Starting phenix.real_space_refine
on Mon Jun  9 09:32:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bbl_44421/06_2025/9bbl_44421_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bbl_44421/06_2025/9bbl_44421.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bbl_44421/06_2025/9bbl_44421.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bbl_44421/06_2025/9bbl_44421.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bbl_44421/06_2025/9bbl_44421_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bbl_44421/06_2025/9bbl_44421_neut.cif"
  }
  resolution = 2.5
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S       9      5.16       5
     C    3198      2.51       5
     N     936      2.21       5
     O     951      1.98       5
     H    5301      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10395
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1121
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "B"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 1121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1121
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "E"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "G"
      Number of atoms: 1121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1121
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "H"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "I"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 6.24, per 1000 atoms: 0.60
  Number of scatterers: 10395
  At special positions: 0
  Unit cell: (151.58, 134.62, 41.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       9     16.00
     O     951      8.00
     N     936      7.00
     C    3198      6.00
     H    5301      1.00
    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: 2.54
  Conformation dependent library (CDL) restraints added in 709.6 milliseconds
  

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1170

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 25 sheets defined
      0.0% alpha, 42.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.823A  pdb=" N   VAL A 313 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 321
      removed outlier: 6.359A  pdb=" N   LYS A 317 " --> pdb=" O   VAL G 318 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   SER G 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   THR A 319 " --> pdb=" O   SER G 320 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330
      removed outlier: 6.561A  pdb=" N   HIS A 329 " --> pdb=" O   HIS G 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 339
      removed outlier: 6.437A  pdb=" N   GLN A 336 " --> pdb=" O   VAL G 337 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   VAL G 339 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLU A 338 " --> pdb=" O   VAL G 339 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347
      removed outlier: 6.431A  pdb=" N   PHE D 346 " --> pdb=" O   LYS G 347 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 356
      removed outlier: 6.836A  pdb=" N   SER G 356 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   SER D 352 " --> pdb=" O   LYS G 353 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   GLY G 355 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   ILE D 354 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362
      removed outlier: 6.252A  pdb=" N   ILE A 360 " --> pdb=" O   THR G 361 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASN D 359 " --> pdb=" O   ILE G 360 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   HIS G 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   THR D 361 " --> pdb=" O   HIS G 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 372
      removed outlier: 6.737A  pdb=" N   LYS A 369 " --> pdb=" O   LYS G 370 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   GLU G 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE A 371 " --> pdb=" O   GLU G 372 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 308
    Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 322
      removed outlier: 6.377A  pdb=" N   LYS B 317 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   SER H 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   THR B 319 " --> pdb=" O   SER H 320 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   CYS H 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LYS B 321 " --> pdb=" O   CYS H 322 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 330
      removed outlier: 8.725A  pdb=" N   LEU B 325 " --> pdb=" O   GLY H 326 " (cutoff:3.500A)
      removed outlier: 9.780A  pdb=" N   ILE H 328 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ASN B 327 " --> pdb=" O   ILE H 328 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   HIS H 330 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   HIS B 329 " --> pdb=" O   HIS H 330 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   GLY E 326 " --> pdb=" O   LEU H 325 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASN H 327 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.338A  pdb=" N   VAL E 337 " --> pdb=" O   GLU H 338 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   LYS H 340 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL E 339 " --> pdb=" O   LYS H 340 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 344 through 347
      removed outlier: 6.695A  pdb=" N   LEU E 344 " --> pdb=" O   ASP H 345 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   LYS H 347 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   PHE E 346 " --> pdb=" O   LYS H 347 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 351 through 354
      removed outlier: 6.448A  pdb=" N   GLN B 351 " --> pdb=" O   SER H 352 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   ILE H 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS B 353 " --> pdb=" O   ILE H 354 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 357 through 362
      removed outlier: 6.501A  pdb=" N   ASP B 358 " --> pdb=" O   ASN H 359 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   THR H 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE B 360 " --> pdb=" O   THR H 361 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 374
      removed outlier: 6.634A  pdb=" N   LYS B 369 " --> pdb=" O   LYS H 370 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   GLU H 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ILE B 371 " --> pdb=" O   GLU H 372 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   HIS H 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   THR B 373 " --> pdb=" O   HIS H 374 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 377 through 378
      removed outlier: 6.394A  pdb=" N   THR B 377 " --> pdb=" O   PHE H 378 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.567A  pdb=" N   GLN C 307 " --> pdb=" O   ILE I 308 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   TYR I 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL C 309 " --> pdb=" O   TYR I 310 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL F 306 " --> pdb=" O   GLN I 307 " (cutoff:3.500A)
      removed outlier: 8.396A  pdb=" N   VAL I 309 " --> pdb=" O   VAL F 306 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ILE F 308 " --> pdb=" O   VAL I 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.399A  pdb=" N   LYS C 317 " --> pdb=" O   VAL I 318 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   SER I 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   THR C 319 " --> pdb=" O   SER I 320 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   CYS I 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LYS C 321 " --> pdb=" O   CYS I 322 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 325 through 330
      removed outlier: 8.706A  pdb=" N   LEU C 325 " --> pdb=" O   GLY I 326 " (cutoff:3.500A)
      removed outlier: 9.917A  pdb=" N   ILE I 328 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ASN C 327 " --> pdb=" O   ILE I 328 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   HIS I 330 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   HIS C 329 " --> pdb=" O   HIS I 330 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   GLY F 326 " --> pdb=" O   LEU I 325 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ASN I 327 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 336 through 340
      removed outlier: 6.430A  pdb=" N   VAL F 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   LYS I 340 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   VAL F 339 " --> pdb=" O   LYS I 340 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 344 through 347
      removed outlier: 6.483A  pdb=" N   LEU F 344 " --> pdb=" O   ASP I 345 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   LYS I 347 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   PHE F 346 " --> pdb=" O   LYS I 347 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 350 through 356
      removed outlier: 6.829A  pdb=" N   SER I 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   VAL F 350 " --> pdb=" O   GLN I 351 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   LYS I 353 " --> pdb=" O   VAL F 350 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   SER F 352 " --> pdb=" O   LYS I 353 " (cutoff:3.500A)
      removed outlier: 8.645A  pdb=" N   GLY I 355 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 8.457A  pdb=" N   ILE F 354 " --> pdb=" O   GLY I 355 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 359 through 362
      removed outlier: 6.553A  pdb=" N   ASN F 359 " --> pdb=" O   ILE I 360 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   HIS I 362 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR F 361 " --> pdb=" O   HIS I 362 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 369 through 377

    91 hydrogen bonds defined for protein.
