 25.13 %
    Favored  : 69.74 %
  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: -2.86 (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   0.009   0.002   PHE A 378 
 TYR   0.010   0.003   TYR B 310 
 ARG   0.001   0.000   ARG E 379 

*********************** 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
  187 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9134 (mttt) cc_final: 0.8554 (pttm)
REVERT: A  379 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7811 (mtp-110)
REVERT: B  317 LYS cc_start: 0.9059 (ptmm) cc_final: 0.8671 (ptpp)
REVERT: B  349 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7470 (ttp80)
REVERT: B  375 LYS cc_start: 0.9047 (ttmt) cc_final: 0.8666 (mttm)
REVERT: B  377 THR cc_start: 0.8609 (m) cc_final: 0.8338 (p)
REVERT: B  378 PHE cc_start: 0.8959 (t80) cc_final: 0.8486 (t80)
REVERT: C  307 GLN cc_start: 0.8579 (tt0) cc_final: 0.8216 (tp-100)
REVERT: C  311 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4652 (mmtt)
REVERT: C  313 VAL cc_start: 0.9291 (t) cc_final: 0.9006 (p)
REVERT: C  317 LYS cc_start: 0.8643 (ptmt) cc_final: 0.8272 (ptpp)
REVERT: C  331 LYS cc_start: 0.9035 (mttm) cc_final: 0.7175 (tmtt)
REVERT: C  378 PHE cc_start: 0.8783 (t80) cc_final: 0.7187 (p90)
REVERT: D  375 LYS cc_start: 0.8374 (tptp) cc_final: 0.7938 (tptm)
REVERT: D  379 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7384 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8927 (mttt)
REVERT: E  379 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7670 (mtm-85)
REVERT: F  317 LYS cc_start: 0.9152 (ptmm) cc_final: 0.8914 (ptmm)
REVERT: F  375 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8481 (mptm)
REVERT: F  377 THR cc_start: 0.8732 (m) cc_final: 0.8446 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 170
  average time/residue: 1.2632
  time to fit residues: 219.9787
Evaluate side-chains
  183 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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  375 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    3.1786

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.137024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.116245 restraints weight = 4368.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 2.41
r_work: 0.3811 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3468  Z= 0.310
  Angle     :  0.721   9.247   4632  Z= 0.352
  Chirality :  0.050   0.149    516
  Planarity :  0.003   0.032    588
  Dihedral  :  5.330  15.561    456
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 24.36 %
    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: -2.77 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.008   0.001   PHE E 378 
 TYR   0.009   0.002   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
  196 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.9146 (mttt) cc_final: 0.8582 (pttm)
REVERT: A  379 ARG cc_start: 0.8224 (mtm110) cc_final: 0.7866 (mtp-110)
REVERT: B  311 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6156 (pptt)
REVERT: B  317 LYS cc_start: 0.9056 (ptmm) cc_final: 0.8687 (ptpp)
REVERT: B  349 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7457 (ttp80)
REVERT: B  375 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8728 (ttmm)
REVERT: B  377 THR cc_start: 0.8602 (m) cc_final: 0.8328 (p)
REVERT: B  378 PHE cc_start: 0.8996 (t80) cc_final: 0.8518 (t80)
REVERT: C  307 GLN cc_start: 0.8547 (tt0) cc_final: 0.8203 (tp-100)
REVERT: C  311 LYS cc_start: 0.4920 (OUTLIER) cc_final: 0.4501 (mmtt)
REVERT: C  313 VAL cc_start: 0.9295 (t) cc_final: 0.9021 (p)
REVERT: C  316 SER cc_start: 0.9421 (p) cc_final: 0.9171 (p)
REVERT: C  317 LYS cc_start: 0.8646 (ptmt) cc_final: 0.8268 (ptpp)
REVERT: C  331 LYS cc_start: 0.9026 (mttm) cc_final: 0.7178 (tmtt)
REVERT: C  378 PHE cc_start: 0.8721 (t80) cc_final: 0.7141 (p90)
REVERT: D  311 LYS cc_start: 0.5180 (OUTLIER) cc_final: 0.3821 (mmpt)
REVERT: D  340 LYS cc_start: 0.8167 (mtpm) cc_final: 0.7695 (mttp)
REVERT: D  379 ARG cc_start: 0.7996 (mtm180) cc_final: 0.7380 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8923 (mttt)
REVERT: F  317 LYS cc_start: 0.9145 (ptmm) cc_final: 0.8917 (ptmm)
REVERT: F  375 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8402 (mptm)
REVERT: F  377 THR cc_start: 0.8727 (m) cc_final: 0.8479 (p)
  outliers start: 25
  outliers final: 16
  residues processed: 173
  average time/residue: 1.2515
  time to fit residues: 221.8839
Evaluate side-chains
  192 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  353 LYS
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  375 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 307 GLN
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.135959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.114587 restraints weight = 4330.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.44
r_work: 0.3794 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3681 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3468  Z= 0.375
  Angle     :  0.766   9.707   4632  Z= 0.376
  Chirality :  0.050   0.162    516
  Planarity :  0.003   0.038    588
  Dihedral  :  5.546  17.626    456
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 24.62 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.81 (0.31), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 330 
 PHE   0.008   0.002   PHE A 378 
 TYR   0.011   0.003   TYR B 310 
 ARG   0.002   0.000   ARG F 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
  189 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.9139 (mttt) cc_final: 0.8569 (pttm)
REVERT: A  379 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7870 (mtp-110)
REVERT: B  311 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6020 (pptt)
REVERT: B  317 LYS cc_start: 0.9051 (ptmm) cc_final: 0.8665 (ptpp)
REVERT: B  349 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7429 (ttp80)
REVERT: B  375 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8697 (ttmm)
REVERT: B  377 THR cc_start: 0.8572 (m) cc_final: 0.8326 (p)
REVERT: B  378 PHE cc_start: 0.9002 (t80) cc_final: 0.8504 (t80)
REVERT: C  307 GLN cc_start: 0.8551 (tt0) cc_final: 0.8177 (tp-100)
REVERT: C  311 LYS cc_start: 0.4643 (OUTLIER) cc_final: 0.3825 (mmtt)
REVERT: C  313 VAL cc_start: 0.9287 (t) cc_final: 0.9007 (p)
REVERT: C  316 SER cc_start: 0.9411 (p) cc_final: 0.9143 (p)
REVERT: C  317 LYS cc_start: 0.8591 (ptmt) cc_final: 0.8171 (ptpp)
REVERT: C  331 LYS cc_start: 0.8971 (mttm) cc_final: 0.7092 (tmtt)
REVERT: C  378 PHE cc_start: 0.8798 (t80) cc_final: 0.7227 (p90)
REVERT: D  311 LYS cc_start: 0.4486 (OUTLIER) cc_final: 0.3000 (mmpt)
REVERT: D  375 LYS cc_start: 0.8302 (tptp) cc_final: 0.7828 (tptm)
REVERT: D  379 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7271 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8854 (mttt)
REVERT: F  317 LYS cc_start: 0.9134 (ptmm) cc_final: 0.8892 (ptmm)
REVERT: F  375 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8482 (mptm)
REVERT: F  377 THR cc_start: 0.8721 (m) cc_final: 0.8484 (p)
  outliers start: 25
  outliers final: 16
  residues processed: 167
  average time/residue: 1.2863
  time to fit residues: 219.8869
Evaluate side-chains
  185 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  353 LYS
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  375 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
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:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   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**
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 = 0.4233 r_free = 0.4233 target = 0.140263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.119380 restraints weight = 4335.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 2.43
r_work: 0.3852 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.4712

