Starting phenix.real_space_refine
on Thu Aug  6 23:10:29 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8c9a_16507/08_2026/8c9a_16507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c9a_16507/08_2026/8c9a_16507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2026/8c9a_16507.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2026/8c9a_16507.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2026/8c9a_16507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2026/8c9a_16507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2026/8c9a_16507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2026/8c9a_16507.cif"
  }
  resolution = 4.86
  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=   0.044
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
     P     650      5.49       5
     S      10      5.16       5
     C    8805      2.51       5
     N    3358      2.21       5
     O    5236      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 18059
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 13953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 650, 13953
          Classifications: {'RNAv2': 650}
          Modifications used: {'rna2p_pur': 70, 'rna2p_pyr': 42, 'rna3p_pur': 314, 'rna3p_pyr': 224}
          Link IDs: {'rna2p': 112, 'rna3p': 537}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'  U%rna2p_pyr:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "2"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 286
          Classifications: {'peptide': 35}
          Link IDs: {'TRANS': 34}
    Chain: "E"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1137
          Classifications: {'peptide': 147}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 144}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 726
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 92}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 779
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "Y"
      Number of atoms: 494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 494
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "T"
      Number of atoms: 684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 684
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
          Chain breaks: 1
  Time building chain proxies: 3.47, per 1000 atoms: 0.19
  Number of scatterers: 18059
  At special positions: 0
  Unit cell: (132.5, 152.5, 148.75, 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      10     16.00
     P     650     15.00
     O    5236      8.00
     N    3358      7.00
     C    8805      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 351.1 milliseconds
  

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  998

  Finding SS restraints...
Warning! N1 atom is missing from residue    G A 356  
  Was trying to link:    G A 356 N1 with    U A 284 O4, Saenger class: 27
Warning! N1 atom is missing from residue    G A 356  
  Was trying to link:    G A 356 N1 with    U A 284 O2, Saenger class: 28
    Secondary structure from input PDB file:
      19 helices and 5 sheets defined
      44.6% alpha, 14.7% beta
      198 base pairs and 310 stacking pairs defined.
    Time for finding SS restraints: 2.62
  Creating SS restraints...
    Processing helix  chain '2' and resid 10 through 17
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 4.282A  pdb=" N   THR 2  24 " --> pdb=" O   ALA 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 24 through 38
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 24 through 38
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
      removed outlier: 3.689A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   MET E 141 " --> pdb=" O   LYS E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 162
    Processing helix  chain 'E' and resid 176 through 183
      removed outlier: 3.566A  pdb=" N   PHE E 183 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 201
    Processing helix  chain 'S' and resid 13 through 22
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 4.349A  pdb=" N   TYR S  38 " --> pdb=" O   ASP S  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 41 through 63
      removed outlier: 3.789A  pdb=" N   VAL S  45 " --> pdb=" O   LYS S  41 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 65 through 67
      No H-bonds generated for 'chain 'U' and resid 65 through 67'
    Processing helix  chain 'Y' and resid 9 through 35
      removed outlier: 3.525A  pdb=" N   GLU Y  13 " --> pdb=" O   LYS Y   9 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLN Y  25 " --> pdb=" O   LEU Y  21 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 56
      removed outlier: 3.817A  pdb=" N   LYS Y  44 " --> pdb=" O   SER Y  40 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU Y  56 " --> pdb=" O   ARG Y  52 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 9
      removed outlier: 3.531A  pdb=" N   LEU T   8 " --> pdb=" O   GLU T   4 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 17 through 27
      removed outlier: 3.847A  pdb=" N   GLU T  25 " --> pdb=" O   SER T  21 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 39 through 52
    Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 121
      removed outlier: 4.005A  pdb=" N   THR E 189 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 3 through 10
      removed outlier: 5.340A  pdb=" N   ILE S   4 " --> pdb=" O   VAL S 107 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   VAL S 107 " --> pdb=" O   ILE S   4 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS S   6 " --> pdb=" O   VAL S 105 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   VAL S 105 " --> pdb=" O   LYS S   6 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   ARG S   8 " --> pdb=" O   ILE S 103 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ILE S 103 " --> pdb=" O   ARG S   8 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   SER S 108 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   VAL S  71 " --> pdb=" O   SER S 108 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'U' and resid 33 through 35
      removed outlier: 7.123A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ASP U   8 " --> pdb=" O   VAL U  24 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'U' and resid 83 through 86
    Processing sheet with id=AA5, first strand: chain 'T' and resid 29 through 34
      removed outlier: 3.604A  pdb=" N   ALA T  83 " --> pdb=" O   LEU T  32 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL T  34 " --> pdb=" O   LYS T  81 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR T  86 " --> pdb=" O   VAL T  57 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   VAL T  57 " --> pdb=" O   THR T  86 " (cutoff:3.500A)

    181 hydrogen bonds defined for protein.
