Starting phenix.real_space_refine
on Tue Feb 11 17:35:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ql0_14059/02_2025/7ql0_14059.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ql0_14059/02_2025/7ql0_14059.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ql0_14059/02_2025/7ql0_14059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ql0_14059/02_2025/7ql0_14059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ql0_14059/02_2025/7ql0_14059.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ql0_14059/02_2025/7ql0_14059.cif"
  }
  resolution = 3.13
  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: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1956      2.51       5
     N     576      2.21       5
     O     594      1.98       5
     H    3258      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6390
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 1065
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
    Chain: "c"
      Number of atoms: 1065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 1065
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
    Chain: "A"
      Number of atoms: 1065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 1065
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
    Chain: "C"
      Number of atoms: 1065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 1065
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
    Chain: "D"
      Number of atoms: 1065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 1065
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
    Chain: "E"
      Number of atoms: 1065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 1065
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
  Time building chain proxies: 4.45, per 1000 atoms: 0.70
  Number of scatterers: 6390
  At special positions: 0
  Unit cell: (93.936, 127.72, 34.608, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     594      8.00
     N     576      7.00
     C    1956      6.00
     H    3258      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 444.5 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  720

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 39.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'c' and resid 313 through 314
      removed outlier: 6.878A  pdb=" N   VAL B 313 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'c' and resid 317 through 318
      removed outlier: 6.340A  pdb=" N   LYS B 317 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'c' and resid 325 through 330
      removed outlier: 6.273A  pdb=" N   GLY B 326 " --> pdb=" O   ASN c 327 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   HIS c 329 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE B 328 " --> pdb=" O   HIS c 329 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   GLY A 326 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ASN B 327 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'c' and resid 337 through 342
      removed outlier: 6.649A  pdb=" N   VAL B 337 " --> pdb=" O   GLU c 338 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   LYS c 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL B 339 " --> pdb=" O   LYS c 340 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   GLU c 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   SER B 341 " --> pdb=" O   GLU c 342 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'c' and resid 345 through 346
      removed outlier: 6.465A  pdb=" N   ASP B 345 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'c' and resid 350 through 357
      removed outlier: 6.243A  pdb=" N   VAL B 350 " --> pdb=" O   GLN c 351 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   LYS c 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   SER B 352 " --> pdb=" O   LYS c 353 " (cutoff:3.500A)
      removed outlier: 8.225A  pdb=" N   GLY c 355 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   ILE B 354 " --> pdb=" O   GLY c 355 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   LEU c 357 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   SER B 356 " --> pdb=" O   LEU c 357 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'c' and resid 360 through 362
      removed outlier: 6.432A  pdb=" N   THR B 361 " --> pdb=" O   HIS c 362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'c' and resid 369 through 375
      removed outlier: 6.544A  pdb=" N   LYS B 369 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   GLU A 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ILE B 371 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   HIS A 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   THR B 373 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.794A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 318
      removed outlier: 6.522A  pdb=" N   LYS C 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 324 through 330
      removed outlier: 9.443A  pdb=" N   SER C 324 " --> pdb=" O   LEU D 325 " (cutoff:3.500A)
      removed outlier: 10.392A  pdb=" N   ASN D 327 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   GLY C 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.397A  pdb=" N   HIS D 329 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ILE C 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   LEU C 325 " --> pdb=" O   SER E 324 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   GLY E 326 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ASN C 327 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 342
    Processing sheet with id=AB4, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.495A  pdb=" N   ASP C 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 357
      removed outlier: 6.215A  pdb=" N   VAL C 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   LYS D 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   SER C 352 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   GLY D 355 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   ILE C 354 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LEU D 357 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   SER C 356 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 360 through 362
      removed outlier: 6.539A  pdb=" N   THR C 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 371
      removed outlier: 6.388A  pdb=" N   LYS C 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)

    56 hydrogen bonds defined for protein.
