Starting phenix.real_space_refine
on Wed Sep 17 18:41:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bbl_44421/09_2025/9bbl_44421_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bbl_44421/09_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_44421/09_2025/9bbl_44421.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bbl_44421/09_2025/9bbl_44421.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bbl_44421/09_2025/9bbl_44421_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bbl_44421/09_2025/9bbl_44421_neut.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.51, per 1000 atoms: 0.24
  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: 1.02
  Conformation dependent library (CDL) restraints added in 263.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.33
  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: 2.09

  Time building geometry restraints manager: 1.37 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: 0.00
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:             3.710
  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:             0.060
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.940
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.470
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (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
 ARG   0.009   0.002   ARG H 349 
 TYR   0.059   0.014   TYR B 310 
 PHE   0.027   0.010   PHE I 346 
 HIS   0.043   0.008   HIS H 329 

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

*********************** 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  : 0.305 
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: 0.6899 (mmtm)
REVERT: B  317 LYS cc_start: 0.7429 (mtmt) cc_final: 0.6528 (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: 0.6765 (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: 0.7515 (t0)
REVERT: B  347 LYS cc_start: 0.7145 (mttp) cc_final: 0.6723 (mttp)
REVERT: B  348 ASP cc_start: 0.7527 (t0) cc_final: 0.7218 (t0)
REVERT: C  311 LYS cc_start: 0.7807 (mttt) cc_final: 0.7001 (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: 0.6914 (tt0)
REVERT: C  345 ASP cc_start: 0.8198 (t0) cc_final: 0.7874 (t0)
REVERT: C  347 LYS cc_start: 0.7187 (mttt) cc_final: 0.6793 (mtpp)
REVERT: C  348 ASP cc_start: 0.7867 (t0) cc_final: 0.7650 (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: 0.7624 (mmmt)
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: 0.7318 (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: 0.7830 (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: 0.7766 (p)
REVERT: E  321 LYS cc_start: 0.7950 (tttt) cc_final: 0.7367 (mmtp)
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: 0.7273 (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: 0.7450 (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: 0.6915 (mtmm)
REVERT: F  349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6837 (mtp180)
REVERT: F  353 LYS cc_start: 0.8380 (tttt) cc_final: 0.8021 (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: 0.7603 (mttp)
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: 0.7760 (p)
REVERT: G  358 ASP cc_start: 0.7738 (m-30) cc_final: 0.7378 (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: 0.7148 (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: 0.6600 (mptt)
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  311 LYS cc_start: 0.7761 (mttt) cc_final: 0.6802 (tttp)
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: 0.6751 (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: 0.6841 (mtpp)
REVERT: I  349 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6515 (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: 1.5111
  time to fit residues: 405.1480
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  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4134 r_free = 0.4134 target = 0.144676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.129515 restraints weight = 19326.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 1.42
r_work: 0.3885 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3812 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3025

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= 0.158
  Angle     :  0.722   6.187   6924  Z= 0.368
  Chirality :  0.053   0.148    780
  Planarity :  0.004   0.043    879
  Dihedral  :  6.592  19.867    681
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 11.45 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.74 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 349 
 TYR   0.009   0.002   TYR F 310 
 PHE   0.017   0.002   PHE E 378 
 HIS   0.009   0.003   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5175)
  covalent geometry    : angle       0.72157 ( 6924)
  hydrogen bonds       : bond        0.03696 (   91)
  hydrogen bonds       : angle       5.49140 (  273)