    534 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      506 hydrogen bonds
      816 hydrogen bond angles
      0 basepair planarities
      198 basepair parallelities
      310 stacking parallelities
  Total time for adding SS restraints: 4.35

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2914
        1.33 -     1.45: 8282
        1.45 -     1.57: 7252
        1.57 -     1.69: 1294
        1.69 -     1.81: 20
  Bond restraints: 19762
  Sorted by residual:
  bond pdb=" N   ALA U   1 "
       pdb=" CA  ALA U   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.07e+00
  bond pdb=" N   MET Y   1 "
       pdb=" CA  MET Y   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" N   MET T   1 "
       pdb=" CA  MET T   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.84e+00
  bond pdb=" C3'   G A 271 "
       pdb=" O3'   G A 271 "
    ideal  model  delta    sigma   weight residual
    1.415  1.436 -0.021 2.00e-02 2.50e+03 1.06e+00
  bond pdb=" C3'   G A 410 "
       pdb=" O3'   G A 410 "
    ideal  model  delta    sigma   weight residual
    1.415  1.435 -0.020 2.00e-02 2.50e+03 9.86e-01
  ... (remaining 19757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.34: 29884
        5.34 -    10.68: 8
       10.68 -    16.03: 0
       16.03 -    21.37: 0
       21.37 -    26.71: 2
  Bond angle restraints: 29894
  Sorted by residual:
  angle pdb=" O3'   C A 624 "
        pdb=" P     G A 625 "
        pdb=" OP1   G A 625 "
      ideal   model   delta    sigma   weight residual
     108.00   81.29   26.71 3.00e+00 1.11e-01 7.93e+01
  angle pdb=" O3'   C A 624 "
        pdb=" P     G A 625 "
        pdb=" OP2   G A 625 "
      ideal   model   delta    sigma   weight residual
     108.00   84.09   23.91 3.00e+00 1.11e-01 6.35e+01
  angle pdb=" OP1   G A 625 "
        pdb=" P     G A 625 "
        pdb=" OP2   G A 625 "
      ideal   model   delta    sigma   weight residual
     119.60  129.76  -10.16 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" C6    A A 278 "
        pdb=" N1    A A 278 "
        pdb=" C2    A A 278 "
      ideal   model   delta    sigma   weight residual
     118.60  127.77   -9.17 3.00e+00 1.11e-01 9.34e+00
  angle pdb=" C5    A A 278 "
        pdb=" C6    A A 278 "
        pdb=" N1    A A 278 "
      ideal   model   delta    sigma   weight residual
     117.70  126.76   -9.06 3.00e+00 1.11e-01 9.13e+00
  ... (remaining 29889 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.82: 9222
       35.82 -    71.63: 1090
       71.63 -   107.45: 75
      107.45 -   143.27: 1
      143.27 -   179.09: 2
  Dihedral angle restraints: 10390
    sinusoidal: 8872
      harmonic: 1518
  Sorted by residual:
  dihedral pdb=" C4'   G A 411 "
           pdb=" C3'   G A 411 "
           pdb=" C2'   G A 411 "
           pdb=" C1'   G A 411 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.32   73.67     1      3.10e+00 1.04e-01 7.18e+02
  dihedral pdb=" C4'   G A 215 "
           pdb=" C3'   G A 215 "
           pdb=" C2'   G A 215 "
           pdb=" C1'   G A 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.19   73.54     1      3.10e+00 1.04e-01 7.16e+02
  dihedral pdb=" C4'   U A 434 "
           pdb=" C3'   U A 434 "
           pdb=" C2'   U A 434 "
           pdb=" C1'   U A 434 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.12   73.47     1      3.10e+00 1.04e-01 7.15e+02
  ... (remaining 10387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.353: 3912
       0.353 -    0.706: 0
       0.706 -    1.059: 0
       1.059 -    1.412: 0
       1.412 -    1.765: 1
  Chirality restraints: 3913
  Sorted by residual:
  chirality pdb=" P     G A 625 "
            pdb=" OP1   G A 625 "
            pdb=" OP2   G A 625 "
            pdb=" O5'   G A 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17    0.41    1.77 2.00e-01 2.50e+01 7.79e+01
  chirality pdb=" C2'   G A 411 "
            pdb=" C3'   G A 411 "
            pdb=" O2'   G A 411 "
