Starting phenix.real_space_refine
on Tue Feb 11 01:52:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q2j_18109/02_2025/8q2j_18109.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q2j_18109/02_2025/8q2j_18109.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q2j_18109/02_2025/8q2j_18109.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q2j_18109/02_2025/8q2j_18109.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q2j_18109/02_2025/8q2j_18109.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q2j_18109/02_2025/8q2j_18109.cif"
  }
  resolution = 2.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2193      2.51       5
     N     648      2.21       5
     O     660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3507
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 582
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "C"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 582
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "E"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 582
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Time building chain proxies: 3.55, per 1000 atoms: 1.01
  Number of scatterers: 3507
  At special positions: 0
  Unit cell: (117.047, 119.228, 37.804, 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     660      8.00
     N     648      7.00
     C    2193      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: 0.80
  Conformation dependent library (CDL) restraints added in 396.3 milliseconds
  

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  798

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 51.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.518A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.781A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.543A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   SER C 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.387A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330
      removed outlier: 6.872A  pdb=" N   GLY C 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ASN A 327 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY A 326 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ASN E 327 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342
      removed outlier: 6.537A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   GLU E 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   SER A 341 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.504A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354
      removed outlier: 6.261A  pdb=" N   VAL A 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   LYS E 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   SER A 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.419A  pdb=" N   LEU A 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   ILE E 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ASN A 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   HIS E 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.423A  pdb=" N   LYS A 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   GLU C 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ILE A 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   HIS C 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   THR A 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   LEU C 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LYS A 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   PHE C 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   THR A 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.580A  pdb=" N   SER B 305 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   ILE D 308 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.935A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325
      removed outlier: 6.525A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   SER D 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   GLY B 323 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.720A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342
      removed outlier: 6.684A  pdb=" N   VAL B 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   LYS F 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   VAL B 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   GLU F 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   SER B 341 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.358A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.190A  pdb=" N   VAL B 350 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   LYS F 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   SER B 352 " --> pdb=" O   LYS F 353 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 357 through 362
