Starting phenix.real_space_refine
on Sun Aug  9 14:52:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hal_51982/08_2026/9hal_51982.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hal_51982/08_2026/9hal_51982.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hal_51982/08_2026/9hal_51982.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hal_51982/08_2026/9hal_51982.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hal_51982/08_2026/9hal_51982.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hal_51982/08_2026/9hal_51982.map"
  }
  resolution = 4.49
  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=  -0.013 sd=   0.109
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    1329      5.49       5
     S      20      5.16       5
     C   17868      2.51       5
     N    6829      2.21       5
     O   10671      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: 36717
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "J"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1129
          Classifications: {'peptide': 142}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 135}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 961
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "Q"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 947
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 116}
    Chain: "R"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 816
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 28562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1329, 28562
          Classifications: {'RNA': 1329}
          Modifications used: {'rna2p_pur': 127, 'rna2p_pyr': 68, 'rna3p_pur': 654, 'rna3p_pyr': 480}
          Link IDs: {'rna2p': 195, 'rna3p': 1133}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 1306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1306
          Classifications: {'peptide': 175}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1438
          Classifications: {'peptide': 187}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 182}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 778
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 106}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 780
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
  Time building chain proxies: 7.31, per 1000 atoms: 0.20
  Number of scatterers: 36717
  At special positions: 0
  Unit cell: (133.866, 215.784, 175.824, 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      20     16.00
     P    1329     15.00
     O   10671      8.00
     N    6829      7.00
     C   17868      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: 2.40
  Conformation dependent library (CDL) restraints added in 781.6 milliseconds
  

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1918

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      34.2% alpha, 15.7% beta
      436 base pairs and 626 stacking pairs defined.
    Time for finding SS restraints: 6.56
  Creating SS restraints...
    Processing helix  chain 'J' and resid 24 through 38
    Processing helix  chain 'J' and resid 58 through 62
    Processing helix  chain 'J' and resid 67 through 72
    Processing helix  chain 'J' and resid 89 through 96
    Processing helix  chain 'J' and resid 96 through 109
      removed outlier: 3.671A  pdb=" N   VAL J 100 " --> pdb=" O   ARG J  96 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 112 through 121
    Processing helix  chain 'J' and resid 130 through 136
      removed outlier: 4.330A  pdb=" N   ALA J 134 " --> pdb=" O   ASN J 131 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 13 through 32
    Processing helix  chain 'N' and resid 37 through 55
      removed outlier: 3.834A  pdb=" N   GLU N  43 " --> pdb=" O   PRO N  39 " (cutoff:3.500A)
      Proline residue:  N  50  - end of helix
    Processing helix  chain 'N' and resid 59 through 71
    Processing helix  chain 'N' and resid 72 through 79
    Processing helix  chain 'N' and resid 82 through 87
    Processing helix  chain 'Q' and resid 5 through 19
      removed outlier: 4.018A  pdb=" N   GLN Q  19 " --> pdb=" O   LYS Q  15 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 25 through 30
    Processing helix  chain 'Q' and resid 30 through 72
      removed outlier: 4.616A  pdb=" N   GLN Q  36 " --> pdb=" O   ARG Q  32 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG Q  50 " --> pdb=" O   TYR Q  46 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LYS Q  53 " --> pdb=" O   ARG Q  49 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ARG Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 74 through 85
    Processing helix  chain 'Q' and resid 90 through 101
      removed outlier: 3.905A  pdb=" N   VAL Q  99 " --> pdb=" O   ALA Q  95 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   PHE Q 100 " --> pdb=" O   ASP Q  96 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 102 through 117
      removed outlier: 4.117A  pdb=" N   ALA Q 117 " --> pdb=" O   LYS Q 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 72
    Processing helix  chain 'D' and resid 98 through 102
      removed outlier: 4.097A  pdb=" N   ALA D 102 " --> pdb=" O   GLU D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 125
    Processing helix  chain 'E' and resid 15 through 21
      removed outlier: 3.705A  pdb=" N   PHE E  19 " --> pdb=" O   SER E  15 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 24 through 39
      removed outlier: 3.600A  pdb=" N   VAL E  28 " --> pdb=" O   ASN E  24 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 142
    Processing helix  chain 'E' and resid 154 through 162
    Processing helix  chain 'E' and resid 176 through 183
    Processing helix  chain 'E' and resid 190 through 199
    Processing helix  chain 'L' and resid 29 through 33
    Processing helix  chain 'L' and resid 70 through 74
    Processing helix  chain 'L' and resid 128 through 138
    Processing sheet with id=AA1, first strand: chain 'J' and resid 122 through 124
      removed outlier: 6.290A  pdb=" N   ILE J  54 " --> pdb=" O   LYS J 123 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   TYR J  16 " --> pdb=" O   ILE J  55 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LEU J  57 " --> pdb=" O   TYR J  16 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL J  18 " --> pdb=" O   LEU J  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 73 through 75
    Processing sheet with id=AA3, first strand: chain 'N' and resid 33 through 36
      removed outlier: 5.776A  pdb=" N   ALA N 108 " --> pdb=" O   PHE N 102 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   PHE N 102 " --> pdb=" O   ALA N 108 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   MET N 110 " --> pdb=" O   CYS N 100 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'R' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'R' and resid 19 through 22