            pdb=" C1'   G A 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.48   -0.31 2.00e-01 2.50e+01 2.35e+00
  chirality pdb=" C2'   G A 410 "
            pdb=" C3'   G A 410 "
            pdb=" O2'   G A 410 "
            pdb=" C1'   G A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.50   -0.29 2.00e-01 2.50e+01 2.10e+00
  ... (remaining 3910 not shown)

  Planarity restraints: 1349
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A  33 "    0.009 2.00e-02 2.50e+03   1.24e-02 3.47e+00
        pdb=" N1    C A  33 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    C A  33 "    0.025 2.00e-02 2.50e+03
        pdb=" O2    C A  33 "   -0.022 2.00e-02 2.50e+03
        pdb=" N3    C A  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    C A  33 "    0.005 2.00e-02 2.50e+03
        pdb=" N4    C A  33 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C A  33 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6    C A  33 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 363 "   -0.007 2.00e-02 2.50e+03   1.00e-02 3.01e+00
        pdb=" N9    G A 363 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    G A 363 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G A 363 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    G A 363 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G A 363 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G A 363 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G A 363 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G A 363 "    0.027 2.00e-02 2.50e+03
        pdb=" N2    G A 363 "   -0.019 2.00e-02 2.50e+03
        pdb=" N3    G A 363 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    G A 363 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 473 "    0.006 2.00e-02 2.50e+03   9.37e-03 2.63e+00
        pdb=" N9    G A 473 "   -0.002 2.00e-02 2.50e+03
        pdb=" C8    G A 473 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    G A 473 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G A 473 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G A 473 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6    G A 473 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    G A 473 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G A 473 "   -0.025 2.00e-02 2.50e+03
        pdb=" N2    G A 473 "    0.017 2.00e-02 2.50e+03
        pdb=" N3    G A 473 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G A 473 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1346 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 160
        2.52 -     3.11: 13075
        3.11 -     3.71: 33605
        3.71 -     4.30: 45916
        4.30 -     4.90: 62873
  Nonbonded interactions: 155629
  Sorted by model distance:
  nonbonded pdb=" O2'   A A 255 "
            pdb=" O4'   A A 256 "
     model   vdw
     1.924 3.040
  nonbonded pdb=" O2    C A  69 "
            pdb=" O2'   A A  73 "
     model   vdw
     1.948 3.040
  nonbonded pdb=" O2    C A 106 "
            pdb=" O2'   A A 294 "
     model   vdw
     1.965 3.040
  nonbonded pdb=" O2'   A A 126 "
            pdb=" O4'   A A 127 "
     model   vdw
     1.975 3.040
  nonbonded pdb=" O2'   A A 299 "
            pdb=" O4'   A A 300 "
     model   vdw
     1.988 3.040
  ... (remaining 155624 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
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:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.810
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
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      :  0.003   0.033  19762  Z= 0.131
  Angle     :  0.922  26.711  29894  Z= 0.371
  Chirality :  0.122   1.765   3913
  Planarity :  0.002   0.022   1349
  Dihedral  : 21.307 179.086   9392
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.39 %
    Favored  : 96.39 %
  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 are not related in a simple way.