      removed outlier: 6.733A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   THR D 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ILE B 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LEU B 357 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ILE F 360 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ASN B 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   HIS F 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   THR B 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'D' and resid 368 through 378
      removed outlier: 6.486A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)

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

  Time building geometry restraints manager: 0.94 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: 1074
        1.33 -     1.45: 374
        1.45 -     1.57: 2107
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 3561
  Sorted by residual:
  bond pdb=" CA  LYS F 331 "
       pdb=" C   LYS F 331 "
    ideal  model  delta    sigma   weight residual
    1.532  1.555 -0.023 6.50e-03 2.37e+04 1.26e+01
  bond pdb=" CZ  ARG F 349 "
       pdb=" NH2 ARG F 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.64e+00
  bond pdb=" CA  LYS F 331 "
       pdb=" CB  LYS F 331 "
    ideal  model  delta    sigma   weight residual
    1.522  1.548 -0.026 8.90e-03 1.26e+04 8.32e+00
  bond pdb=" CA  LYS D 331 "
       pdb=" CB  LYS D 331 "
    ideal  model  delta    sigma   weight residual
    1.522  1.547 -0.025 8.90e-03 1.26e+04 7.63e+00
  bond pdb=" CZ  ARG D 349 "
       pdb=" NH2 ARG D 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.17e+00
  ... (remaining 3556 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 2822
        1.36 -     2.73: 1367
        2.73 -     4.09: 472
        4.09 -     5.46: 86
        5.46 -     6.82: 14
  Bond angle restraints: 4761
  Sorted by residual:
  angle pdb=" N   GLY A 326 "
        pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     110.69  117.51   -6.82 1.33e+00 5.65e-01 2.63e+01
  angle pdb=" CA  ASP B 358 "
        pdb=" CB  ASP B 358 "
        pdb=" CG  ASP B 358 "
      ideal   model   delta    sigma   weight residual
     112.60  117.65   -5.05 1.00e+00 1.00e+00 2.55e+01
  angle pdb=" OE1 GLN B 336 "
        pdb=" CD  GLN B 336 "
        pdb=" NE2 GLN B 336 "
      ideal   model   delta    sigma   weight residual
     122.60  117.74    4.86 1.00e+00 1.00e+00 2.37e+01
  angle pdb=" C   ASP F 348 "
        pdb=" N   ARG F 349 "
        pdb=" CA  ARG F 349 "
      ideal   model   delta    sigma   weight residual
     121.05  127.81   -6.76 1.43e+00 4.89e-01 2.24e+01
  angle pdb=" CB  HIS B 374 "
        pdb=" CG  HIS B 374 "
        pdb=" CD2 HIS B 374 "
      ideal   model   delta    sigma   weight residual
     131.20  125.06    6.14 1.30e+00 5.92e-01 2.23e+01
  ... (remaining 4756 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.74: 2053
       17.74 -    35.48: 92
       35.48 -    53.22: 13
       53.22 -    70.96: 3
       70.96 -    88.69: 2
  Dihedral angle restraints: 2163
    sinusoidal: 903
      harmonic: 1260
  Sorted by residual:
  dihedral pdb=" CA  GLY A 355 "
           pdb=" C   GLY A 355 "
           pdb=" N   SER A 356 "
           pdb=" CA  SER A 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.73   28.27     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  LEU E 357 "
           pdb=" C   LEU E 357 "
           pdb=" N   ASP E 358 "
           pdb=" CA  ASP E 358 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.60   25.40     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  GLY B 355 "
           pdb=" C   GLY B 355 "
           pdb=" N   SER B 356 "
           pdb=" CA  SER B 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.81   25.19     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 2160 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 301
       0.062 -    0.124: 175
       0.124 -    0.186: 42
       0.186 -    0.248: 9
       0.248 -    0.311: 4
  Chirality restraints: 531
  Sorted by residual:
  chirality pdb=" CA  GLU A 372 "
            pdb=" N   GLU A 372 "
