Starting phenix.real_space_refine
on Wed Jun  4 16:25:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qku_14053/06_2025/7qku_14053.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qku_14053/06_2025/7qku_14053.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qku_14053/06_2025/7qku_14053.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qku_14053/06_2025/7qku_14053.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qku_14053/06_2025/7qku_14053.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qku_14053/06_2025/7qku_14053.cif"
  }
  resolution = 2.57
  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: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2166      2.51       5
     N     639      2.21       5
     O     645      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 3.55, per 1000 atoms: 1.03
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (117.008, 120.304, 35.432, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     645      8.00
     N     639      7.00
     C    2166      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 390.1 milliseconds
  

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 50.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  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: 6.709A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322
      removed outlier: 6.310A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.465A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330
      removed outlier: 5.817A  pdb=" N   GLY A 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.579A  pdb=" N   HIS D 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   GLY D 326 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ASN B 327 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.547A  pdb=" N   GLN B 336 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   VAL D 339 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   GLU B 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346
      removed outlier: 6.550A  pdb=" N   LEU A 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354
      removed outlier: 6.522A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   ILE D 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 362
      removed outlier: 6.281A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   THR D 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ILE B 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 378
      removed outlier: 6.433A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 307 through 310
      removed outlier: 6.606A  pdb=" N   GLN C 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   TYR E 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL C 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.872A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 323
      removed outlier: 6.317A  pdb=" N   LYS C 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   SER E 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   THR C 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   CYS E 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS C 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 333 through 334
    Processing sheet with id=AB5, first strand: chain 'E' and resid 337 through 342
      removed outlier: 6.557A  pdb=" N   GLU C 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   SER E 341 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LYS C 340 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346
      removed outlier: 6.402A  pdb=" N   ASP C 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 350 through 362
      removed outlier: 9.068A  pdb=" N   VAL C 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 10.217A  pdb=" N   LYS E 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
      removed outlier: 8.940A  pdb=" N   SER C 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 10.373A  pdb=" N   GLY E 355 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   ILE C 354 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 10.078A  pdb=" N   LEU E 357 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   SER C 356 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   ASN E 359 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ASP C 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   THR E 361 " --> pdb=" O   ASP C 358 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE C 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLN C 351 " --> pdb=" O   VAL F 350 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   SER F 352 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LYS C 353 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE F 354 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLY C 355 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   SER F 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 368 through 377
