Starting phenix.real_space_refine
on Tue Mar  3 11:44:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qku_14053/03_2026/7qku_14053.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qku_14053/03_2026/7qku_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_14053/03_2026/7qku_14053.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qku_14053/03_2026/7qku_14053.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qku_14053/03_2026/7qku_14053.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qku_14053/03_2026/7qku_14053.cif"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.86, per 1000 atoms: 0.25
  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: 0.26
  Conformation dependent library (CDL) restraints added in 130.5 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: 0.15
  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: 0.40

  Time building geometry restraints manager: 0.37 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: 0.00
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:             3.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     5.270
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:7.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.470
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG B 349 
 TYR   0.046   0.014   TYR F 310 
 PHE   0.038   0.012   PHE E 346 
 HIS   0.016   0.004   HIS D 330 

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

*********************** 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  : 0.127 
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: 0.7253
  time to fit residues: 131.4952
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  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3652 r_free = 0.3652 target = 0.111763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.098888 restraints weight = 4677.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.63
r_work: 0.3358 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
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      :  0.002   0.020   3510  Z= 0.112
  Angle     :  0.612   6.339   4695  Z= 0.310
  Chirality :  0.051   0.170    528
  Planarity :  0.003   0.026    597
  Dihedral  :  6.020  20.085    465
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.84
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 349 
 TYR   0.009   0.002   TYR C 310 
 PHE   0.007   0.001   PHE F 346 
 HIS   0.004   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3510)
  covalent geometry    : angle       0.61210 ( 4695)
  hydrogen bonds       : bond        0.02139 (   73)
  hydrogen bonds       : angle       6.00952 (  219)

*********************** 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  : 0.163 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.8386 (tt0) cc_final: 0.7999 (tt0)
REVERT: A  345 ASP cc_start: 0.8565 (t0) cc_final: 0.8314 (t70)
REVERT: A  348 ASP cc_start: 0.7906 (p0) cc_final: 0.7567 (p0)
REVERT: A  353 LYS cc_start: 0.9083 (mttt) cc_final: 0.8844 (mttm)
REVERT: A  373 THR cc_start: 0.8889 (m) cc_final: 0.8555 (p)
REVERT: B  311 LYS cc_start: 0.9076 (ptmt) cc_final: 0.7731 (mmpt)
REVERT: B  319 THR cc_start: 0.8719 (m) cc_final: 0.8502 (p)
REVERT: B  349 ARG cc_start: 0.7440 (ptt180) cc_final: 0.7216 (mtm180)
REVERT: B  373 THR cc_start: 0.9116 (m) cc_final: 0.8770 (p)
REVERT: B  379 ARG cc_start: 0.8189 (ttm170) cc_final: 0.6938 (mmt-90)
REVERT: C  342 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7468 (mp0)
REVERT: D  311 LYS cc_start: 0.9027 (ptmt) cc_final: 0.8686 (pttm)
REVERT: D  348 ASP cc_start: 0.7938 (p0) cc_final: 0.7728 (p0)
REVERT: D  359 ASN cc_start: 0.9228 (m-40) cc_final: 0.8966 (m110)
REVERT: D  375 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8183 (ttmm)
REVERT: D  379 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7723 (mtt180)
REVERT: E  361 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9051 (m)
REVERT: F  317 LYS cc_start: 0.8845 (mtpm) cc_final: 0.8460 (mttm)
REVERT: F  338 GLU cc_start: 0.8482 (tt0) cc_final: 0.7933 (tt0)
REVERT: F  349 ARG cc_start: 0.8135 (ttm170) cc_final: 0.6903 (mmp-170)
  outliers start: 11
  outliers final: 1
  residues processed: 134
  average time/residue: 0.6612
  time to fit residues: 90.5771
Evaluate side-chains
  122 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  361 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0270
   chunk 20 optimal weight:   10.0000
   chunk 28 optimal weight:    0.0070
   chunk 14 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 6 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    2.8062

-------------------------------------------------------------------------------
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 = 0.3551 r_free = 0.3551 target = 0.105131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.092280 restraints weight = 4826.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.64
r_work: 0.3263 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8878
moved from start:          0.3180

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= 0.183
  Angle     :  0.630   7.258   4695  Z= 0.312
  Chirality :  0.051   0.155    528
  Planarity :  0.002   0.013    597
  Dihedral  :  5.926  20.520    465
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.95 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.43 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 379 
 TYR   0.012   0.002   TYR B 310 
 PHE   0.007   0.002   PHE F 346 
 HIS   0.006   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 3510)
  covalent geometry    : angle       0.63016 ( 4695)
  hydrogen bonds       : bond        0.02177 (   73)
  hydrogen bonds       : angle       5.65476 (  219)

