Starting phenix.real_space_refine
on Mon Jul  6 13:36:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hal_51982/07_2026/9hal_51982.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hal_51982/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hal_51982/07_2026/9hal_51982.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hal_51982/07_2026/9hal_51982.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hal_51982/07_2026/9hal_51982.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hal_51982/07_2026/9hal_51982.cif"
  }
  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-dev-6108/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: 7.32, 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: 3.01
  Conformation dependent library (CDL) restraints added in 504.1 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: 5.89
  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: 13.90

  Time building geometry restraints manager: 4.20 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: 59872
        1.23 -     2.46: 981
        2.46 -     3.69: 102
        3.69 -     4.92: 23
        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: 7436
       0.043 -    0.086: 311
       0.086 -    0.129: 143
       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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:             0.020
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.110
  Set scattering table:                    0.080
  Process input model:                     41.350
  Find NCS groups from input model:        0.260
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.270
-------------------------------------------------------------------------------
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      :  0.002   0.033  40250  Z= 0.182
  Angle     :  0.403   6.152  60980  Z= 0.374
  Chirality :  0.027   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        0.00230 /  0.18 (40250)
  covalent geometry    : angle       0.40267 /  0.37 (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  : 0.666 
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: J   14 ASP cc_start: 0.7736 (p0) cc_final: 0.6730 (p0)
REVERT: J   16 TYR cc_start: 0.8740 (m-10) cc_final: 0.8427 (m-10)
REVERT: J   93 ILE cc_start: 0.7463 (pt) cc_final: 0.7150 (pt)
REVERT: J  122 LEU cc_start: 0.9356 (tp) cc_final: 0.8702 (pp)
REVERT: J  132 HIS cc_start: 0.8317 (m170) cc_final: 0.7903 (m-70)
REVERT: Q   23 TYR cc_start: 0.9222 (m-80) cc_final: 0.8499 (m-80)
REVERT: Q   59 LEU cc_start: 0.9445 (mt) cc_final: 0.9208 (mm)
REVERT: R   39 LEU cc_start: 0.9022 (mm) cc_final: 0.8679 (mp)
REVERT: R   48 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7470 (mmtp)
REVERT: R   81 LYS cc_start: 0.5307 (ttmt) cc_final: 0.3775 (tptt)
REVERT: R   95 ASP cc_start: 0.8578 (m-30) cc_final: 0.7396 (m-30)
REVERT: D   96 ILE cc_start: 0.7350 (mt) cc_final: 0.7127 (tp)
REVERT: D  100 LEU cc_start: 0.8988 (tt) cc_final: 0.8767 (tp)
REVERT: D  165 MET cc_start: 0.4932 (pmm) cc_final: 0.3767 (mpp)
REVERT: D  185 ASN cc_start: 0.7141 (m-40) cc_final: 0.6888 (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: 0.8128 (t80)
REVERT: E  101 TYR cc_start: 0.8980 (t80) cc_final: 0.8411 (t80)
REVERT: E  119 ILE cc_start: 0.9492 (mp) cc_final: 0.9250 (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: 0.9003 (mm)
REVERT: E  188 MET cc_start: 0.9243 (ptp) cc_final: 0.8953 (ptm)
REVERT: L  125 LEU cc_start: 0.5831 (mt) cc_final: 0.5464 (mp)
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: 0.2681
  time to fit residues: 108.9670
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  : 0.641 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 194 optimal weight:    7.9990
   chunk 227 optimal weight:    4.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:   30.0000
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:   40.0000
   chunk 103 optimal weight:   40.0000
   chunk 200 optimal weight:   50.0000
   overall best weight:   14.5996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  67 ASN
** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 GLN
N  16 HIS
N 107 ASN
** Q  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 ASN
D  49 GLN
D  94 GLN
** L   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  26 ASN
** 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.055290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.040887 restraints weight = 507180.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.041980 restraints weight = 238176.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.042559 restraints weight = 161145.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.042777 restraints weight = 132654.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.042940 restraints weight = 122469.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.210  40250  Z= 0.459
  Angle     :  1.013  24.431  60980  Z= 0.559
  Chirality :  0.053   0.437   7908
  Planarity :  0.011   0.220   2755
