Starting phenix.real_space_refine
on Wed Mar 12 03:36:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bxo_45007/03_2025/9bxo_45007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bxo_45007/03_2025/9bxo_45007.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bxo_45007/03_2025/9bxo_45007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bxo_45007/03_2025/9bxo_45007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bxo_45007/03_2025/9bxo_45007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bxo_45007/03_2025/9bxo_45007.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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       6      5.16       5
     C    2202      2.51       5
     N     648      2.21       5
     O     672      1.98       5
     H    3654      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7182
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "C"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "E"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Time building chain proxies: 5.17, per 1000 atoms: 0.72
  Number of scatterers: 7182
  At special positions: 0
  Unit cell: (135.942, 105.918, 37.53, 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       6     16.00
     O     672      8.00
     N     648      7.00
     C    2202      6.00
     H    3654      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.06
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  804

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 42.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.746A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322
      removed outlier: 6.646A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   SER C 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.763A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LYS C 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   SER E 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   THR C 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.758A  pdb=" N   CYS E 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LYS C 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354
      removed outlier: 6.706A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.547A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   GLN C 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.551A  pdb=" N   ILE E 354 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LYS C 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 360
      removed outlier: 6.352A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP C 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 377
      removed outlier: 6.649A  pdb=" N   LYS A 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 8.429A  pdb=" N   GLU C 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ILE A 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   HIS C 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   THR A 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   LEU C 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LYS A 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LYS C 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   GLU E 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ILE C 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   HIS E 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   THR C 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   LEU E 376 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   LYS C 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 306 through 310
    Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.731A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   VAL D 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 324
      removed outlier: 6.421A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.613A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   SER D 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   GLY B 323 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LYS D 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   SER F 320 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   THR D 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.640A  pdb=" N   CYS F 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LYS D 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   SER F 324 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   GLY D 323 " --> pdb=" O   SER F 324 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 330
    Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340
    Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 346
      removed outlier: 6.822A  pdb=" N   LYS B 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   PHE D 346 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   LYS D 343 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   PHE F 346 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP D 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 354