*********************** 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
  121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.8427 (tt0) cc_final: 0.8043 (tt0)
REVERT: A  345 ASP cc_start: 0.8479 (t0) cc_final: 0.8233 (t70)
REVERT: A  353 LYS cc_start: 0.9100 (mttt) cc_final: 0.8853 (mttp)
REVERT: A  373 THR cc_start: 0.9105 (m) cc_final: 0.8769 (p)
REVERT: A  379 ARG cc_start: 0.8388 (ttm170) cc_final: 0.8001 (mtt180)
REVERT: B  311 LYS cc_start: 0.9102 (ptmt) cc_final: 0.7872 (mmtp)
REVERT: B  319 THR cc_start: 0.8826 (m) cc_final: 0.8571 (p)
REVERT: B  373 THR cc_start: 0.9173 (m) cc_final: 0.8823 (p)
REVERT: D  311 LYS cc_start: 0.9068 (ptmt) cc_final: 0.8764 (pttt)
REVERT: D  340 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7970 (mtpp)
REVERT: D  375 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8291 (ttmm)
REVERT: D  379 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7884 (mtt180)
REVERT: F  338 GLU cc_start: 0.8549 (tt0) cc_final: 0.8027 (tt0)
REVERT: F  349 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7040 (mmp-170)
  outliers start: 12
  outliers final: 3
  residues processed: 114
  average time/residue: 0.6771
  time to fit residues: 78.8876
Evaluate side-chains
  109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0670
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   overall best weight:    2.1922

-------------------------------------------------------------------------------
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 = 0.3545 r_free = 0.3545 target = 0.104700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.092239 restraints weight = 4846.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.62
r_work: 0.3274 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3510  Z= 0.151
  Angle     :  0.579   6.581   4695  Z= 0.284
  Chirality :  0.049   0.132    528
  Planarity :  0.002   0.022    597
  Dihedral  :  5.501  18.372    465
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 20.71 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 379 
 TYR   0.011   0.002   TYR B 310 
 PHE   0.005   0.001   PHE F 346 
 HIS   0.005   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3510)
  covalent geometry    : angle       0.57924 ( 4695)
  hydrogen bonds       : bond        0.01847 (   73)
  hydrogen bonds       : angle       5.24608 (  219)

*********************** 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
  123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8418 (ptmm) cc_final: 0.8179 (ptmm)
REVERT: A  373 THR cc_start: 0.9097 (m) cc_final: 0.8762 (p)
REVERT: A  379 ARG cc_start: 0.8345 (ttm170) cc_final: 0.8094 (mtm-85)
REVERT: B  311 LYS cc_start: 0.9101 (ptmt) cc_final: 0.7910 (mmtt)
REVERT: B  319 THR cc_start: 0.8818 (m) cc_final: 0.8600 (p)
REVERT: B  373 THR cc_start: 0.9147 (m) cc_final: 0.8788 (p)
REVERT: C  338 GLU cc_start: 0.8498 (tt0) cc_final: 0.8081 (tt0)
REVERT: D  311 LYS cc_start: 0.9026 (ptmt) cc_final: 0.8681 (pttm)
REVERT: D  340 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7959 (mtpp)
REVERT: D  351 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8050 (tm-30)
REVERT: D  375 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8297 (ttmm)
REVERT: D  379 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7929 (mtt180)
REVERT: E  317 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8527 (mttp)
REVERT: F  317 LYS cc_start: 0.8892 (mtpm) cc_final: 0.8529 (mttm)
REVERT: F  338 GLU cc_start: 0.8552 (tt0) cc_final: 0.8124 (tt0)
REVERT: F  349 ARG cc_start: 0.8294 (ttm170) cc_final: 0.6989 (mmp-170)
  outliers start: 10
  outliers final: 3
  residues processed: 118
  average time/residue: 0.7206
  time to fit residues: 86.7626
Evaluate side-chains
  118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  340 LYS
Chi-restraints excluded: chain D residue  351 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 5 optimal weight:    0.8980
   chunk 34 optimal weight:    8.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.104579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.092040 restraints weight = 4831.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.62
r_work: 0.3261 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8880
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3510  Z= 0.171
  Angle     :  0.594   7.426   4695  Z= 0.289
  Chirality :  0.049   0.133    528
  Planarity :  0.002   0.017    597
  Dihedral  :  5.455  18.404    465
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.24), residues: 441