  whole:  1.73 (0.39), residues: 507
  helix:  2.53 (0.37), residues: 213
  sheet:  0.56 (0.67), residues: 71
  loop :  0.03 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG 2  35 
 TYR   0.005   0.001   TYR T  84 
 PHE   0.005   0.001   PHE S  75 
 TRP   0.003   0.001   TRP T  80 
 HIS   0.001   0.000   HIS S 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.13 (19762)
  covalent geometry    : angle       0.92195 /  0.37 (29894)
  hydrogen bonds       : bond        0.07736 /  4.39 (  687)
  hydrogen bonds       : angle       4.05371 /  1.61 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8920 (tm-30)
REVERT: E  149 ILE cc_start: 0.9481 (tp) cc_final: 0.8987 (tp)
REVERT: E  188 MET cc_start: 0.8631 (ttt) cc_final: 0.8222 (tpt)
REVERT: E  195 GLN cc_start: 0.9690 (mt0) cc_final: 0.9289 (mt0)
REVERT: E  199 MET cc_start: 0.8842 (mtm) cc_final: 0.8132 (ptp)
REVERT: S   68 ASP cc_start: 0.9274 (t0) cc_final: 0.8858 (t70)
REVERT: U   12 VAL cc_start: 0.8571 (t) cc_final: 0.8029 (t)
REVERT: T    1 MET cc_start: 0.6162 (pmm) cc_final: 0.5517 (pmm)
REVERT: T   80 TRP cc_start: 0.6633 (p-90) cc_final: 0.6382 (t60)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1666
  time to fit residues: 24.7138
Evaluate side-chains
  63 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
2  13 ASN
E  30 GLN
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 136 GLN
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  48 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.058103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.044372 restraints weight = 213473.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.045495 restraints weight = 87665.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.046114 restraints weight = 55518.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.046310 restraints weight = 44878.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.046310 restraints weight = 41725.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  19762  Z= 0.249
  Angle     :  1.298  25.348  29894  Z= 0.509
  Chirality :  0.094   1.876   3913
  Planarity :  0.005   0.051   1349
  Dihedral  : 20.712 174.542   8343
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.93 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.37), residues: 507
  helix:  1.49 (0.34), residues: 219
  sheet: -0.33 (0.55), residues: 94
  loop : -0.17 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG U  81 
 TYR   0.010   0.001   TYR T  84 
 PHE   0.014   0.002   PHE Y  26 
 TRP   0.002   0.001   TRP T  80 
 HIS   0.002   0.001   HIS 2  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00493 /  0.25 (19762)
  covalent geometry    : angle       1.29846 /  0.51 (29894)
  hydrogen bonds       : bond        0.08981 /  4.68 (  687)
  hydrogen bonds       : angle       3.81342 /  1.52 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   97 ASN cc_start: 0.8778 (t0) cc_final: 0.8021 (t0)
REVERT: E  100 MET cc_start: 0.9387 (mtt) cc_final: 0.9100 (mtt)
REVERT: E  163 ASN cc_start: 0.8121 (t0) cc_final: 0.7809 (t0)
REVERT: E  199 MET cc_start: 0.8900 (mtm) cc_final: 0.8333 (ptp)
REVERT: S   68 ASP cc_start: 0.9460 (t0) cc_final: 0.9199 (t70)
REVERT: U   17 ASP cc_start: 0.7651 (t0) cc_final: 0.7240 (t0)
REVERT: T   11 LEU cc_start: 0.8632 (pt) cc_final: 0.8362 (pp)
REVERT: T   51 PHE cc_start: 0.8761 (m-80) cc_final: 0.8467 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 84
  average time/residue: 0.1634
  time to fit residues: 20.1653
Evaluate side-chains
  65 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 72 optimal weight:    9.9990
   chunk 85 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 59 optimal weight:   20.0000
   chunk 45 optimal weight:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 60 optimal weight:   20.0000
   chunk 58 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 2  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  30 GLN
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  48 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.049367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035795 restraints weight = 220711.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.035994 restraints weight = 148711.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.036063 restraints weight = 95252.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.036206 restraints weight = 83775.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.036209 restraints weight = 75066.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.6976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.049  19762  Z= 0.433
  Angle     :  1.551  24.910  29894  Z= 0.611
  Chirality :  0.101   1.841   3913
  Planarity :  0.007   0.067   1349
  Dihedral  : 21.608 179.071   8343
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 40.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.87 %
    Favored  : 93.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.35), residues: 507
  helix: -0.10 (0.32), residues: 219
  sheet: -1.01 (0.55), residues: 86
  loop : -0.59 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 102 
