Starting phenix.real_space_refine
on Fri Aug 22 17:19:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ql0_14059/08_2025/7ql0_14059.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ql0_14059/08_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_14059/08_2025/7ql0_14059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ql0_14059/08_2025/7ql0_14059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ql0_14059/08_2025/7ql0_14059.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ql0_14059/08_2025/7ql0_14059.cif"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.33, per 1000 atoms: 0.21
  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: 0.53
  Conformation dependent library (CDL) restraints added in 155.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.20
  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: 1.29

  Time building geometry restraints manager: 0.80 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: 0.00
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:             5.460
  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:             0.030
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.250
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.460
-------------------------------------------------------------------------------
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= 0.700
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.006   0.002   ARG D 349 
 TYR   0.128   0.046   TYR c 310 
 PHE   0.046   0.015   PHE A 346 
 HIS   0.019   0.005   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01096 ( 3180)
  covalent geometry    : angle       1.87489 ( 4254)
  hydrogen bonds       : bond        0.12782 (   56)
  hydrogen bonds       : angle       7.72118 (  168)

*********************** 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  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  311 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7261 (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: 0.7417 (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: 0.7075 (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: 0.1864
  time to fit residues: 20.2365
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  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.4468 r_free = 0.4468 target = 0.144720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.116395 restraints weight = 11722.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 2.27
r_work: 0.4072 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3983 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3180  Z= 0.153
  Angle     :  0.676   5.693   4254  Z= 0.347
  Chirality :  0.051   0.142    480
  Planarity :  0.003   0.021    540
  Dihedral  :  7.630  21.073    420
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.61 %
    Favored  : 90.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.33), 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
 ARG   0.001   0.000   ARG c 349 
 TYR   0.013   0.002   TYR E 310 
 PHE   0.006   0.001   PHE c 346 
 HIS   0.004   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3180)
  covalent geometry    : angle       0.67560 ( 4254)
  hydrogen bonds       : bond        0.02672 (   56)
  hydrogen bonds       : angle       5.17154 (  168)

*********************** 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
  67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  311 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7870 (mttm)
REVERT: B  345 ASP cc_start: 0.7679 (m-30) cc_final: 0.7354 (t0)
REVERT: B  347 LYS cc_start: 0.8676 (mttt) cc_final: 0.8170 (mtpt)
REVERT: c  311 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7853 (mmtt)
REVERT: c  377 THR cc_start: 0.6355 (m) cc_final: 0.6070 (p)
REVERT: A  310 TYR cc_start: 0.8012 (t80) cc_final: 0.7798 (t80)
REVERT: A  321 LYS cc_start: 0.8204 (mttt) cc_final: 0.7351 (tttm)
REVERT: A  347 LYS cc_start: 0.8612 (mttt) cc_final: 0.8196 (mtpt)
REVERT: A  348 ASP cc_start: 0.8418 (t70) cc_final: 0.7090 (p0)
REVERT: A  349 ARG cc_start: 0.7265 (mtm180) cc_final: 0.6918 (pmt-80)
REVERT: A  372 GLU cc_start: 0.7792 (tt0) cc_final: 0.7247 (mt-10)
REVERT: A  375 LYS cc_start: 0.7930 (tttt) cc_final: 0.7681 (tttm)
REVERT: D  349 ARG cc_start: 0.6496 (mtm180) cc_final: 0.6293 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8851 (mttt) cc_final: 0.8549 (mttp)
  outliers start: 2
  outliers final: 1
  residues processed: 66
  average time/residue: 0.1968
  time to fit residues: 14.6751
Evaluate side-chains
  51 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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 13 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 12 optimal weight:    0.0980
   chunk 15 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4615 r_free = 0.4615 target = 0.158233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.132077 restraints weight = 11127.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.4295 rms_B_bonded: 2.22
r_work: 0.4221 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.4139 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.4139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3180  Z= 0.087
  Angle     :  0.537   6.550   4254  Z= 0.273
  Chirality :  0.051   0.134    480
  Planarity :  0.002   0.022    540
  Dihedral  :  5.873  17.117    420
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.009   0.002   TYR E 310 
 PHE   0.004   0.001   PHE A 346 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00175 ( 3180)
  covalent geometry    : angle       0.53723 ( 4254)
  hydrogen bonds       : bond        0.02001 (   56)
  hydrogen bonds       : angle       4.52675 (  168)