    168 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: 2.04

  Time building geometry restraints manager: 1.85 seconds

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

  Histogram of bond lengths:
        0.94 -     1.11: 3252
        1.11 -     1.29: 528
        1.29 -     1.46: 885
        1.46 -     1.64: 1767
        1.64 -     1.82: 6
  Bond restraints: 6438
  Sorted by residual:
  bond pdb=" CE1 HIS B 330 "
       pdb=" HE1 HIS B 330 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   LYS c 311 "
       pdb=" H   LYS c 311 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   GLY E 326 "
       pdb=" H   GLY E 326 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   ILE E 328 "
       pdb=" H   ILE E 328 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   SER A 356 "
       pdb=" H   SER A 356 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  ... (remaining 6433 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 9668
        2.42 -     4.85: 1591
        4.85 -     7.27: 464
        7.27 -     9.70: 24
        9.70 -    12.12: 7
  Bond angle restraints: 11754
  Sorted by residual:
  angle pdb=" N   GLY C 326 "
        pdb=" CA  GLY C 326 "
        pdb=" C   GLY C 326 "
      ideal   model   delta    sigma   weight residual
     110.69  118.23   -7.54 1.33e+00 5.65e-01 3.21e+01
  angle pdb=" N   GLY B 326 "
        pdb=" CA  GLY B 326 "
        pdb=" C   GLY B 326 "
      ideal   model   delta    sigma   weight residual
     110.74  117.48   -6.74 1.37e+00 5.33e-01 2.42e+01
  angle pdb=" C   ASP c 348 "
        pdb=" N   ARG c 349 "
        pdb=" CA  ARG c 349 "
      ideal   model   delta    sigma   weight residual
     121.56  129.18   -7.62 1.56e+00 4.11e-01 2.39e+01
  angle pdb=" C   ASP D 348 "
        pdb=" N   ARG D 349 "
        pdb=" CA  ARG D 349 "
      ideal   model   delta    sigma   weight residual
     121.31  128.35   -7.04 1.49e+00 4.50e-01 2.23e+01
  angle pdb=" CB  HIS A 374 "
        pdb=" CG  HIS A 374 "
        pdb=" CD2 HIS A 374 "
      ideal   model   delta    sigma   weight residual
     131.20  125.41    5.79 1.30e+00 5.92e-01 1.98e+01
  ... (remaining 11749 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 2623
       16.08 -    32.16: 148
       32.16 -    48.25: 69
       48.25 -    64.33: 118
       64.33 -    80.41: 6
  Dihedral angle restraints: 2964
    sinusoidal: 1704
      harmonic: 1260
  Sorted by residual:
  dihedral pdb=" CA  GLN A 336 "
           pdb=" C   GLN A 336 "
           pdb=" N   VAL A 337 "
           pdb=" CA  VAL A 337 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.21   27.79     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  LYS E 375 "
           pdb=" C   LYS E 375 "
           pdb=" N   LEU E 376 "
           pdb=" CA  LEU E 376 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.45   26.55     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  VAL C 318 "
           pdb=" C   VAL C 318 "
           pdb=" N   THR C 319 "
           pdb=" CA  THR C 319 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.58  -25.42     0      5.00e+00 4.00e-02 2.58e+01
  ... (remaining 2961 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 282
       0.070 -    0.139: 147
       0.139 -    0.208: 36
       0.208 -    0.278: 10
       0.278 -    0.347: 5
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  ASN D 327 "
            pdb=" N   ASN D 327 "
            pdb=" C   ASN D 327 "
            pdb=" CB  ASN D 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CA  LYS D 321 "
            pdb=" N   LYS D 321 "
            pdb=" C   LYS D 321 "
            pdb=" CB  LYS D 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CA  ASN C 327 "
            pdb=" N   ASN C 327 "
            pdb=" C   ASN C 327 "
            pdb=" CB  ASN C 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 477 not shown)

  Planarity restraints: 930
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR c 310 "   -0.149 2.00e-02 2.50e+03   6.00e-02 1.08e+02
        pdb=" CG  TYR c 310 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR c 310 "    0.054 2.00e-02 2.50e+03