      removed outlier: 6.299A  pdb=" N   LYS C 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   GLU E 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ILE C 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   HIS E 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   THR C 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   LEU E 376 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LYS C 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)

    73 hydrogen bonds defined for protein.
    219 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.80

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1028
        1.33 -     1.45: 388
        1.45 -     1.57: 2088
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 3510
  Sorted by residual:
  bond pdb=" CZ  ARG E 349 "
       pdb=" NH2 ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.35e+00
  bond pdb=" CZ  ARG C 349 "
       pdb=" NH2 ARG C 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.98e+00
  bond pdb=" CZ  ARG B 379 "
       pdb=" NH2 ARG B 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.87e+00
  bond pdb=" CZ  ARG D 379 "
       pdb=" NH2 ARG D 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.64e+00
  bond pdb=" CZ  ARG A 379 "
       pdb=" NH2 ARG A 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.41e+00
  ... (remaining 3505 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 3002
        1.57 -     3.15: 1297
        3.15 -     4.72: 314
        4.72 -     6.30: 79
        6.30 -     7.87: 3
  Bond angle restraints: 4695
  Sorted by residual:
  angle pdb=" CA  GLY F 355 "
        pdb=" C   GLY F 355 "
        pdb=" N   SER F 356 "
      ideal   model   delta    sigma   weight residual
     114.58  119.13   -4.55 8.60e-01 1.35e+00 2.80e+01
  angle pdb=" CA  ASP D 348 "
        pdb=" CB  ASP D 348 "
        pdb=" CG  ASP D 348 "
      ideal   model   delta    sigma   weight residual
     112.60  117.65   -5.05 1.00e+00 1.00e+00 2.55e+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  118.62   -4.82 1.00e+00 1.00e+00 2.32e+01
  angle pdb=" CA  PHE A 346 "
        pdb=" CB  PHE A 346 "
        pdb=" CG  PHE A 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.54   -4.74 1.00e+00 1.00e+00 2.25e+01
  angle pdb=" CA  PHE B 346 "
        pdb=" CB  PHE B 346 "
        pdb=" CG  PHE B 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.54   -4.74 1.00e+00 1.00e+00 2.25e+01
  ... (remaining 4690 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.46: 1864
       12.46 -    24.93: 214
       24.93 -    37.39: 40
       37.39 -    49.86: 15
       49.86 -    62.32: 6
  Dihedral angle restraints: 2139
    sinusoidal: 894
      harmonic: 1245
  Sorted by residual:
  dihedral pdb=" C   LEU E 325 "
           pdb=" N   LEU E 325 "
           pdb=" CA  LEU E 325 "
           pdb=" CB  LEU E 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.42   15.82     0      2.50e+00 1.60e-01 4.00e+01
  dihedral pdb=" C   ARG D 349 "
           pdb=" N   ARG D 349 "
           pdb=" CA  ARG D 349 "
           pdb=" CB  ARG D 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.80   15.20     0      2.50e+00 1.60e-01 3.70e+01
  dihedral pdb=" C   ARG A 349 "
           pdb=" N   ARG A 349 "
           pdb=" CA  ARG A 349 "
           pdb=" CB  ARG A 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.80   15.20     0      2.50e+00 1.60e-01 3.70e+01
  ... (remaining 2136 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.121: 436
       0.121 -    0.240: 77
       0.240 -    0.359: 10
       0.359 -    0.479: 1
       0.479 -    0.598: 4
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  LEU E 325 "
            pdb=" N   LEU E 325 "
            pdb=" C   LEU E 325 "
            pdb=" CB  LEU E 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.94e+00
  chirality pdb=" CA  ARG A 349 "
            pdb=" N   ARG A 349 "
            pdb=" C   ARG A 349 "
            pdb=" CB  ARG A 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.91e+00
  chirality pdb=" CA  ARG D 349 "
            pdb=" N   ARG D 349 "
            pdb=" C   ARG D 349 "
            pdb=" CB  ARG D 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.33e+00
  ... (remaining 525 not shown)

  Planarity restraints: 597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "   -0.046 2.00e-02 2.50e+03   2.70e-02 1.46e+01
        pdb=" CG  TYR F 310 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 330 "    0.032 2.00e-02 2.50e+03   2.60e-02 1.02e+01
        pdb=" CG  HIS D 330 "   -0.020 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 330 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 330 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 330 "    0.027 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 330 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 346 "   -0.038 2.00e-02 2.50e+03   2.37e-02 9.87e+00