      removed outlier: 6.706A  pdb=" N   PHE R  93 " --> pdb=" O   HIS R  66 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   HIS R  66 " --> pdb=" O   PHE R  93 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ASP R  95 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   THR R  99 " --> pdb=" O   LYS R  60 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   LYS R  60 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 72 through 77
    Processing sheet with id=AA7, first strand: chain 'D' and resid 108 through 111
      removed outlier: 6.344A  pdb=" N   LYS D   8 " --> pdb=" O   GLU D  28 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLU D  28 " --> pdb=" O   LYS D   8 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 80 through 83
      removed outlier: 6.671A  pdb=" N   THR D  51 " --> pdb=" O   VAL D  34 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   VAL D  34 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ASN D  32 " --> pdb=" O   ILE D  96 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE D  96 " --> pdb=" O   ASN D  32 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 4
    Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 121
      removed outlier: 6.271A  pdb=" N   ILE E 119 " --> pdb=" O   MET E 188 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   THR E 189 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG E 170 " --> pdb=" O   ILE E 148 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 77 through 78
      removed outlier: 6.491A  pdb=" N   ILE L  77 " --> pdb=" O   ILE L 111 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'U' and resid 63 through 65
      removed outlier: 6.746A  pdb=" N   LYS U  32 " --> pdb=" O   VAL U  27 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   VAL U  27 " --> pdb=" O   LYS U  32 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU U  36 " --> pdb=" O   LYS U  23 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   LYS U  23 " --> pdb=" O   GLU U  36 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   GLU U   9 " --> pdb=" O   PHE U  72 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASN U  73 " --> pdb=" O   LYS U  78 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS U  78 " --> pdb=" O   ASN U  73 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'U' and resid 40 through 44
    Processing sheet with id=AB5, first strand: chain 'U' and resid 82 through 86

    303 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1109 hydrogen bonds
      1768 hydrogen bond angles
      0 basepair planarities
      436 basepair parallelities
      626 stacking parallelities
  Total time for adding SS restraints: 15.86

  Time building geometry restraints manager: 3.39 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 5211
        1.33 -     1.45: 17716
        1.45 -     1.57: 14633
        1.57 -     1.69: 2651
        1.69 -     1.81: 39
  Bond restraints: 40250
  Sorted by residual:
  bond pdb=" N   VAL N  47 "
       pdb=" CA  VAL N  47 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.28e-02 6.10e+03 6.61e+00
  bond pdb=" N   ASN N 107 "
       pdb=" CA  ASN N 107 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.50e+00
  bond pdb=" N   ILE N  97 "
       pdb=" CA  ILE N  97 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.029 1.17e-02 7.31e+03 6.34e+00
  bond pdb=" N   ILE N  34 "
       pdb=" CA  ILE N  34 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.11e-02 8.12e+03 6.31e+00
  bond pdb=" N   ILE N  52 "
       pdb=" CA  ILE N  52 "
    ideal  model  delta    sigma   weight residual
    1.460  1.489 -0.030 1.21e-02 6.83e+03 6.09e+00
  ... (remaining 40245 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 55884
        1.23 -     2.46: 4835
        2.46 -     3.69: 235
        3.69 -     4.92: 24
        4.92 -     6.15: 2
  Bond angle restraints: 60980
  Sorted by residual:
  angle pdb=" O2    C A 635 "
        pdb=" C2    C A 635 "
        pdb=" N3    C A 635 "
      ideal   model   delta    sigma   weight residual
     121.90  117.53    4.37 7.00e-01 2.04e+00 3.91e+01
  angle pdb=" N2    G A 175 "
        pdb=" C2    G A 175 "
        pdb=" N3    G A 175 "
      ideal   model   delta    sigma   weight residual
     119.90  124.02   -4.12 7.00e-01 2.04e+00 3.46e+01
  angle pdb=" N1    C A 394 "
        pdb=" C2    C A 394 "
        pdb=" O2    C A 394 "
      ideal   model   delta    sigma   weight residual
     118.90  122.28   -3.38 6.00e-01 2.78e+00 3.17e+01
  angle pdb=" O2    C A 269 "
        pdb=" C2    C A 269 "
        pdb=" N3    C A 269 "
      ideal   model   delta    sigma   weight residual
     121.90  117.99    3.91 7.00e-01 2.04e+00 3.13e+01
  angle pdb=" N1    G A 175 "
        pdb=" C2    G A 175 "
        pdb=" N2    G A 175 "
      ideal   model   delta    sigma   weight residual
     116.20  111.37    4.83 9.00e-01 1.23e+00 2.88e+01
  ... (remaining 60975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.51: 22677
       35.51 -    71.02: 2665
       71.02 -   106.52: 350
      106.52 -   142.03: 9
      142.03 -   177.54: 3
  Dihedral angle restraints: 25704
    sinusoidal: 22723
      harmonic: 2981
  Sorted by residual:
  dihedral pdb=" O4'   U A 828 "
           pdb=" C1'   U A 828 "
           pdb=" N1    U A 828 "
           pdb=" C2    U A 828 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.54 -177.54     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C A 323 "
           pdb=" C1'   C A 323 "
           pdb=" N1    C A 323 "
           pdb=" C2    C A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   -3.99 -124.01     1      1.70e+01 3.46e-03 5.18e+01
  dihedral pdb=" C4'   G A2763 "
           pdb=" C3'   G A2763 "
           pdb=" O3'   G A2763 "
           pdb=" P     A A2764 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.11  173.89     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 25701 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 6058
       0.043 -    0.086: 480
       0.086 -    0.129: 1352
       0.129 -    0.172: 14
       0.172 -    0.216: 4
  Chirality restraints: 7908
  Sorted by residual:
  chirality pdb=" CA  ILE N 113 "
            pdb=" N   ILE N 113 "
            pdb=" C   ILE N 113 "
            pdb=" CB  ILE N 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  ILE N  97 "
            pdb=" N   ILE N  97 "
            pdb=" C   ILE N  97 "
            pdb=" CB  ILE N  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  VAL N  60 "
            pdb=" N   VAL N  60 "
            pdb=" C   VAL N  60 "
            pdb=" CB  VAL N  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.19 2.00e-01 2.50e+01 9.45e-01
  ... (remaining 7905 not shown)

  Planarity restraints: 2755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 269 "   -0.005 2.00e-02 2.50e+03   1.95e-02 8.54e+00
        pdb=" N1    C A 269 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    C A 269 "   -0.045 2.00e-02 2.50e+03
        pdb=" O2    C A 269 "    0.029 2.00e-02 2.50e+03
        pdb=" N3    C A 269 "    0.008 2.00e-02 2.50e+03
        pdb=" C4    C A 269 "   -0.015 2.00e-02 2.50e+03
        pdb=" N4    C A 269 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    C A 269 "    0.007 2.00e-02 2.50e+03