 TYR   0.023   0.003   TYR T  84 
 PHE   0.027   0.003   PHE Y  26 
 TRP   0.010   0.004   TRP T  80 
 HIS   0.006   0.003   HIS S  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00861 /  0.43 (19762)
  covalent geometry    : angle       1.55059 /  0.61 (29894)
  hydrogen bonds       : bond        0.13796 /  7.24 (  687)
  hydrogen bonds       : angle       4.77222 /  1.91 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8391 (ttt) cc_final: 0.8188 (ttt)
REVERT: E   25 GLU cc_start: 0.9277 (tm-30) cc_final: 0.9050 (tm-30)
REVERT: E  100 MET cc_start: 0.9321 (mtt) cc_final: 0.9067 (mtt)
REVERT: E  199 MET cc_start: 0.9218 (mtm) cc_final: 0.8527 (mtp)
REVERT: S   68 ASP cc_start: 0.9472 (t0) cc_final: 0.9228 (t70)
REVERT: T   32 LEU cc_start: 0.8880 (mt) cc_final: 0.8623 (mp)
REVERT: T   89 GLU cc_start: 0.9133 (pm20) cc_final: 0.8871 (pm20)
  outliers start: 2
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1637
  time to fit residues: 17.9888
Evaluate side-chains
  51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 72 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 101 optimal weight:    0.0470
   chunk 40 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0980
   chunk 52 optimal weight:    9.9990
   overall best weight:    0.7082

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
2  13 ASN
E  24 ASN
E  30 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  41 HIS
T  15 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.054555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.040783 restraints weight = 205868.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.041809 restraints weight = 101920.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.041649 restraints weight = 62042.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.041767 restraints weight = 56160.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.041789 restraints weight = 51723.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.5963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  19762  Z= 0.156
  Angle     :  1.090  24.026  29894  Z= 0.431
  Chirality :  0.082   1.868   3913
  Planarity :  0.004   0.057   1349
  Dihedral  : 20.463 179.808   8343
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  5.19 %
    Favored  : 94.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.37), residues: 507
  helix:  0.68 (0.34), residues: 219
  sheet: -0.54 (0.56), residues: 84
  loop : -0.48 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Y  29 
 TYR   0.008   0.001   TYR S  38 
 PHE   0.011   0.002   PHE U  95 
 TRP   0.023   0.009   TRP T  80 
 HIS   0.002   0.001   HIS S   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.16 (19762)
  covalent geometry    : angle       1.08979 /  0.43 (29894)
  hydrogen bonds       : bond        0.07294 /  3.76 (  687)
  hydrogen bonds       : angle       3.72577 /  1.50 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9294 (tm-30) cc_final: 0.9026 (tm-30)
REVERT: E   97 ASN cc_start: 0.8752 (t0) cc_final: 0.8094 (t0)
REVERT: E  100 MET cc_start: 0.9380 (mtt) cc_final: 0.8991 (mtt)
REVERT: E  163 ASN cc_start: 0.7783 (t0) cc_final: 0.7392 (m-40)
REVERT: E  195 GLN cc_start: 0.9715 (mt0) cc_final: 0.9304 (mt0)
REVERT: E  199 MET cc_start: 0.9262 (mtm) cc_final: 0.8410 (ptm)
REVERT: U    7 ASP cc_start: 0.8708 (m-30) cc_final: 0.8390 (m-30)
REVERT: T   32 LEU cc_start: 0.8732 (mt) cc_final: 0.8417 (mp)
REVERT: T   51 PHE cc_start: 0.8839 (m-80) cc_final: 0.8421 (m-80)
REVERT: T   79 ASP cc_start: 0.8759 (m-30) cc_final: 0.8481 (t70)
REVERT: T   80 TRP cc_start: 0.7808 (t60) cc_final: 0.7028 (p-90)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1624
  time to fit residues: 20.7832
Evaluate side-chains
  65 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 97 optimal weight:    0.1980
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:   20.0000
   chunk 80 optimal weight:    0.0970
   chunk 69 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 108 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    4.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN
Y  20 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.050059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.035801 restraints weight = 214991.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.036765 restraints weight = 91355.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.037198 restraints weight = 60249.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.037495 restraints weight = 50914.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.037495 restraints weight = 46737.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.7154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  19762  Z= 0.312
  Angle     :  1.272  24.875  29894  Z= 0.501
  Chirality :  0.086   1.850   3913
  Planarity :  0.006   0.051   1349
  Dihedral  : 21.000 179.024   8343
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 30.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.39 %
    Favored  : 96.39 %
  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 are not related in a simple way.