            pdb=" C   GLU A 372 "
            pdb=" CB  GLU A 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CA  GLU E 372 "
            pdb=" N   GLU E 372 "
            pdb=" C   GLU E 372 "
            pdb=" CB  GLU E 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" CA  THR B 319 "
            pdb=" N   THR B 319 "
            pdb=" C   THR B 319 "
            pdb=" CB  THR B 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 528 not shown)

  Planarity restraints: 609
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.091 2.00e-02 2.50e+03   5.23e-02 5.48e+01
        pdb=" CG  TYR F 310 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.083 2.00e-02 2.50e+03   4.63e-02 4.29e+01
        pdb=" CG  TYR E 310 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.076 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.072 2.00e-02 2.50e+03   4.13e-02 3.41e+01
        pdb=" CG  TYR A 310 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "   -0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.070 2.00e-02 2.50e+03
  ... (remaining 606 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 1505
        2.97 -     3.45: 2687
        3.45 -     3.94: 5705
        3.94 -     4.42: 5591
        4.42 -     4.90: 10696
  Nonbonded interactions: 26184
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.490 3.040
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.499 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.519 3.040
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.535 3.040
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.535 3.040
  ... (remaining 26179 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 304 through 379)
  selection = (chain 'B' and resid 304 through 379)
  selection = (chain 'C' and resid 304 through 379)
  selection = (chain 'D' and resid 304 through 379)
  selection = (chain 'E' and resid 304 through 379)
  selection = (chain 'F' and resid 304 through 379)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.230
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.530
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:12.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
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   0.038   3561  Z= 0.737
  Angle     :  1.720   6.824   4761  Z= 1.160
  Chirality :  0.079   0.311    531
  Planarity :  0.010   0.071    609
  Dihedral  : 11.078  88.693   1365
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 0.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.004   HIS A 330 
 PHE   0.035   0.012   PHE A 346 
 TYR   0.091   0.026   TYR F 310 
 ARG   0.008   0.001   ARG B 349 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.7818 (mttt) cc_final: 0.7530 (mttm)
REVERT: A  317 LYS cc_start: 0.7043 (mtmt) cc_final: 0.6683 (mtpt)
REVERT: A  338 GLU cc_start: 0.6921 (tt0) cc_final: 0.5878 (mt-10)
REVERT: A  342 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6604 (mt-10)
REVERT: A  343 LYS cc_start: 0.7881 (mttt) cc_final: 0.7614 (mtpp)
REVERT: A  353 LYS cc_start: 0.7411 (tttt) cc_final: 0.5931 (tptt)
REVERT: A  358 ASP cc_start: 0.7242 (m-30) cc_final: 0.6818 (m-30)
REVERT: A  369 LYS cc_start: 0.6714 (mttt) cc_final: 0.6034 (mtpp)
REVERT: A  370 LYS cc_start: 0.7418 (tttp) cc_final: 0.6913 (ttmt)
REVERT: A  373 THR cc_start: 0.7803 (m) cc_final: 0.7345 (p)
REVERT: A  375 LYS cc_start: 0.7255 (tttt) cc_final: 0.7052 (tttt)
REVERT: B  345 ASP cc_start: 0.6846 (m-30) cc_final: 0.6221 (t70)
REVERT: B  348 ASP cc_start: 0.8206 (t70) cc_final: 0.7992 (t0)
REVERT: B  353 LYS cc_start: 0.7015 (tttt) cc_final: 0.6591 (tttm)
REVERT: B  375 LYS cc_start: 0.7608 (tttt) cc_final: 0.7061 (ttpp)
REVERT: C  307 GLN cc_start: 0.8278 (tt0) cc_final: 0.7880 (tt0)
REVERT: C  311 LYS cc_start: 0.8232 (mttt) cc_final: 0.7978 (mttm)
REVERT: C  320 SER cc_start: 0.7604 (t) cc_final: 0.7339 (p)
REVERT: C  336 GLN cc_start: 0.8206 (tt0) cc_final: 0.7923 (tt0)
REVERT: C  338 GLU cc_start: 0.7444 (tt0) cc_final: 0.7002 (tm-30)
REVERT: C  340 LYS cc_start: 0.7880 (mttt) cc_final: 0.7504 (mtmm)
REVERT: C  342 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7127 (mt-10)
REVERT: C  343 LYS cc_start: 0.8064 (mttt) cc_final: 0.7772 (mttm)
REVERT: C  349 ARG cc_start: 0.6452 (mtm180) cc_final: 0.6051 (mtt180)
REVERT: C  353 LYS cc_start: 0.7737 (tttt) cc_final: 0.6777 (tptt)
REVERT: C  369 LYS cc_start: 0.7617 (mttt) cc_final: 0.6980 (mtpp)