        pdb=" C6    C A 269 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 424 "   -0.003 2.00e-02 2.50e+03   1.29e-02 5.03e+00
        pdb=" N9    G A 424 "    0.001 2.00e-02 2.50e+03
        pdb=" C8    G A 424 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G A 424 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    G A 424 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 424 "    0.013 2.00e-02 2.50e+03
        pdb=" O6    G A 424 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    G A 424 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    G A 424 "    0.035 2.00e-02 2.50e+03
        pdb=" N2    G A 424 "   -0.023 2.00e-02 2.50e+03
        pdb=" N3    G A 424 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G A 424 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 175 "   -0.007 2.00e-02 2.50e+03   1.26e-02 4.74e+00
        pdb=" N9    G A 175 "    0.009 2.00e-02 2.50e+03
        pdb=" C8    G A 175 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G A 175 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G A 175 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G A 175 "   -0.033 2.00e-02 2.50e+03
        pdb=" O6    G A 175 "    0.019 2.00e-02 2.50e+03
        pdb=" N1    G A 175 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    G A 175 "   -0.013 2.00e-02 2.50e+03
        pdb=" N2    G A 175 "    0.009 2.00e-02 2.50e+03
        pdb=" N3    G A 175 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G A 175 "    0.005 2.00e-02 2.50e+03
  ... (remaining 2752 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 286
        2.49 -     3.09: 25042
        3.09 -     3.70: 71695
        3.70 -     4.30: 99931
        4.30 -     4.90: 134574
  Nonbonded interactions: 331528
  Sorted by model distance:
  nonbonded pdb=" OP2   G A 636 "
            pdb=" OG1 THR L 128 "
     model   vdw
     1.888 3.040
  nonbonded pdb=" O2'   G A 370 "
            pdb=" O4'   G A 424 "
     model   vdw
     1.930 3.040
  nonbonded pdb=" OP2   C A1007 "
            pdb=" O2'   A A1008 "
     model   vdw
     1.954 3.040
  nonbonded pdb=" O2'   A A 981 "
            pdb=" O2'   C A2036 "
     model   vdw
     1.956 3.040
  nonbonded pdb=" O2'   G A 214 "
            pdb=" O4'   G A 215 "
     model   vdw
     1.969 3.040
  ... (remaining 331523 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:             0.660
  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:          0.620
  Check model and map are aligned:         0.130
  Set scattering table:                    0.110
  Process input model:                     42.890
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.060
  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:1.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
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  40250  Z= 0.204
  Angle     :  0.637   6.152  60980  Z= 0.572
  Chirality :  0.048   0.216   7908
  Planarity :  0.003   0.031   2755
  Dihedral  : 22.665 177.539  23786
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.94 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.29 %
    Favored  : 95.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.27), residues: 1033
  helix:  2.27 (0.30), residues: 314
  sheet: -0.51 (0.42), residues: 160
  loop : -0.86 (0.27), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  64 
 TYR   0.007   0.001   TYR N 112 
 PHE   0.007   0.001   PHE R  53 
 TRP   0.004   0.001   TRP R  92 
 HIS   0.004   0.001   HIS N   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.20 (40250)
  covalent geometry    : angle       0.63678 /  0.57 (60980)
  hydrogen bonds       : bond        0.08780 /  5.82 ( 1412)
  hydrogen bonds       : angle       3.45262 /  2.34 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 259
  time to evaluate  : 0.700 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   14 ASP cc_start: 0.7736 (p0) cc_final: 0.6744 (p0)
REVERT: J   16 TYR cc_start: 0.8740 (m-10) cc_final: 0.8431 (m-10)
REVERT: J   93 ILE cc_start: 0.7463 (pt) cc_final: 0.7147 (pt)
REVERT: J  122 LEU cc_start: 0.9356 (tp) cc_final: 0.8687 (pp)
REVERT: Q   23 TYR cc_start: 0.9222 (m-80) cc_final: 0.8484 (m-80)
REVERT: R   39 LEU cc_start: 0.9022 (mm) cc_final: 0.8678 (mp)
REVERT: R   48 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7469 (mmtp)
REVERT: R   81 LYS cc_start: 0.5307 (ttmt) cc_final: 0.3777 (tptt)
REVERT: R   95 ASP cc_start: 0.8578 (m-30) cc_final: 0.7395 (m-30)
REVERT: D   96 ILE cc_start: 0.7350 (mt) cc_final: 0.7129 (tp)
REVERT: D  100 LEU cc_start: 0.8988 (tt) cc_final: 0.8768 (tp)
REVERT: D  165 MET cc_start: 0.4932 (pmm) cc_final: 0.3766 (mpp)
REVERT: D  185 ASN cc_start: 0.7141 (m-40) cc_final: 0.6889 (m110)
REVERT: D  187 LEU cc_start: 0.7584 (tp) cc_final: 0.6826 (pp)
REVERT: E   23 PHE cc_start: 0.8513 (t80) cc_final: 0.8133 (t80)
REVERT: E  101 TYR cc_start: 0.8980 (t80) cc_final: 0.8267 (t80)
REVERT: E  119 ILE cc_start: 0.9492 (mp) cc_final: 0.9251 (mp)
REVERT: E  129 PRO cc_start: 0.7798 (Cg_endo) cc_final: 0.7573 (Cg_exo)
REVERT: E  138 LEU cc_start: 0.9252 (tt) cc_final: 0.9004 (mm)
REVERT: E  188 MET cc_start: 0.9243 (ptp) cc_final: 0.8953 (ptm)
REVERT: E  200 LEU cc_start: 0.7646 (pt) cc_final: 0.7256 (pt)
REVERT: L  125 LEU cc_start: 0.5831 (mt) cc_final: 0.5467 (mp)
REVERT: L  129 LYS cc_start: 0.9240 (pptt) cc_final: 0.8910 (mttp)
REVERT: U   45 GLN cc_start: 0.3231 (OUTLIER) cc_final: 0.2790 (pm20)
  outliers start: 3
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2563
  time to fit residues: 104.5965
Evaluate side-chains
  143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 216 optimal weight:   30.0000
   chunk 98 optimal weight:   30.0000
   chunk 194 optimal weight:   40.0000
   chunk 227 optimal weight:    4.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:   50.0000
   chunk 130 optimal weight:   40.0000
   chunk 124 optimal weight:   50.0000
   chunk 103 optimal weight:   50.0000
   chunk 200 optimal weight:   50.0000
   overall best weight:   20.9998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
J  67 ASN
** J  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 GLN
N  16 HIS
N 107 ASN
** Q  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.052161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.037891 restraints weight = 513925.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.038945 restraints weight = 245974.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.039538 restraints weight = 168262.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.039735 restraints weight = 139799.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.039883 restraints weight = 129662.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.5136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.394  40250  Z= 0.561
  Angle     :  1.280  19.703  60980  Z= 0.661
  Chirality :  0.081   1.157   7908
  Planarity :  0.012   0.143   2755
  Dihedral  : 24.578 178.166  21798
  Min Nonbonded Distance : 1.732

Molprobity Statistics.