      removed outlier: 6.764A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.661A  pdb=" N   ILE D 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   GLN D 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 8.703A  pdb=" N   ILE F 354 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LYS D 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 357 through 362
      removed outlier: 6.368A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   THR D 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ILE B 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ASP D 358 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   THR F 361 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ILE D 360 " --> pdb=" O   THR F 361 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 372
      removed outlier: 6.606A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.598A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   LYS D 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   GLU F 372 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ILE D 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9

    46 hydrogen bonds defined for protein.
    138 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.32

  Time building geometry restraints manager: 2.77 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 3648
        1.12 -     1.29: 600
        1.29 -     1.46: 963
        1.46 -     1.63: 2019
        1.63 -     1.80: 6
  Bond restraints: 7236
  Sorted by residual:
  bond pdb=" ND2 ASN E 327 "
       pdb="HD21 ASN E 327 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" CD2 HIS D 330 "
       pdb=" HD2 HIS D 330 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" N   VAL C 350 "
       pdb=" H   VAL C 350 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" NE2 GLN D 336 "
       pdb="HE22 GLN D 336 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   LYS D 375 "
       pdb=" H   LYS D 375 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 7231 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 11166
        2.47 -     4.94: 1542
        4.94 -     7.41: 453
        7.41 -     9.89: 21
        9.89 -    12.36: 6
  Bond angle restraints: 13188
  Sorted by residual:
  angle pdb=" CB  HIS E 330 "
        pdb=" CG  HIS E 330 "
        pdb=" CD2 HIS E 330 "
      ideal   model   delta    sigma   weight residual
     131.20  124.69    6.51 1.30e+00 5.92e-01 2.51e+01
  angle pdb=" CB  HIS C 330 "
        pdb=" CG  HIS C 330 "
        pdb=" CD2 HIS C 330 "
      ideal   model   delta    sigma   weight residual
     131.20  124.71    6.49 1.30e+00 5.92e-01 2.49e+01
  angle pdb=" CB  HIS A 330 "
        pdb=" CG  HIS A 330 "
        pdb=" CD2 HIS A 330 "
      ideal   model   delta    sigma   weight residual
     131.20  124.72    6.48 1.30e+00 5.92e-01 2.48e+01
  angle pdb=" CB  HIS F 330 "
        pdb=" CG  HIS F 330 "
        pdb=" CD2 HIS F 330 "
      ideal   model   delta    sigma   weight residual
     131.20  124.73    6.47 1.30e+00 5.92e-01 2.48e+01
  angle pdb=" CB  HIS B 330 "
        pdb=" CG  HIS B 330 "
        pdb=" CD2 HIS B 330 "
      ideal   model   delta    sigma   weight residual
     131.20  124.74    6.46 1.30e+00 5.92e-01 2.47e+01
  ... (remaining 13183 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 3012
       17.00 -    34.00: 135
       34.00 -    51.00: 78
       51.00 -    67.99: 93
       67.99 -    84.99: 6
  Dihedral angle restraints: 3324
    sinusoidal: 1902
      harmonic: 1422
  Sorted by residual:
  dihedral pdb=" CA  SER F 320 "
           pdb=" C   SER F 320 "
           pdb=" N   LYS F 321 "
           pdb=" CA  LYS F 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.05   18.95     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  SER B 320 "
           pdb=" C   SER B 320 "
           pdb=" N   LYS B 321 "
           pdb=" CA  LYS B 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.09   18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  SER D 320 "
           pdb=" C   SER D 320 "
           pdb=" N   LYS D 321 "
           pdb=" CA  LYS D 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.12   18.88     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 3321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 269
       0.057 -    0.114: 170
       0.114 -    0.171: 74
       0.171 -    0.228: 13
       0.228 -    0.285: 8
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" CA  GLU E 380 "
            pdb=" N   GLU E 380 "
            pdb=" C   GLU E 380 "
            pdb=" CB  GLU E 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  GLU A 380 "
            pdb=" N   GLU A 380 "
            pdb=" C   GLU A 380 "
            pdb=" CB  GLU A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  GLU C 380 "
            pdb=" N   GLU C 380 "
            pdb=" C   GLU C 380 "
            pdb=" CB  GLU C 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  ... (remaining 531 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 375 "   -0.021 2.00e-02 2.50e+03   3.83e-02 1.47e+01