    273 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: 3.06

  Time building geometry restraints manager: 3.12 seconds

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

  Histogram of bond lengths:
        0.91 -     1.09: 5292
        1.09 -     1.27: 846
        1.27 -     1.45: 1242
        1.45 -     1.63: 3087
        1.63 -     1.81: 9
  Bond restraints: 10476
  Sorted by residual:
  bond pdb=" N   THR G 361 "
       pdb=" H   THR G 361 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" ND1 HIS D 330 "
       pdb=" HD1 HIS D 330 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CE2 PHE D 378 "
       pdb=" HE2 PHE D 378 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CD1 PHE D 378 "
       pdb=" HD1 PHE D 378 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   SER D 324 "
       pdb=" H   SER D 324 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  ... (remaining 10471 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 15638
        2.46 -     4.93: 2586
        4.93 -     7.39: 807
        7.39 -     9.86: 52
        9.86 -    12.32: 12
  Bond angle restraints: 19095
  Sorted by residual:
  angle pdb=" CA  ASP D 358 "
        pdb=" CB  ASP D 358 "
        pdb=" CG  ASP D 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.26   -5.66 1.00e+00 1.00e+00 3.20e+01
  angle pdb=" C   GLU C 342 "
        pdb=" CA  GLU C 342 "
        pdb=" CB  GLU C 342 "
      ideal   model   delta    sigma   weight residual
     110.42  121.14  -10.72 1.99e+00 2.53e-01 2.90e+01
  angle pdb=" CA  PHE D 346 "
        pdb=" CB  PHE D 346 "
        pdb=" CG  PHE D 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.17   -5.37 1.00e+00 1.00e+00 2.89e+01
  angle pdb=" CA  ASP G 358 "
        pdb=" CB  ASP G 358 "
        pdb=" CG  ASP G 358 "
      ideal   model   delta    sigma   weight residual
     112.60  117.77   -5.17 1.00e+00 1.00e+00 2.67e+01
  angle pdb=" CB  HIS G 329 "
        pdb=" CG  HIS G 329 "
        pdb=" CD2 HIS G 329 "
      ideal   model   delta    sigma   weight residual
     131.20  124.51    6.69 1.30e+00 5.92e-01 2.65e+01
  ... (remaining 19090 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 4344
       17.30 -    34.61: 233
       34.61 -    51.91: 101
       51.91 -    69.22: 143
       69.22 -    86.52: 6
  Dihedral angle restraints: 4827
    sinusoidal: 2757
      harmonic: 2070
  Sorted by residual:
  dihedral pdb=" C   GLU C 342 "
           pdb=" N   GLU C 342 "
           pdb=" CA  GLU C 342 "
           pdb=" CB  GLU C 342 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.00   11.40     0      2.50e+00 1.60e-01 2.08e+01
  dihedral pdb=" C   GLU I 342 "
           pdb=" N   GLU I 342 "
           pdb=" CA  GLU I 342 "
           pdb=" CB  GLU I 342 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.42    9.82     0      2.50e+00 1.60e-01 1.54e+01
  dihedral pdb=" C   ARG B 349 "
           pdb=" N   ARG B 349 "
           pdb=" CA  ARG B 349 "
           pdb=" CB  ARG B 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.72    9.12     0      2.50e+00 1.60e-01 1.33e+01
  ... (remaining 4824 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 463
       0.081 -    0.161: 238
       0.161 -    0.242: 63
       0.242 -    0.323: 11
       0.323 -    0.403: 5
  Chirality restraints: 780
  Sorted by residual:
  chirality pdb=" CA  PRO I 332 "
            pdb=" N   PRO I 332 "
            pdb=" C   PRO I 332 "
            pdb=" CB  PRO I 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.32    0.40 2.00e-01 2.50e+01 4.06e+00
  chirality pdb=" CA  LEU A 325 "
            pdb=" N   LEU A 325 "
            pdb=" C   LEU A 325 "
            pdb=" CB  LEU A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.30e+00
  chirality pdb=" CG  LEU C 357 "
            pdb=" CB  LEU C 357 "
            pdb=" CD1 LEU C 357 "
            pdb=" CD2 LEU C 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.93    0.34 2.00e-01 2.50e+01 2.93e+00
  ... (remaining 777 not shown)

  Planarity restraints: 1509
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 329 "    0.040 2.00e-02 2.50e+03   6.00e-02 8.11e+01
        pdb=" CG  HIS B 329 "   -0.118 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 329 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 329 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 329 "   -0.013 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 329 "   -0.022 2.00e-02 2.50e+03
        pdb=" HD1 HIS B 329 "    0.058 2.00e-02 2.50e+03
        pdb=" HD2 HIS B 329 "    0.091 2.00e-02 2.50e+03
        pdb=" HE1 HIS B 329 "    0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS H 329 "    0.045 2.00e-02 2.50e+03   5.67e-02 7.23e+01
        pdb=" CG  HIS H 329 "   -0.131 2.00e-02 2.50e+03
        pdb=" ND1 HIS H 329 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS H 329 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE1 HIS H 329 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS H 329 "   -0.015 2.00e-02 2.50e+03
        pdb=" HD1 HIS H 329 "    0.032 2.00e-02 2.50e+03
        pdb=" HD2 HIS H 329 "    0.077 2.00e-02 2.50e+03
        pdb=" HE1 HIS H 329 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 329 "   -0.058 2.00e-02 2.50e+03   5.00e-02 5.62e+01
        pdb=" CG  HIS C 329 "    0.101 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 329 "    0.041 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 329 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 329 "    0.009 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 329 "    0.006 2.00e-02 2.50e+03
        pdb=" HD1 HIS C 329 "   -0.032 2.00e-02 2.50e+03
        pdb=" HD2 HIS C 329 "   -0.054 2.00e-02 2.50e+03
        pdb=" HE1 HIS C 329 "   -0.045 2.00e-02 2.50e+03
  ... (remaining 1506 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 542
        2.15 -     2.76: 17211
        2.76 -     3.37: 28116
        3.37 -     3.99: 36273
        3.99 -     4.60: 52416
  Nonbonded interactions: 134558
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP G 314 "
            pdb=" HG  SER G 316 "
     model   vdw
