Starting phenix.real_space_refine
on Fri Aug 22 13:43:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8x_18264/08_2025/8q8x_18264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8x_18264/08_2025/8q8x_18264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q8x_18264/08_2025/8q8x_18264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8x_18264/08_2025/8q8x_18264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8x_18264/08_2025/8q8x_18264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8x_18264/08_2025/8q8x_18264.cif"
  }
  resolution = 2.54
  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    2154      2.51       5
     N     630      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 22 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3435
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      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: "B"
      Number of atoms: 571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 571
          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: 571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 571
          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: 571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 571
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Time building chain proxies: 0.93, per 1000 atoms: 0.27
  Number of scatterers: 3435
  At special positions: 0
  Unit cell: (133.768, 135.222, 56.706, 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     630      7.00
     C    2154      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: 0.22
  Conformation dependent library (CDL) restraints added in 101.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 57.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.547A  pdb=" N   VAL A 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   VAL C 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ILE A 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   GLN A 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   TYR E 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL A 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.878A  pdb=" N   VAL A 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325
      removed outlier: 6.561A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   LYS C 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER A 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   GLY C 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   CYS A 322 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU C 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   SER A 324 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.665A  pdb=" N   ILE A 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346
      removed outlier: 6.773A  pdb=" N   LEU C 344 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ASP A 345 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   PHE C 346 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
      removed outlier: 8.995A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 9.966A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 8.820A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 9.814A  pdb=" N   GLU E 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 8.936A  pdb=" N   SER A 341 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
      removed outlier: 9.397A  pdb=" N   LEU E 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   LYS A 343 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 8.378A  pdb=" N   PHE E 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASP A 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 362
      removed outlier: 8.982A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 10.259A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 9.061A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 10.211A  pdb=" N   SER C 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   GLY A 355 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   ASP C 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   LEU A 357 " --> pdb=" O   ASP C 358 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   ILE C 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASN A 359 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   HIS C 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   THR A 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLN E 351 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   SER A 352 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   LYS E 353 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ILE A 354 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLY E 355 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   SER A 356 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 368 through 378
      removed outlier: 6.486A  pdb=" N   LYS A 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   GLU E 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ILE A 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   HIS E 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   THR A 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   LEU E 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   LYS A 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   PHE E 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   THR A 377 " --> pdb=" O   PHE E 378 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.543A  pdb=" N   GLN B 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   TYR F 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL B 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.832A  pdb=" N   VAL B 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 325
      removed outlier: 6.295A  pdb=" N   LYS B 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   SER F 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   THR B 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   CYS F 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LYS B 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   SER F 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   GLY B 323 " --> pdb=" O   SER F 324 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.516A  pdb=" N   ILE B 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 340
      removed outlier: 6.545A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 343 through 347
      removed outlier: 6.418A  pdb=" N   LEU B 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   LYS D 347 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   PHE B 346 " --> pdb=" O   LYS D 347 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.347A  pdb=" N   GLN B 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   ILE F 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LYS B 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 357 through 362
    Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 377

    88 hydrogen bonds defined for protein.
    264 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: 0.47