        pdb=" N   LEU D 376 "    0.066 2.00e-02 2.50e+03
        pdb=" CA  LEU D 376 "   -0.019 2.00e-02 2.50e+03
        pdb=" H   LEU D 376 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 375 "   -0.021 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" N   LEU B 376 "    0.066 2.00e-02 2.50e+03
        pdb=" CA  LEU B 376 "   -0.019 2.00e-02 2.50e+03
        pdb=" H   LEU B 376 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 375 "   -0.021 2.00e-02 2.50e+03   3.81e-02 1.45e+01
        pdb=" N   LEU F 376 "    0.066 2.00e-02 2.50e+03
        pdb=" CA  LEU F 376 "   -0.019 2.00e-02 2.50e+03
        pdb=" H   LEU F 376 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        0.82 -     1.58: 38
        1.58 -     2.33: 1422
        2.33 -     3.09: 21448
        3.09 -     3.84: 26900
        3.84 -     4.60: 41780
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 91588
  Sorted by model distance:
  nonbonded pdb=" HE1 PHE C 346 "
            pdb=" HD2 PHE E 346 "
     model   vdw
     0.820 2.100
  nonbonded pdb=" HE1 PHE A 346 "
            pdb=" HD2 PHE C 346 "
     model   vdw
     0.821 2.100
  nonbonded pdb=" HD2 HIS A 330 "
            pdb=" OG1 THR C 361 "
     model   vdw
     1.012 2.450
  nonbonded pdb=" HD2 HIS C 330 "
            pdb=" OG1 THR E 361 "
     model   vdw
     1.030 2.450
  nonbonded pdb=" HA  LEU D 325 "
            pdb="HD11 LEU F 325 "
     model   vdw
     1.165 2.440
  ... (remaining 91583 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.480
  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:             0.140
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.860
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.050
  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:21.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
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   0.040   3582  Z= 0.751
  Angle     :  1.741   6.507   4794  Z= 1.146
  Chirality :  0.085   0.285    534
  Planarity :  0.007   0.039    618
  Dihedral  : 12.754  84.993   1380
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 23.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.003   HIS D 362 
 PHE   0.014   0.006   PHE E 346 
 TYR   0.027   0.011   TYR E 310 
 ARG   0.002   0.000   ARG D 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLN cc_start: 0.7791 (tt0) cc_final: 0.7555 (mt0)
REVERT: B  317 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8188 (ptpt)
REVERT: B  321 LYS cc_start: 0.8436 (mttt) cc_final: 0.7971 (mttp)
REVERT: B  336 GLN cc_start: 0.7550 (mt0) cc_final: 0.7293 (tt0)
REVERT: C  369 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8451 (ttpt)
REVERT: D  317 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8164 (ptpt)
REVERT: D  321 LYS cc_start: 0.8332 (mttt) cc_final: 0.8027 (mttm)
REVERT: D  336 GLN cc_start: 0.7572 (mt0) cc_final: 0.6900 (tt0)
REVERT: D  343 LYS cc_start: 0.6808 (mttp) cc_final: 0.6418 (mtpp)
REVERT: D  345 ASP cc_start: 0.6258 (m-30) cc_final: 0.5431 (t70)
REVERT: D  347 LYS cc_start: 0.6455 (mtpt) cc_final: 0.5717 (mttp)
REVERT: E  338 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7145 (mm-30)
REVERT: E  340 LYS cc_start: 0.7031 (mttt) cc_final: 0.6365 (pptt)
REVERT: E  347 LYS cc_start: 0.7436 (mtpt) cc_final: 0.6651 (pptt)
REVERT: E  349 ARG cc_start: 0.6836 (mtt90) cc_final: 0.5870 (ttp-170)
REVERT: E  350 VAL cc_start: 0.7436 (p) cc_final: 0.7107 (m)
REVERT: E  353 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7291 (ttmm)
REVERT: F  317 LYS cc_start: 0.8853 (ptmt) cc_final: 0.8544 (ptpp)
REVERT: F  321 LYS cc_start: 0.8490 (mttt) cc_final: 0.7814 (mptt)
REVERT: F  342 GLU cc_start: 0.6801 (mt-10) cc_final: 0.5514 (pm20)
REVERT: F  343 LYS cc_start: 0.7588 (mttp) cc_final: 0.6688 (ttpp)
REVERT: F  345 ASP cc_start: 0.7228 (m-30) cc_final: 0.6869 (t0)
REVERT: F  347 LYS cc_start: 0.7672 (mtpt) cc_final: 0.6645 (mttp)
REVERT: F  369 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8381 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 3.2444
  time to fit residues: 404.3735
Evaluate side-chains
  78 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
A 374 HIS
B 330 HIS
** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 330 HIS
C 336 GLN
D 330 HIS
D 362 HIS
F 307 GLN
F 336 GLN
F 362 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.157538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.115907 restraints weight = 11580.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.91
r_work: 0.3477 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3582  Z= 0.228
  Angle     :  0.578   3.949   4794  Z= 0.308
  Chirality :  0.050   0.128    534
  Planarity :  0.003   0.033    618
  Dihedral  :  9.763  73.244    480
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.46 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 329 
 PHE   0.014   0.002   PHE C 346 
 TYR   0.012   0.003   TYR F 310 
 ARG   0.003   0.001   ARG D 349 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLN cc_start: 0.7814 (tt0) cc_final: 0.7591 (mt0)