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= 0.238
  Angle     :  0.714   9.148   4632  Z= 0.341
  Chirality :  0.048   0.131    516
  Planarity :  0.003   0.040    588
  Dihedral  :  5.217  17.379    456
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 26.15 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.004   0.001   PHE A 378 
 TYR   0.010   0.002   TYR B 310 
 ARG   0.001   0.000   ARG E 379 

********************** 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
  189 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8095 (pp30)
REVERT: A  311 LYS cc_start: 0.9164 (mttt) cc_final: 0.8954 (mtpt)
REVERT: A  379 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7819 (mtp-110)
REVERT: B  317 LYS cc_start: 0.9043 (ptmm) cc_final: 0.8676 (ptpp)
REVERT: B  375 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8656 (ttmm)
REVERT: B  377 THR cc_start: 0.8528 (m) cc_final: 0.8287 (p)
REVERT: B  378 PHE cc_start: 0.8988 (t80) cc_final: 0.8508 (t80)
REVERT: C  307 GLN cc_start: 0.8556 (tt0) cc_final: 0.8202 (tp-100)
REVERT: C  311 LYS cc_start: 0.4943 (OUTLIER) cc_final: 0.4579 (mmmt)
REVERT: C  313 VAL cc_start: 0.9274 (t) cc_final: 0.9000 (p)
REVERT: C  316 SER cc_start: 0.9415 (p) cc_final: 0.9169 (p)
REVERT: C  317 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8268 (ptpp)
REVERT: C  331 LYS cc_start: 0.9055 (mttm) cc_final: 0.7209 (tmtt)
REVERT: C  378 PHE cc_start: 0.8796 (t80) cc_final: 0.7138 (p90)
REVERT: D  311 LYS cc_start: 0.4837 (OUTLIER) cc_final: 0.3248 (mmpt)
REVERT: D  340 LYS cc_start: 0.8190 (mtpm) cc_final: 0.7706 (mttp)
REVERT: D  375 LYS cc_start: 0.8293 (tptp) cc_final: 0.7828 (tptm)
REVERT: D  379 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7295 (mmp-170)
REVERT: E  331 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8913 (mttt)
REVERT: F  317 LYS cc_start: 0.9127 (ptmm) cc_final: 0.8916 (ptmm)
REVERT: F  375 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8383 (mptm)
REVERT: F  379 ARG cc_start: 0.7064 (mtm180) cc_final: 0.6249 (pmt170)
  outliers start: 19
  outliers final: 13
  residues processed: 171
  average time/residue: 1.3064
  time to fit residues: 228.6867
Evaluate side-chains
  186 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  353 LYS
Chi-restraints excluded: chain D residue  309 VAL
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  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:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   overall best weight:    3.3986

-------------------------------------------------------------------------------
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 = 0.4199 r_free = 0.4199 target = 0.135167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.113321 restraints weight = 4481.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.48
r_work: 0.3796 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3468  Z= 0.337
  Angle     :  0.765   9.662   4632  Z= 0.369
  Chirality :  0.050   0.146    516
  Planarity :  0.003   0.042    588
  Dihedral  :  5.425  19.880    456
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 27.44 %
    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: -2.78 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 330 
 PHE   0.006   0.002   PHE A 378 
 TYR   0.009   0.002   TYR A 310 
 ARG   0.001   0.000   ARG F 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4313.07 seconds
wall clock time: 77 minutes 11.77 seconds (4631.77 seconds total)