        pdb=" CG  PHE E 346 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 346 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 346 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 346 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 346 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 346 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 594 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 1607
        2.99 -     3.47: 2760
        3.47 -     3.95: 5501
        3.95 -     4.42: 5742
        4.42 -     4.90: 10651
  Nonbonded interactions: 26261
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.516 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.539 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.600 3.040
  nonbonded pdb=" OD2 ASP D 314 "
            pdb=" NZ  LYS D 370 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   SER C 316 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.632 3.040
  ... (remaining 26256 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 305 through 379)
  selection = (chain 'B' and resid 305 through 379)
  selection = chain 'C'
  selection = (chain 'D' and resid 305 through 379)
  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:             2.380
  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:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.470
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
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   0.035   3510  Z= 0.670
  Angle     :  1.831   7.874   4695  Z= 1.211
  Chirality :  0.105   0.598    528
  Planarity :  0.009   0.030    597
  Dihedral  : 11.695  62.321   1347
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Cbeta Deviations :  1.26 %
  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: -1.72 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.004   HIS D 330 
 PHE   0.038   0.012   PHE E 346 
 TYR   0.046   0.014   TYR F 310 
 ARG   0.002   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07711 (   73)
  hydrogen bonds       : angle       8.03596 (  219)
  covalent geometry    : bond        0.01079 ( 3510)
  covalent geometry    : angle       1.83125 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLN cc_start: 0.8094 (tt0) cc_final: 0.7628 (tt0)
REVERT: A  345 ASP cc_start: 0.8280 (t0) cc_final: 0.8063 (t0)
REVERT: B  311 LYS cc_start: 0.8643 (ptmt) cc_final: 0.7412 (mmtm)
REVERT: B  351 GLN cc_start: 0.7814 (tt0) cc_final: 0.7591 (tt0)
REVERT: B  375 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7823 (ttmm)
REVERT: B  379 ARG cc_start: 0.7911 (ttm170) cc_final: 0.6900 (mmt-90)
REVERT: C  342 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7636 (mp0)
REVERT: D  311 LYS cc_start: 0.8722 (ptmt) cc_final: 0.8265 (pttm)
REVERT: D  375 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7742 (ttmm)
REVERT: D  379 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7334 (ttm170)
REVERT: F  347 LYS cc_start: 0.9014 (mttt) cc_final: 0.8318 (mmmt)
REVERT: F  349 ARG cc_start: 0.8457 (ttm170) cc_final: 0.7040 (mmp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 1.5325
  time to fit residues: 278.1611
Evaluate side-chains
  118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
A 368 ASN
B 307 GLN
** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
D 336 GLN
E 307 GLN
E 329 HIS
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.109337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.096855 restraints weight = 4846.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.63
r_work: 0.3347 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3510  Z= 0.121
  Angle     :  0.622   6.392   4695  Z= 0.314
  Chirality :  0.051   0.170    528
  Planarity :  0.003   0.024    597
  Dihedral  :  6.049  20.092    465
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.18 %
    Favored  : 79.04 %
  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: -1.81 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.37 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 362 
 PHE   0.008   0.001   PHE F 346 
 TYR   0.009   0.002   TYR D 310 
 ARG   0.004   0.001   ARG D 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02187 (   73)
  hydrogen bonds       : angle       6.04836 (  219)
  covalent geometry    : bond        0.00266 ( 3510)
  covalent geometry    : angle       0.62202 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.8421 (tt0) cc_final: 0.8031 (tt0)
REVERT: A  345 ASP cc_start: 0.8546 (t0) cc_final: 0.8290 (t70)
REVERT: A  348 ASP cc_start: 0.7941 (p0) cc_final: 0.7662 (p0)
REVERT: A  353 LYS cc_start: 0.9081 (mttt) cc_final: 0.8860 (mttm)
REVERT: A  373 THR cc_start: 0.8929 (m) cc_final: 0.8587 (p)
REVERT: B  311 LYS cc_start: 0.9084 (ptmt) cc_final: 0.7811 (mmpt)
REVERT: B  319 THR cc_start: 0.8758 (m) cc_final: 0.8536 (p)
REVERT: B  349 ARG cc_start: 0.7501 (ptt180) cc_final: 0.7118 (mtm180)
REVERT: B  373 THR cc_start: 0.9132 (m) cc_final: 0.8789 (p)
REVERT: B  379 ARG cc_start: 0.8218 (ttm170) cc_final: 0.6959 (mmt-90)
REVERT: C  342 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7452 (mp0)
REVERT: D  311 LYS cc_start: 0.9019 (ptmt) cc_final: 0.8679 (pttm)