REVERT: C  370 LYS cc_start: 0.7871 (tttp) cc_final: 0.7520 (ttmt)
REVERT: C  371 ILE cc_start: 0.8166 (mt) cc_final: 0.7738 (mp)
REVERT: C  372 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6269 (mm-30)
REVERT: C  373 THR cc_start: 0.8235 (m) cc_final: 0.7848 (p)
REVERT: C  375 LYS cc_start: 0.8036 (tttt) cc_final: 0.7709 (tttt)
REVERT: D  314 ASP cc_start: 0.7230 (t0) cc_final: 0.6917 (t0)
REVERT: D  315 LEU cc_start: 0.8312 (mt) cc_final: 0.7971 (mm)
REVERT: D  317 LYS cc_start: 0.7720 (mttt) cc_final: 0.7358 (mtpt)
REVERT: D  321 LYS cc_start: 0.7725 (mttt) cc_final: 0.7197 (mttp)
REVERT: D  338 GLU cc_start: 0.7798 (tt0) cc_final: 0.7137 (tt0)
REVERT: D  345 ASP cc_start: 0.7255 (m-30) cc_final: 0.6768 (t70)
REVERT: D  347 LYS cc_start: 0.7951 (mttt) cc_final: 0.7634 (mmtm)
REVERT: D  353 LYS cc_start: 0.7856 (tttt) cc_final: 0.7582 (tttm)
REVERT: D  373 THR cc_start: 0.8328 (m) cc_final: 0.7952 (p)
REVERT: D  375 LYS cc_start: 0.8246 (tttt) cc_final: 0.7726 (ttpp)
REVERT: D  379 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.6292 (mmp-170)
REVERT: E  311 LYS cc_start: 0.7813 (mttt) cc_final: 0.6878 (mttm)
REVERT: E  336 GLN cc_start: 0.7688 (tt0) cc_final: 0.7391 (tt0)
REVERT: E  338 GLU cc_start: 0.6808 (tt0) cc_final: 0.6077 (mt-10)
REVERT: E  342 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7128 (mt-10)
REVERT: E  343 LYS cc_start: 0.8105 (mttt) cc_final: 0.7855 (mtpp)
REVERT: E  347 LYS cc_start: 0.8048 (mttt) cc_final: 0.7808 (mttm)
REVERT: E  348 ASP cc_start: 0.7897 (t0) cc_final: 0.7658 (t0)
REVERT: E  349 ARG cc_start: 0.6798 (mtm180) cc_final: 0.5746 (mtp180)
REVERT: E  353 LYS cc_start: 0.7295 (tttt) cc_final: 0.5997 (tptt)
REVERT: E  356 SER cc_start: 0.7331 (p) cc_final: 0.7005 (t)
REVERT: E  369 LYS cc_start: 0.6882 (mttt) cc_final: 0.6240 (mtpp)
REVERT: E  373 THR cc_start: 0.7841 (m) cc_final: 0.7121 (p)
REVERT: E  375 LYS cc_start: 0.7191 (tttt) cc_final: 0.6686 (tttp)
REVERT: F  311 LYS cc_start: 0.7444 (mttt) cc_final: 0.6550 (mttm)
REVERT: F  317 LYS cc_start: 0.7056 (mttt) cc_final: 0.6837 (mtpt)
REVERT: F  321 LYS cc_start: 0.6984 (mttt) cc_final: 0.6605 (mttm)
REVERT: F  336 GLN cc_start: 0.7452 (tt0) cc_final: 0.7223 (tt0)
REVERT: F  338 GLU cc_start: 0.7380 (tt0) cc_final: 0.6342 (tt0)
REVERT: F  340 LYS cc_start: 0.6749 (mttt) cc_final: 0.6081 (mmtt)
REVERT: F  347 LYS cc_start: 0.7897 (mttt) cc_final: 0.7408 (mmtp)
REVERT: F  348 ASP cc_start: 0.7818 (t0) cc_final: 0.7552 (t0)
REVERT: F  353 LYS cc_start: 0.7234 (tttt) cc_final: 0.6750 (tttm)
REVERT: F  356 SER cc_start: 0.7261 (p) cc_final: 0.7023 (t)
REVERT: F  375 LYS cc_start: 0.7658 (tttt) cc_final: 0.7126 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 1.3346
  time to fit residues: 278.5431
Evaluate side-chains
  187 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 351 GLN
D 307 GLN
D 327 ASN
F 351 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.125213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.110639 restraints weight = 3860.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.44
r_work: 0.3523 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3561  Z= 0.269
  Angle     :  0.645   5.499   4761  Z= 0.330
  Chirality :  0.051   0.131    531
  Planarity :  0.004   0.026    609
  Dihedral  :  5.389  19.164    474
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.28 %
    Favored  : 88.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 329 
 PHE   0.016   0.003   PHE F 346 
 TYR   0.011   0.003   TYR A 310 
 ARG   0.003   0.001   ARG A 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 183
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8024 (tt0) cc_final: 0.7717 (mt-10)
REVERT: A  353 LYS cc_start: 0.8611 (tttt) cc_final: 0.8237 (tptt)
REVERT: C  342 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: C  345 ASP cc_start: 0.8373 (m-30) cc_final: 0.8015 (t70)
REVERT: C  353 LYS cc_start: 0.8629 (tttt) cc_final: 0.8335 (tptt)
REVERT: C  372 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7779 (mm-30)
REVERT: D  305 SER cc_start: 0.8470 (p) cc_final: 0.8252 (p)
REVERT: D  338 GLU cc_start: 0.8458 (tt0) cc_final: 0.8139 (tt0)
REVERT: E  307 GLN cc_start: 0.8434 (tt0) cc_final: 0.8222 (tt0)
REVERT: E  311 LYS cc_start: 0.8618 (mttt) cc_final: 0.8044 (mttm)
REVERT: E  342 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7799 (mt-10)
REVERT: E  353 LYS cc_start: 0.8618 (tttt) cc_final: 0.8262 (tptt)