  All-atom Clashscore : 65.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.91 %
    Favored  : 88.00 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  8.94 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -2.98 (0.23), residues: 1033
  helix: -1.55 (0.25), residues: 329
  sheet: -2.04 (0.38), residues: 148
  loop : -2.24 (0.23), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.067   0.003   ARG R  68 
 TYR   0.078   0.009   TYR J  74 
 PHE   0.036   0.006   PHE U  84 
 TRP   0.042   0.008   TRP D  80 
 HIS   0.031   0.007   HIS J 130 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00935 /  0.56 (40250)
  covalent geometry    : angle       1.27971 /  0.66 (60980)
  hydrogen bonds       : bond        0.26455 / 18.54 ( 1412)
  hydrogen bonds       : angle       5.47384 /  3.84 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.552 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   15 TRP cc_start: 0.7561 (m100) cc_final: 0.6887 (m100)
REVERT: J   67 ASN cc_start: 0.8893 (m110) cc_final: 0.8471 (t0)
REVERT: J   71 ASP cc_start: 0.9101 (m-30) cc_final: 0.8823 (p0)
REVERT: J  109 LEU cc_start: 0.9723 (tp) cc_final: 0.9502 (tt)
REVERT: J  125 TYR cc_start: 0.9026 (m-80) cc_final: 0.8805 (m-80)
REVERT: N   33 ILE cc_start: 0.5232 (tt) cc_final: 0.4760 (tt)
REVERT: Q   59 LEU cc_start: 0.9657 (mm) cc_final: 0.9447 (mt)
REVERT: Q  116 LEU cc_start: 0.9066 (tt) cc_final: 0.8830 (pp)
REVERT: R   13 ARG cc_start: 0.9213 (tmt170) cc_final: 0.8410 (tmt-80)
REVERT: R   39 LEU cc_start: 0.9497 (mm) cc_final: 0.8986 (mp)
REVERT: R   48 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8318 (mmtt)
REVERT: R   81 LYS cc_start: 0.7329 (ttmt) cc_final: 0.6074 (tptp)
REVERT: R   83 TYR cc_start: 0.8002 (t80) cc_final: 0.6813 (t80)
REVERT: R   95 ASP cc_start: 0.9126 (m-30) cc_final: 0.8254 (m-30)
REVERT: E  124 PHE cc_start: 0.8543 (m-80) cc_final: 0.7984 (m-80)
REVERT: E  188 MET cc_start: 0.9590 (ptp) cc_final: 0.9277 (ptp)
REVERT: L   81 ASP cc_start: 0.8496 (t0) cc_final: 0.8038 (m-30)
REVERT: U   61 GLU cc_start: 0.8217 (pp20) cc_final: 0.7706 (pp20)
REVERT: U   65 GLN cc_start: 0.9227 (mt0) cc_final: 0.8986 (mt0)
  outliers start: 20
  outliers final: 7
  residues processed: 163
  average time/residue: 0.2431
  time to fit residues: 63.3787
Evaluate side-chains
  119 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 58 optimal weight:   40.0000
   chunk 65 optimal weight:   30.0000
   chunk 72 optimal weight:   40.0000
   chunk 64 optimal weight:   40.0000
   chunk 75 optimal weight:   40.0000
   chunk 88 optimal weight:   50.0000
   chunk 218 optimal weight:    4.9990
   chunk 122 optimal weight:   50.0000
   chunk 206 optimal weight:    5.9990
   chunk 181 optimal weight:    5.9990
   chunk 106 optimal weight:   30.0000
   overall best weight:   15.3994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J  58 ASN
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 ASN
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 GLN
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.050967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.037041 restraints weight = 522932.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.037591 restraints weight = 247646.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.038074 restraints weight = 163696.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.038337 restraints weight = 135293.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.038397 restraints weight = 123932.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.6473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.149  40250  Z= 0.356
  Angle     :  0.873  14.004  60980  Z= 0.471
  Chirality :  0.054   0.398   7908
  Planarity :  0.008   0.077   2755
  Dihedral  : 25.150 176.087  21798
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 44.82
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.20 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  9.18 %
    Favored  : 90.23 %
  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: -3.08 (0.23), residues: 1033
  helix: -1.41 (0.26), residues: 323
  sheet: -2.27 (0.40), residues: 148
  loop : -2.40 (0.22), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.041   0.002   ARG R  68 
 TYR   0.036   0.006   TYR R  83 
 PHE   0.025   0.005   PHE U  72 
 TRP   0.026   0.005   TRP R  92 
 HIS   0.020   0.004   HIS R  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00588 /  0.36 (40250)
  covalent geometry    : angle       0.87312 /  0.47 (60980)
  hydrogen bonds       : bond        0.15743 / 11.24 ( 1412)
  hydrogen bonds       : angle       4.64758 /  3.27 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 143
  time to evaluate  : 0.625 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   49 ASP cc_start: 0.8290 (p0) cc_final: 0.7968 (p0)
REVERT: J   67 ASN cc_start: 0.9319 (m110) cc_final: 0.8866 (t0)
REVERT: J   71 ASP cc_start: 0.9319 (m-30) cc_final: 0.8353 (m-30)
REVERT: J  103 ILE cc_start: 0.9501 (mm) cc_final: 0.9253 (pt)
REVERT: J  120 ARG cc_start: 0.9289 (mtm-85) cc_final: 0.8873 (mtt-85)
REVERT: Q   23 TYR cc_start: 0.9638 (m-80) cc_final: 0.8852 (m-80)
REVERT: Q  116 LEU cc_start: 0.9296 (tt) cc_final: 0.8922 (pp)
REVERT: R   13 ARG cc_start: 0.9398 (tmt170) cc_final: 0.8657 (ttp80)
REVERT: R   37 GLU cc_start: 0.7700 (pp20) cc_final: 0.7448 (pp20)
REVERT: R   39 LEU cc_start: 0.9408 (mm) cc_final: 0.8300 (mt)
REVERT: R   48 LYS cc_start: 0.9018 (mmtm) cc_final: 0.8783 (mmtp)
REVERT: R   81 LYS cc_start: 0.7594 (ttmt) cc_final: 0.6971 (tptt)
REVERT: R   95 ASP cc_start: 0.8745 (m-30) cc_final: 0.8337 (m-30)
REVERT: D   46 ARG cc_start: 0.9536 (tpp80) cc_final: 0.8805 (tpp80)
REVERT: D  173 GLN cc_start: 0.5958 (pp30) cc_final: 0.4663 (pp30)
REVERT: E   41 GLN cc_start: 0.9210 (tp40) cc_final: 0.8954 (tp40)
REVERT: E   83 VAL cc_start: 0.6663 (t) cc_final: 0.6404 (t)
REVERT: E  100 MET cc_start: 0.9514 (mmp) cc_final: 0.9305 (mmm)
REVERT: E  138 LEU cc_start: 0.9670 (tt) cc_final: 0.9400 (mt)
REVERT: E  188 MET cc_start: 0.9471 (ptp) cc_final: 0.9081 (ptp)
REVERT: L   81 ASP cc_start: 0.8526 (t0) cc_final: 0.8169 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 148
  average time/residue: 0.2528
  time to fit residues: 59.0617
Evaluate side-chains
  113 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 47 optimal weight:   30.0000
   chunk 27 optimal weight:    6.9990
   chunk 89 optimal weight:   50.0000
   chunk 143 optimal weight:   30.0000
   chunk 189 optimal weight:    7.9990
   chunk 73 optimal weight:   30.0000
   chunk 111 optimal weight:   50.0000
   chunk 202 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 115 optimal weight:   40.0000
   overall best weight:    5.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   4 ASN