  whole: -0.56 (0.35), residues: 507
  helix:  0.15 (0.33), residues: 219
  sheet: -0.25 (0.65), residues: 68
  loop : -0.83 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG U  93 
 TYR   0.021   0.003   TYR T  84 
 PHE   0.017   0.002   PHE Y  26 
 TRP   0.002   0.001   TRP T  80 
 HIS   0.005   0.002   HIS S  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00620 /  0.31 (19762)
  covalent geometry    : angle       1.27201 /  0.50 (29894)
  hydrogen bonds       : bond        0.10261 /  5.44 (  687)
  hydrogen bonds       : angle       4.32176 /  1.72 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9275 (tm-30) cc_final: 0.9057 (tm-30)
REVERT: E   97 ASN cc_start: 0.8660 (t0) cc_final: 0.7911 (t0)
REVERT: E  100 MET cc_start: 0.9451 (mtt) cc_final: 0.8913 (mtp)
REVERT: E  199 MET cc_start: 0.9205 (mtm) cc_final: 0.8715 (mtm)
REVERT: U    7 ASP cc_start: 0.9008 (m-30) cc_final: 0.8741 (m-30)
REVERT: T    1 MET cc_start: 0.7079 (pmm) cc_final: 0.6588 (pmm)
REVERT: T   51 PHE cc_start: 0.8738 (m-80) cc_final: 0.8451 (m-80)
REVERT: T   79 ASP cc_start: 0.8788 (m-30) cc_final: 0.8576 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 80
  average time/residue: 0.1514
  time to fit residues: 18.1396
Evaluate side-chains
  57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 91 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 44 optimal weight:    8.9990
   chunk 62 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    8.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 136 GLN
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  60 HIS
S  61 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.046949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.032713 restraints weight = 221100.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.033620 restraints weight = 97168.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.034044 restraints weight = 64459.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.034331 restraints weight = 54834.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.034384 restraints weight = 50165.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.9193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.053  19762  Z= 0.485
  Angle     :  1.590  25.380  29894  Z= 0.624
  Chirality :  0.102   1.843   3913
  Planarity :  0.008   0.078   1349
  Dihedral  : 22.007 179.233   8343
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 48.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  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 are not related in a simple way.
  whole: -1.89 (0.34), residues: 507
  helix: -0.71 (0.32), residues: 218
  sheet: -1.62 (0.61), residues: 74
  loop : -1.55 (0.38), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG U  93 
 TYR   0.022   0.003   TYR T  84 
 PHE   0.022   0.003   PHE Y  26 
 TRP   0.012   0.004   TRP T  80 
 HIS   0.011   0.003   HIS S   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00960 /  0.48 (19762)
  covalent geometry    : angle       1.59030 /  0.62 (29894)
  hydrogen bonds       : bond        0.14883 /  7.89 (  687)
  hydrogen bonds       : angle       5.10258 /  2.04 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   16 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9201 (tp30)
REVERT: E   25 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9096 (tm-30)
REVERT: E  100 MET cc_start: 0.9425 (mtt) cc_final: 0.9155 (mtt)
REVERT: E  102 ARG cc_start: 0.9074 (ptp-170) cc_final: 0.8688 (ptt-90)
REVERT: E  199 MET cc_start: 0.9363 (mtm) cc_final: 0.8846 (mtm)
REVERT: Y   24 GLU cc_start: 0.9393 (mp0) cc_final: 0.9164 (mp0)
REVERT: T   51 PHE cc_start: 0.8666 (m-80) cc_final: 0.8412 (m-80)
REVERT: T   79 ASP cc_start: 0.8547 (m-30) cc_final: 0.8328 (m-30)
REVERT: T   80 TRP cc_start: 0.6904 (t60) cc_final: 0.6545 (t60)
REVERT: T   87 LEU cc_start: 0.8661 (mt) cc_final: 0.8417 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1581
  time to fit residues: 16.2274
Evaluate side-chains
  53 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  15 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.047856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.033736 restraints weight = 215752.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.034676 restraints weight = 90878.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.035215 restraints weight = 59074.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.035394 restraints weight = 48655.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.035448 restraints weight = 45553.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.9068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035  19762  Z= 0.334
  Angle     :  1.320  24.448  29894  Z= 0.518
  Chirality :  0.090   1.859   3913
  Planarity :  0.006   0.060   1349
  Dihedral  : 21.639 177.094   8343
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 32.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.81 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.35), residues: 507
  helix: -0.27 (0.33), residues: 218