REVERT: E  372 GLU cc_start: 0.8123 (tt0) cc_final: 0.7903 (tp30)
REVERT: F  311 LYS cc_start: 0.8362 (mttt) cc_final: 0.7851 (mttm)
REVERT: F  338 GLU cc_start: 0.8327 (tt0) cc_final: 0.7960 (tt0)
REVERT: F  340 LYS cc_start: 0.8237 (mttt) cc_final: 0.7955 (mmtt)
  outliers start: 5
  outliers final: 2
  residues processed: 185
  average time/residue: 1.3900
  time to fit residues: 262.8920
Evaluate side-chains
  161 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  341 SER
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 307 GLN
C 307 GLN
C 330 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.120206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.105408 restraints weight = 3920.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.46
r_work: 0.3431 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   3561  Z= 0.489
  Angle     :  0.742   6.014   4761  Z= 0.376
  Chirality :  0.054   0.154    531
  Planarity :  0.004   0.023    609
  Dihedral  :  5.438  18.783    474
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.30 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D 329 
 PHE   0.017   0.003   PHE B 346 
 TYR   0.015   0.003   TYR E 310 
 ARG   0.004   0.001   ARG E 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8577 (tttt) cc_final: 0.8281 (tptt)
REVERT: C  321 LYS cc_start: 0.8616 (mttt) cc_final: 0.8343 (mtpp)
REVERT: C  342 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7815 (mt-10)
REVERT: C  353 LYS cc_start: 0.8662 (tttt) cc_final: 0.8385 (tptp)
REVERT: C  372 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7858 (mm-30)
REVERT: D  305 SER cc_start: 0.8489 (p) cc_final: 0.8283 (p)
REVERT: D  338 GLU cc_start: 0.8506 (tt0) cc_final: 0.8165 (tt0)
REVERT: E  307 GLN cc_start: 0.8467 (tt0) cc_final: 0.8247 (tt0)
REVERT: E  311 LYS cc_start: 0.8745 (mttt) cc_final: 0.8135 (mttm)
REVERT: E  340 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8159 (mttm)
REVERT: E  349 ARG cc_start: 0.8265 (mtt180) cc_final: 0.6808 (mmp80)
REVERT: E  353 LYS cc_start: 0.8662 (tttt) cc_final: 0.8261 (tptt)
REVERT: E  370 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8470 (ttmp)
REVERT: E  375 LYS cc_start: 0.8602 (tttt) cc_final: 0.8331 (tttp)
REVERT: F  311 LYS cc_start: 0.8457 (mttt) cc_final: 0.7839 (mttm)
REVERT: F  338 GLU cc_start: 0.8392 (tt0) cc_final: 0.7962 (tt0)
  outliers start: 10
  outliers final: 4
  residues processed: 160
  average time/residue: 1.5692
  time to fit residues: 256.3488
Evaluate side-chains
  147 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 142
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain E residue  341 SER
Chi-restraints excluded: chain E residue  370 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 307 GLN
C 330 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.119087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.104823 restraints weight = 4087.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.43
r_work: 0.3433 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3561  Z= 0.396
  Angle     :  0.691   8.219   4761  Z= 0.347
  Chirality :  0.051   0.136    531
  Planarity :  0.003   0.025    609
  Dihedral  :  5.282  18.517    474
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.05 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 329 
 PHE   0.015   0.003   PHE F 346 
 TYR   0.013   0.003   TYR E 310 
 ARG   0.004   0.001   ARG A 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8600 (tttt) cc_final: 0.8255 (tptt)
REVERT: C  321 LYS cc_start: 0.8603 (mttt) cc_final: 0.8321 (mtpp)
REVERT: C  342 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7769 (mt-10)
REVERT: C  353 LYS cc_start: 0.8649 (tttt) cc_final: 0.8380 (tptp)
REVERT: C  372 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7870 (mm-30)
REVERT: D  338 GLU cc_start: 0.8490 (tt0) cc_final: 0.8138 (tt0)
REVERT: E  311 LYS cc_start: 0.8714 (mttt) cc_final: 0.8127 (mttm)
REVERT: E  349 ARG cc_start: 0.8226 (mtt180) cc_final: 0.6782 (mmp80)
REVERT: F  311 LYS cc_start: 0.8419 (mttt) cc_final: 0.7832 (mttm)
REVERT: F  338 GLU cc_start: 0.8352 (tt0) cc_final: 0.7907 (tt0)
REVERT: F  340 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7916 (mmtt)
  outliers start: 9
  outliers final: 5
  residues processed: 145
  average time/residue: 1.5223
  time to fit residues: 225.5049
Evaluate side-chains
  139 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain E residue  341 SER