*********************** 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
  76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.7877 (mttt) cc_final: 0.7072 (tttm)
REVERT: B  347 LYS cc_start: 0.8547 (mttt) cc_final: 0.8091 (mtpt)
REVERT: B  351 GLN cc_start: 0.7857 (mt0) cc_final: 0.7294 (tt0)
REVERT: B  375 LYS cc_start: 0.7277 (tttt) cc_final: 0.6896 (tttm)
REVERT: c  311 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7905 (mmtm)
REVERT: c  321 LYS cc_start: 0.8285 (mttt) cc_final: 0.7430 (tttm)
REVERT: c  347 LYS cc_start: 0.8563 (mttt) cc_final: 0.8088 (mtpt)
REVERT: c  375 LYS cc_start: 0.7998 (tttp) cc_final: 0.7523 (tptt)
REVERT: c  377 THR cc_start: 0.6320 (m) cc_final: 0.6101 (p)
REVERT: A  311 LYS cc_start: 0.8042 (mttp) cc_final: 0.7441 (ptpp)
REVERT: A  321 LYS cc_start: 0.8150 (mttt) cc_final: 0.7305 (tttm)
REVERT: A  347 LYS cc_start: 0.8510 (mttt) cc_final: 0.8107 (mtpt)
REVERT: A  348 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7337 (p0)
REVERT: A  349 ARG cc_start: 0.7322 (mtm180) cc_final: 0.6708 (pmt-80)
REVERT: A  372 GLU cc_start: 0.7869 (tt0) cc_final: 0.7496 (mt-10)
REVERT: A  375 LYS cc_start: 0.7995 (tttt) cc_final: 0.7607 (tttm)
REVERT: C  349 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6862 (mtm110)
REVERT: E  343 LYS cc_start: 0.8951 (mttt) cc_final: 0.8653 (mttp)
  outliers start: 3
  outliers final: 2
  residues processed: 73
  average time/residue: 0.2434
  time to fit residues: 19.8000
Evaluate side-chains
  58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
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 18 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0470
   chunk 8 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    2.4084

-------------------------------------------------------------------------------
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 = 0.4429 r_free = 0.4429 target = 0.141287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.115512 restraints weight = 12286.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 2.23
r_work: 0.4055 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3971 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4781

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= 0.143
  Angle     :  0.539   5.036   4254  Z= 0.280
  Chirality :  0.050   0.134    480
  Planarity :  0.002   0.017    540
  Dihedral  :  5.768  16.340    420
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.72 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.34), 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
 ARG   0.002   0.000   ARG C 349 
 TYR   0.016   0.003   TYR C 310 
 PHE   0.006   0.001   PHE A 346 
 HIS   0.003   0.001   HIS c 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3180)
  covalent geometry    : angle       0.53856 ( 4254)
  hydrogen bonds       : bond        0.02068 (   56)
  hydrogen bonds       : angle       3.99843 (  168)

*********************** 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
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.7881 (mttt) cc_final: 0.7101 (tttm)
REVERT: B  347 LYS cc_start: 0.8617 (mttt) cc_final: 0.8091 (mtpt)
REVERT: B  375 LYS cc_start: 0.7323 (tttt) cc_final: 0.6995 (tttm)
REVERT: c  311 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7868 (mmtm)
REVERT: c  321 LYS cc_start: 0.8301 (mttt) cc_final: 0.7354 (tttm)
REVERT: c  347 LYS cc_start: 0.8733 (mttt) cc_final: 0.8181 (mtpt)
REVERT: c  375 LYS cc_start: 0.7946 (tttp) cc_final: 0.7400 (tptt)
REVERT: A  311 LYS cc_start: 0.8004 (mttp) cc_final: 0.7404 (ptpp)
REVERT: A  321 LYS cc_start: 0.8108 (mttt) cc_final: 0.7295 (tttm)
REVERT: A  347 LYS cc_start: 0.8571 (mttt) cc_final: 0.8097 (mtpt)
REVERT: A  348 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.7341 (p0)
REVERT: A  349 ARG cc_start: 0.7433 (mtm180) cc_final: 0.6985 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7932 (tttt) cc_final: 0.7577 (tttp)
REVERT: C  349 ARG cc_start: 0.6808 (mtm-85) cc_final: 0.5947 (mtt90)
REVERT: E  343 LYS cc_start: 0.8912 (mttt) cc_final: 0.8611 (mttp)
  outliers start: 5
  outliers final: 4
  residues processed: 63
  average time/residue: 0.2177
  time to fit residues: 15.4715
Evaluate side-chains
  61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain D residue  324 SER
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 18 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0010
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.9994