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.048108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.032036 restraints weight = 412690.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.033085 restraints weight = 193765.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.033629 restraints weight = 129557.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.033907 restraints weight = 105956.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.034063 restraints weight = 95932.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.6484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087  40250  Z= 0.187
  Angle     :  0.600  13.585  60980  Z= 0.340
  Chirality :  0.041   0.376   7908
  Planarity :  0.006   0.055   2755
  Dihedral  : 24.894 179.472  21798
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 27.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.94 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  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: -2.47 (0.23), residues: 1033
  helix: -0.71 (0.27), residues: 327
  sheet: -2.07 (0.42), residues: 124
  loop : -2.14 (0.22), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E  49 
 TYR   0.023   0.003   TYR J  75 
 PHE   0.026   0.002   PHE R  53 
 TRP   0.019   0.002   TRP R  92 
 HIS   0.013   0.003   HIS J  76 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.19 (40250)
  covalent geometry    : angle       0.59993 /  0.34 (60980)
  hydrogen bonds       : bond        0.12375 /  8.75 ( 1412)
  hydrogen bonds       : angle       4.12929 /  2.86 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.670 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   49 ASP cc_start: 0.8126 (p0) cc_final: 0.7755 (p0)
REVERT: J   67 ASN cc_start: 0.9325 (m110) cc_final: 0.8698 (t0)
REVERT: Q   19 GLN cc_start: 0.9464 (mp10) cc_final: 0.9173 (mp10)
REVERT: Q   23 TYR cc_start: 0.9652 (m-80) cc_final: 0.8927 (m-80)
REVERT: Q  105 PHE cc_start: 0.9123 (t80) cc_final: 0.8874 (t80)
REVERT: Q  116 LEU cc_start: 0.9370 (tt) cc_final: 0.8995 (pp)
REVERT: R   13 ARG cc_start: 0.9394 (tmt170) cc_final: 0.8557 (ttp80)
REVERT: R   35 PHE cc_start: 0.9419 (m-80) cc_final: 0.9163 (m-80)
REVERT: R   39 LEU cc_start: 0.9586 (mm) cc_final: 0.8220 (mt)
REVERT: R   81 LYS cc_start: 0.7709 (ttmt) cc_final: 0.7054 (tptt)
REVERT: R   92 TRP cc_start: 0.9216 (m100) cc_final: 0.8915 (m100)
REVERT: R   95 ASP cc_start: 0.9101 (m-30) cc_final: 0.8289 (m-30)
REVERT: D    4 LEU cc_start: 0.9636 (tp) cc_final: 0.9432 (tt)
REVERT: E  100 MET cc_start: 0.9643 (mmp) cc_final: 0.9325 (mmm)
REVERT: E  188 MET cc_start: 0.9575 (ptp) cc_final: 0.9307 (ptp)
REVERT: E  195 GLN cc_start: 0.9463 (mt0) cc_final: 0.9226 (mm110)
REVERT: E  199 MET cc_start: 0.8643 (tpt) cc_final: 0.8395 (tpt)
REVERT: L   81 ASP cc_start: 0.8554 (t0) cc_final: 0.8082 (m-30)
REVERT: U   65 GLN cc_start: 0.9459 (mt0) cc_final: 0.8957 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.2283
  time to fit residues: 53.6527
Evaluate side-chains
  118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 216 optimal weight:   50.0000
   chunk 212 optimal weight:   10.0000
   chunk 127 optimal weight:   50.0000
   chunk 148 optimal weight:   50.0000
   chunk 211 optimal weight:    7.9990
   chunk 231 optimal weight:   20.0000
   chunk 130 optimal weight:   40.0000
   chunk 165 optimal weight:   50.0000
   chunk 7 optimal weight:    5.9990
   chunk 154 optimal weight:   40.0000
   chunk 30 optimal weight:    7.9990
   overall best weight:   10.3994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 GLN
Q  43 GLN
** R  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   9 GLN
E 195 GLN
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.045350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.029958 restraints weight = 424111.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.030907 restraints weight = 199847.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.031389 restraints weight = 134525.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.031633 restraints weight = 110537.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.031753 restraints weight = 100670.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.7637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  40250  Z= 0.295
  Angle     :  0.740  15.205  60980  Z= 0.411
  Chirality :  0.049   0.370   7908
  Planarity :  0.008   0.169   2755
  Dihedral  : 25.168 178.765  21798
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 47.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.42 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  8.10 %
    Favored  : 91.66 %
  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: -2.81 (0.23), residues: 1033
  helix: -1.12 (0.26), residues: 326
  sheet: -2.33 (0.41), residues: 133
  loop : -2.24 (0.22), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.002   ARG R  21 
 TYR   0.023   0.004   TYR J  74 
 PHE   0.036   0.004   PHE R  93 
 TRP   0.010   0.003   TRP R  92 
 HIS   0.015   0.004   HIS J 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00460 /  0.29 (40250)
  covalent geometry    : angle       0.73985 /  0.41 (60980)
  hydrogen bonds       : bond        0.15180 / 10.68 ( 1412)
  hydrogen bonds       : angle       4.48345 /  3.11 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.398 
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: J    1 MET cc_start: 0.8768 (tmm) cc_final: 0.8179 (tmm)
REVERT: J   49 ASP cc_start: 0.8223 (p0) cc_final: 0.7800 (p0)
REVERT: Q   19 GLN cc_start: 0.9424 (mp10) cc_final: 0.9216 (mp10)
REVERT: Q   23 TYR cc_start: 0.9637 (m-80) cc_final: 0.8816 (m-80)
REVERT: Q  105 PHE cc_start: 0.9302 (t80) cc_final: 0.8895 (t80)
REVERT: Q  116 LEU cc_start: 0.9392 (tt) cc_final: 0.9037 (pp)
REVERT: R   13 ARG cc_start: 0.9409 (tmt170) cc_final: 0.8671 (ttp80)
REVERT: R   35 PHE cc_start: 0.9434 (m-80) cc_final: 0.9190 (m-80)
REVERT: R   37 GLU cc_start: 0.8209 (pp20) cc_final: 0.7727 (pp20)
REVERT: R   39 LEU cc_start: 0.9557 (mm) cc_final: 0.8083 (mt)
REVERT: R   81 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6271 (tptt)
REVERT: R   95 ASP cc_start: 0.9140 (m-30) cc_final: 0.8874 (m-30)
REVERT: D   46 ARG cc_start: 0.9349 (tpp80) cc_final: 0.8799 (tpp-160)
REVERT: D  173 GLN cc_start: 0.5939 (pp30) cc_final: 0.4874 (pp30)
REVERT: E   53 THR cc_start: 0.6739 (m) cc_final: 0.6331 (t)
REVERT: E  100 MET cc_start: 0.9146 (mmp) cc_final: 0.8745 (mmm)
REVERT: E  188 MET cc_start: 0.9335 (ptp) cc_final: 0.9061 (ptp)
REVERT: E  195 GLN cc_start: 0.9513 (mt0) cc_final: 0.9173 (mt0)
REVERT: L   14 LYS cc_start: 0.8448 (tmmt) cc_final: 0.8179 (tmtt)
REVERT: L   79 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7935 (mm)
REVERT: L   81 ASP cc_start: 0.8773 (t0) cc_final: 0.8372 (m-30)
REVERT: L  104 GLN cc_start: 0.4850 (pp30) cc_final: 0.4524 (pp30)
REVERT: U   90 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8143 (mttt)
  outliers start: 2
  outliers final: 1
  residues processed: 142
  average time/residue: 0.2356
  time to fit residues: 53.7152