*********************** 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
  208 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 205
  time to evaluate  : 0.282 
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: A  342 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7517 (mp0)
REVERT: B  311 LYS cc_start: 0.8190 (mttt) cc_final: 0.7582 (mmtm)
REVERT: B  338 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7992 (tt0)
REVERT: B  348 ASP cc_start: 0.8493 (t0) cc_final: 0.8144 (t0)
REVERT: C  311 LYS cc_start: 0.8419 (mttt) cc_final: 0.7818 (mmtm)
REVERT: C  321 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8083 (tmtm)
REVERT: D  317 LYS cc_start: 0.8207 (mttt) cc_final: 0.7914 (mtpt)
REVERT: D  342 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7503 (mp0)
REVERT: D  343 LYS cc_start: 0.8545 (mttt) cc_final: 0.8345 (mttm)
REVERT: E  336 GLN cc_start: 0.8544 (mt0) cc_final: 0.8198 (mt0)
REVERT: F  311 LYS cc_start: 0.8626 (mttt) cc_final: 0.8171 (ttpp)
REVERT: F  345 ASP cc_start: 0.8624 (t0) cc_final: 0.8398 (t0)
REVERT: F  373 THR cc_start: 0.8822 (m) cc_final: 0.8589 (p)
REVERT: G  340 LYS cc_start: 0.8705 (mttt) cc_final: 0.8426 (mttm)
REVERT: G  342 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7738 (mp0)
REVERT: H  336 GLN cc_start: 0.8478 (mt0) cc_final: 0.8220 (mt0)
REVERT: H  338 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7913 (mt-10)
REVERT: H  375 LYS cc_start: 0.8448 (tttt) cc_final: 0.8211 (tttm)
REVERT: H  379 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.6946 (mtt-85)
REVERT: I  311 LYS cc_start: 0.8440 (mttt) cc_final: 0.7784 (tttp)
  outliers start: 3
  outliers final: 1
  residues processed: 206
  average time/residue: 1.6581
  time to fit residues: 351.4172
Evaluate side-chains
  154 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
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 3 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 GLN
C 336 GLN
G 330 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.138103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.122006 restraints weight = 19553.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 1.43
r_work: 0.3796 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3725 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   5175  Z= 0.251
  Angle     :  0.674   5.136   6924  Z= 0.345
  Chirality :  0.050   0.137    780
  Planarity :  0.004   0.041    879
  Dihedral  :  6.578  18.748    681
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.58 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.80 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 379 
 TYR   0.010   0.002   TYR F 310 
 PHE   0.017   0.002   PHE E 378 
 HIS   0.010   0.003   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 5175)
  covalent geometry    : angle       0.67364 ( 6924)
  hydrogen bonds       : bond        0.03109 (   91)
  hydrogen bonds       : angle       5.14601 (  273)

*********************** 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
  171 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8950 (mp) cc_final: 0.8606 (mp)
REVERT: A  342 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7486 (mp0)
REVERT: B  311 LYS cc_start: 0.8309 (mttt) cc_final: 0.7695 (mmtm)
REVERT: B  338 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7980 (tt0)
REVERT: B  348 ASP cc_start: 0.8313 (t0) cc_final: 0.8032 (t70)
REVERT: C  311 LYS cc_start: 0.8442 (mttt) cc_final: 0.7946 (mmtm)
REVERT: C  321 LYS cc_start: 0.8334 (ttmt) cc_final: 0.8118 (tmtm)
REVERT: D  314 ASP cc_start: 0.8738 (t0) cc_final: 0.8470 (t0)
REVERT: E  336 GLN cc_start: 0.8578 (mt0) cc_final: 0.8318 (mt0)
REVERT: F  311 LYS cc_start: 0.8748 (mttt) cc_final: 0.7709 (pmtt)
REVERT: F  349 ARG cc_start: 0.8344 (mtp180) cc_final: 0.8085 (mtm180)
REVERT: F  373 THR cc_start: 0.8829 (m) cc_final: 0.8526 (p)
REVERT: G  340 LYS cc_start: 0.8662 (mttt) cc_final: 0.8306 (mtpp)
REVERT: G  342 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7652 (mp0)
REVERT: G  349 ARG cc_start: 0.7771 (mtm180) cc_final: 0.7100 (mtm180)
REVERT: H  336 GLN cc_start: 0.8565 (mt0) cc_final: 0.8299 (mt0)
REVERT: H  375 LYS cc_start: 0.8382 (tttt) cc_final: 0.7750 (ttmm)
REVERT: I  311 LYS cc_start: 0.8437 (mttt) cc_final: 0.7847 (tttp)
REVERT: I  347 LYS cc_start: 0.8586 (mtpp) cc_final: 0.7659 (mmtm)
  outliers start: 11
  outliers final: 3
  residues processed: 166
  average time/residue: 1.4454
  time to fit residues: 247.9145
Evaluate side-chains
  148 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 145
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
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 17 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.1786