REVERT: B  317 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8348 (ptpt)
REVERT: B  321 LYS cc_start: 0.8793 (mttt) cc_final: 0.8483 (mttp)
REVERT: B  336 GLN cc_start: 0.8189 (mt0) cc_final: 0.7853 (tt0)
REVERT: B  372 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7932 (mt-10)
REVERT: C  369 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8505 (tppt)
REVERT: D  314 ASP cc_start: 0.8847 (t70) cc_final: 0.8623 (t0)
REVERT: D  336 GLN cc_start: 0.8142 (mt0) cc_final: 0.7719 (tt0)
REVERT: D  342 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7817 (mm-30)
REVERT: D  343 LYS cc_start: 0.7780 (mttp) cc_final: 0.7259 (mtpp)
REVERT: D  347 LYS cc_start: 0.7291 (mtpt) cc_final: 0.6538 (mttp)
REVERT: E  338 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6965 (mm-30)
REVERT: E  340 LYS cc_start: 0.6945 (mttt) cc_final: 0.6259 (pptt)
REVERT: E  347 LYS cc_start: 0.7526 (mtpt) cc_final: 0.6452 (pptt)
REVERT: E  349 ARG cc_start: 0.6824 (mtt90) cc_final: 0.5681 (ttp80)
REVERT: E  350 VAL cc_start: 0.7045 (p) cc_final: 0.6814 (m)
REVERT: E  353 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7507 (ttmm)
REVERT: F  321 LYS cc_start: 0.8621 (mttt) cc_final: 0.8099 (mptt)
REVERT: F  342 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6307 (pm20)
REVERT: F  347 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7644 (mtmm)
REVERT: F  369 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8465 (mtpt)
  outliers start: 5
  outliers final: 1
  residues processed: 85
  average time/residue: 3.7329
  time to fit residues: 323.8665
Evaluate side-chains
  74 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  358 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.0040
   chunk 39 optimal weight:    0.1980
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 37 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
B 374 HIS
** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 336 GLN
C 374 HIS
D 329 HIS
D 374 HIS
E 374 HIS
F 374 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.160923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.119285 restraints weight = 11512.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.86
r_work: 0.3503 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3582  Z= 0.131
  Angle     :  0.487   4.913   4794  Z= 0.256
  Chirality :  0.051   0.135    534
  Planarity :  0.002   0.026    618
  Dihedral  :  9.091  68.616    480
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.45 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 330 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.010   0.002   TYR F 310 
 ARG   0.002   0.000   ARG D 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  311 LYS cc_start: 0.8437 (tmmt) cc_final: 0.8200 (mtmm)
REVERT: B  317 LYS cc_start: 0.8586 (ptmt) cc_final: 0.8351 (ptpt)
REVERT: B  321 LYS cc_start: 0.8730 (mttt) cc_final: 0.8432 (mttp)
REVERT: B  336 GLN cc_start: 0.8224 (mt0) cc_final: 0.7789 (tt0)
REVERT: B  372 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7964 (mm-30)
REVERT: C  369 LYS cc_start: 0.8828 (ttpp) cc_final: 0.8520 (tppt)
REVERT: D  314 ASP cc_start: 0.8812 (t70) cc_final: 0.8578 (t0)
REVERT: D  342 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7783 (mm-30)
REVERT: D  343 LYS cc_start: 0.7811 (mttp) cc_final: 0.7296 (mtpp)
REVERT: D  347 LYS cc_start: 0.7357 (mtpt) cc_final: 0.6550 (mttp)
REVERT: D  351 GLN cc_start: 0.8227 (pt0) cc_final: 0.8026 (pt0)
REVERT: E  338 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6926 (mm-30)
REVERT: E  340 LYS cc_start: 0.6973 (mttt) cc_final: 0.6216 (pptt)
REVERT: E  347 LYS cc_start: 0.7462 (mtpt) cc_final: 0.6364 (pptt)
REVERT: E  349 ARG cc_start: 0.6877 (mtt90) cc_final: 0.6489 (mtp-110)
REVERT: E  350 VAL cc_start: 0.7140 (p) cc_final: 0.6931 (m)
REVERT: E  353 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7591 (ttmm)
REVERT: F  321 LYS cc_start: 0.8421 (mttt) cc_final: 0.7870 (mptt)
REVERT: F  342 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6530 (pm20)
REVERT: F  347 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7602 (mtmm)
REVERT: F  369 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8463 (mtpt)
  outliers start: 6
  outliers final: 3
  residues processed: 77
  average time/residue: 3.6088
  time to fit residues: 283.6765
Evaluate side-chains
  71 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  358 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0670
   chunk 5 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 4 optimal weight:   50.0000
   overall best weight:    1.3724

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

Flipped N/Q/H residues before XYZ refinement:
** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 336 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 = 0.157056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.114489 restraints weight = 11678.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.89
r_work: 0.3439 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3582  Z= 0.202