     1.532 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.539 2.450
  nonbonded pdb=" OD1 ASP I 314 "
            pdb=" HG  SER I 316 "
     model   vdw
     1.543 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.548 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.552 2.450
  ... (remaining 134553 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 307 through 378)
  selection = (chain 'C' and resid 307 through 378)
  selection = chain 'D'
  selection = (chain 'E' and resid 307 through 378)
  selection = (chain 'F' and resid 307 through 378)
  selection = chain 'G'
  selection = (chain 'H' and resid 307 through 378)
  selection = (chain 'I' and resid 307 through 378)
}

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:             4.240
  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:             0.170
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     25.350
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  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:12.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6397
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      :  0.011   0.045   5175  Z= 0.692
  Angle     :  2.112  10.719   6924  Z= 1.371
  Chirality :  0.102   0.403    780
  Planarity :  0.013   0.110    879
  Dihedral  : 10.019  86.521   1986
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 0.19
  Ramachandran Plot:
    Outliers :  1.39 %
    Allowed  :  9.72 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.34 %
  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: -2.48 (0.26), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.20), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.043   0.008   HIS H 329 
 PHE   0.027   0.010   PHE I 346 
 TYR   0.059   0.014   TYR B 310 
 ARG   0.009   0.002   ARG H 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12064 (   91)
  hydrogen bonds       : angle       7.19332 (  273)
  covalent geometry    : bond        0.01098 ( 5175)
  covalent geometry    : angle       2.11181 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8083 (mtmt) cc_final: 0.6036 (tptp)
REVERT: A  342 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6624 (mp0)
REVERT: A  343 LYS cc_start: 0.8253 (mttt) cc_final: 0.8044 (mtmt)
REVERT: A  356 SER cc_start: 0.7966 (p) cc_final: 0.7681 (t)
REVERT: A  358 ASP cc_start: 0.7916 (m-30) cc_final: 0.7523 (m-30)
REVERT: B  307 GLN cc_start: 0.7736 (pt0) cc_final: 0.7487 (pt0)
REVERT: B  311 LYS cc_start: 0.7880 (mttt) cc_final: 0.6900 (mmtm)
REVERT: B  317 LYS cc_start: 0.7429 (mtmt) cc_final: 0.6527 (tttp)
REVERT: B  321 LYS cc_start: 0.7563 (tttt) cc_final: 0.7139 (tmmm)
REVERT: B  336 GLN cc_start: 0.7656 (mt0) cc_final: 0.7398 (mt0)
REVERT: B  338 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6766 (mt-10)
REVERT: B  340 LYS cc_start: 0.7572 (tttt) cc_final: 0.7152 (mtpp)
REVERT: B  345 ASP cc_start: 0.7816 (t0) cc_final: 0.7469 (t0)
REVERT: B  347 LYS cc_start: 0.7145 (mttp) cc_final: 0.6716 (mttp)
REVERT: B  348 ASP cc_start: 0.7527 (t0) cc_final: 0.7217 (t0)
REVERT: C  311 LYS cc_start: 0.7807 (mttt) cc_final: 0.6969 (mmtm)
REVERT: C  321 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6426 (tmtm)
REVERT: C  331 LYS cc_start: 0.7388 (mttt) cc_final: 0.6965 (mtpt)
REVERT: C  338 GLU cc_start: 0.7151 (tt0) cc_final: 0.6913 (tt0)
REVERT: C  345 ASP cc_start: 0.8198 (t0) cc_final: 0.7530 (t0)
REVERT: C  347 LYS cc_start: 0.7187 (mttt) cc_final: 0.6769 (mtpp)
REVERT: C  348 ASP cc_start: 0.7867 (t0) cc_final: 0.7647 (t0)
REVERT: C  372 GLU cc_start: 0.8161 (tt0) cc_final: 0.7899 (tt0)
REVERT: D  311 LYS cc_start: 0.8118 (tttt) cc_final: 0.7580 (ttmp)
REVERT: D  317 LYS cc_start: 0.8165 (mttt) cc_final: 0.7523 (mtpt)
REVERT: D  321 LYS cc_start: 0.8220 (mttt) cc_final: 0.7463 (tptp)
REVERT: D  331 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7851 (mtpt)
REVERT: D  340 LYS cc_start: 0.8093 (mttt) cc_final: 0.7431 (mttm)
REVERT: D  341 SER cc_start: 0.8729 (m) cc_final: 0.8525 (m)
REVERT: D  342 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6985 (mp0)
REVERT: D  343 LYS cc_start: 0.8306 (mttt) cc_final: 0.7838 (mttm)
REVERT: D  347 LYS cc_start: 0.7821 (mttt) cc_final: 0.7319 (mtmm)
REVERT: D  356 SER cc_start: 0.8138 (p) cc_final: 0.7878 (t)
REVERT: D  358 ASP cc_start: 0.7682 (m-30) cc_final: 0.7250 (m-30)
REVERT: D  369 LYS cc_start: 0.8145 (mttt) cc_final: 0.7845 (mttp)
REVERT: D  372 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: D  375 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7831 (ttmt)
REVERT: E  317 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7509 (mtpm)
REVERT: E  320 SER cc_start: 0.7993 (t) cc_final: 0.7773 (p)
REVERT: E  321 LYS cc_start: 0.7950 (tttt) cc_final: 0.7587 (tmmt)
REVERT: E  331 LYS cc_start: 0.8589 (mttt) cc_final: 0.8358 (mttp)
REVERT: E  336 GLN cc_start: 0.8036 (mt0) cc_final: 0.7421 (mt0)
REVERT: E  338 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7235 (tt0)
REVERT: E  340 LYS cc_start: 0.7734 (tttt) cc_final: 0.7431 (tptp)
REVERT: E  341 SER cc_start: 0.8173 (m) cc_final: 0.7835 (t)
REVERT: E  342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6370 (mp0)
REVERT: E  347 LYS cc_start: 0.7662 (mttp) cc_final: 0.7173 (mmtm)
REVERT: E  369 LYS cc_start: 0.8492 (mttt) cc_final: 0.8172 (mttp)
REVERT: F  311 LYS cc_start: 0.8344 (mttt) cc_final: 0.7480 (ttpp)
REVERT: F  317 LYS cc_start: 0.7870 (pttt) cc_final: 0.7669 (ptmt)
REVERT: F  342 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6057 (mp0)
REVERT: F  345 ASP cc_start: 0.8372 (t0) cc_final: 0.7979 (t0)
REVERT: F  347 LYS cc_start: 0.7694 (mttt) cc_final: 0.6913 (mtmm)
REVERT: F  349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6836 (mtp180)
REVERT: F  353 LYS cc_start: 0.8380 (tttt) cc_final: 0.8022 (tttp)
REVERT: F  369 LYS cc_start: 0.7983 (mttt) cc_final: 0.7404 (mtpp)
REVERT: F  375 LYS cc_start: 0.8054 (tttt) cc_final: 0.7849 (ttmt)
REVERT: G  311 LYS cc_start: 0.7831 (tttt) cc_final: 0.7403 (tppp)
REVERT: G  317 LYS cc_start: 0.7457 (mttt) cc_final: 0.7166 (mtpm)
REVERT: G  321 LYS cc_start: 0.7936 (mttt) cc_final: 0.7362 (mptt)