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.139625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.123562 restraints weight = 19194.565|
|-----------------------------------------------------------------------------|
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: 0.3746 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.5024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5175  Z= 0.160
  Angle     :  0.586   5.388   6924  Z= 0.298
  Chirality :  0.050   0.135    780
  Planarity :  0.004   0.036    879
  Dihedral  :  6.221  18.482    681
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.77 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 379 
 TYR   0.008   0.002   TYR F 310 
 PHE   0.014   0.001   PHE E 378 
 HIS   0.005   0.002   HIS C 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5175)
  covalent geometry    : angle       0.58609 ( 6924)
  hydrogen bonds       : bond        0.02468 (   91)
  hydrogen bonds       : angle       4.84070 (  273)

*********************** 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
  161 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8963 (mp) cc_final: 0.8646 (mp)
REVERT: A  342 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7470 (mp0)
REVERT: B  311 LYS cc_start: 0.8302 (mttt) cc_final: 0.7673 (mmtm)
REVERT: B  338 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7996 (tt0)
REVERT: B  348 ASP cc_start: 0.8210 (t0) cc_final: 0.7877 (t70)
REVERT: B  379 ARG cc_start: 0.7072 (ttp-110) cc_final: 0.6500 (mtt90)
REVERT: C  311 LYS cc_start: 0.8390 (mttt) cc_final: 0.7899 (mmtm)
REVERT: C  321 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8105 (tmtm)
REVERT: E  336 GLN cc_start: 0.8566 (mt0) cc_final: 0.8307 (mt0)
REVERT: E  342 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7138 (mp0)
REVERT: F  311 LYS cc_start: 0.8670 (mttt) cc_final: 0.7607 (pmtt)
REVERT: F  345 ASP cc_start: 0.8577 (t70) cc_final: 0.8276 (t0)
REVERT: F  347 LYS cc_start: 0.8472 (mttt) cc_final: 0.8193 (mtmm)
REVERT: G  321 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8332 (mttt)
REVERT: G  340 LYS cc_start: 0.8624 (mttt) cc_final: 0.8377 (mttm)
REVERT: G  342 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7672 (mp0)
REVERT: G  349 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7087 (mtm180)
REVERT: G  369 LYS cc_start: 0.8729 (mttp) cc_final: 0.8524 (mttp)
REVERT: H  336 GLN cc_start: 0.8541 (mt0) cc_final: 0.8261 (mt0)
REVERT: H  375 LYS cc_start: 0.8367 (tttt) cc_final: 0.7764 (ttmm)
REVERT: I  311 LYS cc_start: 0.8402 (mttt) cc_final: 0.7828 (tttp)
REVERT: I  347 LYS cc_start: 0.8562 (mtpp) cc_final: 0.7612 (mmtm)
  outliers start: 14
  outliers final: 5
  residues processed: 151
  average time/residue: 1.3329
  time to fit residues: 208.0811
Evaluate side-chains
  149 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 143
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  338 GLU
Chi-restraints excluded: chain D residue  345 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 17 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.4786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.137840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.121973 restraints weight = 19447.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 1.44
r_work: 0.3794 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3722 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.5209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5175  Z= 0.192
  Angle     :  0.586   4.834   6924  Z= 0.298
  Chirality :  0.049   0.134    780
  Planarity :  0.004   0.039    879
  Dihedral  :  6.187  18.539    681
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 19.66 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.85 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 379 
 TYR   0.009   0.002   TYR B 310 
 PHE   0.014   0.001   PHE E 378 
 HIS   0.006   0.002   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 5175)
  covalent geometry    : angle       0.58563 ( 6924)
  hydrogen bonds       : bond        0.02512 (   91)
  hydrogen bonds       : angle       4.74171 (  273)