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 307 GLN
C 330 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.119883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.105658 restraints weight = 4068.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.43
r_work: 0.3441 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3561  Z= 0.301
  Angle     :  0.624   5.821   4761  Z= 0.314
  Chirality :  0.050   0.129    531
  Planarity :  0.003   0.023    609
  Dihedral  :  5.084  17.945    474
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.80 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 PHE   0.014   0.002   PHE F 346 
 TYR   0.012   0.003   TYR A 310 
 ARG   0.005   0.001   ARG A 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8626 (tttt) cc_final: 0.8236 (tptt)
REVERT: C  321 LYS cc_start: 0.8592 (mttt) cc_final: 0.8314 (mtpp)
REVERT: C  342 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7793 (mt-10)
REVERT: C  353 LYS cc_start: 0.8659 (tttt) cc_final: 0.8391 (tptt)
REVERT: C  379 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6910 (mtm180)
REVERT: D  338 GLU cc_start: 0.8453 (tt0) cc_final: 0.8119 (tt0)
REVERT: E  311 LYS cc_start: 0.8733 (mttt) cc_final: 0.8149 (mttm)
REVERT: E  340 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8136 (mttm)
REVERT: E  353 LYS cc_start: 0.8686 (tttt) cc_final: 0.8292 (tptt)
REVERT: E  370 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8388 (ttmp)
REVERT: F  338 GLU cc_start: 0.8321 (tt0) cc_final: 0.7894 (tt0)
REVERT: F  340 LYS cc_start: 0.8480 (mtmt) cc_final: 0.7941 (mmtt)
  outliers start: 11
  outliers final: 4
  residues processed: 142
  average time/residue: 1.4768
  time to fit residues: 214.2451
Evaluate side-chains
  141 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain E residue  341 SER
Chi-restraints excluded: chain E residue  370 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.119475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.105247 restraints weight = 4136.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.44
r_work: 0.3431 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3561  Z= 0.332
  Angle     :  0.651   8.642   4761  Z= 0.325
  Chirality :  0.050   0.131    531
  Planarity :  0.003   0.023    609
  Dihedral  :  5.109  17.930    474
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.05 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 PHE   0.013   0.002   PHE F 346 
 TYR   0.012   0.003   TYR A 310 
 ARG   0.005   0.001   ARG A 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 137
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8615 (tttt) cc_final: 0.8232 (tptt)
REVERT: C  321 LYS cc_start: 0.8608 (mttt) cc_final: 0.8337 (mtpp)
REVERT: C  342 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7790 (mt-10)
REVERT: C  347 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7405 (pmtt)
REVERT: C  353 LYS cc_start: 0.8657 (tttt) cc_final: 0.8392 (tptt)
REVERT: D  338 GLU cc_start: 0.8471 (tt0) cc_final: 0.8131 (tt0)
REVERT: D  373 THR cc_start: 0.8918 (m) cc_final: 0.8693 (p)
REVERT: E  311 LYS cc_start: 0.8735 (mttt) cc_final: 0.8151 (mttm)
REVERT: E  340 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8140 (mttm)
REVERT: E  370 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8375 (ttmp)
REVERT: F  338 GLU cc_start: 0.8333 (tt0) cc_final: 0.7946 (tt0)
  outliers start: 8
  outliers final: 3
  residues processed: 143
  average time/residue: 1.4687
  time to fit residues: 214.5679
Evaluate side-chains
  140 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 135
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  347 LYS
Chi-restraints excluded: chain E residue  341 SER
Chi-restraints excluded: chain E residue  370 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 34 optimal weight:    0.7980
   chunk 32 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.120696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.106576 restraints weight = 4029.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 1.41
r_work: 0.3453 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3561  Z= 0.247
  Angle     :  0.596   5.726   4761  Z= 0.298
  Chirality :  0.049   0.125    531
  Planarity :  0.003   0.024    609
  Dihedral  :  4.918  17.480    474
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.30 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.50 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.012   0.002   PHE F 346 