REVERT: G  340 LYS cc_start: 0.7876 (mttt) cc_final: 0.6960 (mtpp)
REVERT: G  342 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6768 (mp0)
REVERT: G  343 LYS cc_start: 0.8061 (mttt) cc_final: 0.7729 (mttp)
REVERT: G  345 ASP cc_start: 0.7417 (m-30) cc_final: 0.7113 (m-30)
REVERT: G  353 LYS cc_start: 0.7471 (mttt) cc_final: 0.7243 (mtmt)
REVERT: G  356 SER cc_start: 0.8045 (p) cc_final: 0.7759 (p)
REVERT: G  358 ASP cc_start: 0.7738 (m-30) cc_final: 0.7379 (m-30)
REVERT: G  369 LYS cc_start: 0.7434 (mttt) cc_final: 0.7052 (mttp)
REVERT: G  371 ILE cc_start: 0.8054 (mt) cc_final: 0.7747 (mp)
REVERT: H  317 LYS cc_start: 0.7620 (mtmt) cc_final: 0.7378 (ttmm)
REVERT: H  321 LYS cc_start: 0.7702 (tttt) cc_final: 0.7142 (mttp)
REVERT: H  331 LYS cc_start: 0.8066 (mttt) cc_final: 0.7774 (mttp)
REVERT: H  336 GLN cc_start: 0.7517 (mt0) cc_final: 0.6995 (mt0)
REVERT: H  347 LYS cc_start: 0.7097 (mttp) cc_final: 0.6517 (mmtm)
REVERT: H  356 SER cc_start: 0.8112 (m) cc_final: 0.7533 (p)
REVERT: H  375 LYS cc_start: 0.7688 (tttt) cc_final: 0.7232 (tttm)
REVERT: I  317 LYS cc_start: 0.7575 (pttt) cc_final: 0.7242 (pttt)
REVERT: I  321 LYS cc_start: 0.7401 (ttmt) cc_final: 0.6922 (ttmm)
REVERT: I  331 LYS cc_start: 0.7229 (mttt) cc_final: 0.6750 (mtpt)
REVERT: I  338 GLU cc_start: 0.7508 (tt0) cc_final: 0.6791 (tt0)
REVERT: I  347 LYS cc_start: 0.7326 (mttt) cc_final: 0.6226 (mmtm)
REVERT: I  349 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6545 (mtm180)
REVERT: I  369 LYS cc_start: 0.7510 (mttt) cc_final: 0.6963 (mtpm)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 2.9422
  time to fit residues: 792.4018
Evaluate side-chains
  206 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 GLN
I 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.144726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.129647 restraints weight = 19137.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 1.42
r_work: 0.3884 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3812 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5175  Z= 0.161
  Angle     :  0.714   5.357   6924  Z= 0.369
  Chirality :  0.051   0.151    780
  Planarity :  0.004   0.040    879
  Dihedral  :  6.450  18.856    681
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 11.79 %
    Favored  : 87.86 %
  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: -2.68 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS B 362 
 PHE   0.016   0.002   PHE E 378 
 TYR   0.007   0.001   TYR F 310 
 ARG   0.004   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (   91)
  hydrogen bonds       : angle       5.43394 (  273)
  covalent geometry    : bond        0.00356 ( 5175)
  covalent geometry    : angle       0.71356 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7544 (mp0)
REVERT: B  311 LYS cc_start: 0.8199 (mttt) cc_final: 0.7599 (mmtm)
REVERT: B  338 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7936 (tt0)
REVERT: B  348 ASP cc_start: 0.8436 (t0) cc_final: 0.8124 (t0)
REVERT: C  311 LYS cc_start: 0.8387 (mttt) cc_final: 0.7923 (mmtm)
REVERT: C  321 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8086 (tmtm)
REVERT: C  345 ASP cc_start: 0.8382 (t0) cc_final: 0.8083 (t0)
REVERT: D  317 LYS cc_start: 0.8227 (mttt) cc_final: 0.7930 (mtpt)
REVERT: D  342 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7487 (mp0)
REVERT: D  343 LYS cc_start: 0.8551 (mttt) cc_final: 0.8337 (mttm)
REVERT: E  336 GLN cc_start: 0.8545 (mt0) cc_final: 0.8207 (mt0)
REVERT: E  379 ARG cc_start: 0.5515 (pmt170) cc_final: 0.5011 (pmt-80)
REVERT: F  311 LYS cc_start: 0.8639 (mttt) cc_final: 0.8182 (ttpp)
REVERT: F  345 ASP cc_start: 0.8595 (t0) cc_final: 0.8362 (t0)
REVERT: F  373 THR cc_start: 0.8803 (m) cc_final: 0.8521 (p)
REVERT: G  340 LYS cc_start: 0.8701 (mttt) cc_final: 0.8423 (mttm)
REVERT: G  342 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7745 (mp0)
REVERT: H  336 GLN cc_start: 0.8493 (mt0) cc_final: 0.8233 (mt0)
REVERT: H  338 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7928 (mt-10)
REVERT: I  311 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7740 (tttp)
REVERT: I  347 LYS cc_start: 0.8538 (mttt) cc_final: 0.7995 (mmtm)
  outliers start: 2
  outliers final: 1
  residues processed: 203
  average time/residue: 3.0593
  time to fit residues: 641.5538
Evaluate side-chains
  153 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  315 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0020
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0170
   chunk 52 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.9830

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 351 GLN
C 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.142217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.126500 restraints weight = 19402.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 1.44
r_work: 0.3872 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3802 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5175  Z= 0.144
  Angle     :  0.594   4.507   6924  Z= 0.303
  Chirality :  0.050   0.142    780
  Planarity :  0.003   0.034    879
  Dihedral  :  6.213  18.108    681
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 17.44 %
    Favored  : 81.20 %
  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: -2.64 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS H 329 
 PHE   0.004   0.001   PHE D 346 
 TYR   0.008   0.002   TYR F 310 
 ARG   0.003   0.001   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02730 (   91)
  hydrogen bonds       : angle       5.07006 (  273)
  covalent geometry    : bond        0.00330 ( 5175)
  covalent geometry    : angle       0.59447 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7519 (mp0)
REVERT: B  311 LYS cc_start: 0.8196 (mttt) cc_final: 0.7644 (mmtm)
REVERT: B  321 LYS cc_start: 0.8510 (tmmm) cc_final: 0.8260 (tmmt)
REVERT: B  338 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8033 (tt0)
REVERT: B  348 ASP cc_start: 0.8331 (t0) cc_final: 0.8060 (t70)
REVERT: C  311 LYS cc_start: 0.8341 (mttt) cc_final: 0.7867 (mmtm)