*********************** 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
  155 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8985 (mp) cc_final: 0.8674 (mp)
REVERT: A  342 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7430 (mp0)
REVERT: B  311 LYS cc_start: 0.8425 (mttt) cc_final: 0.7724 (mmtm)
REVERT: B  321 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8291 (tmmt)
REVERT: B  338 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8002 (tt0)
REVERT: B  348 ASP cc_start: 0.8156 (t0) cc_final: 0.7836 (t70)
REVERT: C  311 LYS cc_start: 0.8472 (mttt) cc_final: 0.7955 (mmtm)
REVERT: C  321 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8105 (tmtm)
REVERT: D  342 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7720 (tt0)
REVERT: E  336 GLN cc_start: 0.8560 (mt0) cc_final: 0.8288 (mt0)
REVERT: E  379 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.3232 (ptt90)
REVERT: F  311 LYS cc_start: 0.8647 (mttt) cc_final: 0.7616 (pmtt)
REVERT: F  349 ARG cc_start: 0.8313 (mtp180) cc_final: 0.8091 (mtm180)
REVERT: G  321 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8156 (tptm)
REVERT: G  340 LYS cc_start: 0.8581 (mttt) cc_final: 0.8322 (mttm)
REVERT: G  342 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7493 (mp0)
REVERT: G  349 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7187 (mtm180)
REVERT: H  336 GLN cc_start: 0.8631 (mt0) cc_final: 0.8342 (mt0)
REVERT: H  375 LYS cc_start: 0.8390 (tttt) cc_final: 0.7795 (ttmm)
REVERT: I  311 LYS cc_start: 0.8453 (mttt) cc_final: 0.7851 (tttp)
REVERT: I  347 LYS cc_start: 0.8525 (mtpp) cc_final: 0.7590 (mptp)
  outliers start: 9
  outliers final: 5
  residues processed: 148
  average time/residue: 1.4203
  time to fit residues: 217.2675
Evaluate side-chains
  143 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain C residue  338 GLU
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain E residue  356 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.9382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.139349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.123650 restraints weight = 19487.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.45
r_work: 0.3815 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3743 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.5290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5175  Z= 0.132
  Angle     :  0.550   4.403   6924  Z= 0.279
  Chirality :  0.049   0.131    780
  Planarity :  0.004   0.037    879
  Dihedral  :  5.947  18.770    681
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.86 (0.26), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.20), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 379 
 TYR   0.007   0.001   TYR E 310 
 PHE   0.013   0.001   PHE E 378 
 HIS   0.004   0.001   HIS I 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5175)
  covalent geometry    : angle       0.55015 ( 6924)
  hydrogen bonds       : bond        0.02184 (   91)
  hydrogen bonds       : angle       4.55469 (  273)