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 3510)
  covalent geometry    : angle       0.59392 ( 4695)
  hydrogen bonds       : bond        0.01826 (   73)
  hydrogen bonds       : angle       5.14981 (  219)

*********************** 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
  129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 THR cc_start: 0.9109 (m) cc_final: 0.8763 (p)
REVERT: A  379 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8015 (mtt180)
REVERT: B  311 LYS cc_start: 0.9094 (ptmt) cc_final: 0.7894 (mmtm)
REVERT: B  319 THR cc_start: 0.8858 (m) cc_final: 0.8638 (p)
REVERT: B  331 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8423 (mttt)
REVERT: B  351 GLN cc_start: 0.8333 (tt0) cc_final: 0.8041 (tm-30)
REVERT: B  373 THR cc_start: 0.9131 (m) cc_final: 0.8761 (p)
REVERT: C  338 GLU cc_start: 0.8532 (tt0) cc_final: 0.8105 (tt0)
REVERT: D  311 LYS cc_start: 0.9021 (ptmt) cc_final: 0.8683 (pttm)
REVERT: D  340 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7978 (mtpp)
REVERT: D  375 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8322 (ttmm)
REVERT: D  379 ARG cc_start: 0.8322 (ttm170) cc_final: 0.7949 (mtt180)
REVERT: E  317 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8578 (mttm)
REVERT: F  317 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8531 (mttm)
REVERT: F  338 GLU cc_start: 0.8572 (tt0) cc_final: 0.8139 (tt0)
REVERT: F  349 ARG cc_start: 0.8295 (ttm170) cc_final: 0.6995 (mmp-170)
  outliers start: 12
  outliers final: 4
  residues processed: 122
  average time/residue: 0.6930
  time to fit residues: 86.2561
Evaluate side-chains
  118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
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 D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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
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 = 0.3508 r_free = 0.3508 target = 0.102372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.089647 restraints weight = 4814.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.64
r_work: 0.3225 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   3510  Z= 0.230
  Angle     :  0.645   8.705   4695  Z= 0.313
  Chirality :  0.050   0.146    528
  Planarity :  0.003   0.023    597
  Dihedral  :  5.635  20.381    465
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 20.45 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 379 
 TYR   0.013   0.002   TYR B 310 
 PHE   0.006   0.002   PHE F 346 
 HIS   0.007   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 3510)
  covalent geometry    : angle       0.64482 ( 4695)
  hydrogen bonds       : bond        0.02017 (   73)
  hydrogen bonds       : angle       5.24855 (  219)

*********************** 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
  123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 THR cc_start: 0.9142 (m) cc_final: 0.8783 (p)
REVERT: A  379 ARG cc_start: 0.8462 (ttm170) cc_final: 0.8179 (mtt180)
REVERT: B  311 LYS cc_start: 0.9091 (ptmt) cc_final: 0.7959 (mmtm)
REVERT: B  373 THR cc_start: 0.9126 (m) cc_final: 0.8738 (p)
REVERT: C  338 GLU cc_start: 0.8518 (tt0) cc_final: 0.8060 (tt0)
REVERT: D  311 LYS cc_start: 0.9037 (ptmt) cc_final: 0.8684 (pttm)
REVERT: D  340 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8001 (mtpp)
REVERT: D  379 ARG cc_start: 0.8371 (ttm170) cc_final: 0.8006 (mtt180)
REVERT: F  338 GLU cc_start: 0.8561 (tt0) cc_final: 0.8104 (tt0)
REVERT: F  349 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7000 (mmp-170)
  outliers start: 17
  outliers final: 7
  residues processed: 113
  average time/residue: 0.6956
  time to fit residues: 80.2570
Evaluate side-chains
  116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
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 D residue  377 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 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 = 0.3514 r_free = 0.3514 target = 0.102733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.090016 restraints weight = 4904.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.65
r_work: 0.3231 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   3510  Z= 0.208
  Angle     :  0.630   8.347   4695  Z= 0.305
  Chirality :  0.050   0.136    528
  Planarity :  0.003   0.021    597
  Dihedral  :  5.513  19.309    465
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 22.22 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.32), 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
 ARG   0.005   0.001   ARG F 379 
 TYR   0.012   0.002   TYR B 310 
 PHE   0.006   0.002   PHE F 346 
 HIS   0.005   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 3510)
  covalent geometry    : angle       0.63010 ( 4695)
  hydrogen bonds       : bond        0.01949 (   73)
  hydrogen bonds       : angle       5.24577 (  219)