REVERT: C  345 ASP cc_start: 0.8303 (t0) cc_final: 0.8044 (t0)
REVERT: D  317 LYS cc_start: 0.8162 (mttt) cc_final: 0.7898 (mtpt)
REVERT: D  342 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7482 (mp0)
REVERT: E  336 GLN cc_start: 0.8543 (mt0) cc_final: 0.8205 (mt0)
REVERT: E  342 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7130 (mp0)
REVERT: F  311 LYS cc_start: 0.8666 (mttt) cc_final: 0.7538 (pmtt)
REVERT: F  345 ASP cc_start: 0.8553 (t0) cc_final: 0.8263 (t0)
REVERT: F  373 THR cc_start: 0.8810 (m) cc_final: 0.8526 (p)
REVERT: G  340 LYS cc_start: 0.8656 (mttt) cc_final: 0.8260 (mtpp)
REVERT: G  342 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7702 (mp0)
REVERT: G  349 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7080 (mtm180)
REVERT: H  336 GLN cc_start: 0.8478 (mt0) cc_final: 0.8220 (mt0)
REVERT: H  338 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7939 (mt-10)
REVERT: H  375 LYS cc_start: 0.8378 (tttt) cc_final: 0.8098 (tttm)
REVERT: I  311 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7720 (tttp)
REVERT: I  347 LYS cc_start: 0.8495 (mttt) cc_final: 0.7942 (mmtm)
  outliers start: 8
  outliers final: 3
  residues processed: 164
  average time/residue: 3.1515
  time to fit residues: 535.4438
Evaluate side-chains
  156 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 153
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain G residue  356 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 351 GLN
C 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.142678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.126691 restraints weight = 18841.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 1.47
r_work: 0.3865 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3793 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.4926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5175  Z= 0.130
  Angle     :  0.556   4.938   6924  Z= 0.283
  Chirality :  0.050   0.139    780
  Planarity :  0.004   0.034    879
  Dihedral  :  5.927  17.570    681
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.63 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.26), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.20), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 362 
 PHE   0.012   0.001   PHE D 378 
 TYR   0.007   0.001   TYR F 310 
 ARG   0.002   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02273 (   91)
  hydrogen bonds       : angle       4.67061 (  273)
  covalent geometry    : bond        0.00290 ( 5175)
  covalent geometry    : angle       0.55636 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 158
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8932 (mp) cc_final: 0.8611 (mp)
REVERT: A  342 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7523 (mp0)
REVERT: B  311 LYS cc_start: 0.8214 (mttt) cc_final: 0.7659 (mmtm)
REVERT: B  321 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8225 (tmmt)
REVERT: B  338 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8022 (tt0)
REVERT: B  348 ASP cc_start: 0.8297 (t0) cc_final: 0.7977 (t70)
REVERT: B  379 ARG cc_start: 0.7004 (ttp-110) cc_final: 0.6434 (mtt90)
REVERT: C  311 LYS cc_start: 0.8317 (mttt) cc_final: 0.7857 (mmtm)
REVERT: C  345 ASP cc_start: 0.8260 (t0) cc_final: 0.7932 (t70)
REVERT: D  342 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7464 (mp0)
REVERT: E  336 GLN cc_start: 0.8525 (mt0) cc_final: 0.8191 (mt0)
REVERT: E  342 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7105 (mp0)
REVERT: F  311 LYS cc_start: 0.8651 (mttt) cc_final: 0.7584 (pmtt)
REVERT: G  321 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8318 (mttt)
REVERT: G  340 LYS cc_start: 0.8653 (mttt) cc_final: 0.8245 (mtpp)
REVERT: G  342 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7684 (mp0)
REVERT: G  349 ARG cc_start: 0.7777 (mtm180) cc_final: 0.7221 (mtm180)
REVERT: H  336 GLN cc_start: 0.8515 (mt0) cc_final: 0.8244 (mt0)
REVERT: H  375 LYS cc_start: 0.8249 (tttt) cc_final: 0.7973 (tttm)
REVERT: I  311 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7713 (tttp)
REVERT: I  347 LYS cc_start: 0.8449 (mttt) cc_final: 0.7874 (mmtm)
  outliers start: 11
  outliers final: 3
  residues processed: 160
  average time/residue: 2.6645
  time to fit residues: 441.9995
Evaluate side-chains
  156 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain G residue  321 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0570
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0170
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.9940

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 351 GLN
C 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.141377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.125467 restraints weight = 18828.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 1.46
r_work: 0.3830 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3753 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.5079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5175  Z= 0.139
  Angle     :  0.548   5.035   6924  Z= 0.279
  Chirality :  0.049   0.132    780
  Planarity :  0.004   0.036    879
  Dihedral  :  5.896  17.939    681
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.63 %
    Favored  : 79.32 %
  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: -2.63 (0.26), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.20), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 362 
 PHE   0.013   0.001   PHE E 378 
 TYR   0.008   0.001   TYR E 310 
 ARG   0.002   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02226 (   91)
  hydrogen bonds       : angle       4.55274 (  273)
  covalent geometry    : bond        0.00309 ( 5175)
  covalent geometry    : angle       0.54753 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8962 (mp) cc_final: 0.8640 (mp)
REVERT: A  342 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7577 (mp0)
REVERT: A  378 PHE cc_start: 0.6745 (m-80) cc_final: 0.6461 (m-80)
REVERT: B  311 LYS cc_start: 0.8290 (mttt) cc_final: 0.7696 (mmtm)
REVERT: B  321 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8256 (tmmt)