        pdb=" CD2 TYR c 310 "    0.041 2.00e-02 2.50e+03
        pdb=" CE1 TYR c 310 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR c 310 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR c 310 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR c 310 "   -0.099 2.00e-02 2.50e+03
        pdb=" HD1 TYR c 310 "    0.059 2.00e-02 2.50e+03
        pdb=" HD2 TYR c 310 "    0.019 2.00e-02 2.50e+03
        pdb=" HE1 TYR c 310 "   -0.008 2.00e-02 2.50e+03
        pdb=" HE2 TYR c 310 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.149 2.00e-02 2.50e+03   5.96e-02 1.07e+02
        pdb=" CG  TYR E 310 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "    0.020 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.095 2.00e-02 2.50e+03
        pdb=" HD1 TYR E 310 "   -0.033 2.00e-02 2.50e+03
        pdb=" HD2 TYR E 310 "   -0.064 2.00e-02 2.50e+03
        pdb=" HE1 TYR E 310 "   -0.015 2.00e-02 2.50e+03
        pdb=" HE2 TYR E 310 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "    0.139 2.00e-02 2.50e+03   5.47e-02 8.98e+01
        pdb=" CG  TYR C 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "    0.019 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "    0.070 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 310 "   -0.067 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 310 "   -0.016 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 310 "    0.018 2.00e-02 2.50e+03
  ... (remaining 927 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 424
        2.17 -     2.77: 11012
        2.77 -     3.38: 16927
        3.38 -     3.99: 22645
        3.99 -     4.60: 31452
  Nonbonded interactions: 82460
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.557 2.450
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.571 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.596 2.450
  ... (remaining 82455 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 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'c'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.140
  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:             0.110
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     18.690
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.035   3180  Z= 0.747
  Angle     :  1.875   7.621   4254  Z= 1.238
  Chirality :  0.093   0.347    480
  Planarity :  0.011   0.068    540
  Dihedral  : 12.058  80.411   1224
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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: -2.04 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.019   0.005   HIS D 362 
 PHE   0.046   0.015   PHE A 346 
 TYR   0.128   0.046   TYR c 310 
 ARG   0.006   0.002   ARG D 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  311 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7232 (mttm)
REVERT: B  345 ASP cc_start: 0.7855 (m-30) cc_final: 0.7438 (t0)
REVERT: B  347 LYS cc_start: 0.8736 (mttt) cc_final: 0.8320 (mtpt)
REVERT: c  311 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7363 (mmtt)
REVERT: A  310 TYR cc_start: 0.6480 (t80) cc_final: 0.6174 (t80)
REVERT: A  311 LYS cc_start: 0.7317 (mtmt) cc_final: 0.7076 (mttp)
REVERT: A  345 ASP cc_start: 0.8253 (m-30) cc_final: 0.8015 (t0)
REVERT: A  347 LYS cc_start: 0.8685 (mttt) cc_final: 0.8282 (mtpt)
REVERT: A  348 ASP cc_start: 0.8307 (t70) cc_final: 0.7492 (p0)
REVERT: A  349 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7304 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7516 (tttt) cc_final: 0.7044 (tttm)
REVERT: D  311 LYS cc_start: 0.6375 (mtmt) cc_final: 0.5530 (mmtm)
REVERT: D  349 ARG cc_start: 0.6886 (mtm180) cc_final: 0.6646 (mmp-170)
REVERT: E  317 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7387 (mttm)
REVERT: E  343 LYS cc_start: 0.8872 (mttt) cc_final: 0.8639 (mttp)
REVERT: E  349 ARG cc_start: 0.7244 (mtm180) cc_final: 0.6352 (pmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.4624
  time to fit residues: 50.3591
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 362 HIS
c 362 HIS
A 362 HIS
C 362 HIS
D 362 HIS
E 351 GLN