Evaluate side-chains
  112 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 217 optimal weight:    0.0980
   chunk 48 optimal weight:   40.0000
   chunk 153 optimal weight:   50.0000
   chunk 86 optimal weight:   50.0000
   chunk 136 optimal weight:   40.0000
   chunk 193 optimal weight:    7.9990
   chunk 119 optimal weight:   40.0000
   chunk 188 optimal weight:    0.8980
   chunk 127 optimal weight:   50.0000
   chunk 155 optimal weight:   40.0000
   chunk 106 optimal weight:   30.0000
   overall best weight:   15.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 195 GLN
** U  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.042769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.027725 restraints weight = 448554.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.028547 restraints weight = 214168.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.028974 restraints weight = 148501.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.029112 restraints weight = 124456.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.029112 restraints weight = 116136.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.9578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.125  40250  Z= 0.406
  Angle     :  0.968  15.484  60980  Z= 0.530
  Chirality :  0.063   0.558   7908
  Planarity :  0.010   0.188   2755
  Dihedral  : 25.953 177.413  21798
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 64.14
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 13.07 %
    Favored  : 86.74 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  6.67 %
    Favored  : 93.21 %
  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: -3.92 (0.21), residues: 1033
  helix: -2.19 (0.24), residues: 318
  sheet: -3.03 (0.44), residues: 113
  loop : -2.84 (0.20), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.002   ARG Q   2 
 TYR   0.029   0.005   TYR J  74 
 PHE   0.041   0.006   PHE E  23 
 TRP   0.078   0.008   TRP E  78 
 HIS   0.021   0.005   HIS J  76 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00642 /  0.41 (40250)
  covalent geometry    : angle       0.96788 /  0.53 (60980)
  hydrogen bonds       : bond        0.20485 / 14.38 ( 1412)
  hydrogen bonds       : angle       5.13752 /  3.57 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.652 
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: J    1 MET cc_start: 0.8419 (tmm) cc_final: 0.7971 (tmm)
REVERT: J   49 ASP cc_start: 0.8490 (p0) cc_final: 0.7991 (p0)
REVERT: J   67 ASN cc_start: 0.9038 (t0) cc_final: 0.8585 (t0)
REVERT: J   71 ASP cc_start: 0.8895 (p0) cc_final: 0.8559 (p0)
REVERT: J   92 MET cc_start: 0.9312 (tpt) cc_final: 0.8811 (tpp)
REVERT: J  103 ILE cc_start: 0.9630 (mm) cc_final: 0.9333 (mt)
REVERT: N   42 LYS cc_start: 0.9251 (pttm) cc_final: 0.8766 (tptt)
REVERT: Q   19 GLN cc_start: 0.9543 (mp10) cc_final: 0.9275 (mp10)
REVERT: Q   23 TYR cc_start: 0.9591 (m-80) cc_final: 0.8608 (m-80)
REVERT: R   13 ARG cc_start: 0.9371 (tmt170) cc_final: 0.8787 (ttp80)
REVERT: R   35 PHE cc_start: 0.9435 (m-80) cc_final: 0.9211 (m-80)
REVERT: R   39 LEU cc_start: 0.9337 (mm) cc_final: 0.8617 (mt)
REVERT: R   41 ILE cc_start: 0.9316 (mp) cc_final: 0.9055 (mp)
REVERT: R   48 LYS cc_start: 0.9447 (mmtt) cc_final: 0.9193 (mmtt)
REVERT: R   81 LYS cc_start: 0.7283 (ttmt) cc_final: 0.6805 (tptt)
REVERT: D   43 ASP cc_start: 0.9185 (t70) cc_final: 0.8030 (p0)
REVERT: D  173 GLN cc_start: 0.6276 (pp30) cc_final: 0.5595 (pp30)
REVERT: E  100 MET cc_start: 0.9033 (mmp) cc_final: 0.8815 (mmm)
REVERT: E  188 MET cc_start: 0.9441 (ptp) cc_final: 0.9237 (ptp)
REVERT: E  199 MET cc_start: 0.8637 (tpt) cc_final: 0.8400 (tpt)
REVERT: L  104 GLN cc_start: 0.5370 (pp30) cc_final: 0.5110 (pp30)
  outliers start: 1
  outliers final: 1
  residues processed: 139
  average time/residue: 0.2601
  time to fit residues: 57.4909
Evaluate side-chains
  106 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 107 optimal weight:   40.0000
   chunk 133 optimal weight:   50.0000
   chunk 121 optimal weight:   50.0000
   chunk 177 optimal weight:   50.0000
   chunk 126 optimal weight:   40.0000
   chunk 212 optimal weight:    0.8980
   chunk 79 optimal weight:   30.0000
   chunk 116 optimal weight:   50.0000
   chunk 64 optimal weight:   50.0000
   chunk 185 optimal weight:    3.9990
   chunk 192 optimal weight:   20.0000
   overall best weight:   18.9794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.041452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.026744 restraints weight = 458077.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.027493 restraints weight = 223399.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.027868 restraints weight = 157240.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.028060 restraints weight = 132232.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.028149 restraints weight = 121796.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          1.0512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.158  40250  Z= 0.451
  Angle     :  1.014  13.251  60980  Z= 0.553
  Chirality :  0.066   0.484   7908
  Planarity :  0.009   0.093   2755
  Dihedral  : 26.255 173.789  21798
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 74.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 14.52 %
    Favored  : 85.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.94 (0.22), residues: 1033
  helix: -2.06 (0.25), residues: 319
  sheet: -3.30 (0.40), residues: 113
  loop : -2.90 (0.21), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.042   0.003   ARG D  13 
 TYR   0.030   0.005   TYR E 101 
 PHE   0.039   0.006   PHE D  15 
 TRP   0.029   0.006   TRP E  78 
 HIS   0.020   0.005   HIS R  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00716 /  0.45 (40250)
  covalent geometry    : angle       1.01429 /  0.55 (60980)
  hydrogen bonds       : bond        0.20978 / 14.74 ( 1412)
  hydrogen bonds       : angle       5.41490 /  3.76 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.576 
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: J   67 ASN cc_start: 0.9248 (t0) cc_final: 0.8863 (t0)
REVERT: J   71 ASP cc_start: 0.8849 (p0) cc_final: 0.8447 (p0)
REVERT: J   92 MET cc_start: 0.9467 (tpt) cc_final: 0.9109 (tpp)
REVERT: R   13 ARG cc_start: 0.9300 (tmt170) cc_final: 0.8554 (ttp80)
REVERT: R   39 LEU cc_start: 0.9378 (mm) cc_final: 0.8661 (mt)
REVERT: R   41 ILE cc_start: 0.9305 (mp) cc_final: 0.9062 (mp)
REVERT: R   53 PHE cc_start: 0.9480 (p90) cc_final: 0.8840 (p90)
REVERT: R   73 LYS cc_start: 0.9557 (mppt) cc_final: 0.9320 (mmtm)
REVERT: R   81 LYS cc_start: 0.7154 (ttmt) cc_final: 0.6675 (tptt)
REVERT: D   43 ASP cc_start: 0.9176 (t70) cc_final: 0.7687 (p0)
REVERT: D   79 LEU cc_start: 0.9123 (mp) cc_final: 0.8850 (mp)
REVERT: E  100 MET cc_start: 0.8844 (mmp) cc_final: 0.8584 (mmm)
REVERT: L  104 GLN cc_start: 0.7025 (pp30) cc_final: 0.6664 (pp30)