*********************** 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
  152 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8994 (mp) cc_final: 0.8695 (mp)
REVERT: A  340 LYS cc_start: 0.8573 (mttt) cc_final: 0.8364 (mttp)
REVERT: A  342 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7482 (mp0)
REVERT: B  311 LYS cc_start: 0.8403 (mttt) cc_final: 0.7619 (mmtm)
REVERT: B  338 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8016 (tt0)
REVERT: B  348 ASP cc_start: 0.8120 (t0) cc_final: 0.7796 (t70)
REVERT: C  311 LYS cc_start: 0.8422 (mttt) cc_final: 0.7877 (mmtm)
REVERT: C  321 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8095 (tmtm)
REVERT: D  342 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7744 (tt0)
REVERT: E  336 GLN cc_start: 0.8538 (mt0) cc_final: 0.8257 (mt0)
REVERT: E  342 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7212 (mp0)
REVERT: F  311 LYS cc_start: 0.8663 (mttt) cc_final: 0.7589 (pmtt)
REVERT: F  349 ARG cc_start: 0.8327 (mtp180) cc_final: 0.8104 (mtm180)
REVERT: G  321 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8147 (tptm)
REVERT: G  342 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7532 (mp0)
REVERT: G  349 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7115 (mtm180)
REVERT: H  336 GLN cc_start: 0.8591 (mt0) cc_final: 0.8292 (mt0)
REVERT: H  375 LYS cc_start: 0.8392 (tttt) cc_final: 0.7796 (ttmm)
REVERT: I  311 LYS cc_start: 0.8387 (mttt) cc_final: 0.7830 (tttp)
  outliers start: 11
  outliers final: 6
  residues processed: 144
  average time/residue: 1.3473
  time to fit residues: 201.0116
Evaluate side-chains
  141 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  338 GLU
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain E residue  356 SER
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 12 optimal weight:    0.0470
   chunk 52 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.3878

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.143953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.128558 restraints weight = 18660.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 1.46
r_work: 0.3917 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3845 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5175  Z= 0.089
  Angle     :  0.503   4.208   6924  Z= 0.255
  Chirality :  0.050   0.133    780
  Planarity :  0.003   0.033    879
  Dihedral  :  5.508  18.200    681
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 20.68 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.83 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 379 
 TYR   0.004   0.001   TYR E 310 
 PHE   0.003   0.001   PHE A 378 
 HIS   0.003   0.001   HIS F 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 5175)
  covalent geometry    : angle       0.50253 ( 6924)
  hydrogen bonds       : bond        0.01857 (   91)
  hydrogen bonds       : angle       4.30204 (  273)

*********************** 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
  152 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8962 (mp) cc_final: 0.8673 (mp)
REVERT: A  340 LYS cc_start: 0.8525 (mttt) cc_final: 0.8283 (mttp)
REVERT: A  342 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7482 (mp0)
REVERT: B  311 LYS cc_start: 0.8358 (mttt) cc_final: 0.7712 (mmtt)
REVERT: B  338 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8006 (tt0)
REVERT: C  311 LYS cc_start: 0.8375 (mttt) cc_final: 0.7786 (mmtm)
REVERT: C  321 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8071 (tmtm)
REVERT: C  340 LYS cc_start: 0.8730 (tttt) cc_final: 0.8337 (tptt)
REVERT: D  342 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7469 (mp0)
REVERT: D  378 PHE cc_start: 0.6694 (t80) cc_final: 0.6493 (m-80)
REVERT: E  336 GLN cc_start: 0.8465 (mt0) cc_final: 0.8113 (mt0)
REVERT: E  342 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7109 (mp0)
REVERT: E  379 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.3467 (ptt90)
REVERT: F  311 LYS cc_start: 0.8642 (mttt) cc_final: 0.7528 (pmtt)
REVERT: F  317 LYS cc_start: 0.8429 (ptmt) cc_final: 0.8215 (pttt)
REVERT: G  321 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8044 (tptm)
REVERT: G  342 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7502 (mp0)
REVERT: G  349 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7263 (mtm180)
REVERT: H  336 GLN cc_start: 0.8540 (mt0) cc_final: 0.8245 (mt0)
REVERT: H  375 LYS cc_start: 0.8326 (tttt) cc_final: 0.7709 (ttmm)
REVERT: I  311 LYS cc_start: 0.8300 (mttt) cc_final: 0.7785 (tttp)
  outliers start: 8
  outliers final: 4
  residues processed: 147
  average time/residue: 1.3030
  time to fit residues: 198.4055
Evaluate side-chains
  139 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  338 GLU
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 61 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.143150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.127808 restraints weight = 18759.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 1.44
r_work: 0.3904 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3833 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.5532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5175  Z= 0.101
  Angle     :  0.512   4.553   6924  Z= 0.258
  Chirality :  0.049   0.130    780
  Planarity :  0.003   0.036    879
  Dihedral  :  5.461  17.689    681
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 20.85 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.83 (0.25), residues: 648
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 379 
 TYR   0.006   0.001   TYR E 310 
 PHE   0.005   0.001   PHE G 378 
 HIS   0.003   0.001   HIS G 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 5175)
  covalent geometry    : angle       0.51172 ( 6924)
  hydrogen bonds       : bond        0.01875 (   91)
  hydrogen bonds       : angle       4.21465 (  273)