REVERT: B  338 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8062 (tt0)
REVERT: B  348 ASP cc_start: 0.8275 (t0) cc_final: 0.7975 (t70)
REVERT: B  379 ARG cc_start: 0.7016 (ttp-110) cc_final: 0.6367 (mtt90)
REVERT: C  311 LYS cc_start: 0.8360 (mttt) cc_final: 0.7869 (mmtm)
REVERT: C  345 ASP cc_start: 0.8331 (t0) cc_final: 0.8039 (t70)
REVERT: D  342 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7509 (mp0)
REVERT: E  336 GLN cc_start: 0.8577 (mt0) cc_final: 0.8230 (mt0)
REVERT: E  342 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7118 (mp0)
REVERT: F  311 LYS cc_start: 0.8648 (mttt) cc_final: 0.7610 (pmtt)
REVERT: F  347 LYS cc_start: 0.8404 (mttt) cc_final: 0.8148 (mtmm)
REVERT: G  321 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8171 (tptm)
REVERT: G  340 LYS cc_start: 0.8625 (mttt) cc_final: 0.8246 (mtpp)
REVERT: G  342 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7681 (mp0)
REVERT: G  349 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7277 (mtm180)
REVERT: G  378 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.6035 (t80)
REVERT: H  336 GLN cc_start: 0.8510 (mt0) cc_final: 0.8242 (mt0)
REVERT: H  375 LYS cc_start: 0.8273 (tttt) cc_final: 0.7978 (tttm)
REVERT: I  311 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7662 (tttp)
REVERT: I  345 ASP cc_start: 0.8584 (t0) cc_final: 0.8309 (t0)
REVERT: I  347 LYS cc_start: 0.8384 (mttt) cc_final: 0.7830 (mptp)
  outliers start: 12
  outliers final: 4
  residues processed: 159
  average time/residue: 2.8677
  time to fit residues: 473.4188
Evaluate side-chains
  159 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain G residue  321 LYS
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain G residue  378 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 351 GLN
C 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.138603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.122784 restraints weight = 19383.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.44
r_work: 0.3806 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3732 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.5231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5175  Z= 0.197
  Angle     :  0.587   5.341   6924  Z= 0.299
  Chirality :  0.050   0.139    780
  Planarity :  0.004   0.039    879
  Dihedral  :  6.060  18.340    681
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.97 %
    Favored  : 78.80 %
  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: -2.76 (0.26), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.20), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B 362 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.010   0.002   TYR F 310 
 ARG   0.003   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02395 (   91)
  hydrogen bonds       : angle       4.57756 (  273)
  covalent geometry    : bond        0.00433 ( 5175)
  covalent geometry    : angle       0.58660 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8975 (mp) cc_final: 0.8679 (mp)
REVERT: A  340 LYS cc_start: 0.8547 (mttt) cc_final: 0.8340 (mttp)
REVERT: A  342 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7435 (mp0)
REVERT: B  311 LYS cc_start: 0.8416 (mttt) cc_final: 0.7745 (mmtm)
REVERT: B  338 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8041 (tt0)
REVERT: B  348 ASP cc_start: 0.8138 (t0) cc_final: 0.7802 (t70)
REVERT: B  379 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6386 (mtt90)
REVERT: C  311 LYS cc_start: 0.8456 (mttt) cc_final: 0.7930 (mmtm)
REVERT: C  345 ASP cc_start: 0.8313 (t0) cc_final: 0.8034 (t70)
REVERT: D  342 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7477 (mp0)
REVERT: E  336 GLN cc_start: 0.8571 (mt0) cc_final: 0.8297 (mt0)
REVERT: E  342 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7131 (mp0)
REVERT: F  311 LYS cc_start: 0.8667 (mttt) cc_final: 0.7700 (pmtt)
REVERT: G  321 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8166 (tptm)
REVERT: G  340 LYS cc_start: 0.8599 (mttt) cc_final: 0.8219 (mtpp)
REVERT: G  342 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7701 (mp0)
REVERT: G  349 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7073 (mtm180)
REVERT: H  336 GLN cc_start: 0.8594 (mt0) cc_final: 0.8326 (mt0)
REVERT: I  311 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7694 (tttp)
REVERT: I  347 LYS cc_start: 0.8393 (mttt) cc_final: 0.7829 (mptp)
  outliers start: 13
  outliers final: 4
  residues processed: 155
  average time/residue: 2.9776
  time to fit residues: 478.7321
Evaluate side-chains
  150 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 145
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain G residue  321 LYS
Chi-restraints excluded: chain G residue  356 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 351 GLN
C 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.138792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.122960 restraints weight = 18927.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 1.45
r_work: 0.3817 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.5390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5175  Z= 0.181
  Angle     :  0.578   5.483   6924  Z= 0.293
  Chirality :  0.049   0.133    780
  Planarity :  0.004   0.054    879
  Dihedral  :  6.037  18.525    681
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 19.83 %
    Favored  : 78.63 %
  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: -2.84 (0.26), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.20), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 362 
 PHE   0.016   0.001   PHE G 378 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.006   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02336 (   91)
  hydrogen bonds       : angle       4.52180 (  273)
  covalent geometry    : bond        0.00402 ( 5175)
  covalent geometry    : angle       0.57786 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8966 (mp) cc_final: 0.8676 (mp)
REVERT: A  340 LYS cc_start: 0.8576 (mttt) cc_final: 0.8367 (mttp)
REVERT: A  342 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7369 (mp0)