 TYR   0.011   0.002   TYR F 310 
 ARG   0.004   0.000   ARG A 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8654 (tttt) cc_final: 0.8273 (tptt)
REVERT: C  321 LYS cc_start: 0.8599 (mttt) cc_final: 0.8323 (mtpp)
REVERT: C  340 LYS cc_start: 0.8391 (mtmm) cc_final: 0.8186 (mttt)
REVERT: C  342 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7728 (mt-10)
REVERT: C  347 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7396 (pmtt)
REVERT: C  353 LYS cc_start: 0.8649 (tttt) cc_final: 0.8397 (tptt)
REVERT: D  324 SER cc_start: 0.8999 (t) cc_final: 0.8765 (m)
REVERT: D  338 GLU cc_start: 0.8457 (tt0) cc_final: 0.8113 (tt0)
REVERT: D  353 LYS cc_start: 0.8658 (tttm) cc_final: 0.8430 (tttt)
REVERT: E  311 LYS cc_start: 0.8691 (mttt) cc_final: 0.8109 (mttm)
REVERT: E  340 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8147 (mttm)
REVERT: E  353 LYS cc_start: 0.8676 (tttt) cc_final: 0.8286 (tptt)
REVERT: E  370 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8405 (ttmp)
REVERT: F  338 GLU cc_start: 0.8315 (tt0) cc_final: 0.7908 (tt0)
  outliers start: 8
  outliers final: 4
  residues processed: 144
  average time/residue: 1.4287
  time to fit residues: 210.3359
Evaluate side-chains
  143 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  347 LYS
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  341 SER
Chi-restraints excluded: chain E residue  370 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   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 336 GLN
B 307 GLN
C 307 GLN
C 330 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.119346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.105178 restraints weight = 4050.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.41
r_work: 0.3431 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3561  Z= 0.343
  Angle     :  0.649   5.933   4761  Z= 0.327
  Chirality :  0.050   0.130    531
  Planarity :  0.003   0.024    609
  Dihedral  :  5.086  17.868    474
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.05 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 PHE   0.014   0.002   PHE F 346 
 TYR   0.013   0.003   TYR F 310 
 ARG   0.006   0.001   ARG A 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  353 LYS cc_start: 0.8603 (tttt) cc_final: 0.8221 (tptt)
REVERT: A  372 GLU cc_start: 0.8128 (tt0) cc_final: 0.7909 (mm-30)
REVERT: C  321 LYS cc_start: 0.8633 (mttt) cc_final: 0.8357 (mtpp)
REVERT: C  342 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7753 (mt-10)
REVERT: C  347 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7405 (pmtt)
REVERT: C  353 LYS cc_start: 0.8657 (tttt) cc_final: 0.8389 (tptt)
REVERT: D  338 GLU cc_start: 0.8460 (tt0) cc_final: 0.8110 (tt0)
REVERT: E  311 LYS cc_start: 0.8724 (mttt) cc_final: 0.8145 (mttm)
REVERT: E  340 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8147 (mttm)
REVERT: E  370 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8384 (ttmp)
REVERT: F  338 GLU cc_start: 0.8329 (tt0) cc_final: 0.7938 (tt0)
REVERT: F  347 LYS cc_start: 0.8965 (mptm) cc_final: 0.8709 (mmtm)
  outliers start: 8
  outliers final: 3
  residues processed: 138
  average time/residue: 1.4186
  time to fit residues: 200.2067
Evaluate side-chains
  136 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  347 LYS
Chi-restraints excluded: chain E residue  341 SER
Chi-restraints excluded: chain E residue  370 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0270
   overall best weight:    2.1644

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 307 GLN
C 307 GLN
C 330 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.122588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108285 restraints weight = 3878.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.45
r_work: 0.3459 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3561  Z= 0.214
  Angle     :  0.599   8.532   4761  Z= 0.295
  Chirality :  0.049   0.124    531
  Planarity :  0.003   0.023    609
  Dihedral  :  4.840  17.258    474
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 20.05 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.49 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.010   0.002   PHE F 346 
 TYR   0.012   0.002   TYR F 310 
 ARG   0.003   0.000   ARG A 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 141