REVERT: L  141 LYS cc_start: 0.9125 (mppt) cc_final: 0.8924 (mppt)
REVERT: U   88 ASP cc_start: 0.9182 (m-30) cc_final: 0.8844 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2569
  time to fit residues: 53.3330
Evaluate side-chains
  99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 62 optimal weight:   50.0000
   chunk 207 optimal weight:    5.9990
   chunk 176 optimal weight:   50.0000
   chunk 224 optimal weight:    3.9990
   chunk 189 optimal weight:    6.9990
   chunk 143 optimal weight:   30.0000
   chunk 77 optimal weight:   40.0000
   chunk 231 optimal weight:    7.9990
   chunk 126 optimal weight:   40.0000
   chunk 61 optimal weight:   50.0000
   chunk 164 optimal weight:   50.0000
   overall best weight:   10.9992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  43 GLN
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  29 HIS
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U  45 GLN
** U  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.042425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.027469 restraints weight = 439534.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.028311 restraints weight = 205140.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.028729 restraints weight = 139285.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.028934 restraints weight = 115959.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.029025 restraints weight = 106393.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          1.0490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  40250  Z= 0.276
  Angle     :  0.764  12.839  60980  Z= 0.430
  Chirality :  0.051   0.409   7908
  Planarity :  0.007   0.065   2755
  Dihedral  : 26.054 175.006  21798
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 46.54
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.10 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.74 %
    Favored  : 97.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.66 (0.22), residues: 1033
  helix: -1.82 (0.25), residues: 318
  sheet: -2.92 (0.40), residues: 138
  loop : -2.72 (0.22), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG D  83 
 TYR   0.016   0.003   TYR E 101 
 PHE   0.021   0.003   PHE N  80 
 TRP   0.016   0.003   TRP D  80 
 HIS   0.017   0.003   HIS J 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.28 (40250)
  covalent geometry    : angle       0.76403 /  0.43 (60980)
  hydrogen bonds       : bond        0.15656 / 11.04 ( 1412)
  hydrogen bonds       : angle       4.81342 /  3.32 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.852 
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: J   49 ASP cc_start: 0.8483 (p0) cc_final: 0.8031 (p0)
REVERT: J   67 ASN cc_start: 0.9180 (t0) cc_final: 0.8739 (t0)
REVERT: J   71 ASP cc_start: 0.8848 (p0) cc_final: 0.8408 (p0)
REVERT: J   74 TYR cc_start: 0.8502 (m-10) cc_final: 0.8256 (m-80)
REVERT: J   92 MET cc_start: 0.9340 (tpt) cc_final: 0.8867 (tpp)
REVERT: J  103 ILE cc_start: 0.9729 (mm) cc_final: 0.9480 (pt)
REVERT: N   42 LYS cc_start: 0.9162 (pttm) cc_final: 0.8552 (tptt)
REVERT: Q   23 TYR cc_start: 0.9616 (m-80) cc_final: 0.8535 (m-80)
REVERT: R   13 ARG cc_start: 0.9228 (tmt170) cc_final: 0.8692 (ttp80)
REVERT: R   35 PHE cc_start: 0.9464 (m-80) cc_final: 0.9207 (m-80)
REVERT: R   37 GLU cc_start: 0.8093 (pp20) cc_final: 0.7264 (pp20)
REVERT: R   39 LEU cc_start: 0.9438 (mm) cc_final: 0.8269 (mt)
REVERT: R   40 MET cc_start: 0.9102 (ppp) cc_final: 0.8808 (ppp)
REVERT: R   53 PHE cc_start: 0.9338 (p90) cc_final: 0.8726 (p90)
REVERT: R   71 LYS cc_start: 0.9408 (tptt) cc_final: 0.9110 (tptt)
REVERT: R   81 LYS cc_start: 0.7164 (ttmt) cc_final: 0.6337 (tptt)
REVERT: D  173 GLN cc_start: 0.6951 (pp30) cc_final: 0.6192 (pp30)
REVERT: D  184 ARG cc_start: 0.8971 (ptt180) cc_final: 0.8560 (ptt90)
REVERT: E  100 MET cc_start: 0.9168 (mmp) cc_final: 0.8854 (mmm)
REVERT: E  181 ILE cc_start: 0.9612 (tp) cc_final: 0.9379 (tp)
REVERT: E  199 MET cc_start: 0.8769 (tpt) cc_final: 0.8491 (tpp)
REVERT: L   17 LYS cc_start: 0.9321 (mppt) cc_final: 0.8973 (mptt)
REVERT: L  104 GLN cc_start: 0.6916 (pp30) cc_final: 0.6567 (pp30)
REVERT: U   45 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7813 (pp30)
REVERT: U   88 ASP cc_start: 0.9176 (m-30) cc_final: 0.8900 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2654
  time to fit residues: 58.7080
Evaluate side-chains
  110 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 165 optimal weight:   50.0000
   chunk 227 optimal weight:    5.9990
   chunk 87 optimal weight:   50.0000
   chunk 110 optimal weight:   50.0000
   chunk 160 optimal weight:   50.0000
   chunk 0 optimal weight:   10.0000
   chunk 176 optimal weight:   50.0000
   chunk 229 optimal weight:   40.0000
   chunk 14 optimal weight:   50.0000
   chunk 145 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   overall best weight:   21.1998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.040369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.026090 restraints weight = 470831.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.026845 restraints weight = 230257.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.027179 restraints weight = 160708.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.027352 restraints weight = 135485.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.027447 restraints weight = 125406.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          1.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.101  40250  Z= 0.520
  Angle     :  1.091  21.766  60980  Z= 0.591
  Chirality :  0.071   0.424   7908
  Planarity :  0.010   0.084   2755
  Dihedral  : 26.518 174.305  21798
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 83.81
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 17.62 %
    Favored  : 82.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -4.30 (0.21), residues: 1033
  helix: -2.35 (0.23), residues: 320
  sheet: -3.29 (0.37), residues: 139
  loop : -3.12 (0.21), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.031   0.002   ARG L   2 
 TYR   0.030   0.005   TYR E 101 
 PHE   0.025   0.004   PHE D 101 
 TRP   0.023   0.005   TRP Q  60 
 HIS   0.020   0.006   HIS J 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00791 /  0.52 (40250)
  covalent geometry    : angle       1.09079 /  0.59 (60980)
  hydrogen bonds       : bond        0.23221 / 16.23 ( 1412)
  hydrogen bonds       : angle       5.58954 /  3.88 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.569 
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: J    1 MET cc_start: 0.8970 (tmm) cc_final: 0.8266 (tmm)
REVERT: J   67 ASN cc_start: 0.9165 (t0) cc_final: 0.8771 (t0)
REVERT: J   71 ASP cc_start: 0.8936 (p0) cc_final: 0.8470 (p0)
REVERT: J   74 TYR cc_start: 0.8684 (m-10) cc_final: 0.8403 (m-80)
REVERT: J   92 MET cc_start: 0.9455 (tpt) cc_final: 0.9050 (tpp)
REVERT: Q   10 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8548 (tpt-90)