E 362 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.147553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.119474 restraints weight = 11422.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.4206 rms_B_bonded: 2.23
r_work: 0.4098 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4012 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3180  Z= 0.194
  Angle     :  0.656   5.714   4254  Z= 0.338
  Chirality :  0.051   0.139    480
  Planarity :  0.003   0.020    540
  Dihedral  :  7.513  20.691    420
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 1.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.89 %
    Favored  : 90.56 %
  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: -1.88 (0.32), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 330 
 PHE   0.006   0.001   PHE c 346 
 TYR   0.012   0.002   TYR E 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  311 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7876 (mttm)
REVERT: B  345 ASP cc_start: 0.7694 (m-30) cc_final: 0.7427 (t0)
REVERT: B  347 LYS cc_start: 0.8662 (mttt) cc_final: 0.8170 (mtpt)
REVERT: B  372 GLU cc_start: 0.7260 (tt0) cc_final: 0.6716 (mt-10)
REVERT: c  311 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7850 (mmtt)
REVERT: c  377 THR cc_start: 0.6428 (m) cc_final: 0.6139 (p)
REVERT: A  310 TYR cc_start: 0.7997 (t80) cc_final: 0.7778 (t80)
REVERT: A  321 LYS cc_start: 0.8186 (mttt) cc_final: 0.7354 (tmtt)
REVERT: A  347 LYS cc_start: 0.8581 (mttt) cc_final: 0.8187 (mtpt)
REVERT: A  348 ASP cc_start: 0.8395 (t70) cc_final: 0.7072 (p0)
REVERT: A  349 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6939 (pmt-80)
REVERT: A  372 GLU cc_start: 0.7754 (tt0) cc_final: 0.7233 (mt-10)
REVERT: A  375 LYS cc_start: 0.7899 (tttt) cc_final: 0.7661 (tttm)
REVERT: D  311 LYS cc_start: 0.8433 (mtmt) cc_final: 0.7550 (mmtm)
REVERT: E  343 LYS cc_start: 0.8869 (mttt) cc_final: 0.8570 (mttp)
  outliers start: 2
  outliers final: 1
  residues processed: 68
  average time/residue: 0.5158
  time to fit residues: 39.6270
Evaluate side-chains
  53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  315 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
A 336 GLN
C 359 ASN
D 359 ASN
E 359 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.145582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.119303 restraints weight = 11952.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.4199 rms_B_bonded: 2.23
r_work: 0.4118 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4035 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3180  Z= 0.135
  Angle     :  0.546   5.989   4254  Z= 0.279
  Chirality :  0.051   0.144    480
  Planarity :  0.002   0.021    540
  Dihedral  :  6.031  17.310    420
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.72 %
    Favored  : 89.17 %
  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: -1.75 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 330 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.014   0.002   TYR E 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.7856 (mttt) cc_final: 0.7062 (tttm)
REVERT: B  347 LYS cc_start: 0.8542 (mttt) cc_final: 0.8048 (mtpt)
REVERT: B  375 LYS cc_start: 0.7282 (tttt) cc_final: 0.6893 (tttm)
REVERT: c  311 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7891 (mmtm)
REVERT: c  321 LYS cc_start: 0.8318 (mttt) cc_final: 0.7410 (tttm)
REVERT: c  347 LYS cc_start: 0.8625 (mttt) cc_final: 0.8077 (mtpt)
REVERT: c  375 LYS cc_start: 0.7984 (tttp) cc_final: 0.7464 (tptt)
REVERT: c  377 THR cc_start: 0.6349 (m) cc_final: 0.6091 (p)
REVERT: A  311 LYS cc_start: 0.8055 (mttp) cc_final: 0.7478 (ptpp)
REVERT: A  321 LYS cc_start: 0.8182 (mttt) cc_final: 0.7389 (tttm)
REVERT: A  347 LYS cc_start: 0.8542 (mttt) cc_final: 0.8136 (mtpt)
REVERT: A  348 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7296 (p0)
REVERT: A  349 ARG cc_start: 0.7322 (mtm180) cc_final: 0.6884 (pmt-80)
REVERT: A  372 GLU cc_start: 0.7938 (tt0) cc_final: 0.7499 (mt-10)
REVERT: A  375 LYS cc_start: 0.8004 (tttt) cc_final: 0.7629 (tttm)
REVERT: C  349 ARG cc_start: 0.6892 (mtm-85) cc_final: 0.6040 (mtt90)