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A  353 LYS cc_start: 0.8661 (tttt) cc_final: 0.8351 (tptt)
REVERT: A  372 GLU cc_start: 0.8128 (tt0) cc_final: 0.7849 (mm-30)
REVERT: C  342 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7691 (mt-10)
REVERT: C  353 LYS cc_start: 0.8657 (tttt) cc_final: 0.8348 (tptt)
REVERT: D  324 SER cc_start: 0.8993 (t) cc_final: 0.8758 (m)
REVERT: D  338 GLU cc_start: 0.8455 (tt0) cc_final: 0.8118 (tt0)
REVERT: D  353 LYS cc_start: 0.8622 (tttm) cc_final: 0.8390 (tttt)
REVERT: E  311 LYS cc_start: 0.8657 (mttt) cc_final: 0.8062 (mttm)
REVERT: E  340 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8145 (mttm)
REVERT: E  349 ARG cc_start: 0.8079 (mtt180) cc_final: 0.6690 (mtp180)
REVERT: E  353 LYS cc_start: 0.8671 (tttt) cc_final: 0.8296 (tptt)
REVERT: E  370 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8397 (ttmp)
REVERT: E  372 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8006 (tp30)
REVERT: F  338 GLU cc_start: 0.8337 (tt0) cc_final: 0.7935 (tt0)
REVERT: F  347 LYS cc_start: 0.8945 (mptm) cc_final: 0.8698 (mmtm)
  outliers start: 4
  outliers final: 2
  residues processed: 145
  average time/residue: 1.4472
  time to fit residues: 214.4630
Evaluate side-chains
  133 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain E residue  370 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 21 optimal weight:    0.1980
   chunk 14 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 307 GLN
C 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.120950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.106905 restraints weight = 4109.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 1.43
r_work: 0.3459 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3561  Z= 0.231
  Angle     :  0.608   5.722   4761  Z= 0.305
  Chirality :  0.049   0.124    531
  Planarity :  0.003   0.023    609
  Dihedral  :  4.816  17.375    474
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 21.05 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.011   0.002   PHE B 346 
 TYR   0.012   0.002   TYR F 310 
 ARG   0.005   0.001   ARG A 379 

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

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  353 LYS cc_start: 0.8642 (tttt) cc_final: 0.8341 (tptt)
REVERT: A  372 GLU cc_start: 0.8124 (tt0) cc_final: 0.7832 (mm-30)
REVERT: C  342 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7709 (mt-10)
REVERT: C  353 LYS cc_start: 0.8649 (tttt) cc_final: 0.8348 (tptt)
REVERT: D  324 SER cc_start: 0.8979 (t) cc_final: 0.8755 (m)
REVERT: D  338 GLU cc_start: 0.8466 (tt0) cc_final: 0.8129 (tt0)
REVERT: D  353 LYS cc_start: 0.8616 (tttm) cc_final: 0.8388 (tttt)
REVERT: E  311 LYS cc_start: 0.8667 (mttt) cc_final: 0.8078 (mttm)
REVERT: E  340 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8133 (mttm)
REVERT: E  349 ARG cc_start: 0.8055 (mtt180) cc_final: 0.6693 (mtp180)
REVERT: E  353 LYS cc_start: 0.8671 (tttt) cc_final: 0.8300 (tptt)
REVERT: E  370 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8372 (ttmp)
REVERT: E  372 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7946 (tp30)
REVERT: F  338 GLU cc_start: 0.8313 (tt0) cc_final: 0.7932 (tt0)
REVERT: F  347 LYS cc_start: 0.8932 (mptm) cc_final: 0.8677 (mmtm)
  outliers start: 4
  outliers final: 2
  residues processed: 142
  average time/residue: 1.5067
  time to fit residues: 218.7151
Evaluate side-chains
  133 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain E residue  370 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 17 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 307 GLN
C 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.121358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.107413 restraints weight = 4059.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.42
r_work: 0.3466 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3561  Z= 0.219
  Angle     :  0.599   5.900   4761  Z= 0.301
  Chirality :  0.049   0.123    531
  Planarity :  0.003   0.024    609
  Dihedral  :  4.790  17.283    474
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 22.06 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.46 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 329 
 PHE   0.012   0.002   PHE B 346 
 TYR   0.011   0.002   TYR F 310 
 ARG   0.004   0.001   ARG A 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4995.20 seconds
wall clock time: 88 minutes 35.01 seconds (5315.01 seconds total)