  Time building geometry restraints manager: 0.30 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: 1021
        1.33 -     1.46: 381
        1.46 -     1.58: 2081
        1.58 -     1.70: 0
        1.70 -     1.82: 6
  Bond restraints: 3489
  Sorted by residual:
  bond pdb=" CZ  ARG E 349 "
       pdb=" NH2 ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.69e+00
  bond pdb=" CZ  ARG A 349 "
       pdb=" NH2 ARG A 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.37e+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 6.66e+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 6.54e+00
  bond pdb=" CA  LYS C 331 "
       pdb=" C   LYS C 331 "
    ideal  model  delta    sigma   weight residual
    1.532  1.548 -0.016 6.50e-03 2.37e+04 6.24e+00
  ... (remaining 3484 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 2676
        1.26 -     2.52: 1298
        2.52 -     3.79: 527
        3.79 -     5.05: 122
        5.05 -     6.31: 45
  Bond angle restraints: 4668
  Sorted by residual:
  angle pdb=" CA  ASP B 358 "
        pdb=" CB  ASP B 358 "
        pdb=" CG  ASP B 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.91   -6.31 1.00e+00 1.00e+00 3.98e+01
  angle pdb=" CA  ASP F 358 "
        pdb=" CB  ASP F 358 "
        pdb=" CG  ASP F 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.64   -6.04 1.00e+00 1.00e+00 3.65e+01
  angle pdb=" CA  ASP A 358 "
        pdb=" CB  ASP A 358 "
        pdb=" CG  ASP A 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.56   -5.96 1.00e+00 1.00e+00 3.55e+01
  angle pdb=" OE1 GLN A 336 "
        pdb=" CD  GLN A 336 "
        pdb=" NE2 GLN A 336 "
      ideal   model   delta    sigma   weight residual
     122.60  116.93    5.67 1.00e+00 1.00e+00 3.22e+01
  angle pdb=" CA  GLY C 355 "
        pdb=" C   GLY C 355 "
        pdb=" N   SER C 356 "
      ideal   model   delta    sigma   weight residual
     114.58  119.19   -4.61 8.60e-01 1.35e+00 2.88e+01
  ... (remaining 4663 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 2014
       17.67 -    35.35: 76
       35.35 -    53.02: 18
       53.02 -    70.69: 7
       70.69 -    88.37: 3
  Dihedral angle restraints: 2118
    sinusoidal: 879
      harmonic: 1239
  Sorted by residual:
  dihedral pdb=" CA  LYS F 343 "
           pdb=" C   LYS F 343 "
           pdb=" N   LEU F 344 "
           pdb=" CA  LEU F 344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.22   24.78     0      5.00e+00 4.00e-02 2.46e+01
  dihedral pdb=" CA  ASP E 358 "
           pdb=" C   ASP E 358 "
           pdb=" N   ASN E 359 "
           pdb=" CA  ASN E 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.72   24.28     0      5.00e+00 4.00e-02 2.36e+01
  dihedral pdb=" CA  SER B 341 "
           pdb=" C   SER B 341 "
           pdb=" N   GLU B 342 "
           pdb=" CA  GLU B 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.72   23.28     0      5.00e+00 4.00e-02 2.17e+01
  ... (remaining 2115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 276
       0.058 -    0.117: 185
       0.117 -    0.175: 48
       0.175 -    0.233: 14
       0.233 -    0.291: 2
  Chirality restraints: 525
  Sorted by residual:
  chirality pdb=" CA  THR A 319 "
            pdb=" N   THR A 319 "
            pdb=" C   THR A 319 "
            pdb=" CB  THR A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.23    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  THR E 319 "
            pdb=" N   THR E 319 "
            pdb=" C   THR E 319 "
            pdb=" CB  THR E 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.27    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  GLU E 342 "
            pdb=" N   GLU E 342 "
            pdb=" C   GLU E 342 "
            pdb=" CB  GLU E 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 522 not shown)

  Planarity restraints: 594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "    0.110 2.00e-02 2.50e+03   6.34e-02 8.03e+01
        pdb=" CG  TYR C 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "   -0.052 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "   -0.044 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "    0.106 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.064 2.00e-02 2.50e+03   3.56e-02 2.53e+01
        pdb=" CG  TYR A 310 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.049 2.00e-02 2.50e+03   2.60e-02 1.35e+01
        pdb=" CG  TYR E 310 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.036 2.00e-02 2.50e+03
  ... (remaining 591 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 1594
        2.99 -     3.47: 2668
        3.47 -     3.95: 5618
        3.95 -     4.42: 5438
        4.42 -     4.90: 10758
  Nonbonded interactions: 26076
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.517 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.521 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.529 3.040
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.532 3.040
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.535 3.040
  ... (remaining 26071 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  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:             4.110
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.990
  Find NCS groups from input model:        0.030
  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:6.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
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   0.036   3489  Z= 0.679
  Angle     :  1.745   6.308   4668  Z= 1.165
  Chirality :  0.079   0.291    525
  Planarity :  0.009   0.063    594
  Dihedral  : 11.916  88.368   1332
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  4.33 %
    Favored  : 94.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.34), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.26), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 349 
 TYR   0.110   0.022   TYR C 310 
 PHE   0.034   0.011   PHE E 346 
 HIS   0.009   0.003   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01104 ( 3489)
  covalent geometry    : angle       1.74485 ( 4668)
  hydrogen bonds       : bond        0.07336 (   88)
  hydrogen bonds       : angle       7.58586 (  264)