REVERT: R   13 ARG cc_start: 0.9282 (tmt170) cc_final: 0.8699 (ttp80)
REVERT: R   39 LEU cc_start: 0.9378 (mm) cc_final: 0.8865 (mt)
REVERT: R   41 ILE cc_start: 0.9247 (mp) cc_final: 0.9021 (mp)
REVERT: R   53 PHE cc_start: 0.9544 (p90) cc_final: 0.8884 (p90)
REVERT: R   81 LYS cc_start: 0.7292 (ttmt) cc_final: 0.6624 (tptt)
REVERT: D   79 LEU cc_start: 0.9207 (mp) cc_final: 0.8848 (mp)
REVERT: D  184 ARG cc_start: 0.8846 (ptt180) cc_final: 0.8373 (ptt90)
REVERT: E  100 MET cc_start: 0.8877 (mmp) cc_final: 0.8659 (mmm)
REVERT: E  188 MET cc_start: 0.9514 (ptp) cc_final: 0.9248 (ptm)
REVERT: L   14 LYS cc_start: 0.9281 (tmmt) cc_final: 0.8832 (pptt)
REVERT: L   17 LYS cc_start: 0.9285 (mppt) cc_final: 0.8988 (mptt)
REVERT: L  104 GLN cc_start: 0.6998 (pp30) cc_final: 0.6613 (pp30)
REVERT: U   88 ASP cc_start: 0.9066 (m-30) cc_final: 0.8782 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2684
  time to fit residues: 54.2582
Evaluate side-chains
  96 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 129 optimal weight:   30.0000
   chunk 178 optimal weight:   50.0000
   chunk 10 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 173 optimal weight:   50.0000
   chunk 20 optimal weight:    8.9990
   chunk 85 optimal weight:   50.0000
   chunk 59 optimal weight:   40.0000
   chunk 153 optimal weight:   50.0000
   chunk 157 optimal weight:   50.0000
   chunk 44 optimal weight:    7.9990
   overall best weight:   11.5992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.041411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026811 restraints weight = 450414.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.027634 restraints weight = 206844.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.028037 restraints weight = 139878.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.028228 restraints weight = 116498.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.028313 restraints weight = 106864.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          1.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  40250  Z= 0.298
  Angle     :  0.809  12.534  60980  Z= 0.454
  Chirality :  0.053   0.404   7908
  Planarity :  0.008   0.110   2755
  Dihedral  : 26.275 173.983  21798
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 52.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 13.75 %
    Favored  : 86.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.96 (0.22), residues: 1033
  helix: -2.02 (0.24), residues: 317
  sheet: -3.20 (0.39), residues: 128
  loop : -2.93 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG Q   2 
 TYR   0.019   0.003   TYR N 112 
 PHE   0.026   0.003   PHE E 183 
 TRP   0.015   0.003   TRP E  78 
 HIS   0.019   0.003   HIS U  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00465 /  0.30 (40250)
  covalent geometry    : angle       0.80919 /  0.45 (60980)
  hydrogen bonds       : bond        0.16409 / 11.53 ( 1412)
  hydrogen bonds       : angle       4.99891 /  3.43 ( 2626)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.646 
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: J    1 MET cc_start: 0.8886 (tmm) cc_final: 0.8192 (tmm)
REVERT: J   67 ASN cc_start: 0.9242 (t0) cc_final: 0.8815 (t0)
REVERT: J   71 ASP cc_start: 0.8867 (p0) cc_final: 0.8428 (p0)
REVERT: J   74 TYR cc_start: 0.8420 (m-10) cc_final: 0.8169 (m-80)
REVERT: J   92 MET cc_start: 0.9378 (tpt) cc_final: 0.8962 (tpp)
REVERT: N   42 LYS cc_start: 0.9276 (pttm) cc_final: 0.8710 (tptt)
REVERT: Q   10 ARG cc_start: 0.9152 (tpp80) cc_final: 0.8609 (ttt180)
REVERT: R   13 ARG cc_start: 0.9143 (tmt170) cc_final: 0.8457 (ttp80)
REVERT: R   39 LEU cc_start: 0.9557 (mm) cc_final: 0.8949 (mt)
REVERT: R   40 MET cc_start: 0.9121 (ppp) cc_final: 0.8815 (ppp)
REVERT: R   53 PHE cc_start: 0.9454 (p90) cc_final: 0.8827 (p90)
REVERT: R   79 ARG cc_start: 0.6978 (tpt170) cc_final: 0.6771 (tpt170)
REVERT: R   80 ARG cc_start: 0.7352 (mmm-85) cc_final: 0.6357 (mmm160)
REVERT: R   81 LYS cc_start: 0.7155 (ttmt) cc_final: 0.6503 (tptt)
REVERT: D   43 ASP cc_start: 0.9088 (t0) cc_final: 0.8627 (p0)
REVERT: D   79 LEU cc_start: 0.9240 (mp) cc_final: 0.8887 (mp)
REVERT: D  173 GLN cc_start: 0.7015 (pp30) cc_final: 0.6226 (pp30)
REVERT: D  184 ARG cc_start: 0.8790 (ptt180) cc_final: 0.8051 (ptt90)
REVERT: E  100 MET cc_start: 0.9141 (mmp) cc_final: 0.8857 (mmm)
REVERT: E  188 MET cc_start: 0.9542 (ptp) cc_final: 0.9333 (pmm)
REVERT: L   17 LYS cc_start: 0.9259 (mppt) cc_final: 0.8933 (mptt)
REVERT: L  104 GLN cc_start: 0.7001 (pp30) cc_final: 0.6653 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2724
  time to fit residues: 57.8821
Evaluate side-chains
  102 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 66 optimal weight:   50.0000
   chunk 174 optimal weight:   50.0000
   chunk 69 optimal weight:   50.0000
   chunk 45 optimal weight:   10.0000
   chunk 137 optimal weight:   40.0000
   chunk 211 optimal weight:    4.9990
   chunk 166 optimal weight:   50.0000
   chunk 104 optimal weight:   50.0000
   chunk 77 optimal weight:   40.0000
   chunk 92 optimal weight:   40.0000
   chunk 112 optimal weight:   50.0000
   overall best weight:   26.9998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.039135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.025316 restraints weight = 477806.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.026002 restraints weight = 235322.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.026341 restraints weight = 164783.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.026504 restraints weight = 139284.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.026582 restraints weight = 128764.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          1.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.115  40250  Z= 0.646
  Angle     :  1.298  19.459  60980  Z= 0.696
  Chirality :  0.083   0.535   7908
  Planarity :  0.012   0.160   2755
  Dihedral  : 26.998 172.341  21798
  Min Nonbonded Distance : 1.762

Molprobity Statistics.
  All-atom Clashscore : 103.65
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 20.72 %
    Favored  : 78.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -4.69 (0.21), residues: 1033
  helix: -2.62 (0.23), residues: 305
  sheet: -3.64 (0.33), residues: 160
  loop : -3.32 (0.21), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.051   0.003   ARG D 184 
 TYR   0.038   0.006   TYR Q  23 
 PHE   0.035   0.005   PHE D 101 
 TRP   0.031   0.007   TRP Q  60 
 HIS   0.023   0.006   HIS J  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00984 /  0.65 (40250)
  covalent geometry    : angle       1.29842 /  0.70 (60980)
  hydrogen bonds       : bond        0.27205 / 18.88 ( 1412)
  hydrogen bonds       : angle       6.13553 /  4.26 ( 2626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5781.09 seconds
wall clock time: 102 minutes 35.02 seconds (6155.02 seconds total)