  Dihedral  : 24.379 176.481  21798
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 46.37
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.07 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.58 %
    Favored  : 89.75 %
  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: -2.22 (0.23), residues: 1033
  helix: -0.68 (0.26), residues: 330
  sheet: -1.83 (0.36), residues: 158
  loop : -1.85 (0.24), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.036   0.003   ARG R  68 
 TYR   0.042   0.008   TYR J  75 
 PHE   0.031   0.005   PHE N  67 
 TRP   0.026   0.007   TRP D  80 
 HIS   0.027   0.005   HIS J  76 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00780 /  0.46 (40250)
  covalent geometry    : angle       1.01272 /  0.56 (60980)
  hydrogen bonds       : bond        0.21482 / 15.07 ( 1412)
  hydrogen bonds       : angle       4.83308 /  3.39 ( 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
  174 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.638 
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: 0.8348 (p0) cc_final: 0.8132 (p0)
REVERT: J   53 TYR cc_start: 0.8792 (m-10) cc_final: 0.8232 (m-10)
REVERT: J   67 ASN cc_start: 0.8530 (m110) cc_final: 0.8283 (t0)
REVERT: J   71 ASP cc_start: 0.8994 (m-30) cc_final: 0.8540 (p0)
REVERT: J  120 ARG cc_start: 0.9055 (ptp90) cc_final: 0.8688 (ptp90)
REVERT: J  125 TYR cc_start: 0.9070 (m-80) cc_final: 0.8755 (m-80)
REVERT: N   33 ILE cc_start: 0.5172 (tt) cc_final: 0.4736 (tt)
REVERT: Q   58 GLN cc_start: 0.9531 (tp-100) cc_final: 0.9003 (tp-100)
REVERT: Q  116 LEU cc_start: 0.9015 (tt) cc_final: 0.8747 (pp)
REVERT: R   13 ARG cc_start: 0.9161 (tmt170) cc_final: 0.8490 (tmt-80)
REVERT: R   39 LEU cc_start: 0.9517 (mm) cc_final: 0.8977 (mp)
REVERT: R   81 LYS cc_start: 0.7325 (ttmt) cc_final: 0.5956 (tptt)
REVERT: R   95 ASP cc_start: 0.9250 (m-30) cc_final: 0.8643 (m-30)
REVERT: D   49 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6889 (tp-100)
REVERT: D  187 LEU cc_start: 0.8334 (tp) cc_final: 0.7552 (pp)
REVERT: E   12 LEU cc_start: 0.9661 (tp) cc_final: 0.9435 (tp)
REVERT: E   90 GLN cc_start: 0.9080 (pt0) cc_final: 0.8231 (pp30)
REVERT: E  124 PHE cc_start: 0.8436 (m-80) cc_final: 0.7808 (m-80)
REVERT: E  188 MET cc_start: 0.9578 (ptp) cc_final: 0.9175 (ptp)
REVERT: L   81 ASP cc_start: 0.8293 (t0) cc_final: 0.7831 (m-30)
REVERT: U   61 GLU cc_start: 0.8044 (pp20) cc_final: 0.7177 (pp20)
  outliers start: 14
  outliers final: 4
  residues processed: 172
  average time/residue: 0.2522
  time to fit residues: 68.8509
Evaluate side-chains
  120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 72 optimal weight:   30.0000
   chunk 64 optimal weight:   40.0000
   chunk 75 optimal weight:   30.0000
   chunk 88 optimal weight:   40.0000
   chunk 218 optimal weight:    1.9990
   chunk 122 optimal weight:   50.0000
   chunk 206 optimal weight:    9.9990
   chunk 181 optimal weight:    5.9990
   chunk 106 optimal weight:   30.0000
   overall best weight:   13.5994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J  58 ASN
** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  51 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**
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   4 ASN
** 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**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.051844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.037487 restraints weight = 518605.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.038552 restraints weight = 240185.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.038962 restraints weight = 164123.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.039280 restraints weight = 139744.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.039407 restraints weight = 126581.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.6092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.138  40250  Z= 0.352
  Angle     :  0.788  18.342  60980  Z= 0.451
  Chirality :  0.049   0.603   7908
  Planarity :  0.008   0.107   2755
  Dihedral  : 25.056 175.782  21798
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 40.68
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.10 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 10.37 %
    Favored  : 89.39 %
  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: -2.71 (0.23), residues: 1033
  helix: -0.92 (0.27), residues: 332
  sheet: -2.27 (0.37), residues: 145
  loop : -2.24 (0.22), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.002   ARG R  84 
 TYR   0.031   0.005   TYR J  53 
 PHE   0.026   0.004   PHE U  86 
 TRP   0.018   0.004   TRP R  92 
 HIS   0.058   0.005   HIS R  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00594 /  0.35 (40250)
  covalent geometry    : angle       0.78803 /  0.45 (60980)
  hydrogen bonds       : bond        0.14136 / 10.07 ( 1412)
  hydrogen bonds       : angle       4.53183 /  3.17 ( 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
  145 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 0.648 