REVERT: D  348 ASP cc_start: 0.7912 (p0) cc_final: 0.7711 (p0)
REVERT: D  359 ASN cc_start: 0.9220 (m-40) cc_final: 0.8954 (m110)
REVERT: D  375 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8210 (ttmm)
REVERT: D  379 ARG cc_start: 0.8116 (ttm170) cc_final: 0.7759 (mtt180)
REVERT: F  317 LYS cc_start: 0.8838 (mtpm) cc_final: 0.8439 (mttm)
REVERT: F  338 GLU cc_start: 0.8487 (tt0) cc_final: 0.7951 (tt0)
REVERT: F  349 ARG cc_start: 0.8197 (ttm170) cc_final: 0.6927 (mmp-170)
  outliers start: 11
  outliers final: 1
  residues processed: 134
  average time/residue: 1.3989
  time to fit residues: 191.6251
Evaluate side-chains
  123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0070
   chunk 36 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    4.0004

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
A 359 ASN
B 307 GLN
C 307 GLN
** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
D 351 GLN
E 307 GLN
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.102776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.090109 restraints weight = 4753.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.62
r_work: 0.3226 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3510  Z= 0.247
  Angle     :  0.678   8.060   4695  Z= 0.337
  Chirality :  0.052   0.168    528
  Planarity :  0.003   0.014    597
  Dihedral  :  6.192  21.726    465
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.19 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.31), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS E 362 
 PHE   0.008   0.002   PHE F 346 
 TYR   0.014   0.003   TYR B 310 
 ARG   0.005   0.001   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02343 (   73)
  hydrogen bonds       : angle       5.69654 (  219)
  covalent geometry    : bond        0.00581 ( 3510)
  covalent geometry    : angle       0.67762 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8545 (ptmm) cc_final: 0.8336 (ptmm)
REVERT: A  345 ASP cc_start: 0.8504 (t0) cc_final: 0.8244 (t70)
REVERT: A  373 THR cc_start: 0.9133 (m) cc_final: 0.8794 (p)
REVERT: A  379 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8003 (mtt180)
REVERT: B  311 LYS cc_start: 0.9113 (ptmt) cc_final: 0.7912 (mmtt)
REVERT: B  373 THR cc_start: 0.9162 (m) cc_final: 0.8804 (p)
REVERT: D  311 LYS cc_start: 0.9050 (ptmt) cc_final: 0.8742 (pttt)
REVERT: D  340 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7962 (mtpp)
REVERT: D  379 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7839 (mtt180)
REVERT: F  338 GLU cc_start: 0.8564 (tt0) cc_final: 0.8027 (tt0)
REVERT: F  349 ARG cc_start: 0.8338 (ttm170) cc_final: 0.7058 (mmp-170)
  outliers start: 11
  outliers final: 2
  residues processed: 110
  average time/residue: 1.4657
  time to fit residues: 164.8844
Evaluate side-chains
  104 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  351 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
C 307 GLN
** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
D 351 GLN
E 307 GLN
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.105277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.092828 restraints weight = 4805.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.62
r_work: 0.3290 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3510  Z= 0.123
  Angle     :  0.562   5.567   4695  Z= 0.275
  Chirality :  0.049   0.129    528
  Planarity :  0.002   0.011    597
  Dihedral  :  5.449  17.131    465
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.22 %
    Favored  : 75.51 %
  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: -2.03 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 362 
 PHE   0.005   0.001   PHE F 346 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.003   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01745 (   73)
  hydrogen bonds       : angle       5.20659 (  219)
  covalent geometry    : bond        0.00274 ( 3510)
  covalent geometry    : angle       0.56158 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8521 (ptmm) cc_final: 0.8288 (ptmm)
REVERT: A  351 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8253 (tt0)
REVERT: A  353 LYS cc_start: 0.9021 (mttt) cc_final: 0.8791 (mttp)
REVERT: A  373 THR cc_start: 0.9017 (m) cc_final: 0.8688 (p)
REVERT: A  379 ARG cc_start: 0.8365 (ttm170) cc_final: 0.8047 (mtm-85)
REVERT: B  311 LYS cc_start: 0.9101 (ptmt) cc_final: 0.7800 (mmpt)
REVERT: B  319 THR cc_start: 0.8808 (m) cc_final: 0.8545 (p)
REVERT: B  373 THR cc_start: 0.9139 (m) cc_final: 0.8782 (p)
REVERT: C  338 GLU cc_start: 0.8496 (tt0) cc_final: 0.8078 (tt0)
REVERT: D  311 LYS cc_start: 0.9008 (ptmt) cc_final: 0.8674 (pttm)
REVERT: D  340 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7949 (mtpp)
REVERT: D  379 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7855 (mtt180)
REVERT: E  317 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8543 (mttp)
REVERT: F  317 LYS cc_start: 0.8865 (mtpm) cc_final: 0.8529 (mttm)