REVERT: E  343 LYS cc_start: 0.8933 (mttt) cc_final: 0.8634 (mttp)
  outliers start: 4
  outliers final: 2
  residues processed: 68
  average time/residue: 0.5903
  time to fit residues: 44.7929
Evaluate side-chains
  57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  315 LEU
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.142276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.116204 restraints weight = 12065.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 2.24
r_work: 0.4075 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3988 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   3180  Z= 0.177
  Angle     :  0.526   5.291   4254  Z= 0.273
  Chirality :  0.050   0.135    480
  Planarity :  0.002   0.017    540
  Dihedral  :  5.678  16.153    420
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.44 %
    Favored  : 89.44 %
  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: -1.78 (0.34), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS c 374 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.014   0.003   TYR E 310 
 ARG   0.001   0.000   ARG c 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.7879 (mttt) cc_final: 0.7072 (tttm)
REVERT: B  347 LYS cc_start: 0.8582 (mttt) cc_final: 0.8037 (mtpt)
REVERT: B  375 LYS cc_start: 0.7281 (tttt) cc_final: 0.6960 (tttm)
REVERT: c  311 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7867 (mmtm)
REVERT: c  321 LYS cc_start: 0.8306 (mttt) cc_final: 0.7361 (tttm)
REVERT: c  347 LYS cc_start: 0.8728 (mttt) cc_final: 0.8162 (mtpt)
REVERT: c  375 LYS cc_start: 0.7913 (tttp) cc_final: 0.7371 (tptt)
REVERT: A  311 LYS cc_start: 0.7990 (mttp) cc_final: 0.7375 (ptpp)
REVERT: A  321 LYS cc_start: 0.8191 (mttt) cc_final: 0.7343 (tttm)
REVERT: A  347 LYS cc_start: 0.8576 (mttt) cc_final: 0.8056 (mtpt)
REVERT: A  348 ASP cc_start: 0.8504 (t70) cc_final: 0.7313 (p0)
REVERT: A  349 ARG cc_start: 0.7460 (mtm180) cc_final: 0.6990 (pmt-80)
REVERT: A  372 GLU cc_start: 0.8036 (tt0) cc_final: 0.7572 (mt-10)
REVERT: A  375 LYS cc_start: 0.7868 (tttt) cc_final: 0.7497 (tttp)
REVERT: C  349 ARG cc_start: 0.6740 (mtm-85) cc_final: 0.5879 (mtt90)
REVERT: E  343 LYS cc_start: 0.8906 (mttt) cc_final: 0.8630 (mttp)
  outliers start: 4
  outliers final: 4
  residues processed: 59
  average time/residue: 0.5578
  time to fit residues: 37.1940
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain c residue  315 LEU
Chi-restraints excluded: chain c residue  376 LEU
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 29 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.142663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.117017 restraints weight = 12309.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.4169 rms_B_bonded: 2.19
r_work: 0.4086 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.4003 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.4945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3180  Z= 0.183
  Angle     :  0.516   5.452   4254  Z= 0.265
  Chirality :  0.050   0.135    480
  Planarity :  0.002   0.015    540
  Dihedral  :  5.468  15.832    420
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.72 %
    Favored  : 89.44 %
  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: -1.72 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS c 374 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.013   0.003   TYR C 310 
 ARG   0.002   0.000   ARG c 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.7952 (mttt) cc_final: 0.7121 (tttm)
REVERT: B  347 LYS cc_start: 0.8631 (mttt) cc_final: 0.8077 (mtpt)
REVERT: B  375 LYS cc_start: 0.7305 (tttt) cc_final: 0.6869 (tttm)
REVERT: c  311 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7839 (mmtm)
REVERT: c  321 LYS cc_start: 0.8268 (mttt) cc_final: 0.7290 (tttm)
REVERT: c  347 LYS cc_start: 0.8793 (mttt) cc_final: 0.8232 (mtpt)
REVERT: c  375 LYS cc_start: 0.7994 (tttp) cc_final: 0.7423 (tptt)
REVERT: A  311 LYS cc_start: 0.7989 (mttp) cc_final: 0.7349 (ptpp)
REVERT: A  321 LYS cc_start: 0.8276 (mttt) cc_final: 0.7345 (tttm)
REVERT: A  347 LYS cc_start: 0.8535 (mttt) cc_final: 0.8011 (mtpt)