REVERT: B  311 LYS cc_start: 0.8440 (mttt) cc_final: 0.7717 (mmtm)
REVERT: B  338 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8039 (tt0)
REVERT: B  348 ASP cc_start: 0.8078 (t0) cc_final: 0.7763 (t70)
REVERT: B  379 ARG cc_start: 0.7084 (ttp-110) cc_final: 0.6408 (mtt90)
REVERT: C  311 LYS cc_start: 0.8496 (mttt) cc_final: 0.8007 (mmtm)
REVERT: C  321 LYS cc_start: 0.8501 (tmtm) cc_final: 0.8186 (ttmm)
REVERT: C  345 ASP cc_start: 0.8309 (t0) cc_final: 0.8035 (t70)
REVERT: D  342 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7496 (mp0)
REVERT: E  336 GLN cc_start: 0.8517 (mt0) cc_final: 0.8235 (mt0)
REVERT: E  342 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7129 (mp0)
REVERT: E  379 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.3369 (ptt90)
REVERT: G  321 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8126 (tptm)
REVERT: G  340 LYS cc_start: 0.8601 (mttt) cc_final: 0.8207 (mtpp)
REVERT: G  342 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7710 (mp0)
REVERT: G  349 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7249 (mtm180)
REVERT: H  336 GLN cc_start: 0.8577 (mt0) cc_final: 0.8312 (mt0)
REVERT: H  375 LYS cc_start: 0.8397 (tttt) cc_final: 0.8110 (tttm)
REVERT: I  311 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7679 (tttp)
REVERT: I  317 LYS cc_start: 0.8476 (ptpp) cc_final: 0.8132 (ttpt)
REVERT: I  345 ASP cc_start: 0.8550 (t0) cc_final: 0.8303 (t0)
REVERT: I  347 LYS cc_start: 0.8356 (mttt) cc_final: 0.7830 (mptp)
  outliers start: 9
  outliers final: 4
  residues processed: 150
  average time/residue: 3.1242
  time to fit residues: 486.3250
Evaluate side-chains
  147 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain E residue  379 ARG
Chi-restraints excluded: chain G residue  321 LYS
Chi-restraints excluded: chain G residue  356 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0770
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.3344

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 351 GLN
C 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.138933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.123112 restraints weight = 18715.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.45
r_work: 0.3812 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3739 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.5476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5175  Z= 0.176
  Angle     :  0.578   5.579   6924  Z= 0.292
  Chirality :  0.050   0.132    780
  Planarity :  0.004   0.037    879
  Dihedral  :  5.986  18.746    681
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.51 %
    Favored  : 77.95 %
  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: -2.89 (0.26), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS G 330 
 PHE   0.011   0.001   PHE G 378 
 TYR   0.009   0.002   TYR E 310 
 ARG   0.002   0.000   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02282 (   91)
  hydrogen bonds       : angle       4.47381 (  273)
  covalent geometry    : bond        0.00389 ( 5175)
  covalent geometry    : angle       0.57765 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 1.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8963 (mp) cc_final: 0.8675 (mp)
REVERT: A  340 LYS cc_start: 0.8557 (mttt) cc_final: 0.8342 (mttp)
REVERT: A  342 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7398 (mp0)
REVERT: B  311 LYS cc_start: 0.8476 (mttt) cc_final: 0.7647 (mmtm)
REVERT: B  338 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7983 (tt0)
REVERT: C  311 LYS cc_start: 0.8507 (mttt) cc_final: 0.7990 (mmtm)
REVERT: C  321 LYS cc_start: 0.8517 (tmtm) cc_final: 0.8192 (ttmm)
REVERT: C  345 ASP cc_start: 0.8294 (t0) cc_final: 0.8011 (t70)
REVERT: D  342 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7512 (mp0)
REVERT: E  336 GLN cc_start: 0.8510 (mt0) cc_final: 0.8228 (mt0)
REVERT: E  342 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7121 (mp0)
REVERT: E  379 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.3554 (ptt90)
REVERT: G  321 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8106 (tptm)
REVERT: G  340 LYS cc_start: 0.8589 (mttt) cc_final: 0.8185 (mtpp)
REVERT: G  342 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7690 (mp0)
REVERT: G  349 ARG cc_start: 0.7810 (mtm180) cc_final: 0.7254 (mtm180)
REVERT: I  311 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7683 (tttp)
REVERT: I  317 LYS cc_start: 0.8462 (ptpp) cc_final: 0.8188 (ttpt)
REVERT: I  347 LYS cc_start: 0.8345 (mttt) cc_final: 0.7800 (mptp)
  outliers start: 9
  outliers final: 4
  residues processed: 149
  average time/residue: 3.3812
  time to fit residues: 527.2683
Evaluate side-chains
  148 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain E residue  379 ARG
Chi-restraints excluded: chain G residue  321 LYS
Chi-restraints excluded: chain G residue  356 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 351 GLN
C 336 GLN
H 336 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.136433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.120560 restraints weight = 19624.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 1.43
r_work: 0.3781 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.5586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5175  Z= 0.251
  Angle     :  0.635   5.716   6924  Z= 0.321
  Chirality :  0.050   0.136    780
  Planarity :  0.005   0.067    879
  Dihedral  :  6.205  18.423    681
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.85 %
    Favored  : 77.61 %
  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: -2.98 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS G 330 
 PHE   0.011   0.002   PHE A 378 
 TYR   0.011   0.002   TYR B 310 
 ARG   0.009   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02607 (   91)
  hydrogen bonds       : angle       4.60536 (  273)
  covalent geometry    : bond        0.00558 ( 5175)
  covalent geometry    : angle       0.63535 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8961 (mp) cc_final: 0.8695 (mp)
REVERT: A  340 LYS cc_start: 0.8517 (mttt) cc_final: 0.8312 (mttp)