*********************** 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
  198 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 193
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.6907 (mttt) cc_final: 0.6561 (mttp)
REVERT: A  319 THR cc_start: 0.7218 (p) cc_final: 0.6909 (m)
REVERT: A  340 LYS cc_start: 0.6452 (mttt) cc_final: 0.6212 (mtpt)
REVERT: A  353 LYS cc_start: 0.6522 (mttt) cc_final: 0.6138 (tttm)
REVERT: A  360 ILE cc_start: 0.7388 (mt) cc_final: 0.7123 (mm)
REVERT: A  375 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7636 (ttpt)
REVERT: B  317 LYS cc_start: 0.7768 (mttt) cc_final: 0.7187 (mtpt)
REVERT: B  340 LYS cc_start: 0.7795 (tttt) cc_final: 0.7100 (ttpp)
REVERT: B  343 LYS cc_start: 0.6437 (ttmt) cc_final: 0.6233 (tppt)
REVERT: B  369 LYS cc_start: 0.7528 (tttt) cc_final: 0.7197 (tttm)
REVERT: C  317 LYS cc_start: 0.6966 (mttt) cc_final: 0.6617 (mttm)
REVERT: C  347 LYS cc_start: 0.7934 (mttt) cc_final: 0.7723 (mptp)
REVERT: C  349 ARG cc_start: 0.6327 (mtm180) cc_final: 0.5897 (mmp-170)
REVERT: C  353 LYS cc_start: 0.6576 (mttt) cc_final: 0.6256 (tttp)
REVERT: C  360 ILE cc_start: 0.7478 (mt) cc_final: 0.7230 (mp)
REVERT: D  311 LYS cc_start: 0.7803 (mttt) cc_final: 0.6972 (mttm)
REVERT: D  317 LYS cc_start: 0.7712 (mttt) cc_final: 0.7230 (mtpt)
REVERT: D  340 LYS cc_start: 0.7711 (tttt) cc_final: 0.7270 (tptt)
REVERT: D  369 LYS cc_start: 0.7514 (tttt) cc_final: 0.7255 (tttm)
REVERT: D  375 LYS cc_start: 0.7125 (tttt) cc_final: 0.6874 (ttpt)
REVERT: E  317 LYS cc_start: 0.7829 (mttt) cc_final: 0.7495 (mttm)
REVERT: E  320 SER cc_start: 0.8379 (m) cc_final: 0.7846 (p)
REVERT: E  340 LYS cc_start: 0.7676 (mttt) cc_final: 0.7251 (mtpt)
REVERT: F  315 LEU cc_start: 0.8983 (mp) cc_final: 0.8775 (mp)
REVERT: F  317 LYS cc_start: 0.8233 (mttt) cc_final: 0.7728 (mtpt)
REVERT: F  340 LYS cc_start: 0.8303 (tttt) cc_final: 0.7869 (tppt)
REVERT: F  343 LYS cc_start: 0.6977 (ttmt) cc_final: 0.6744 (tppt)
REVERT: F  369 LYS cc_start: 0.8123 (tttt) cc_final: 0.7811 (tttm)
  outliers start: 5
  outliers final: 0
  residues processed: 193
  average time/residue: 0.6314
  time to fit residues: 124.7136
Evaluate side-chains
  138 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
B 351 GLN
C 327 ASN
C 351 GLN
D 351 GLN
E 327 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.119945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.105672 restraints weight = 4156.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.45
r_work: 0.3383 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3489  Z= 0.134
  Angle     :  0.630   7.926   4668  Z= 0.304
  Chirality :  0.050   0.132    525
  Planarity :  0.003   0.016    594
  Dihedral  :  5.496  16.007    462
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 14.50 %
    Favored  : 84.48 %
  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 aren not related in a simple way.
  whole: -1.40 (0.34), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.06 (0.26), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.018   0.004   TYR B 310 
 PHE   0.009   0.002   PHE A 346 
 HIS   0.003   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3489)
  covalent geometry    : angle       0.62963 ( 4668)
  hydrogen bonds       : bond        0.02075 (   88)
  hydrogen bonds       : angle       5.34693 (  264)

*********************** 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
  150 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 146
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8544 (mttt) cc_final: 0.8296 (mttp)
REVERT: A  338 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7821 (tt0)
REVERT: B  317 LYS cc_start: 0.8887 (mttt) cc_final: 0.8651 (mtpt)
REVERT: C  317 LYS cc_start: 0.8563 (mttt) cc_final: 0.8349 (mtmt)
REVERT: C  349 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7413 (tpt90)
REVERT: D  311 LYS cc_start: 0.8507 (mttt) cc_final: 0.7936 (mttm)
REVERT: D  340 LYS cc_start: 0.8544 (tttt) cc_final: 0.8308 (tptm)
REVERT: D  358 ASP cc_start: 0.8580 (m-30) cc_final: 0.8370 (m-30)
REVERT: E  317 LYS cc_start: 0.8592 (mttt) cc_final: 0.8370 (mttp)
  outliers start: 4
  outliers final: 2
  residues processed: 147
  average time/residue: 0.7171
  time to fit residues: 107.6059
Evaluate side-chains
  123 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain E residue  347 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    5.7990