REVERT: F  338 GLU cc_start: 0.8556 (tt0) cc_final: 0.8120 (tt0)
REVERT: F  349 ARG cc_start: 0.8283 (ttm170) cc_final: 0.6967 (mmp-170)
  outliers start: 9
  outliers final: 5
  residues processed: 119
  average time/residue: 1.5114
  time to fit residues: 183.7858
Evaluate side-chains
  116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain D residue  340 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 35 optimal weight:    0.2980
   chunk 32 optimal weight:    3.9990
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
A 359 ASN
B 307 GLN
C 307 GLN
** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
D 351 GLN
E 307 GLN
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.104218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.091753 restraints weight = 4911.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.63
r_work: 0.3257 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3510  Z= 0.176
  Angle     :  0.601   7.664   4695  Z= 0.292
  Chirality :  0.049   0.134    528
  Planarity :  0.002   0.025    597
  Dihedral  :  5.501  18.652    465
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.72 %
    Favored  : 75.00 %
  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: -2.14 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.005   0.001   PHE F 346 
 TYR   0.011   0.002   TYR B 310 
 ARG   0.004   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01874 (   73)
  hydrogen bonds       : angle       5.12275 (  219)
  covalent geometry    : bond        0.00406 ( 3510)
  covalent geometry    : angle       0.60052 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 THR cc_start: 0.9105 (m) cc_final: 0.8767 (p)
REVERT: A  379 ARG cc_start: 0.8415 (ttm170) cc_final: 0.8034 (mtt180)
REVERT: B  311 LYS cc_start: 0.9103 (ptmt) cc_final: 0.7910 (mmtt)
REVERT: B  373 THR cc_start: 0.9132 (m) cc_final: 0.8753 (p)
REVERT: C  338 GLU cc_start: 0.8529 (tt0) cc_final: 0.8106 (tt0)
REVERT: D  311 LYS cc_start: 0.9027 (ptmt) cc_final: 0.8688 (pttm)
REVERT: D  340 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7990 (mtpp)
REVERT: D  379 ARG cc_start: 0.8301 (ttm170) cc_final: 0.7878 (mtt180)
REVERT: E  317 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8598 (mttm)
REVERT: F  338 GLU cc_start: 0.8576 (tt0) cc_final: 0.8146 (tt0)
REVERT: F  349 ARG cc_start: 0.8305 (ttm170) cc_final: 0.7018 (mmp-170)
  outliers start: 13
  outliers final: 6
  residues processed: 115
  average time/residue: 1.4299
  time to fit residues: 168.0590
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  351 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 34 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
C 307 GLN
** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
D 351 GLN
E 307 GLN
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.101530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.088799 restraints weight = 4941.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.66
r_work: 0.3207 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   3510  Z= 0.283
  Angle     :  0.684   9.671   4695  Z= 0.334
  Chirality :  0.051   0.156    528
  Planarity :  0.003   0.026    597
  Dihedral  :  5.801  21.080    465
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 22.22 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS E 362 
 PHE   0.007   0.002   PHE F 346 
 TYR   0.014   0.003   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02174 (   73)
  hydrogen bonds       : angle       5.37719 (  219)
  covalent geometry    : bond        0.00667 ( 3510)
  covalent geometry    : angle       0.68376 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 THR cc_start: 0.9143 (m) cc_final: 0.8797 (p)
REVERT: A  379 ARG cc_start: 0.8496 (ttm170) cc_final: 0.8122 (mtt180)
REVERT: B  311 LYS cc_start: 0.9106 (ptmt) cc_final: 0.7984 (mmtt)
REVERT: B  373 THR cc_start: 0.9113 (m) cc_final: 0.8712 (p)
REVERT: D  311 LYS cc_start: 0.9036 (ptmt) cc_final: 0.8675 (pttm)
REVERT: D  340 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8010 (mtpp)
REVERT: D  379 ARG cc_start: 0.8385 (ttm170) cc_final: 0.7916 (mtt180)
REVERT: E  311 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8398 (ptpt)
REVERT: F  338 GLU cc_start: 0.8579 (tt0) cc_final: 0.8007 (tt0)
REVERT: F  349 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7012 (mmp-170)
  outliers start: 16
  outliers final: 5
  residues processed: 109
  average time/residue: 1.4549
  time to fit residues: 162.1811
Evaluate side-chains
  108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  311 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0870
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.1162

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
C 307 GLN
C 362 HIS
D 307 GLN
D 351 GLN
E 327 ASN
** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.106624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.094129 restraints weight = 4814.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.63
r_work: 0.3302 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3510  Z= 0.103