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: J   25 LEU cc_start: 0.9697 (tt) cc_final: 0.9444 (pp)
REVERT: J   49 ASP cc_start: 0.8140 (p0) cc_final: 0.7832 (p0)
REVERT: J   67 ASN cc_start: 0.9133 (m110) cc_final: 0.8744 (t0)
REVERT: J   74 TYR cc_start: 0.8259 (m-80) cc_final: 0.8020 (m-80)
REVERT: Q   19 GLN cc_start: 0.9415 (mp10) cc_final: 0.9201 (mp10)
REVERT: Q   23 TYR cc_start: 0.9672 (m-80) cc_final: 0.8955 (m-80)
REVERT: Q  116 LEU cc_start: 0.9285 (tt) cc_final: 0.9058 (pp)
REVERT: R   37 GLU cc_start: 0.7766 (pm20) cc_final: 0.7491 (pm20)
REVERT: R   39 LEU cc_start: 0.9515 (mm) cc_final: 0.8729 (mp)
REVERT: R   59 ILE cc_start: 0.9609 (mp) cc_final: 0.9397 (mp)
REVERT: R   81 LYS cc_start: 0.6701 (ttmt) cc_final: 0.5885 (tptt)
REVERT: R   95 ASP cc_start: 0.8953 (m-30) cc_final: 0.8316 (m-30)
REVERT: R   98 ILE cc_start: 0.9342 (mm) cc_final: 0.9088 (mm)
REVERT: E  100 MET cc_start: 0.9532 (mmp) cc_final: 0.9189 (mmm)
REVERT: E  188 MET cc_start: 0.9411 (ptp) cc_final: 0.9064 (ptp)
REVERT: L   81 ASP cc_start: 0.8383 (t0) cc_final: 0.8100 (m-30)
REVERT: U   61 GLU cc_start: 0.8460 (pp20) cc_final: 0.8091 (pp20)
  outliers start: 2
  outliers final: 1
  residues processed: 145
  average time/residue: 0.2549
  time to fit residues: 58.3081
Evaluate side-chains
  111 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 89 optimal weight:   40.0000
   chunk 143 optimal weight:   20.0000
   chunk 189 optimal weight:    9.9990
   chunk 73 optimal weight:   30.0000
   chunk 111 optimal weight:   40.0000
   chunk 202 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 115 optimal weight:   30.0000
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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  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  94 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.049304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.033221 restraints weight = 396955.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.034327 restraints weight = 185543.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.034904 restraints weight = 122642.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.035193 restraints weight = 99021.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.035346 restraints weight = 89267.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.5959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.124  40250  Z= 0.167
  Angle     :  0.526  11.831  60980  Z= 0.315
  Chirality :  0.035   0.349   7908
  Planarity :  0.005   0.090   2755
  Dihedral  : 24.822 179.771  21798
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 23.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.55 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  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: -2.17 (0.24), residues: 1033
  helix: -0.44 (0.27), residues: 336
  sheet: -1.93 (0.40), residues: 138
  loop : -1.96 (0.23), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG E  49 
 TYR   0.014   0.002   TYR J  16 
 PHE   0.024   0.003   PHE E  85 
 TRP   0.011   0.002   TRP R  92 
 HIS   0.019   0.002   HIS R  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.17 (40250)
  covalent geometry    : angle       0.52580 /  0.31 (60980)
  hydrogen bonds       : bond        0.10551 /  7.43 ( 1412)
  hydrogen bonds       : angle       3.89308 /  2.68 ( 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
  149 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.616 
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: 0.8161 (p0) cc_final: 0.7807 (p0)
REVERT: J   71 ASP cc_start: 0.9182 (p0) cc_final: 0.8636 (p0)
REVERT: J   93 ILE cc_start: 0.8383 (pt) cc_final: 0.7751 (pt)
REVERT: J  122 LEU cc_start: 0.9796 (tp) cc_final: 0.9407 (pp)
REVERT: Q   19 GLN cc_start: 0.9439 (mp10) cc_final: 0.9185 (mp10)
REVERT: Q   23 TYR cc_start: 0.9647 (m-80) cc_final: 0.8999 (m-80)
REVERT: Q   88 GLU cc_start: 0.8861 (pm20) cc_final: 0.8654 (mp0)
REVERT: Q  116 LEU cc_start: 0.9340 (tt) cc_final: 0.9084 (pp)
REVERT: R   37 GLU cc_start: 0.7506 (pm20) cc_final: 0.7305 (pm20)
REVERT: R   39 LEU cc_start: 0.9561 (mm) cc_final: 0.7609 (mm)
REVERT: R   70 GLU cc_start: 0.9120 (mp0) cc_final: 0.8863 (pp20)
REVERT: R   81 LYS cc_start: 0.7949 (ttmt) cc_final: 0.6982 (tptt)
REVERT: R   98 ILE cc_start: 0.9362 (mm) cc_final: 0.9078 (mm)
REVERT: E    1 MET cc_start: 0.7823 (pmm) cc_final: 0.6959 (pmm)
REVERT: E  100 MET cc_start: 0.9449 (mmp) cc_final: 0.9037 (mmm)
REVERT: E  188 MET cc_start: 0.9537 (ptp) cc_final: 0.9263 (ptp)
REVERT: E  199 MET cc_start: 0.8226 (tpt) cc_final: 0.7978 (tpt)
REVERT: L   81 ASP cc_start: 0.8456 (t0) cc_final: 0.7939 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2523
  time to fit residues: 59.9395
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  : 0.640 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 127 optimal weight:   40.0000
   chunk 148 optimal weight:   40.0000
   chunk 211 optimal weight:    3.9990