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.112384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.098687 restraints weight = 4232.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.41
r_work: 0.3285 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8937
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   3489  Z= 0.315
  Angle     :  0.723   9.767   4668  Z= 0.351
  Chirality :  0.051   0.130    525
  Planarity :  0.004   0.023    594
  Dihedral  :  5.488  14.728    462
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.07 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 349 
 TYR   0.009   0.002   TYR A 310 
 PHE   0.015   0.003   PHE C 346 
 HIS   0.003   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 ( 3489)
  covalent geometry    : angle       0.72299 ( 4668)
  hydrogen bonds       : bond        0.02249 (   88)
  hydrogen bonds       : angle       5.28641 (  264)

*********************** 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
  135 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8816 (mttt) cc_final: 0.8549 (mtpt)
REVERT: C  349 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7425 (tpt90)
REVERT: D  311 LYS cc_start: 0.8729 (mttt) cc_final: 0.8071 (mttm)
REVERT: D  358 ASP cc_start: 0.8606 (m-30) cc_final: 0.8397 (m-30)
REVERT: E  317 LYS cc_start: 0.8731 (mttt) cc_final: 0.8461 (mttm)
REVERT: E  372 GLU cc_start: 0.8536 (tt0) cc_final: 0.8313 (tt0)
REVERT: F  340 LYS cc_start: 0.8758 (tptp) cc_final: 0.8468 (tptt)
  outliers start: 12
  outliers final: 5
  residues processed: 124
  average time/residue: 0.7646
  time to fit residues: 96.7331
Evaluate side-chains
  108 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  369 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0670
   chunk 9 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.6126

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.116209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.102556 restraints weight = 4063.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.41
r_work: 0.3328 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3489  Z= 0.169
  Angle     :  0.581   7.538   4668  Z= 0.281
  Chirality :  0.049   0.121    525
  Planarity :  0.003   0.018    594
  Dihedral  :  5.039  13.110    462
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 1.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.30 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 349 
 TYR   0.009   0.001   TYR F 310 
 PHE   0.009   0.002   PHE C 346 
 HIS   0.002   0.000   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3489)
  covalent geometry    : angle       0.58136 ( 4668)
  hydrogen bonds       : bond        0.01788 (   88)
  hydrogen bonds       : angle       4.99084 (  264)

*********************** 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
  120 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8726 (mttt) cc_final: 0.8491 (mtpt)
REVERT: C  349 ARG cc_start: 0.8108 (mtm180) cc_final: 0.7394 (tpt90)
REVERT: D  311 LYS cc_start: 0.8715 (mttt) cc_final: 0.8055 (mttm)
REVERT: D  358 ASP cc_start: 0.8583 (m-30) cc_final: 0.8305 (m-30)
REVERT: E  317 LYS cc_start: 0.8664 (mttt) cc_final: 0.8423 (mtmt)
  outliers start: 10
  outliers final: 4
  residues processed: 112
  average time/residue: 0.7539
  time to fit residues: 86.2808
Evaluate side-chains
  108 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  369 LYS
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  369 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 41 optimal weight:    0.3980
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.2386

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.117723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.104011 restraints weight = 4094.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.43
r_work: 0.3361 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3489  Z= 0.105
  Angle     :  0.528   6.733   4668  Z= 0.253
  Chirality :  0.048   0.117    525
  Planarity :  0.002   0.018    594
  Dihedral  :  4.641  12.216    462
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.08 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.33), 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   0.001   0.000   ARG E 349 
 TYR   0.019   0.002   TYR B 310 
 PHE   0.005   0.001   PHE C 346 
 HIS   0.001   0.000   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3489)
  covalent geometry    : angle       0.52835 ( 4668)
  hydrogen bonds       : bond        0.01525 (   88)
  hydrogen bonds       : angle       4.65784 (  264)