-------------------------------------------------------------------------------
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 = 0.4425 r_free = 0.4425 target = 0.142133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.116262 restraints weight = 12145.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 2.20
r_work: 0.4062 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3978 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.5007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3180  Z= 0.119
  Angle     :  0.516   4.314   4254  Z= 0.266
  Chirality :  0.050   0.134    480
  Planarity :  0.002   0.015    540
  Dihedral  :  5.451  16.208    420
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.28 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (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
 ARG   0.001   0.000   ARG c 349 
 TYR   0.012   0.003   TYR E 310 
 PHE   0.004   0.001   PHE A 346 
 HIS   0.002   0.001   HIS c 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3180)
  covalent geometry    : angle       0.51581 ( 4254)
  hydrogen bonds       : bond        0.01897 (   56)
  hydrogen bonds       : angle       3.84522 (  168)

*********************** 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
  64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.7983 (mttt) cc_final: 0.7190 (tttm)
REVERT: B  347 LYS cc_start: 0.8652 (mttt) cc_final: 0.8113 (mtpt)
REVERT: B  375 LYS cc_start: 0.7410 (tttt) cc_final: 0.6986 (tttm)
REVERT: c  311 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7861 (mmtm)
REVERT: c  321 LYS cc_start: 0.8301 (mttt) cc_final: 0.7349 (tttm)
REVERT: c  347 LYS cc_start: 0.8748 (mttt) cc_final: 0.8213 (mtpt)
REVERT: c  375 LYS cc_start: 0.8034 (tttp) cc_final: 0.7493 (tptt)
REVERT: A  311 LYS cc_start: 0.7945 (mttp) cc_final: 0.7321 (ptpp)
REVERT: A  321 LYS cc_start: 0.8239 (mttt) cc_final: 0.7337 (tttm)
REVERT: A  347 LYS cc_start: 0.8558 (mttt) cc_final: 0.8039 (mtpt)
REVERT: A  348 ASP cc_start: 0.8540 (t70) cc_final: 0.7375 (p0)
REVERT: A  349 ARG cc_start: 0.7421 (mtm180) cc_final: 0.6980 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7946 (tttt) cc_final: 0.7568 (tttm)
REVERT: C  349 ARG cc_start: 0.6800 (mtm-85) cc_final: 0.5948 (mtt90)
REVERT: E  343 LYS cc_start: 0.8948 (mttt) cc_final: 0.8500 (mttp)
  outliers start: 4
  outliers final: 4
  residues processed: 63
  average time/residue: 0.2150
  time to fit residues: 15.2985
Evaluate side-chains
  60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue  376 LEU
Chi-restraints excluded: chain c residue  377 THR
Chi-restraints excluded: chain D residue  324 SER
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 35 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 14 optimal weight:    0.4980
   chunk 21 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    3.4988

-------------------------------------------------------------------------------
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 = 0.4383 r_free = 0.4383 target = 0.136996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.111442 restraints weight = 12735.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.4090 rms_B_bonded: 2.18
r_work: 0.4006 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3923 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3180  Z= 0.197
  Angle     :  0.566   6.130   4254  Z= 0.292
  Chirality :  0.050   0.137    480
  Planarity :  0.002   0.014    540
  Dihedral  :  5.658  16.641    420
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.28 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c 349 
 TYR   0.021   0.003   TYR C 310 
 PHE   0.005   0.001   PHE B 346 
 HIS   0.004   0.001   HIS c 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 3180)
  covalent geometry    : angle       0.56645 ( 4254)
  hydrogen bonds       : bond        0.02026 (   56)
  hydrogen bonds       : angle       3.76508 (  168)