  Angle     :  0.519   5.742   4794  Z= 0.274
  Chirality :  0.051   0.134    534
  Planarity :  0.003   0.032    618
  Dihedral  :  8.775  68.099    480
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.70 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.49 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 330 
 PHE   0.008   0.002   PHE B 378 
 TYR   0.011   0.002   TYR F 310 
 ARG   0.004   0.001   ARG D 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8349 (ptpt)
REVERT: B  321 LYS cc_start: 0.8740 (mttt) cc_final: 0.8445 (mttp)
REVERT: B  372 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8012 (mt-10)
REVERT: C  369 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8524 (tppt)
REVERT: D  314 ASP cc_start: 0.8892 (t70) cc_final: 0.8663 (t0)
REVERT: D  342 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7805 (mm-30)
REVERT: D  343 LYS cc_start: 0.7878 (mttp) cc_final: 0.7398 (mtpp)
REVERT: D  347 LYS cc_start: 0.7281 (mtpt) cc_final: 0.6414 (mttp)
REVERT: E  338 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6854 (mm-30)
REVERT: E  340 LYS cc_start: 0.7041 (mttt) cc_final: 0.6258 (pptt)
REVERT: E  347 LYS cc_start: 0.7306 (mtpt) cc_final: 0.6209 (pptt)
REVERT: E  349 ARG cc_start: 0.6841 (mtt90) cc_final: 0.6459 (mtp-110)
REVERT: E  350 VAL cc_start: 0.7136 (p) cc_final: 0.6918 (m)
REVERT: E  353 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7642 (ttmm)
REVERT: F  342 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6520 (pm20)
REVERT: F  369 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8532 (mtpt)
  outliers start: 6
  outliers final: 4
  residues processed: 71
  average time/residue: 3.5536
  time to fit residues: 257.5827
Evaluate side-chains
  69 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  356 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.2786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.157798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.115403 restraints weight = 11510.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 1.90
r_work: 0.3457 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3582  Z= 0.180
  Angle     :  0.486   3.705   4794  Z= 0.254
  Chirality :  0.050   0.131    534
  Planarity :  0.003   0.029    618
  Dihedral  :  8.608  67.206    480
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.44 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.24), residues: 450

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8325 (ptpt)
REVERT: B  321 LYS cc_start: 0.8775 (mttt) cc_final: 0.8462 (mttp)
REVERT: B  372 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: C  369 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8542 (tppt)
REVERT: D  314 ASP cc_start: 0.8879 (t70) cc_final: 0.8659 (t0)
REVERT: D  342 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7694 (mm-30)
REVERT: D  343 LYS cc_start: 0.7890 (mttp) cc_final: 0.7338 (mtpp)
REVERT: D  347 LYS cc_start: 0.7300 (mtpt) cc_final: 0.6439 (mttp)
REVERT: E  338 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6748 (mm-30)
REVERT: E  340 LYS cc_start: 0.7059 (mttt) cc_final: 0.6196 (pptt)
REVERT: E  347 LYS cc_start: 0.7212 (mtpt) cc_final: 0.6134 (pptt)
REVERT: E  349 ARG cc_start: 0.6760 (mtt90) cc_final: 0.6406 (mtp-110)
REVERT: E  350 VAL cc_start: 0.7119 (p) cc_final: 0.6894 (m)
REVERT: E  353 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7642 (ttmm)
REVERT: F  342 GLU cc_start: 0.7851 (mt-10) cc_final: 0.6550 (pm20)
REVERT: F  369 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8528 (mtpt)
  outliers start: 5
  outliers final: 4
  residues processed: 72
  average time/residue: 3.5754
  time to fit residues: 262.8117
Evaluate side-chains
  68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain E residue  356 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 4 optimal weight:   30.0000
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.148742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.106239 restraints weight = 11853.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.94
r_work: 0.3388 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.5017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3582  Z= 0.283
  Angle     :  0.554   6.126   4794  Z= 0.293
  Chirality :  0.051   0.136    534
  Planarity :  0.003   0.031    618
  Dihedral  :  8.633  68.025    480
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.94 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 330 
 PHE   0.009   0.002   PHE B 378 
 TYR   0.012   0.002   TYR F 310 
 ARG   0.004   0.001   ARG B 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8669 (mttt) cc_final: 0.8380 (mttp)
REVERT: B  317 LYS cc_start: 0.8551 (ptmt) cc_final: 0.8276 (ptpt)
REVERT: B  321 LYS cc_start: 0.8865 (mttt) cc_final: 0.8523 (mttp)
REVERT: B  372 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: C  369 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8568 (tppt)
REVERT: D  314 ASP cc_start: 0.8956 (t70) cc_final: 0.8732 (t0)