  sheet: -1.26 (0.59), residues: 69
  loop : -1.53 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG U  81 
 TYR   0.023   0.003   TYR T  84 
 PHE   0.019   0.003   PHE Y  26 
 TRP   0.012   0.003   TRP T  80 
 HIS   0.008   0.002   HIS S   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00664 /  0.33 (19762)
  covalent geometry    : angle       1.32036 /  0.52 (29894)
  hydrogen bonds       : bond        0.10997 /  5.84 (  687)
  hydrogen bonds       : angle       4.55386 /  1.82 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9290 (tm-30) cc_final: 0.9077 (tm-30)
REVERT: E   97 ASN cc_start: 0.8636 (t0) cc_final: 0.8408 (t0)
REVERT: E  100 MET cc_start: 0.9369 (mtt) cc_final: 0.9026 (mtt)
REVERT: E  102 ARG cc_start: 0.9067 (ptp-170) cc_final: 0.8702 (ptt-90)
REVERT: E  195 GLN cc_start: 0.9678 (mt0) cc_final: 0.9065 (mt0)
REVERT: E  199 MET cc_start: 0.9510 (mtm) cc_final: 0.8768 (mtp)
REVERT: Y    4 LYS cc_start: 0.9219 (pttm) cc_final: 0.8971 (pptt)
REVERT: T   51 PHE cc_start: 0.8748 (m-80) cc_final: 0.8495 (m-80)
REVERT: T   79 ASP cc_start: 0.8409 (m-30) cc_final: 0.8076 (m-30)
REVERT: T   87 LEU cc_start: 0.8687 (mt) cc_final: 0.8428 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1622
  time to fit residues: 17.8798
Evaluate side-chains
  52 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 114 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   overall best weight:    7.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 2  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.047347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.033841 restraints weight = 228015.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.034838 restraints weight = 88437.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.035365 restraints weight = 56224.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.035628 restraints weight = 46097.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.035696 restraints weight = 42181.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          1.0124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.061  19762  Z= 0.456
  Angle     :  1.535  25.323  29894  Z= 0.603
  Chirality :  0.100   1.840   3913
  Planarity :  0.007   0.067   1349
  Dihedral  : 22.152 177.482   8343
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 45.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.34), residues: 507
  helix: -0.68 (0.33), residues: 222
  sheet: -2.01 (0.49), residues: 84
  loop : -1.86 (0.40), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG U  81 
 TYR   0.023   0.003   TYR T  84 
 PHE   0.022   0.003   PHE Y  26 
 TRP   0.005   0.002   TRP T  80 
 HIS   0.013   0.003   HIS S   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00904 /  0.46 (19762)
  covalent geometry    : angle       1.53538 /  0.60 (29894)
  hydrogen bonds       : bond        0.14465 /  7.67 (  687)
  hydrogen bonds       : angle       5.02304 /  2.02 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9248 (tm-30) cc_final: 0.9046 (tm-30)
REVERT: E  100 MET cc_start: 0.9358 (mtt) cc_final: 0.9122 (mtt)
REVERT: E  102 ARG cc_start: 0.9095 (ptp-170) cc_final: 0.8744 (ptt-90)
REVERT: E  184 ASP cc_start: 0.9244 (t0) cc_final: 0.8946 (t0)
REVERT: E  199 MET cc_start: 0.9537 (mtm) cc_final: 0.8777 (mtp)
REVERT: U    7 ASP cc_start: 0.9228 (m-30) cc_final: 0.9022 (m-30)
REVERT: Y   24 GLU cc_start: 0.9359 (mp0) cc_final: 0.9145 (mp0)
REVERT: T   51 PHE cc_start: 0.8650 (m-80) cc_final: 0.8327 (m-80)
REVERT: T   79 ASP cc_start: 0.8318 (m-30) cc_final: 0.7945 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1550
  time to fit residues: 15.7525
Evaluate side-chains
  50 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN
T  15 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.048651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.035345 restraints weight = 216390.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.036333 restraints weight = 82845.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.036895 restraints weight = 51693.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.037144 restraints weight = 41914.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.037144 restraints weight = 38432.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.9815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  19762  Z= 0.299
  Angle     :  1.286  24.387  29894  Z= 0.507
  Chirality :  0.090   1.860   3913
  Planarity :  0.006   0.057   1349
  Dihedral  : 21.724 178.644   8343
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 31.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.68 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.34), residues: 507
  helix: -0.38 (0.33), residues: 222
  sheet: -1.77 (0.53), residues: 70
  loop : -1.84 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG U  81 
 TYR   0.011   0.002   TYR T  84 
 PHE   0.019   0.002   PHE Y  26 
 TRP   0.015   0.010   TRP T  80 
 HIS   0.007   0.002   HIS S   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00595 /  0.30 (19762)