REVERT: A  348 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.7357 (p0)
REVERT: A  349 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7027 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7916 (tttt) cc_final: 0.7516 (tttm)
REVERT: C  349 ARG cc_start: 0.6792 (mtm-85) cc_final: 0.5923 (mtt90)
REVERT: E  343 LYS cc_start: 0.8934 (mttt) cc_final: 0.8496 (mttp)
  outliers start: 3
  outliers final: 2
  residues processed: 57
  average time/residue: 0.6111
  time to fit residues: 38.9993
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  377 THR
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    4.3990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.135010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.109349 restraints weight = 12715.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.4060 rms_B_bonded: 2.17
r_work: 0.3977 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3891 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3180  Z= 0.365
  Angle     :  0.597   4.157   4254  Z= 0.310
  Chirality :  0.050   0.139    480
  Planarity :  0.003   0.017    540
  Dihedral  :  5.904  17.303    420
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.28 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS c 374 
 PHE   0.006   0.001   PHE B 346 
 TYR   0.026   0.004   TYR C 310 
 ARG   0.004   0.000   ARG c 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8020 (mttt) cc_final: 0.7198 (tttm)
REVERT: B  347 LYS cc_start: 0.8706 (mttt) cc_final: 0.8157 (mtpt)
REVERT: B  375 LYS cc_start: 0.7449 (tttt) cc_final: 0.7000 (tttm)
REVERT: c  311 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7861 (mmtm)
REVERT: c  321 LYS cc_start: 0.8360 (mttt) cc_final: 0.7369 (tttm)
REVERT: c  347 LYS cc_start: 0.8830 (mttt) cc_final: 0.8242 (mtpt)
REVERT: c  375 LYS cc_start: 0.8002 (tttp) cc_final: 0.7447 (tptt)
REVERT: A  311 LYS cc_start: 0.7917 (mttp) cc_final: 0.7308 (ptpp)
REVERT: A  321 LYS cc_start: 0.8387 (mttt) cc_final: 0.7467 (tttm)
REVERT: A  347 LYS cc_start: 0.8585 (mttt) cc_final: 0.8065 (mtpt)
REVERT: A  348 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.7415 (p0)
REVERT: A  349 ARG cc_start: 0.7565 (mtm180) cc_final: 0.7088 (pmt-80)
REVERT: A  375 LYS cc_start: 0.8003 (tttt) cc_final: 0.7606 (tttm)
REVERT: C  349 ARG cc_start: 0.6826 (mtm-85) cc_final: 0.5946 (mtt90)
REVERT: E  338 GLU cc_start: 0.7973 (tt0) cc_final: 0.7688 (mp0)
REVERT: E  343 LYS cc_start: 0.8893 (mttt) cc_final: 0.8508 (mttp)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 0.5796
  time to fit residues: 36.9372
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain c residue  376 LEU
Chi-restraints excluded: chain c residue  377 THR
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.139834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.114631 restraints weight = 12628.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.4141 rms_B_bonded: 2.15
r_work: 0.4058 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3973 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.5249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3180  Z= 0.173
  Angle     :  0.515   4.143   4254  Z= 0.265
  Chirality :  0.050   0.134    480
  Planarity :  0.002   0.015    540
  Dihedral  :  5.381  15.719    420
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.67 %
    Favored  : 87.22 %
  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 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS c 374 
 PHE   0.002   0.001   PHE A 346 
 TYR   0.012   0.002   TYR C 310 
 ARG   0.002   0.000   ARG c 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8049 (mttt) cc_final: 0.7236 (tttm)
REVERT: B  347 LYS cc_start: 0.8685 (mttt) cc_final: 0.8117 (mtpt)
REVERT: B  375 LYS cc_start: 0.7397 (tttt) cc_final: 0.6984 (tttm)
REVERT: c  321 LYS cc_start: 0.8399 (mttt) cc_final: 0.7426 (tttm)
REVERT: c  347 LYS cc_start: 0.8782 (mttt) cc_final: 0.8176 (mtpt)
REVERT: c  375 LYS cc_start: 0.7965 (tttp) cc_final: 0.7426 (tptt)
REVERT: A  311 LYS cc_start: 0.7965 (mttp) cc_final: 0.7342 (ptpp)