   chunk 231 optimal weight:    7.9990
   chunk 130 optimal weight:   30.0000
   chunk 165 optimal weight:   50.0000
   chunk 7 optimal weight:    3.9990
   chunk 154 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   overall best weight:    6.5992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 132 HIS
** Q  43 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 ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.051889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.037637 restraints weight = 514817.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.038733 restraints weight = 232934.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.039138 restraints weight = 156953.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.039456 restraints weight = 132964.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.039619 restraints weight = 120783.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.6528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  40250  Z= 0.218
  Angle     :  0.552  12.607  60980  Z= 0.328
  Chirality :  0.036   0.204   7908
  Planarity :  0.005   0.049   2755
  Dihedral  : 24.854 179.980  21798
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 30.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.20 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    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: -2.14 (0.24), residues: 1033
  helix: -0.32 (0.28), residues: 330
  sheet: -1.97 (0.40), residues: 139
  loop : -1.98 (0.23), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG U  21 
 TYR   0.020   0.003   TYR J  74 
 PHE   0.025   0.003   PHE R  53 
 TRP   0.010   0.002   TRP R  92 
 HIS   0.009   0.002   HIS R  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.22 (40250)
  covalent geometry    : angle       0.55227 /  0.33 (60980)
  hydrogen bonds       : bond        0.11118 /  7.79 ( 1412)
  hydrogen bonds       : angle       3.84358 /  2.64 ( 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
  143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.559 
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: J    1 MET cc_start: 0.8675 (tmm) cc_final: 0.8092 (tmm)
REVERT: J   49 ASP cc_start: 0.8207 (p0) cc_final: 0.7799 (p0)
REVERT: J   67 ASN cc_start: 0.8848 (t0) cc_final: 0.8005 (t0)
REVERT: J   71 ASP cc_start: 0.8847 (p0) cc_final: 0.8412 (p0)
REVERT: J  141 ASP cc_start: 0.9068 (p0) cc_final: 0.8738 (p0)
REVERT: Q   23 TYR cc_start: 0.9557 (m-80) cc_final: 0.8789 (m-80)
REVERT: Q  116 LEU cc_start: 0.9334 (tt) cc_final: 0.8965 (pp)
REVERT: R   11 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8781 (mm-40)
REVERT: R   37 GLU cc_start: 0.7878 (pm20) cc_final: 0.7550 (pm20)
REVERT: R   39 LEU cc_start: 0.9396 (mm) cc_final: 0.8238 (mm)
REVERT: R   81 LYS cc_start: 0.7665 (ttmt) cc_final: 0.6670 (tptt)
REVERT: R   98 ILE cc_start: 0.9483 (mm) cc_final: 0.9195 (mm)
REVERT: E  100 MET cc_start: 0.9409 (mmp) cc_final: 0.9114 (mmm)
REVERT: E  188 MET cc_start: 0.9569 (ptp) cc_final: 0.9359 (ptm)
REVERT: L   17 LYS cc_start: 0.8290 (ptpp) cc_final: 0.7999 (pttm)
REVERT: L   81 ASP cc_start: 0.8336 (t0) cc_final: 0.8058 (m-30)
REVERT: U   90 LYS cc_start: 0.8440 (mmmt) cc_final: 0.7546 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2414
  time to fit residues: 55.4765
Evaluate side-chains
  113 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 48 optimal weight:   30.0000
   chunk 153 optimal weight:   40.0000
   chunk 86 optimal weight:   50.0000
   chunk 136 optimal weight:   20.0000
   chunk 193 optimal weight:   20.0000
   chunk 119 optimal weight:   30.0000
   chunk 188 optimal weight:   20.0000
   chunk 127 optimal weight:   40.0000
   chunk 155 optimal weight:   30.0000
   chunk 106 optimal weight:   30.0000
   overall best weight:   24.0000

-------------------------------------------------------------------------------
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 136 GLN
Q  43 GLN
** 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 ** 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   9 GLN
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 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 = 0.3096 r_free = 0.3096 target = 0.041811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.027227 restraints weight = 467677.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.027997 restraints weight = 236171.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.028387 restraints weight = 166071.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.028581 restraints weight = 139778.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.028660 restraints weight = 128911.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.9534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.194  40250  Z= 0.685
  Angle     :  1.298  17.069  60980  Z= 0.725
  Chirality :  0.077   0.395   7908
  Planarity :  0.012   0.130   2755
  Dihedral  : 26.174 179.766  21798
  Min Nonbonded Distance : 1.788

Molprobity Statistics.