REVERT: D  342 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7701 (mm-30)
REVERT: D  343 LYS cc_start: 0.7903 (mttp) cc_final: 0.7338 (mtpp)
REVERT: D  347 LYS cc_start: 0.7270 (mtpt) cc_final: 0.6385 (mttp)
REVERT: E  338 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6771 (mm-30)
REVERT: E  340 LYS cc_start: 0.7107 (mttt) cc_final: 0.6022 (pptt)
REVERT: E  349 ARG cc_start: 0.6677 (mtt90) cc_final: 0.6253 (mtp-110)
REVERT: E  350 VAL cc_start: 0.7276 (p) cc_final: 0.7021 (m)
REVERT: E  353 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7656 (ttmm)
REVERT: F  342 GLU cc_start: 0.7717 (mt-10) cc_final: 0.6449 (pm20)
  outliers start: 6
  outliers final: 4
  residues processed: 71
  average time/residue: 3.5179
  time to fit residues: 255.3795
Evaluate side-chains
  67 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  356 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.3184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.154417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.112869 restraints weight = 11682.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.93
r_work: 0.3432 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.5165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3582  Z= 0.186
  Angle     :  0.487   3.837   4794  Z= 0.253
  Chirality :  0.050   0.130    534
  Planarity :  0.003   0.029    618
  Dihedral  :  8.554  66.644    480
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.94 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 330 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.002   0.000   ARG F 349 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8300 (ptpt)
REVERT: B  321 LYS cc_start: 0.8832 (mttt) cc_final: 0.8480 (mttp)
REVERT: B  372 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8048 (mt-10)
REVERT: C  369 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8539 (tppt)
REVERT: D  314 ASP cc_start: 0.8922 (t70) cc_final: 0.8698 (t0)
REVERT: D  342 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7742 (mm-30)
REVERT: D  343 LYS cc_start: 0.7912 (mttp) cc_final: 0.7346 (mtpp)
REVERT: D  347 LYS cc_start: 0.7323 (mtpt) cc_final: 0.6478 (mttp)
REVERT: E  338 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6753 (mm-30)
REVERT: E  340 LYS cc_start: 0.7122 (mttt) cc_final: 0.6032 (pptt)
REVERT: E  342 GLU cc_start: 0.5036 (pm20) cc_final: 0.4675 (pm20)
REVERT: E  349 ARG cc_start: 0.6681 (mtt90) cc_final: 0.6293 (mtp-110)
REVERT: E  350 VAL cc_start: 0.7198 (p) cc_final: 0.6955 (m)
REVERT: E  353 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7640 (ttmm)
REVERT: F  342 GLU cc_start: 0.7717 (mt-10) cc_final: 0.6399 (pm20)
  outliers start: 6
  outliers final: 3
  residues processed: 67
  average time/residue: 3.7174
  time to fit residues: 254.1430
Evaluate side-chains
  68 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  356 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.155362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.113978 restraints weight = 11712.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.92
r_work: 0.3465 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.5204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3582  Z= 0.140
  Angle     :  0.472   5.139   4794  Z= 0.241
  Chirality :  0.050   0.130    534
  Planarity :  0.004   0.057    618
  Dihedral  :  8.391  66.148    480
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.93 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.004   0.001   PHE C 378 
 TYR   0.007   0.001   TYR F 310 
 ARG   0.009   0.001   ARG F 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8562 (ptmt) cc_final: 0.8293 (ptpt)
REVERT: B  321 LYS cc_start: 0.8790 (mttt) cc_final: 0.8455 (mttp)
REVERT: B  353 LYS cc_start: 0.7492 (ttmt) cc_final: 0.7210 (ttmt)
REVERT: B  372 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8017 (mm-30)
REVERT: C  369 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8552 (tppt)
REVERT: D  314 ASP cc_start: 0.8901 (t70) cc_final: 0.8683 (t0)
REVERT: D  342 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7778 (mm-30)
REVERT: D  343 LYS cc_start: 0.7904 (mttp) cc_final: 0.7347 (mtpp)
REVERT: D  347 LYS cc_start: 0.7334 (mtpt) cc_final: 0.6423 (mttp)
REVERT: E  338 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6752 (mm-30)
REVERT: E  340 LYS cc_start: 0.7157 (mttt) cc_final: 0.6061 (pptt)
REVERT: E  342 GLU cc_start: 0.5020 (pm20) cc_final: 0.4649 (pm20)
REVERT: E  349 ARG cc_start: 0.6571 (mtt90) cc_final: 0.6167 (mtp-110)
REVERT: E  350 VAL cc_start: 0.7056 (p) cc_final: 0.6808 (m)
REVERT: E  353 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7636 (ttmm)
REVERT: F  342 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6378 (pm20)
  outliers start: 4
  outliers final: 4
  residues processed: 67
  average time/residue: 4.0892
  time to fit residues: 279.7691
Evaluate side-chains