*********************** 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
  142 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8970 (mp) cc_final: 0.8683 (mp)
REVERT: A  340 LYS cc_start: 0.8569 (mttt) cc_final: 0.8368 (mttp)
REVERT: A  342 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7531 (mp0)
REVERT: B  311 LYS cc_start: 0.8354 (mttt) cc_final: 0.7747 (mmtt)
REVERT: C  311 LYS cc_start: 0.8379 (mttt) cc_final: 0.7842 (mmtm)
REVERT: C  321 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8144 (tmtm)
REVERT: C  340 LYS cc_start: 0.8737 (tttt) cc_final: 0.8396 (tptt)
REVERT: D  342 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7517 (mp0)
REVERT: E  336 GLN cc_start: 0.8483 (mt0) cc_final: 0.8147 (mt0)
REVERT: E  342 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7153 (mp0)
REVERT: E  379 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.3550 (ptt90)
REVERT: F  345 ASP cc_start: 0.8489 (t70) cc_final: 0.8268 (t0)
REVERT: G  321 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8142 (tptm)
REVERT: G  342 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7562 (mp0)
REVERT: G  349 ARG cc_start: 0.7710 (mtm180) cc_final: 0.7307 (mtm180)
REVERT: H  336 GLN cc_start: 0.8539 (mt0) cc_final: 0.8265 (mt0)
REVERT: H  375 LYS cc_start: 0.8368 (tttt) cc_final: 0.7780 (ttmm)
REVERT: I  311 LYS cc_start: 0.8311 (mttt) cc_final: 0.7828 (tttp)
  outliers start: 8
  outliers final: 5
  residues processed: 136
  average time/residue: 1.2380
  time to fit residues: 174.8154
Evaluate side-chains
  138 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  338 GLU
Chi-restraints excluded: chain E residue  379 ARG
Chi-restraints excluded: chain F residue  372 GLU
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 9 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0170
   chunk 17 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.1222

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.140600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.125046 restraints weight = 18655.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 1.43
r_work: 0.3864 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3793 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5175  Z= 0.147
  Angle     :  0.534   4.209   6924  Z= 0.271
  Chirality :  0.049   0.130    780
  Planarity :  0.004   0.036    879
  Dihedral  :  5.603  17.702    681
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 20.68 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (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
 ARG   0.007   0.001   ARG B 379 
 TYR   0.008   0.001   TYR E 310 
 PHE   0.007   0.001   PHE G 378 
 HIS   0.004   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5175)
  covalent geometry    : angle       0.53410 ( 6924)
  hydrogen bonds       : bond        0.02095 (   91)
  hydrogen bonds       : angle       4.27156 (  273)

*********************** 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
  140 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 133
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8980 (mp) cc_final: 0.8719 (mp)
REVERT: A  342 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7487 (mp0)
REVERT: B  311 LYS cc_start: 0.8400 (mttt) cc_final: 0.7645 (mmtm)
REVERT: C  311 LYS cc_start: 0.8420 (mttt) cc_final: 0.7878 (mmtm)
REVERT: C  321 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8193 (tmtm)
REVERT: D  342 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7506 (mp0)
REVERT: E  336 GLN cc_start: 0.8488 (mt0) cc_final: 0.8235 (mt0)
REVERT: E  342 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7187 (mp0)
REVERT: E  379 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.3551 (ptt90)
REVERT: F  345 ASP cc_start: 0.8466 (t70) cc_final: 0.8244 (t0)
REVERT: F  379 ARG cc_start: 0.7409 (mmm-85) cc_final: 0.6412 (mtm180)
REVERT: G  321 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8112 (tptm)
REVERT: G  342 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7582 (mp0)
REVERT: G  349 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7274 (mtm180)
REVERT: H  375 LYS cc_start: 0.8402 (tttt) cc_final: 0.7814 (ttmm)
REVERT: I  311 LYS cc_start: 0.8398 (mttt) cc_final: 0.7891 (tttp)
  outliers start: 7
  outliers final: 4
  residues processed: 134
  average time/residue: 1.1852
  time to fit residues: 165.2169
Evaluate side-chains
  135 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 129
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain C residue  338 GLU
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 61 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 50 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0770
   chunk 52 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.5738