  All-atom Clashscore : 95.31
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 15.20 %
    Favored  : 84.51 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  9.77 %
    Favored  : 90.11 %
  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: -4.23 (0.21), residues: 1033
  helix: -2.47 (0.23), residues: 325
  sheet: -3.48 (0.40), residues: 110
  loop : -2.97 (0.20), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.003   ARG U  21 
 TYR   0.053   0.007   TYR R   2 
 PHE   0.044   0.006   PHE R  53 
 TRP   0.081   0.010   TRP E  78 
 HIS   0.024   0.007   HIS J  76 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01101 /  0.69 (40250)
  covalent geometry    : angle       1.29753 /  0.72 (60980)
  hydrogen bonds       : bond        0.29041 / 20.34 ( 1412)
  hydrogen bonds       : angle       5.79001 /  4.02 ( 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
  128 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.564 
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: J   67 ASN cc_start: 0.9263 (t0) cc_final: 0.8745 (t0)
REVERT: J   71 ASP cc_start: 0.9330 (p0) cc_final: 0.8939 (p0)
REVERT: J   74 TYR cc_start: 0.8486 (m-80) cc_final: 0.8090 (m-80)
REVERT: J   92 MET cc_start: 0.9384 (tpt) cc_final: 0.8954 (tpp)
REVERT: Q   59 LEU cc_start: 0.9620 (mm) cc_final: 0.9375 (mt)
REVERT: Q  116 LEU cc_start: 0.9310 (tt) cc_final: 0.8928 (pp)
REVERT: R    2 TYR cc_start: 0.9194 (p90) cc_final: 0.8993 (p90)
REVERT: R   31 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8745 (tm-30)
REVERT: R   39 LEU cc_start: 0.9140 (mm) cc_final: 0.8582 (mm)
REVERT: R   53 PHE cc_start: 0.9463 (p90) cc_final: 0.9011 (p90)
REVERT: R   73 LYS cc_start: 0.9572 (mppt) cc_final: 0.9340 (mmtm)
REVERT: R   81 LYS cc_start: 0.6888 (ttmt) cc_final: 0.6354 (tptt)
REVERT: D   43 ASP cc_start: 0.9264 (t70) cc_final: 0.8114 (p0)
REVERT: E  199 MET cc_start: 0.8922 (tpt) cc_final: 0.8614 (tpt)
REVERT: L   81 ASP cc_start: 0.9008 (t0) cc_final: 0.8706 (m-30)
REVERT: U   61 GLU cc_start: 0.8142 (pp20) cc_final: 0.7916 (pp20)
REVERT: U   90 LYS cc_start: 0.8375 (mttm) cc_final: 0.7913 (mttp)
  outliers start: 1
  outliers final: 1
  residues processed: 128
  average time/residue: 0.2459
  time to fit residues: 49.3740
Evaluate side-chains
  101 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 133 optimal weight:   30.0000
   chunk 121 optimal weight:   50.0000
   chunk 177 optimal weight:   50.0000
   chunk 126 optimal weight:   30.0000
   chunk 212 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 116 optimal weight:   30.0000
   chunk 64 optimal weight:   30.0000
   chunk 185 optimal weight:    5.9990
   chunk 192 optimal weight:    7.9990
   overall best weight:    9.9994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  77 HIS
** 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  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.043615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.028372 restraints weight = 441740.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.029244 restraints weight = 212447.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.029672 restraints weight = 146495.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.029874 restraints weight = 121927.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.029959 restraints weight = 112293.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.9235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  40250  Z= 0.295
  Angle     :  0.723  13.017  60980  Z= 0.433
  Chirality :  0.047   0.581   7908
  Planarity :  0.007   0.112   2755
  Dihedral  : 25.920 175.209  21798
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 42.48
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.94 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  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: -3.48 (0.22), residues: 1033
  helix: -1.69 (0.25), residues: 314
  sheet: -3.17 (0.39), residues: 131
  loop : -2.51 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG D  83 
 TYR   0.049   0.004   TYR J  75 
 PHE   0.026   0.004   PHE R  53 
 TRP   0.019   0.003   TRP E  78 
 HIS   0.012   0.002   HIS R  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00487 /  0.30 (40250)
  covalent geometry    : angle       0.72298 /  0.43 (60980)
  hydrogen bonds       : bond        0.16014 / 11.31 ( 1412)
  hydrogen bonds       : angle       4.59898 /  3.17 ( 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
  150 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.663 
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: J    1 MET cc_start: 0.8504 (tmm) cc_final: 0.8144 (tmm)
REVERT: J   49 ASP cc_start: 0.8419 (p0) cc_final: 0.8050 (p0)
REVERT: J   67 ASN cc_start: 0.9285 (t0) cc_final: 0.8786 (t0)
REVERT: J   71 ASP cc_start: 0.8830 (p0) cc_final: 0.8354 (p0)
REVERT: J   74 TYR cc_start: 0.8584 (m-80) cc_final: 0.8380 (m-80)
REVERT: J   92 MET cc_start: 0.9306 (tpt) cc_final: 0.8823 (tpp)
REVERT: J  109 LEU cc_start: 0.9680 (tp) cc_final: 0.9398 (tt)
REVERT: J  141 ASP cc_start: 0.9195 (p0) cc_final: 0.8901 (p0)
REVERT: N   42 LYS cc_start: 0.9224 (pttm) cc_final: 0.8685 (tptt)