*********************** 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
  119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8741 (mttt) cc_final: 0.8469 (mtpt)
REVERT: C  349 ARG cc_start: 0.8168 (mtm180) cc_final: 0.7425 (tpt90)
REVERT: D  311 LYS cc_start: 0.8689 (mttt) cc_final: 0.8063 (mttm)
REVERT: E  317 LYS cc_start: 0.8610 (mttt) cc_final: 0.8388 (mtmt)
REVERT: E  347 LYS cc_start: 0.8893 (mptp) cc_final: 0.8486 (mppt)
  outliers start: 7
  outliers final: 2
  residues processed: 114
  average time/residue: 0.7069
  time to fit residues: 82.4069
Evaluate side-chains
  105 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain F residue  369 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0980
   chunk 14 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    4.2188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.112583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.099070 restraints weight = 4192.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.43
r_work: 0.3300 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   3489  Z= 0.246
  Angle     :  0.621   7.598   4668  Z= 0.302
  Chirality :  0.049   0.120    525
  Planarity :  0.003   0.017    594
  Dihedral  :  5.003  14.155    462
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.59 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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   0.002   0.001   ARG A 349 
 TYR   0.008   0.002   TYR A 310 
 PHE   0.013   0.002   PHE C 346 
 HIS   0.002   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 ( 3489)
  covalent geometry    : angle       0.62133 ( 4668)
  hydrogen bonds       : bond        0.01884 (   88)
  hydrogen bonds       : angle       4.93016 (  264)

*********************** 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 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8725 (mttt) cc_final: 0.8480 (mtpt)
REVERT: C  349 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7417 (tpt90)
REVERT: D  311 LYS cc_start: 0.8719 (mttt) cc_final: 0.8059 (mttm)
REVERT: E  317 LYS cc_start: 0.8665 (mttt) cc_final: 0.8426 (mtmt)
REVERT: F  311 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8576 (mtmt)
  outliers start: 11
  outliers final: 5
  residues processed: 110
  average time/residue: 0.7538
  time to fit residues: 84.6673
Evaluate side-chains
  109 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  369 LYS
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  369 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    2.7386

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.114229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.100555 restraints weight = 4235.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.45
r_work: 0.3318 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8909
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3489  Z= 0.171
  Angle     :  0.583   7.568   4668  Z= 0.278
  Chirality :  0.049   0.120    525
  Planarity :  0.003   0.018    594
  Dihedral  :  4.887  17.486    462
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.87 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 349 
 TYR   0.019   0.002   TYR D 310 
 PHE   0.009   0.002   PHE C 346 
 HIS   0.002   0.000   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 3489)
  covalent geometry    : angle       0.58323 ( 4668)
  hydrogen bonds       : bond        0.01700 (   88)
  hydrogen bonds       : angle       4.83890 (  264)

*********************** 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
  114 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8713 (mttt) cc_final: 0.8475 (mtpt)
REVERT: C  349 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7402 (tpt90)
REVERT: D  311 LYS cc_start: 0.8707 (mttt) cc_final: 0.8046 (mttm)
REVERT: D  343 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7561 (tppt)
REVERT: E  317 LYS cc_start: 0.8643 (mttt) cc_final: 0.8414 (mtmt)
REVERT: E  347 LYS cc_start: 0.8902 (mptp) cc_final: 0.8521 (mppt)
REVERT: F  311 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8574 (mtmt)
  outliers start: 7
  outliers final: 6
  residues processed: 109
  average time/residue: 0.7317
  time to fit residues: 81.4692
Evaluate side-chains
  111 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  369 LYS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  369 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.1980
   chunk 7 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    2.0186

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.115542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.102023 restraints weight = 4194.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.43
r_work: 0.3339 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3489  Z= 0.138
  Angle     :  0.555   7.326   4668  Z= 0.265
  Chirality :  0.049   0.118    525
  Planarity :  0.002   0.017    594
  Dihedral  :  4.728  17.468    462
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.34 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.49 (0.24), residues: 441

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3489)
  covalent geometry    : angle       0.55524 ( 4668)
  hydrogen bonds       : bond        0.01592 (   88)
  hydrogen bonds       : angle       4.71351 (  264)