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.142919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.127392 restraints weight = 18710.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 1.45
r_work: 0.3898 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3827 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.5678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5175  Z= 0.102
  Angle     :  0.514   5.142   6924  Z= 0.261
  Chirality :  0.050   0.130    780
  Planarity :  0.003   0.038    879
  Dihedral  :  5.450  17.771    681
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 21.54 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.88 (0.25), 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
 ARG   0.008   0.000   ARG B 379 
 TYR   0.005   0.001   TYR E 310 
 PHE   0.007   0.001   PHE G 378 
 HIS   0.003   0.001   HIS G 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 5175)
  covalent geometry    : angle       0.51417 ( 6924)
  hydrogen bonds       : bond        0.01832 (   91)
  hydrogen bonds       : angle       4.15167 (  273)

********************** 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
  138 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 133
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 LEU cc_start: 0.8962 (mp) cc_final: 0.8692 (mp)
REVERT: A  342 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7542 (mp0)
REVERT: B  311 LYS cc_start: 0.8402 (mttt) cc_final: 0.7794 (mmtt)
REVERT: C  311 LYS cc_start: 0.8393 (mttt) cc_final: 0.7843 (mmtm)
REVERT: C  321 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8185 (tmtm)
REVERT: D  342 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7513 (mp0)
REVERT: D  345 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7589 (m-30)
REVERT: E  336 GLN cc_start: 0.8467 (mt0) cc_final: 0.8151 (mt0)
REVERT: E  342 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7161 (mp0)
REVERT: F  345 ASP cc_start: 0.8390 (t70) cc_final: 0.8189 (t0)
REVERT: F  379 ARG cc_start: 0.7406 (mmm-85) cc_final: 0.6449 (mtm110)
REVERT: G  321 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8572 (ttmt)
REVERT: G  342 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7571 (mp0)
REVERT: G  349 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7214 (mtm180)
REVERT: H  375 LYS cc_start: 0.8400 (tttt) cc_final: 0.7813 (ttmm)
REVERT: I  311 LYS cc_start: 0.8411 (mttt) cc_final: 0.7956 (tttp)
  outliers start: 5
  outliers final: 3
  residues processed: 134
  average time/residue: 1.2411
  time to fit residues: 173.1445
Evaluate side-chains
  134 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain C residue  338 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.141426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.125717 restraints weight = 18825.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 1.45
r_work: 0.3863 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3792 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.5740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5175  Z= 0.119
  Angle     :  0.522   4.725   6924  Z= 0.263
  Chirality :  0.049   0.129    780
  Planarity :  0.004   0.039    879
  Dihedral  :  5.459  17.408    681
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 21.71 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (0.25), 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
 ARG   0.009   0.001   ARG B 379 
 TYR   0.007   0.001   TYR E 310 
 PHE   0.007   0.001   PHE G 378 
 HIS   0.003   0.001   HIS H 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5175)
  covalent geometry    : angle       0.52243 ( 6924)
  hydrogen bonds       : bond        0.01931 (   91)
  hydrogen bonds       : angle       4.15219 (  273)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5566.85 seconds
wall clock time: 95 minutes 3.26 seconds (5703.26 seconds total)