*********************** 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
  60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8010 (mttt) cc_final: 0.7194 (tttm)
REVERT: B  347 LYS cc_start: 0.8699 (mttt) cc_final: 0.8144 (mtpt)
REVERT: B  375 LYS cc_start: 0.7414 (tttt) cc_final: 0.6981 (tttm)
REVERT: c  311 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7845 (mmtm)
REVERT: c  321 LYS cc_start: 0.8384 (mttt) cc_final: 0.7422 (tttm)
REVERT: c  347 LYS cc_start: 0.8812 (mttt) cc_final: 0.8229 (mtpt)
REVERT: c  375 LYS cc_start: 0.8033 (tttp) cc_final: 0.7476 (tptt)
REVERT: A  311 LYS cc_start: 0.7942 (mttp) cc_final: 0.7321 (ptpp)
REVERT: A  321 LYS cc_start: 0.8306 (mttt) cc_final: 0.7379 (tttm)
REVERT: A  347 LYS cc_start: 0.8576 (mttt) cc_final: 0.8053 (mtpt)
REVERT: A  348 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.7412 (p0)
REVERT: A  349 ARG cc_start: 0.7594 (mtm180) cc_final: 0.7068 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7961 (tttt) cc_final: 0.7540 (tttm)
REVERT: C  349 ARG cc_start: 0.6800 (mtm-85) cc_final: 0.5916 (mtt90)
REVERT: E  343 LYS cc_start: 0.8904 (mttt) cc_final: 0.8479 (mttp)
  outliers start: 6
  outliers final: 5
  residues processed: 58
  average time/residue: 0.2268
  time to fit residues: 14.8311
Evaluate side-chains
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
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  320 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain D residue  324 SER
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 33 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.4438 r_free = 0.4438 target = 0.141147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.116255 restraints weight = 12600.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 2.15
r_work: 0.4080 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3992 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.5313

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= 0.099
  Angle     :  0.498   4.720   4254  Z= 0.256
  Chirality :  0.050   0.133    480
  Planarity :  0.002   0.012    540
  Dihedral  :  5.215  15.254    420
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.39 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.89 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.43 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG c 349 
 TYR   0.011   0.002   TYR C 310 
 PHE   0.002   0.001   PHE A 346 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 3180)
  covalent geometry    : angle       0.49847 ( 4254)
  hydrogen bonds       : bond        0.01604 (   56)
  hydrogen bonds       : angle       3.61233 (  168)

*********************** 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
  59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8053 (mttt) cc_final: 0.7244 (tttm)
REVERT: B  347 LYS cc_start: 0.8645 (mttt) cc_final: 0.8070 (mtpt)
REVERT: B  375 LYS cc_start: 0.7429 (tttt) cc_final: 0.7038 (tttm)
REVERT: c  311 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7821 (mmtm)
REVERT: c  321 LYS cc_start: 0.8418 (mttt) cc_final: 0.7443 (tttm)
REVERT: c  347 LYS cc_start: 0.8780 (mttt) cc_final: 0.8181 (mtpt)
REVERT: c  375 LYS cc_start: 0.7972 (tttp) cc_final: 0.7426 (tptt)
REVERT: A  311 LYS cc_start: 0.7953 (mttp) cc_final: 0.7287 (ptpp)
REVERT: A  321 LYS cc_start: 0.8385 (mttt) cc_final: 0.7395 (tttm)
REVERT: A  347 LYS cc_start: 0.8526 (mttt) cc_final: 0.8005 (mtpt)
REVERT: A  348 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.7433 (p0)
REVERT: A  349 ARG cc_start: 0.7604 (mtm180) cc_final: 0.7051 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7929 (tttt) cc_final: 0.7514 (tttm)
REVERT: C  349 ARG cc_start: 0.6720 (mtm-85) cc_final: 0.5949 (mtt90)
REVERT: D  349 ARG cc_start: 0.5220 (mmp-170) cc_final: 0.4611 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8892 (mttt) cc_final: 0.8464 (mttp)
  outliers start: 6
  outliers final: 5
  residues processed: 57
  average time/residue: 0.2315
  time to fit residues: 14.7286
Evaluate side-chains
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
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  324 SER
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 7 optimal weight:    7.9990
   chunk 8 optimal weight:    0.1980
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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 = 0.4417 r_free = 0.4417 target = 0.139570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.114678 restraints weight = 12729.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 2.15
r_work: 0.4059 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3976 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.5393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3180  Z= 0.124
  Angle     :  0.514   6.584   4254  Z= 0.263
  Chirality :  0.049   0.135    480
  Planarity :  0.002   0.015    540
  Dihedral  :  5.151  14.891    420
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.39 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG c 349 
 TYR   0.014   0.002   TYR C 310 
 PHE   0.003   0.001   PHE A 346 
 HIS   0.003   0.001   HIS c 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3180)
  covalent geometry    : angle       0.51423 ( 4254)
  hydrogen bonds       : bond        0.01621 (   56)
  hydrogen bonds       : angle       3.54824 (  168)