*********************** 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
  119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8719 (mttt) cc_final: 0.8491 (mtpt)
REVERT: C  349 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7400 (tpt90)
REVERT: D  311 LYS cc_start: 0.8710 (mttt) cc_final: 0.8055 (mttm)
REVERT: D  343 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7586 (tppt)
REVERT: E  317 LYS cc_start: 0.8643 (mttt) cc_final: 0.8412 (mtmt)
REVERT: E  347 LYS cc_start: 0.8876 (mptp) cc_final: 0.8505 (mppt)
REVERT: F  311 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8570 (mtmt)
REVERT: F  343 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8225 (ttpt)
  outliers start: 11
  outliers final: 5
  residues processed: 113
  average time/residue: 0.7480
  time to fit residues: 86.3626
Evaluate side-chains
  114 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  369 LYS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain F residue  369 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0870
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0060
   chunk 33 optimal weight:   10.0000
   overall best weight:    1.3778

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.117134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.103604 restraints weight = 4134.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.43
r_work: 0.3362 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8880
moved from start:          0.3966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3489  Z= 0.112
  Angle     :  0.535   8.097   4668  Z= 0.257
  Chirality :  0.049   0.120    525
  Planarity :  0.002   0.016    594
  Dihedral  :  4.635  20.591    462
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.36 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 379 
 TYR   0.022   0.003   TYR B 310 
 PHE   0.005   0.001   PHE C 346 
 HIS   0.001   0.000   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 3489)
  covalent geometry    : angle       0.53454 ( 4668)
  hydrogen bonds       : bond        0.01487 (   88)
  hydrogen bonds       : angle       4.57254 (  264)

*********************** 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
  118 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8711 (mttt) cc_final: 0.8442 (mtpt)
REVERT: C  349 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7318 (tpt90)
REVERT: D  311 LYS cc_start: 0.8686 (mttt) cc_final: 0.8043 (mttm)
REVERT: D  343 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7531 (tppt)
REVERT: E  317 LYS cc_start: 0.8598 (mttt) cc_final: 0.8363 (mtmt)
REVERT: E  347 LYS cc_start: 0.8842 (mptp) cc_final: 0.8468 (mppt)
  outliers start: 7
  outliers final: 3
  residues processed: 113
  average time/residue: 0.7133
  time to fit residues: 82.3312
Evaluate side-chains
  110 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  369 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.0470
   chunk 4 optimal weight:    0.0470
   chunk 27 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.2182

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.118382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.104850 restraints weight = 4131.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.42
r_work: 0.3376 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   3489  Z= 0.104
  Angle     :  0.548   8.671   4668  Z= 0.258
  Chirality :  0.049   0.125    525
  Planarity :  0.002   0.020    594
  Dihedral  :  4.544  20.588    462
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.61 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.25), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 379 
 TYR   0.008   0.001   TYR F 310 
 PHE   0.005   0.001   PHE C 346 
 HIS   0.001   0.000   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3489)
  covalent geometry    : angle       0.54792 ( 4668)
  hydrogen bonds       : bond        0.01449 (   88)
  hydrogen bonds       : angle       4.45710 (  264)

********************** 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
  117 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.8700 (mttt) cc_final: 0.8439 (mtpt)
REVERT: C  349 ARG cc_start: 0.8121 (mtm180) cc_final: 0.7310 (tpt90)
REVERT: D  311 LYS cc_start: 0.8667 (mttt) cc_final: 0.8030 (mttm)
REVERT: D  343 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7561 (tppt)
REVERT: E  317 LYS cc_start: 0.8604 (mttt) cc_final: 0.8370 (mtmt)
REVERT: E  347 LYS cc_start: 0.8796 (mptp) cc_final: 0.8435 (mppt)
  outliers start: 7
  outliers final: 4
  residues processed: 113
  average time/residue: 0.7234
  time to fit residues: 83.5379
Evaluate side-chains
  112 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  369 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    2.5788

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.114450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.101119 restraints weight = 4282.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.43
r_work: 0.3336 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8906
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3489  Z= 0.166
  Angle     :  0.574   8.351   4668  Z= 0.278
  Chirality :  0.049   0.119    525
  Planarity :  0.003   0.023    594
  Dihedral  :  4.831  22.429    462
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 21.88 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.93 (0.32), residues: 441
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.46 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 379 
 TYR   0.020   0.002   TYR D 310 
 PHE   0.009   0.002   PHE C 346 
 HIS   0.002   0.000   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3489)
  covalent geometry    : angle       0.57368 ( 4668)
  hydrogen bonds       : bond        0.01659 (   88)
  hydrogen bonds       : angle       4.59535 (  264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2404.82 seconds
wall clock time: 41 minutes 47.30 seconds (2507.30 seconds total)