REVERT: Q   15 LYS cc_start: 0.9348 (ptpp) cc_final: 0.9144 (pttt)
REVERT: Q   19 GLN cc_start: 0.9592 (mp10) cc_final: 0.9227 (mp10)
REVERT: Q   23 TYR cc_start: 0.9544 (m-80) cc_final: 0.8555 (m-80)
REVERT: Q  105 PHE cc_start: 0.9263 (t80) cc_final: 0.8999 (t80)
REVERT: R   11 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8257 (mm-40)
REVERT: R   13 ARG cc_start: 0.9103 (tmt-80) cc_final: 0.8153 (tpt90)
REVERT: R   39 LEU cc_start: 0.9237 (mm) cc_final: 0.8391 (mm)
REVERT: R   53 PHE cc_start: 0.9442 (p90) cc_final: 0.9024 (p90)
REVERT: R   73 LYS cc_start: 0.9634 (mppt) cc_final: 0.8742 (tppt)
REVERT: R   81 LYS cc_start: 0.7066 (ttmt) cc_final: 0.6312 (tptt)
REVERT: R   95 ASP cc_start: 0.8558 (m-30) cc_final: 0.8228 (m-30)
REVERT: E  100 MET cc_start: 0.9607 (mmp) cc_final: 0.9089 (mmm)
REVERT: E  188 MET cc_start: 0.9589 (ptp) cc_final: 0.9346 (ptp)
REVERT: U   90 LYS cc_start: 0.8742 (mttm) cc_final: 0.8295 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2489
  time to fit residues: 59.0329
Evaluate side-chains
  110 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 207 optimal weight:    1.9990
   chunk 176 optimal weight:   50.0000
   chunk 224 optimal weight:    8.9990
   chunk 189 optimal weight:    3.9990
   chunk 143 optimal weight:   30.0000
   chunk 77 optimal weight:   30.0000
   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:   10.5992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** 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  58 ASN
D  94 GLN
** U  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.043002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.028056 restraints weight = 439302.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.028904 restraints weight = 207599.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.029342 restraints weight = 141262.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.029557 restraints weight = 117587.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.029650 restraints weight = 107543.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.9653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  40250  Z= 0.320
  Angle     :  0.724  20.516  60980  Z= 0.427
  Chirality :  0.046   0.335   7908
  Planarity :  0.007   0.084   2755
  Dihedral  : 25.929 177.426  21798
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 47.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 13.94 %
    Favored  : 85.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.23), residues: 1033
  helix: -1.35 (0.26), residues: 317
  sheet: -3.04 (0.41), residues: 126
  loop : -2.58 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG E  49 
 TYR   0.021   0.004   TYR J  74 
 PHE   0.028   0.004   PHE R  53 
 TRP   0.023   0.003   TRP D  80 
 HIS   0.014   0.003   HIS J  76 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00520 /  0.32 (40250)
  covalent geometry    : angle       0.72420 /  0.43 (60980)
  hydrogen bonds       : bond        0.15417 / 10.80 ( 1412)
  hydrogen bonds       : angle       4.56948 /  3.14 ( 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: 0
    poor density    : 140
  time to evaluate  : 0.633 
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: J    1 MET cc_start: 0.8511 (tmm) cc_final: 0.8264 (tmm)
REVERT: J   49 ASP cc_start: 0.8475 (p0) cc_final: 0.8150 (p0)
REVERT: J   67 ASN cc_start: 0.9257 (t0) cc_final: 0.8729 (t0)
REVERT: J   71 ASP cc_start: 0.8813 (p0) cc_final: 0.8336 (p0)
REVERT: J   74 TYR cc_start: 0.8636 (m-80) cc_final: 0.8409 (m-80)
REVERT: J   92 MET cc_start: 0.9412 (tpt) cc_final: 0.8877 (tpp)
REVERT: J  102 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8800 (pt0)
REVERT: J  141 ASP cc_start: 0.9217 (p0) cc_final: 0.8911 (p0)
REVERT: Q   15 LYS cc_start: 0.9393 (ptpp) cc_final: 0.8972 (pttt)
REVERT: Q   19 GLN cc_start: 0.9595 (mp10) cc_final: 0.9261 (mp10)
REVERT: Q   23 TYR cc_start: 0.9606 (m-80) cc_final: 0.8642 (m-80)
REVERT: Q  116 LEU cc_start: 0.9339 (tp) cc_final: 0.8875 (pp)
REVERT: R   31 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8707 (tm-30)
REVERT: R   39 LEU cc_start: 0.9337 (mm) cc_final: 0.8959 (mm)
REVERT: R   53 PHE cc_start: 0.9441 (p90) cc_final: 0.9002 (p90)
REVERT: R   73 LYS cc_start: 0.9587 (mppt) cc_final: 0.8571 (tppt)
REVERT: R   81 LYS cc_start: 0.7117 (ttmt) cc_final: 0.6436 (tptt)
REVERT: R   95 ASP cc_start: 0.8512 (m-30) cc_final: 0.8184 (m-30)
REVERT: E  100 MET cc_start: 0.9557 (mmp) cc_final: 0.9192 (mmm)
REVERT: E  199 MET cc_start: 0.8905 (tpt) cc_final: 0.8625 (tpt)
REVERT: L  104 GLN cc_start: 0.6696 (pp30) cc_final: 0.6386 (pp30)
REVERT: U   61 GLU cc_start: 0.7644 (pp20) cc_final: 0.7431 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2345
  time to fit residues: 52.0074
Evaluate side-chains
  112 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
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:    3.9990
   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:    9.9990
   chunk 14 optimal weight:   50.0000
   chunk 145 optimal weight:   30.0000
   chunk 3 optimal weight:    8.9990