  Angle     :  0.539   7.019   4695  Z= 0.262
  Chirality :  0.049   0.130    528
  Planarity :  0.002   0.014    597
  Dihedral  :  5.039  15.088    465
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 22.73 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.33), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 329 
 PHE   0.004   0.001   PHE F 346 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.004   0.000   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01560 (   73)
  hydrogen bonds       : angle       4.97679 (  219)
  covalent geometry    : bond        0.00233 ( 3510)
  covalent geometry    : angle       0.53882 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  373 THR cc_start: 0.9039 (m) cc_final: 0.8715 (p)
REVERT: A  379 ARG cc_start: 0.8445 (ttm170) cc_final: 0.8177 (mtt180)
REVERT: B  305 SER cc_start: 0.8510 (m) cc_final: 0.8298 (t)
REVERT: B  311 LYS cc_start: 0.9140 (ptmt) cc_final: 0.8110 (mtpt)
REVERT: B  319 THR cc_start: 0.8760 (m) cc_final: 0.8559 (p)
REVERT: B  324 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8567 (t)
REVERT: B  373 THR cc_start: 0.9166 (m) cc_final: 0.8837 (p)
REVERT: C  338 GLU cc_start: 0.8516 (tt0) cc_final: 0.8176 (tt0)
REVERT: D  311 LYS cc_start: 0.9023 (ptmt) cc_final: 0.8704 (pttm)
REVERT: D  340 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7971 (mtpp)
REVERT: D  379 ARG cc_start: 0.8333 (ttm170) cc_final: 0.7964 (mtt180)
REVERT: E  338 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8332 (tt0)
REVERT: F  338 GLU cc_start: 0.8589 (tt0) cc_final: 0.8166 (tt0)
REVERT: F  347 LYS cc_start: 0.9118 (mttp) cc_final: 0.8856 (mmtm)
REVERT: F  349 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7059 (mmp-170)
  outliers start: 11
  outliers final: 4
  residues processed: 116
  average time/residue: 1.4576
  time to fit residues: 172.9017
Evaluate side-chains
  114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  338 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
D 351 GLN
F 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.102219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.089460 restraints weight = 4848.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.64
r_work: 0.3228 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   3510  Z= 0.222
  Angle     :  0.637   8.755   4695  Z= 0.307
  Chirality :  0.050   0.139    528
  Planarity :  0.003   0.033    597
  Dihedral  :  5.440  19.792    465
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 23.48 %
    Favored  : 72.98 %
  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: -2.23 (0.33), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.006   0.002   PHE F 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01960 (   73)
  hydrogen bonds       : angle       5.17209 (  219)
  covalent geometry    : bond        0.00527 ( 3510)
  covalent geometry    : angle       0.63710 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A  373 THR cc_start: 0.9127 (m) cc_final: 0.8778 (p)
REVERT: A  379 ARG cc_start: 0.8503 (ttm170) cc_final: 0.8212 (mtt180)
REVERT: B  311 LYS cc_start: 0.9098 (ptmt) cc_final: 0.7957 (mmtm)
REVERT: B  373 THR cc_start: 0.9140 (m) cc_final: 0.8737 (p)
REVERT: C  338 GLU cc_start: 0.8509 (tt0) cc_final: 0.8110 (tt0)
REVERT: D  311 LYS cc_start: 0.9018 (ptmt) cc_final: 0.8670 (pttm)
REVERT: D  340 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7996 (mtpp)
REVERT: D  379 ARG cc_start: 0.8368 (ttm170) cc_final: 0.7952 (mtt180)
REVERT: E  311 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8406 (ptpt)
REVERT: E  338 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8210 (tt0)
REVERT: E  349 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8355 (mtt180)
REVERT: F  338 GLU cc_start: 0.8553 (tt0) cc_final: 0.8096 (tt0)
REVERT: F  349 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7006 (mmp-170)
  outliers start: 14
  outliers final: 6
  residues processed: 109
  average time/residue: 1.4544
  time to fit residues: 162.1966
Evaluate side-chains
  114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  349 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 37 optimal weight:    0.3980
   overall best weight:    3.4788

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
A 359 ASN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
D 351 GLN
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.102127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.089516 restraints weight = 4779.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.61
r_work: 0.3221 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   3510  Z= 0.226
  Angle     :  0.651   8.996   4695  Z= 0.314
  Chirality :  0.050   0.140    528
  Planarity :  0.003   0.033    597
  Dihedral  :  5.523  19.946    465
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 23.48 %
    Favored  : 72.47 %