REVERT: A  342 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7386 (mp0)
REVERT: B  311 LYS cc_start: 0.8555 (mttt) cc_final: 0.7828 (mmtm)
REVERT: B  338 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8013 (tt0)
REVERT: C  311 LYS cc_start: 0.8547 (mttt) cc_final: 0.7991 (mmtm)
REVERT: C  321 LYS cc_start: 0.8567 (tmtm) cc_final: 0.8254 (ttmm)
REVERT: C  345 ASP cc_start: 0.8310 (t0) cc_final: 0.8039 (t70)
REVERT: D  342 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7569 (mp0)
REVERT: E  336 GLN cc_start: 0.8512 (mt0) cc_final: 0.8262 (mt0)
REVERT: E  342 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7126 (mp0)
REVERT: E  379 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.3448 (ptt90)
REVERT: G  321 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8116 (tptm)
REVERT: G  340 LYS cc_start: 0.8571 (mttt) cc_final: 0.8191 (mtpp)
REVERT: G  342 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7704 (mp0)
REVERT: G  349 ARG cc_start: 0.7788 (mtm180) cc_final: 0.7105 (mtm180)
REVERT: H  336 GLN cc_start: 0.8555 (mt0) cc_final: 0.8239 (mt0)
REVERT: H  375 LYS cc_start: 0.8428 (tttt) cc_final: 0.8146 (tttm)
REVERT: I  311 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7681 (tttp)
REVERT: I  317 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8210 (ttpp)
REVERT: I  347 LYS cc_start: 0.8377 (mttt) cc_final: 0.7839 (mptp)
  outliers start: 9
  outliers final: 3
  residues processed: 147
  average time/residue: 3.4571
  time to fit residues: 526.9215
Evaluate side-chains
  140 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 135
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain E residue  379 ARG
Chi-restraints excluded: chain G residue  321 LYS
Chi-restraints excluded: chain G residue  356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
C 336 GLN
G 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.138110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.122208 restraints weight = 18755.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 1.44
r_work: 0.3816 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.5634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5175  Z= 0.178
  Angle     :  0.589   6.145   6924  Z= 0.298
  Chirality :  0.049   0.133    780
  Planarity :  0.004   0.040    879
  Dihedral  :  6.052  18.648    681
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 22.05 %
    Favored  : 76.75 %
  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: -2.99 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.19), residues: 648

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02297 (   91)
  hydrogen bonds       : angle       4.53840 (  273)
  covalent geometry    : bond        0.00395 ( 5175)
  covalent geometry    : angle       0.58911 ( 6924)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8954 (mp) cc_final: 0.8675 (mp)
REVERT: A  342 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7410 (mp0)
REVERT: B  311 LYS cc_start: 0.8525 (mttt) cc_final: 0.7865 (mmtt)
REVERT: B  338 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8018 (tt0)
REVERT: C  311 LYS cc_start: 0.8544 (mttt) cc_final: 0.8011 (mmtm)
REVERT: C  321 LYS cc_start: 0.8557 (tmtm) cc_final: 0.8282 (ttmm)
REVERT: C  345 ASP cc_start: 0.8287 (t0) cc_final: 0.8017 (t70)
REVERT: D  342 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7585 (mp0)
REVERT: E  336 GLN cc_start: 0.8503 (mt0) cc_final: 0.8247 (mt0)
REVERT: E  342 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7138 (mp0)
REVERT: E  379 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.3495 (ptt90)
REVERT: F  342 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6755 (mp0)
REVERT: G  308 ILE cc_start: 0.8733 (mp) cc_final: 0.8508 (mt)
REVERT: G  321 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8132 (tptm)
REVERT: G  340 LYS cc_start: 0.8569 (mttt) cc_final: 0.8192 (mtpp)
REVERT: G  342 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7717 (mp0)
REVERT: G  349 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7089 (mtm180)
REVERT: H  375 LYS cc_start: 0.8448 (tttt) cc_final: 0.8172 (tttm)
REVERT: I  311 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7706 (tttp)
REVERT: I  317 LYS cc_start: 0.8429 (ptpp) cc_final: 0.8206 (ttpp)
REVERT: I  345 ASP cc_start: 0.8527 (t0) cc_final: 0.8273 (t0)
REVERT: I  347 LYS cc_start: 0.8360 (mttt) cc_final: 0.7844 (mptp)
  outliers start: 7
  outliers final: 3
  residues processed: 142
  average time/residue: 2.7067
  time to fit residues: 398.7625
Evaluate side-chains
  142 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain E residue  379 ARG
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  321 LYS
Chi-restraints excluded: chain G residue  356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 15 optimal weight:    0.0670
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7718

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
H 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.140293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.124616 restraints weight = 18593.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 1.43
r_work: 0.3839 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3767 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5175  Z= 0.122
  Angle     :  0.559   6.766   6924  Z= 0.280
  Chirality :  0.050   0.131    780
  Planarity :  0.004   0.047    879
  Dihedral  :  5.797  18.181    681
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 22.39 %
    Favored  : 76.58 %
  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: -2.96 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 329 
 PHE   0.006   0.001   PHE G 378 
 TYR   0.006   0.001   TYR E 310 
 ARG   0.008   0.001   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02054 (   91)
  hydrogen bonds       : angle       4.38372 (  273)
  covalent geometry    : bond        0.00280 ( 5175)
  covalent geometry    : angle       0.55883 ( 6924)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11790.61 seconds
wall clock time: 208 minutes 58.32 seconds (12538.32 seconds total)