   overall best weight:   12.5994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** 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  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 GLN
** D 173 GLN ** 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
** U  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.042084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.027321 restraints weight = 455020.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.028140 restraints weight = 217275.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.028538 restraints weight = 148738.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.028735 restraints weight = 124609.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.028822 restraints weight = 114919.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          1.0479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.110  40250  Z= 0.348
  Angle     :  0.769  11.874  60980  Z= 0.454
  Chirality :  0.049   0.337   7908
  Planarity :  0.008   0.136   2755
  Dihedral  : 26.156 175.893  21798
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 52.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 13.36 %
    Favored  : 86.54 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.91 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.59 (0.22), residues: 1033
  helix: -1.50 (0.26), residues: 316
  sheet: -3.24 (0.42), residues: 127
  loop : -2.78 (0.21), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG E  49 
 TYR   0.030   0.004   TYR R   2 
 PHE   0.031   0.004   PHE D 118 
 TRP   0.015   0.003   TRP E  78 
 HIS   0.013   0.003   HIS R  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00572 /  0.35 (40250)
  covalent geometry    : angle       0.76901 /  0.45 (60980)
  hydrogen bonds       : bond        0.16028 / 11.24 ( 1412)
  hydrogen bonds       : angle       4.78606 /  3.29 ( 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
  140 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.594 
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: J   67 ASN cc_start: 0.9247 (t0) cc_final: 0.8715 (t0)
REVERT: J   71 ASP cc_start: 0.8830 (p0) cc_final: 0.8374 (p0)
REVERT: J   74 TYR cc_start: 0.8552 (m-80) cc_final: 0.8330 (m-80)
REVERT: J   92 MET cc_start: 0.9413 (tpt) cc_final: 0.8890 (tpp)
REVERT: J  102 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8814 (pt0)
REVERT: N   42 LYS cc_start: 0.9401 (pttm) cc_final: 0.8937 (tptt)
REVERT: Q   15 LYS cc_start: 0.9479 (ptpp) cc_final: 0.9027 (pttt)
REVERT: Q   19 GLN cc_start: 0.9657 (mp10) cc_final: 0.9268 (mp10)
REVERT: Q   23 TYR cc_start: 0.9461 (m-80) cc_final: 0.8546 (m-80)
REVERT: Q  110 GLU cc_start: 0.8903 (pm20) cc_final: 0.8460 (pm20)
REVERT: R   13 ARG cc_start: 0.9086 (tmt-80) cc_final: 0.8176 (ttp80)
REVERT: R   31 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8776 (tm-30)
REVERT: R   35 PHE cc_start: 0.9070 (m-80) cc_final: 0.8835 (m-80)
REVERT: R   39 LEU cc_start: 0.9324 (mm) cc_final: 0.8827 (mm)
REVERT: R   73 LYS cc_start: 0.9489 (mppt) cc_final: 0.9190 (mmtm)
REVERT: R   81 LYS cc_start: 0.6959 (ttmt) cc_final: 0.6315 (tptt)
REVERT: R   86 GLN cc_start: 0.8725 (pm20) cc_final: 0.8514 (pm20)
REVERT: R   95 ASP cc_start: 0.8589 (m-30) cc_final: 0.8240 (m-30)
REVERT: D   43 ASP cc_start: 0.8794 (t70) cc_final: 0.8236 (p0)
REVERT: D   58 ASN cc_start: 0.9118 (m110) cc_final: 0.8880 (p0)
REVERT: D  173 GLN cc_start: 0.6737 (pp30) cc_final: 0.6468 (pp30)
REVERT: E  100 MET cc_start: 0.9471 (mmp) cc_final: 0.9044 (mmm)
REVERT: L   17 LYS cc_start: 0.9389 (mppt) cc_final: 0.9039 (mppt)
REVERT: L  104 GLN cc_start: 0.7291 (pp30) cc_final: 0.6927 (pp30)
REVERT: U   45 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7762 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2479
  time to fit residues: 54.7502
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  : 0.510 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 173 optimal weight:   50.0000
   chunk 20 optimal weight:    8.9990
   chunk 85 optimal weight:   50.0000
   chunk 59 optimal weight:   30.0000
   chunk 153 optimal weight:   50.0000
   chunk 157 optimal weight:   50.0000
   chunk 44 optimal weight:    5.9990
   overall best weight:   11.7992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** 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  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 GLN
** U  44 HIS ** 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 = 0.3091 r_free = 0.3091 target = 0.041868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.027249 restraints weight = 453020.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.028011 restraints weight = 212038.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.028438 restraints weight = 142162.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.028637 restraints weight = 118253.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.028737 restraints weight = 108904.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          1.0750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094  40250  Z= 0.327
  Angle     :  0.725  11.910  60980  Z= 0.430
  Chirality :  0.047   0.303   7908