REVERT: A  321 LYS cc_start: 0.8438 (mttt) cc_final: 0.7447 (tttm)
REVERT: A  347 LYS cc_start: 0.8544 (mttt) cc_final: 0.8034 (mtpt)
REVERT: A  348 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7418 (p0)
REVERT: A  349 ARG cc_start: 0.7589 (mtm180) cc_final: 0.7051 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7965 (tttt) cc_final: 0.7565 (tttm)
REVERT: C  349 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.5964 (mtt90)
REVERT: D  349 ARG cc_start: 0.5184 (mmp-170) cc_final: 0.4568 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8908 (mttt) cc_final: 0.8511 (mttp)
  outliers start: 4
  outliers final: 3
  residues processed: 54
  average time/residue: 0.5913
  time to fit residues: 35.8460
Evaluate side-chains
  52 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  376 LEU
Chi-restraints excluded: chain c residue  377 THR
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.138699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.113899 restraints weight = 12696.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 2.14
r_work: 0.4045 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3962 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.5434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3180  Z= 0.201
  Angle     :  0.526   6.817   4254  Z= 0.268
  Chirality :  0.050   0.135    480
  Planarity :  0.002   0.010    540
  Dihedral  :  5.273  14.860    420
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.39 %
    Favored  : 87.50 %
  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: -2.04 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS c 374 
 PHE   0.003   0.001   PHE A 346 
 TYR   0.015   0.002   TYR C 310 
 ARG   0.002   0.000   ARG c 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8069 (mttt) cc_final: 0.7255 (tttm)
REVERT: B  347 LYS cc_start: 0.8690 (mttt) cc_final: 0.8115 (mtpt)
REVERT: B  375 LYS cc_start: 0.7498 (tttt) cc_final: 0.7096 (tttm)
REVERT: c  321 LYS cc_start: 0.8445 (mttt) cc_final: 0.7481 (tttm)
REVERT: c  347 LYS cc_start: 0.8798 (mttt) cc_final: 0.8190 (mtpt)
REVERT: c  375 LYS cc_start: 0.7994 (tttp) cc_final: 0.7453 (tptt)
REVERT: A  311 LYS cc_start: 0.7916 (mttp) cc_final: 0.7324 (ptpp)
REVERT: A  321 LYS cc_start: 0.8463 (mttt) cc_final: 0.7451 (tttm)
REVERT: A  347 LYS cc_start: 0.8556 (mttt) cc_final: 0.8029 (mtpt)
REVERT: A  348 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7414 (p0)
REVERT: A  349 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7106 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7953 (tttt) cc_final: 0.7561 (tttm)
REVERT: C  349 ARG cc_start: 0.6730 (mtm-85) cc_final: 0.5962 (mtt90)
REVERT: D  349 ARG cc_start: 0.5288 (mmp-170) cc_final: 0.4642 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8897 (mttt) cc_final: 0.8496 (mttp)
  outliers start: 4
  outliers final: 3
  residues processed: 52
  average time/residue: 0.6119
  time to fit residues: 35.6062
Evaluate side-chains
  53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  376 LEU
Chi-restraints excluded: chain c residue  377 THR
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
D 330 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.143279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.118498 restraints weight = 12475.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 2.16
r_work: 0.4111 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.4029 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.5584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   3180  Z= 0.111
  Angle     :  0.478   5.873   4254  Z= 0.243
  Chirality :  0.050   0.132    480
  Planarity :  0.002   0.016    540
  Dihedral  :  4.878  14.241    420
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 11.94 %
    Favored  : 87.50 %
  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: -2.04 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 330 
 PHE   0.002   0.000   PHE C 346 
 TYR   0.009   0.002   TYR c 310 
 ARG   0.001   0.000   ARG C 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8128 (mttt) cc_final: 0.7315 (tttm)
REVERT: B  347 LYS cc_start: 0.8616 (mttt) cc_final: 0.8044 (mtpt)