*********************** 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
  122 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 THR cc_start: 0.9142 (m) cc_final: 0.8810 (p)
REVERT: B  311 LYS cc_start: 0.9126 (ptmt) cc_final: 0.7995 (mmtt)
REVERT: B  373 THR cc_start: 0.9138 (m) cc_final: 0.8761 (p)
REVERT: C  338 GLU cc_start: 0.8532 (tt0) cc_final: 0.8181 (tt0)
REVERT: D  311 LYS cc_start: 0.9039 (ptmt) cc_final: 0.8693 (pttm)
REVERT: D  340 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8018 (mtpp)
REVERT: D  379 ARG cc_start: 0.8389 (ttm170) cc_final: 0.8053 (mtt180)
REVERT: E  338 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8289 (tt0)
REVERT: E  349 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8355 (mtt180)
REVERT: F  338 GLU cc_start: 0.8608 (tt0) cc_final: 0.8178 (tt0)
REVERT: F  349 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7013 (mmp-170)
  outliers start: 15
  outliers final: 6
  residues processed: 111
  average time/residue: 0.6775
  time to fit residues: 76.8733
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
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 D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  377 THR
Chi-restraints excluded: chain E residue  338 GLU
Chi-restraints excluded: chain E residue  349 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    4.1788

-------------------------------------------------------------------------------
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 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 = 0.3493 r_free = 0.3493 target = 0.101479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.088762 restraints weight = 4972.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.65
r_work: 0.3203 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8913
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   3510  Z= 0.265
  Angle     :  0.681   9.501   4695  Z= 0.329
  Chirality :  0.051   0.150    528
  Planarity :  0.003   0.037    597
  Dihedral  :  5.686  20.581    465
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 23.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 379 
 TYR   0.013   0.003   TYR B 310 
 PHE   0.006   0.002   PHE F 346 
 HIS   0.006   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 3510)
  covalent geometry    : angle       0.68089 ( 4695)
  hydrogen bonds       : bond        0.02148 (   73)
  hydrogen bonds       : angle       5.38790 (  219)

*********************** 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: 15
    poor density    : 103
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 THR cc_start: 0.9144 (m) cc_final: 0.8796 (p)
REVERT: B  311 LYS cc_start: 0.9098 (ptmt) cc_final: 0.8004 (mmtt)
REVERT: B  373 THR cc_start: 0.9122 (m) cc_final: 0.8740 (p)
REVERT: C  349 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8127 (mtt180)
REVERT: D  311 LYS cc_start: 0.9028 (ptmt) cc_final: 0.8679 (pttm)
REVERT: D  340 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7992 (mtpp)
REVERT: D  379 ARG cc_start: 0.8436 (ttm170) cc_final: 0.8073 (mtt180)
REVERT: E  311 LYS cc_start: 0.8573 (pttp) cc_final: 0.8279 (ptpt)
REVERT: E  349 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8364 (mtt180)
REVERT: F  338 GLU cc_start: 0.8553 (tt0) cc_final: 0.7985 (tt0)
REVERT: F  349 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7027 (mmp-170)
  outliers start: 15
  outliers final: 5
  residues processed: 108
  average time/residue: 0.7142
  time to fit residues: 78.7299
Evaluate side-chains
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
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 C residue  349 ARG
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  377 THR
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 10 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 362 HIS
D 307 GLN
D 351 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 = 0.3556 r_free = 0.3556 target = 0.105557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093043 restraints weight = 4831.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.64
r_work: 0.3290 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3510  Z= 0.121
  Angle     :  0.568   7.907   4695  Z= 0.272
  Chirality :  0.049   0.131    528
  Planarity :  0.002   0.029    597
  Dihedral  :  5.056  15.404    465
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 24.24 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.33), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 379 
 TYR   0.009   0.002   TYR B 310 
 PHE   0.004   0.001   PHE A 378 
 HIS   0.002   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3510)
  covalent geometry    : angle       0.56836 ( 4695)
  hydrogen bonds       : bond        0.01611 (   73)
  hydrogen bonds       : angle       4.99849 (  219)