  65 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  356 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 5 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.157297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.115966 restraints weight = 11601.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.93
r_work: 0.3476 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.5302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3582  Z= 0.134
  Angle     :  0.460   3.989   4794  Z= 0.236
  Chirality :  0.049   0.130    534
  Planarity :  0.004   0.054    618
  Dihedral  :  8.280  65.200    480
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.43 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.004   0.001   PHE C 378 
 TYR   0.008   0.002   TYR D 310 
 ARG   0.009   0.001   ARG F 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8557 (ptmt) cc_final: 0.8282 (ptpt)
REVERT: B  321 LYS cc_start: 0.8782 (mttt) cc_final: 0.8441 (mttp)
REVERT: B  353 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7230 (ttmt)
REVERT: B  372 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8020 (mm-30)
REVERT: C  369 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8562 (tppt)
REVERT: D  314 ASP cc_start: 0.8878 (t70) cc_final: 0.8662 (t0)
REVERT: D  342 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7765 (mm-30)
REVERT: D  343 LYS cc_start: 0.7872 (mttp) cc_final: 0.7306 (mtpp)
REVERT: D  347 LYS cc_start: 0.7321 (mtpt) cc_final: 0.6478 (mttp)
REVERT: E  338 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6746 (mm-30)
REVERT: E  340 LYS cc_start: 0.7229 (mttt) cc_final: 0.6118 (pptt)
REVERT: E  342 GLU cc_start: 0.5050 (pm20) cc_final: 0.4692 (pm20)
REVERT: E  349 ARG cc_start: 0.6530 (mtt90) cc_final: 0.6136 (mtp-110)
REVERT: E  350 VAL cc_start: 0.6910 (p) cc_final: 0.6660 (m)
REVERT: E  353 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7592 (ttmm)
REVERT: F  342 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6422 (pm20)
  outliers start: 5
  outliers final: 5
  residues processed: 61
  average time/residue: 3.7624
  time to fit residues: 234.5406
Evaluate side-chains
  64 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.4980
   chunk 23 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0370
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.158755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.117898 restraints weight = 11691.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.92
r_work: 0.3505 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.5367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3582  Z= 0.122
  Angle     :  0.446   4.290   4794  Z= 0.228
  Chirality :  0.049   0.128    534
  Planarity :  0.004   0.062    618
  Dihedral  :  8.149  64.248    480
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.43 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 362 
 PHE   0.003   0.001   PHE C 378 
 TYR   0.007   0.001   TYR F 310 
 ARG   0.009   0.001   ARG F 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8301 (ptpt)
REVERT: B  321 LYS cc_start: 0.8770 (mttt) cc_final: 0.8424 (mttp)
REVERT: B  372 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8038 (mm-30)
REVERT: C  369 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8550 (tppt)
REVERT: D  314 ASP cc_start: 0.8880 (t70) cc_final: 0.8625 (t0)
REVERT: D  342 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7789 (mm-30)
REVERT: D  343 LYS cc_start: 0.7870 (mttp) cc_final: 0.7337 (mtpp)
REVERT: D  347 LYS cc_start: 0.7340 (mtpt) cc_final: 0.6440 (mttp)
REVERT: E  338 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6779 (mm-30)
REVERT: E  340 LYS cc_start: 0.7273 (mttt) cc_final: 0.6157 (pptt)
REVERT: E  342 GLU cc_start: 0.4966 (pm20) cc_final: 0.4630 (pm20)
REVERT: E  349 ARG cc_start: 0.6376 (mtt90) cc_final: 0.6036 (mtp-110)
REVERT: E  353 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7525 (ttmm)
REVERT: F  342 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6428 (pm20)
REVERT: F  379 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.6736 (mmt-90)
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 4.7860
  time to fit residues: 303.4595
Evaluate side-chains
  63 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 18 optimal weight:    9.9990
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.157598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.116718 restraints weight = 11601.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.91
r_work: 0.3491 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.5397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3582  Z= 0.134
  Angle     :  0.459   4.423   4794  Z= 0.236
  Chirality :  0.049   0.128    534
  Planarity :  0.004   0.056    618
  Dihedral  :  8.129  64.682    480
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 15.17 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 362 
 PHE   0.004   0.001   PHE C 346 
 TYR   0.007   0.001   TYR B 310 
 ARG   0.009   0.001   ARG F 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7973.45 seconds
wall clock time: 139 minutes 46.16 seconds (8386.16 seconds total)