  covalent geometry    : angle       1.28634 /  0.51 (29894)
  hydrogen bonds       : bond        0.10592 /  5.61 (  687)
  hydrogen bonds       : angle       4.59479 /  1.84 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8990 (tm-30)
REVERT: E  100 MET cc_start: 0.9353 (mtt) cc_final: 0.9070 (mtt)
REVERT: E  102 ARG cc_start: 0.9015 (ptp-170) cc_final: 0.8693 (ptt-90)
REVERT: E  199 MET cc_start: 0.9339 (mtm) cc_final: 0.8708 (ptm)
REVERT: Y    4 LYS cc_start: 0.9264 (pttm) cc_final: 0.9022 (pptt)
REVERT: T   32 LEU cc_start: 0.8346 (mt) cc_final: 0.8095 (mp)
REVERT: T   51 PHE cc_start: 0.8803 (m-80) cc_final: 0.8471 (m-80)
REVERT: T   79 ASP cc_start: 0.8599 (m-30) cc_final: 0.8249 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1627
  time to fit residues: 17.3696
Evaluate side-chains
  51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    8.9990
   chunk 64 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 81 optimal weight:    0.5980
   chunk 96 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    2.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.049324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.035485 restraints weight = 206553.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.036499 restraints weight = 84713.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.037043 restraints weight = 54116.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.037298 restraints weight = 44282.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.037342 restraints weight = 40625.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.9469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  19762  Z= 0.206
  Angle     :  1.144  24.470  29894  Z= 0.452
  Chirality :  0.084   1.869   3913
  Planarity :  0.005   0.040   1349
  Dihedral  : 21.196 179.870   8343
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 21.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.35), residues: 507
  helix: -0.07 (0.33), residues: 225
  sheet: -1.63 (0.51), residues: 79
  loop : -1.54 (0.42), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 117 
 TYR   0.013   0.002   TYR T  84 
 PHE   0.016   0.002   PHE U  95 
 TRP   0.017   0.004   TRP T  80 
 HIS   0.004   0.001   HIS S   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.21 (19762)
  covalent geometry    : angle       1.14365 /  0.45 (29894)
  hydrogen bonds       : bond        0.08425 /  4.40 (  687)
  hydrogen bonds       : angle       4.25394 /  1.71 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8955 (tm-30)
REVERT: E  100 MET cc_start: 0.9330 (mtt) cc_final: 0.9022 (mtt)
REVERT: E  102 ARG cc_start: 0.8993 (ptp-170) cc_final: 0.8747 (ptt-90)
REVERT: E  114 ARG cc_start: 0.8822 (ptp90) cc_final: 0.8452 (ptt180)
REVERT: E  117 ARG cc_start: 0.6634 (ttt180) cc_final: 0.6076 (ttt180)
REVERT: E  184 ASP cc_start: 0.9336 (t70) cc_final: 0.9113 (t0)
REVERT: E  199 MET cc_start: 0.9251 (mtm) cc_final: 0.8659 (ptm)
REVERT: T   29 THR cc_start: 0.7854 (m) cc_final: 0.7615 (m)
REVERT: T   51 PHE cc_start: 0.8780 (m-80) cc_final: 0.8437 (m-80)
REVERT: T   79 ASP cc_start: 0.8328 (m-30) cc_final: 0.7939 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1474
  time to fit residues: 17.6999
Evaluate side-chains
  51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 64 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 21 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    4.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 115 GLN
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.049002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.035781 restraints weight = 218143.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.036726 restraints weight = 83921.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.037264 restraints weight = 52287.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.037553 restraints weight = 42550.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.037553 restraints weight = 38714.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.9840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  19762  Z= 0.291
  Angle     :  1.241  24.669  29894  Z= 0.489
  Chirality :  0.087   1.863   3913
  Planarity :  0.005   0.055   1349
  Dihedral  : 21.422 176.232   8343
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 29.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.35), residues: 507
  helix: -0.07 (0.33), residues: 224
  sheet: -1.70 (0.51), residues: 79
  loop : -1.69 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG U  81 
 TYR   0.019   0.002   TYR T  84 
 PHE   0.017   0.002   PHE Y  26 
 TRP   0.019   0.005   TRP T  80 
 HIS   0.009   0.002   HIS S   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00578 /  0.29 (19762)
  covalent geometry    : angle       1.24135 /  0.49 (29894)
  hydrogen bonds       : bond        0.10178 /  5.37 (  687)
  hydrogen bonds       : angle       4.43255 /  1.79 ( 1350)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2636.51 seconds
wall clock time: 47 minutes 0.46 seconds (2820.46 seconds total)