  Planarity :  0.007   0.066   2755
  Dihedral  : 26.127 176.285  21798
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 49.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 13.36 %
    Favored  : 86.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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: -3.52 (0.23), residues: 1033
  helix: -1.45 (0.26), residues: 317
  sheet: -3.11 (0.41), residues: 129
  loop : -2.74 (0.22), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG E  49 
 TYR   0.025   0.004   TYR J  16 
 PHE   0.025   0.003   PHE R  53 
 TRP   0.013   0.003   TRP R  92 
 HIS   0.013   0.003   HIS R  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00534 /  0.33 (40250)
  covalent geometry    : angle       0.72523 /  0.43 (60980)
  hydrogen bonds       : bond        0.15358 / 10.76 ( 1412)
  hydrogen bonds       : angle       4.69401 /  3.21 ( 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
  140 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.657 
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: J   67 ASN cc_start: 0.9251 (t0) cc_final: 0.8635 (t0)
REVERT: J   71 ASP cc_start: 0.8780 (p0) cc_final: 0.8324 (p0)
REVERT: J   74 TYR cc_start: 0.8595 (m-80) cc_final: 0.8356 (m-80)
REVERT: J   92 MET cc_start: 0.9374 (tpt) cc_final: 0.8882 (tpp)
REVERT: J  102 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8843 (pt0)
REVERT: N   42 LYS cc_start: 0.9387 (pttm) cc_final: 0.8944 (tptt)
REVERT: Q   15 LYS cc_start: 0.9487 (ptpp) cc_final: 0.9035 (pttt)
REVERT: Q   19 GLN cc_start: 0.9657 (mp10) cc_final: 0.9259 (mp10)
REVERT: Q   23 TYR cc_start: 0.9453 (m-80) cc_final: 0.8624 (m-80)
REVERT: Q  110 GLU cc_start: 0.8808 (pm20) cc_final: 0.8601 (pm20)
REVERT: R   11 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8093 (mm110)
REVERT: R   13 ARG cc_start: 0.9037 (tmt-80) cc_final: 0.8186 (ttp80)
REVERT: R   39 LEU cc_start: 0.9366 (mm) cc_final: 0.8652 (mm)
REVERT: R   53 PHE cc_start: 0.9415 (p90) cc_final: 0.8897 (p90)
REVERT: R   73 LYS cc_start: 0.9556 (mppt) cc_final: 0.9251 (mmtm)
REVERT: R   81 LYS cc_start: 0.6926 (ttmt) cc_final: 0.6058 (tptt)
REVERT: R   86 GLN cc_start: 0.8751 (pm20) cc_final: 0.8537 (pm20)
REVERT: R   95 ASP cc_start: 0.8551 (m-30) cc_final: 0.8178 (m-30)
REVERT: D   43 ASP cc_start: 0.8792 (t70) cc_final: 0.8284 (p0)
REVERT: D   58 ASN cc_start: 0.9132 (m110) cc_final: 0.8905 (p0)
REVERT: E  100 MET cc_start: 0.9445 (mmp) cc_final: 0.9120 (mmm)
REVERT: E  199 MET cc_start: 0.8777 (tpt) cc_final: 0.8488 (tpt)
REVERT: L   17 LYS cc_start: 0.9371 (mppt) cc_final: 0.9034 (mppt)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2558
  time to fit residues: 56.4134
Evaluate side-chains
  112 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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:   40.0000
   chunk 174 optimal weight:   50.0000
   chunk 69 optimal weight:   50.0000
   chunk 45 optimal weight:   10.0000
   chunk 137 optimal weight:   30.0000
   chunk 211 optimal weight:    0.3980
   chunk 166 optimal weight:   40.0000
   chunk 104 optimal weight:   50.0000
   chunk 77 optimal weight:   30.0000
   chunk 92 optimal weight:   30.0000
   chunk 112 optimal weight:   40.0000
   overall best weight:   20.0796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  80 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 GLN
D 126 ASN
** D 173 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.040037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.025992 restraints weight = 471286.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.026736 restraints weight = 227691.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.027090 restraints weight = 158363.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.027272 restraints weight = 132977.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.027345 restraints weight = 122858.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          1.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.169  40250  Z= 0.523
  Angle     :  1.020  17.481  60980  Z= 0.587
  Chirality :  0.063   0.438   7908
  Planarity :  0.010   0.129   2755
  Dihedral  : 26.673 174.112  21798
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 81.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 17.33 %
    Favored  : 82.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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: -4.29 (0.21), residues: 1033
  helix: -2.16 (0.24), residues: 309
  sheet: -3.45 (0.39), residues: 133
  loop : -3.20 (0.21), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG J  34 
 TYR   0.054   0.006   TYR R   2 
 PHE   0.038   0.004   PHE D  15 
 TRP   0.036   0.006   TRP D 125 
 HIS   0.015   0.004   HIS J  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00843 /  0.52 (40250)
  covalent geometry    : angle       1.01954 /  0.59 (60980)
  hydrogen bonds       : bond        0.23132 / 16.17 ( 1412)
  hydrogen bonds       : angle       5.44105 /  3.76 ( 2626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5872.51 seconds
wall clock time: 103 minutes 53.49 seconds (6233.49 seconds total)