*********************** 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
  58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8079 (mttt) cc_final: 0.7262 (tttm)
REVERT: B  347 LYS cc_start: 0.8686 (mttt) cc_final: 0.8120 (mtpt)
REVERT: B  375 LYS cc_start: 0.7453 (tttt) cc_final: 0.7064 (tttm)
REVERT: B  377 THR cc_start: 0.5681 (OUTLIER) cc_final: 0.5307 (p)
REVERT: c  311 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7824 (mmtm)
REVERT: c  321 LYS cc_start: 0.8421 (mttt) cc_final: 0.7460 (tttm)
REVERT: c  347 LYS cc_start: 0.8780 (mttt) cc_final: 0.8177 (mtpt)
REVERT: c  375 LYS cc_start: 0.7984 (tttp) cc_final: 0.7441 (tptt)
REVERT: A  321 LYS cc_start: 0.8378 (mttt) cc_final: 0.7395 (tttm)
REVERT: A  347 LYS cc_start: 0.8527 (mttt) cc_final: 0.8018 (mtpt)
REVERT: A  348 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.7423 (p0)
REVERT: A  349 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7070 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7942 (tttt) cc_final: 0.7531 (tttm)
REVERT: C  349 ARG cc_start: 0.6699 (mtm-85) cc_final: 0.5952 (mtt90)
REVERT: D  349 ARG cc_start: 0.5239 (mmp-170) cc_final: 0.4577 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8898 (mttt) cc_final: 0.8476 (mttp)
  outliers start: 6
  outliers final: 4
  residues processed: 56
  average time/residue: 0.2416
  time to fit residues: 15.2134
Evaluate side-chains
  58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
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  324 SER
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 18 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.4415 r_free = 0.4415 target = 0.139257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.114336 restraints weight = 12923.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.4142 rms_B_bonded: 2.16
r_work: 0.4049 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3967 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.5450

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= 0.127
  Angle     :  0.509   5.795   4254  Z= 0.261
  Chirality :  0.049   0.135    480
  Planarity :  0.002   0.012    540
  Dihedral  :  5.110  14.816    420
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.35), 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
 ARG   0.002   0.000   ARG c 349 
 TYR   0.014   0.002   TYR C 310 
 PHE   0.003   0.001   PHE A 346 
 HIS   0.003   0.001   HIS c 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3180)
  covalent geometry    : angle       0.50909 ( 4254)
  hydrogen bonds       : bond        0.01568 (   56)
  hydrogen bonds       : angle       3.50594 (  168)