  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: -2.29 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.006   0.002   PHE F 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01996 (   73)
  hydrogen bonds       : angle       5.25141 (  219)
  covalent geometry    : bond        0.00534 ( 3510)
  covalent geometry    : angle       0.65122 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  351 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8306 (tt0)
REVERT: A  373 THR cc_start: 0.9134 (m) cc_final: 0.8789 (p)
REVERT: A  379 ARG cc_start: 0.8508 (ttm170) cc_final: 0.8217 (mtt180)
REVERT: B  311 LYS cc_start: 0.9095 (ptmt) cc_final: 0.7989 (mmtt)
REVERT: B  373 THR cc_start: 0.9130 (m) cc_final: 0.8737 (p)
REVERT: C  338 GLU cc_start: 0.8500 (tt0) cc_final: 0.8102 (tt0)
REVERT: D  311 LYS cc_start: 0.9011 (ptmt) cc_final: 0.8658 (pttm)
REVERT: D  340 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7967 (mtpp)
REVERT: D  379 ARG cc_start: 0.8391 (ttm170) cc_final: 0.7983 (mtt180)
REVERT: E  311 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8406 (ptpt)
REVERT: E  338 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8192 (tt0)
REVERT: E  349 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8355 (mtt180)
REVERT: F  338 GLU cc_start: 0.8555 (tt0) cc_final: 0.8100 (tt0)
REVERT: F  349 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7007 (mmp-170)
  outliers start: 16
  outliers final: 6
  residues processed: 105
  average time/residue: 1.4649
  time to fit residues: 157.3359
Evaluate side-chains
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
A 359 ASN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
D 351 GLN
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.102460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.089729 restraints weight = 4893.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.65
r_work: 0.3228 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3510  Z= 0.211
  Angle     :  0.650   8.807   4695  Z= 0.311
  Chirality :  0.050   0.135    528
  Planarity :  0.003   0.045    597
  Dihedral  :  5.498  19.369    465
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 23.74 %
    Favored  : 72.73 %
  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: -2.30 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.005   0.002   PHE F 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.006   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01979 (   73)
  hydrogen bonds       : angle       5.23523 (  219)
  covalent geometry    : bond        0.00498 ( 3510)
  covalent geometry    : angle       0.64988 ( 4695)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  373 THR cc_start: 0.9123 (m) cc_final: 0.8768 (p)
REVERT: A  379 ARG cc_start: 0.8518 (ttm170) cc_final: 0.8231 (mtt180)
REVERT: B  311 LYS cc_start: 0.9103 (ptmt) cc_final: 0.7990 (mmtt)
REVERT: B  373 THR cc_start: 0.9130 (m) cc_final: 0.8736 (p)
REVERT: C  338 GLU cc_start: 0.8505 (tt0) cc_final: 0.8101 (tt0)
REVERT: D  311 LYS cc_start: 0.9016 (ptmt) cc_final: 0.8660 (pttm)
REVERT: D  340 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7968 (mtpp)
REVERT: D  379 ARG cc_start: 0.8395 (ttm170) cc_final: 0.7983 (mtt180)
REVERT: E  311 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8405 (ptpt)
REVERT: E  338 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8207 (tt0)
REVERT: E  349 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8350 (mtt180)
REVERT: F  338 GLU cc_start: 0.8562 (tt0) cc_final: 0.8107 (tt0)
REVERT: F  349 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7000 (mmp-170)
  outliers start: 14
  outliers final: 6
  residues processed: 103
  average time/residue: 1.4863
  time to fit residues: 156.5554
Evaluate side-chains
  108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0570
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.2104

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
A 359 ASN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
D 351 GLN
F 307 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.106629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.094064 restraints weight = 4843.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.65
r_work: 0.3308 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3510  Z= 0.108
  Angle     :  0.558   7.699   4695  Z= 0.267
  Chirality :  0.048   0.130    528
  Planarity :  0.002   0.023    597
  Dihedral  :  4.944  14.654    465
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 24.49 %
    Favored  : 72.73 %
  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: -2.19 (0.33), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.008   0.002   TYR B 310 
 ARG   0.005   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01539 (   73)
  hydrogen bonds       : angle       4.89426 (  219)
  covalent geometry    : bond        0.00246 ( 3510)
  covalent geometry    : angle       0.55827 ( 4695)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4215.73 seconds
wall clock time: 72 minutes 33.99 seconds (4353.99 seconds total)