*********************** 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
  121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  373 THR cc_start: 0.9036 (m) cc_final: 0.8692 (p)
REVERT: B  305 SER cc_start: 0.8508 (m) cc_final: 0.8286 (t)
REVERT: B  311 LYS cc_start: 0.9075 (ptmt) cc_final: 0.7970 (mmtt)
REVERT: B  319 THR cc_start: 0.8790 (m) cc_final: 0.8512 (p)
REVERT: B  373 THR cc_start: 0.9140 (m) cc_final: 0.8803 (p)
REVERT: C  338 GLU cc_start: 0.8540 (tt0) cc_final: 0.8183 (tt0)
REVERT: C  379 ARG cc_start: 0.7544 (tpp-160) cc_final: 0.7050 (tpp-160)
REVERT: D  311 LYS cc_start: 0.9015 (ptmt) cc_final: 0.8671 (pttm)
REVERT: D  340 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7911 (mtpp)
REVERT: D  379 ARG cc_start: 0.8326 (ttm170) cc_final: 0.8080 (mmm-85)
REVERT: E  311 LYS cc_start: 0.8508 (pttp) cc_final: 0.8228 (ptpt)
REVERT: E  338 GLU cc_start: 0.8610 (tt0) cc_final: 0.8356 (tt0)
REVERT: E  349 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8329 (mtt180)
REVERT: E  379 ARG cc_start: 0.7368 (tpp-160) cc_final: 0.7164 (tpp-160)
REVERT: F  338 GLU cc_start: 0.8578 (tt0) cc_final: 0.8138 (tt0)
REVERT: F  349 ARG cc_start: 0.8241 (ttm170) cc_final: 0.6994 (mmp-170)
  outliers start: 9
  outliers final: 3
  residues processed: 115
  average time/residue: 0.6896
  time to fit residues: 80.9067
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
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 41 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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
D 307 GLN
D 351 GLN
E 327 ASN
E 362 HIS
F 307 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.108041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.095722 restraints weight = 4875.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.63
r_work: 0.3334 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.3855

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= 0.096
  Angle     :  0.542   8.213   4695  Z= 0.256
  Chirality :  0.048   0.131    528
  Planarity :  0.002   0.018    597
  Dihedral  :  4.727  14.012    465
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 24.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.34), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.26), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 379 
 TYR   0.008   0.002   TYR D 310 
 PHE   0.004   0.001   PHE D 346 
 HIS   0.002   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 3510)
  covalent geometry    : angle       0.54159 ( 4695)
  hydrogen bonds       : bond        0.01424 (   73)
  hydrogen bonds       : angle       4.72976 (  219)

********************** 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
  128 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  351 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8337 (tt0)
REVERT: A  373 THR cc_start: 0.9022 (m) cc_final: 0.8676 (p)
REVERT: B  311 LYS cc_start: 0.9082 (ptmt) cc_final: 0.7971 (mmtt)
REVERT: B  331 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8414 (mttt)
REVERT: B  351 GLN cc_start: 0.8413 (tt0) cc_final: 0.8127 (tm-30)
REVERT: B  373 THR cc_start: 0.9171 (m) cc_final: 0.8849 (p)
REVERT: C  338 GLU cc_start: 0.8537 (tt0) cc_final: 0.8177 (tt0)
REVERT: C  379 ARG cc_start: 0.7590 (tpp-160) cc_final: 0.7129 (tpp-160)
REVERT: D  311 LYS cc_start: 0.9004 (ptmt) cc_final: 0.8663 (pttm)
REVERT: D  340 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7899 (mtpp)
REVERT: E  311 LYS cc_start: 0.8505 (pttp) cc_final: 0.8238 (ptpt)
REVERT: E  317 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8540 (mttm)
REVERT: E  338 GLU cc_start: 0.8599 (tt0) cc_final: 0.8378 (tt0)
REVERT: E  349 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8331 (mtt180)
REVERT: F  338 GLU cc_start: 0.8547 (tt0) cc_final: 0.8137 (tt0)
REVERT: F  349 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7022 (mmp-170)
  outliers start: 9
  outliers final: 3
  residues processed: 122
  average time/residue: 0.7045
  time to fit residues: 87.7581
Evaluate side-chains
  121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
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 D residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
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 9 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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
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 = 0.3573 r_free = 0.3573 target = 0.106298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.093912 restraints weight = 4873.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.63
r_work: 0.3291 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.3889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3510  Z= 0.131
  Angle     :  0.577   8.423   4695  Z= 0.272
  Chirality :  0.048   0.134    528
  Planarity :  0.002   0.033    597
  Dihedral  :  4.871  15.986    465
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 24.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.34), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.26), residues: 441

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3510)
  covalent geometry    : angle       0.57721 ( 4695)
  hydrogen bonds       : bond        0.01500 (   73)
  hydrogen bonds       : angle       4.73946 (  219)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2052.02 seconds
wall clock time: 35 minutes 40.10 seconds (2140.10 seconds total)