*********************** 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
  57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8114 (mttt) cc_final: 0.7290 (tttm)
REVERT: B  347 LYS cc_start: 0.8699 (mttt) cc_final: 0.8130 (mtpt)
REVERT: B  375 LYS cc_start: 0.7531 (tttt) cc_final: 0.7144 (tttm)
REVERT: B  377 THR cc_start: 0.5802 (OUTLIER) cc_final: 0.5442 (p)
REVERT: c  311 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7833 (mmtm)
REVERT: c  321 LYS cc_start: 0.8443 (mttt) cc_final: 0.7493 (tttm)
REVERT: c  347 LYS cc_start: 0.8791 (mttt) cc_final: 0.8197 (mtpt)
REVERT: c  375 LYS cc_start: 0.8033 (tttp) cc_final: 0.7504 (tptt)
REVERT: A  321 LYS cc_start: 0.8414 (mttt) cc_final: 0.7409 (tttm)
REVERT: A  347 LYS cc_start: 0.8550 (mttt) cc_final: 0.8034 (mtpt)
REVERT: A  348 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.7423 (p0)
REVERT: A  349 ARG cc_start: 0.7599 (mtm180) cc_final: 0.7103 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7976 (tttt) cc_final: 0.7573 (tttm)
REVERT: C  349 ARG cc_start: 0.6740 (mtm-85) cc_final: 0.6011 (mtt90)
REVERT: D  349 ARG cc_start: 0.5280 (mmp-170) cc_final: 0.4620 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8898 (mttt) cc_final: 0.8480 (mttp)
  outliers start: 6
  outliers final: 4
  residues processed: 55
  average time/residue: 0.2301
  time to fit residues: 14.0718
Evaluate side-chains
  57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
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  324 SER
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 25 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.4381 r_free = 0.4381 target = 0.136399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.111234 restraints weight = 12838.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.4094 rms_B_bonded: 2.17
r_work: 0.4010 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.5489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3180  Z= 0.178
  Angle     :  0.542   5.062   4254  Z= 0.279
  Chirality :  0.049   0.137    480
  Planarity :  0.002   0.015    540
  Dihedral  :  5.274  15.168    420
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c 349 
 TYR   0.019   0.003   TYR C 310 
 PHE   0.004   0.001   PHE A 346 
 HIS   0.004   0.001   HIS c 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3180)
  covalent geometry    : angle       0.54225 ( 4254)
  hydrogen bonds       : bond        0.01744 (   56)
  hydrogen bonds       : angle       3.54235 (  168)

********************** 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
  57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.8156 (mttt) cc_final: 0.7348 (tttm)
REVERT: B  347 LYS cc_start: 0.8696 (mttt) cc_final: 0.8127 (mtpt)
REVERT: B  375 LYS cc_start: 0.7568 (tttt) cc_final: 0.7188 (tttm)
REVERT: B  377 THR cc_start: 0.5893 (OUTLIER) cc_final: 0.5536 (p)
REVERT: c  311 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7829 (mmtm)
REVERT: c  321 LYS cc_start: 0.8460 (mttt) cc_final: 0.7517 (tttm)
REVERT: c  347 LYS cc_start: 0.8803 (mttt) cc_final: 0.8189 (mtpt)
REVERT: c  375 LYS cc_start: 0.7998 (tttp) cc_final: 0.7395 (tptt)
REVERT: A  321 LYS cc_start: 0.8440 (mttt) cc_final: 0.7421 (tttm)
REVERT: A  347 LYS cc_start: 0.8549 (mttt) cc_final: 0.8019 (mtpt)
REVERT: A  348 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.7426 (p0)
REVERT: A  349 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7123 (pmt-80)
REVERT: A  375 LYS cc_start: 0.7991 (tttt) cc_final: 0.7576 (tttm)
REVERT: C  349 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.5972 (mtt90)
REVERT: D  349 ARG cc_start: 0.5222 (mmp-170) cc_final: 0.4577 (mmp-170)
REVERT: E  343 LYS cc_start: 0.8882 (mttt) cc_final: 0.8469 (mttp)
  outliers start: 6
  outliers final: 4
  residues processed: 55
  average time/residue: 0.2297
  time to fit residues: 14.1829
Evaluate side-chains
  57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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  324 SER
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 3 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4436 r_free = 0.4436 target = 0.140918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.116058 restraints weight = 12590.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 2.16
r_work: 0.4081 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.4000 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.5585

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= 0.083
  Angle     :  0.504   8.715   4254  Z= 0.251
  Chirality :  0.050   0.132    480
  Planarity :  0.002   0.022    540
  Dihedral  :  4.886  14.774    420
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 12.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.27), residues: 402

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 3180)
  covalent geometry    : angle       0.50394 ( 4254)
  hydrogen bonds       : bond        0.01387 (   56)
  hydrogen bonds       : angle       3.48052 (  168)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1964.21 seconds
wall clock time: 34 minutes 0.40 seconds (2040.40 seconds total)