REVERT: B  375 LYS cc_start: 0.7419 (tttt) cc_final: 0.7027 (tttm)
REVERT: c  321 LYS cc_start: 0.8406 (mttt) cc_final: 0.7453 (tttm)
REVERT: c  347 LYS cc_start: 0.8775 (mttt) cc_final: 0.8170 (mtpt)
REVERT: c  375 LYS cc_start: 0.8016 (tttp) cc_final: 0.7501 (tptt)
REVERT: A  321 LYS cc_start: 0.8431 (mttt) cc_final: 0.7470 (tttm)
REVERT: A  347 LYS cc_start: 0.8540 (mttt) cc_final: 0.8040 (mtpt)
REVERT: A  348 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7370 (p0)
REVERT: A  349 ARG cc_start: 0.7574 (mtm180) cc_final: 0.7023 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7955 (tttt) cc_final: 0.7551 (tttm)
REVERT: C  349 ARG cc_start: 0.6722 (mtm-85) cc_final: 0.5983 (mtt90)
REVERT: D  349 ARG cc_start: 0.5279 (mmp-170) cc_final: 0.4630 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8905 (mttt) cc_final: 0.8511 (mttp)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.5365
  time to fit residues: 34.6253
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  376 LEU
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.140431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.115490 restraints weight = 12671.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.4154 rms_B_bonded: 2.15
r_work: 0.4066 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3984 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.5613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   3180  Z= 0.178
  Angle     :  0.520   9.304   4254  Z= 0.258
  Chirality :  0.049   0.134    480
  Planarity :  0.002   0.018    540
  Dihedral  :  4.926  14.281    420
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 12.78 %
    Favored  : 86.39 %
  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: -2.01 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS c 374 
 PHE   0.002   0.001   PHE A 346 
 TYR   0.012   0.002   TYR C 310 
 ARG   0.002   0.000   ARG c 349 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8135 (mttt) cc_final: 0.7340 (tttm)
REVERT: B  347 LYS cc_start: 0.8631 (mttt) cc_final: 0.8059 (mtpt)
REVERT: B  375 LYS cc_start: 0.7472 (tttt) cc_final: 0.7066 (tttm)
REVERT: c  321 LYS cc_start: 0.8432 (mttt) cc_final: 0.7482 (tttm)
REVERT: c  347 LYS cc_start: 0.8791 (mttt) cc_final: 0.8195 (mtpt)
REVERT: c  375 LYS cc_start: 0.8017 (tttp) cc_final: 0.7495 (tptt)
REVERT: A  321 LYS cc_start: 0.8439 (mttt) cc_final: 0.7460 (tttm)
REVERT: A  347 LYS cc_start: 0.8555 (mttt) cc_final: 0.8043 (mtpt)
REVERT: A  348 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.7374 (p0)
REVERT: A  349 ARG cc_start: 0.7584 (mtm180) cc_final: 0.7061 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7950 (tttt) cc_final: 0.7435 (tttp)
REVERT: C  349 ARG cc_start: 0.6733 (mtm-85) cc_final: 0.6020 (mtt90)
REVERT: D  349 ARG cc_start: 0.5289 (mmp-170) cc_final: 0.4631 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8876 (mttt) cc_final: 0.8483 (mttp)
  outliers start: 3
  outliers final: 2
  residues processed: 53
  average time/residue: 0.6030
  time to fit residues: 36.1936
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  376 LEU
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    2.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.137042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.112086 restraints weight = 13031.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.4107 rms_B_bonded: 2.17
r_work: 0.4016 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3932 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.5628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3180  Z= 0.251
  Angle     :  0.551   9.444   4254  Z= 0.277
  Chirality :  0.049   0.137    480
  Planarity :  0.002   0.020    540
  Dihedral  :  5.149  14.875    420
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 12.78 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS c 374 
 PHE   0.003   0.001   PHE B 346 
 TYR   0.017   0.003   TYR C 310 
 ARG   0.003   0.001   ARG c 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4210.90 seconds
wall clock time: 74 minutes 47.02 seconds (4487.02 seconds total)