Starting phenix.real_space_refine
on Sun Sep 13 01:23:06 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6j99_9783/09_2026/6j99_9783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6j99_9783/09_2026/6j99_9783.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6j99_9783/09_2026/6j99_9783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6j99_9783/09_2026/6j99_9783.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6j99_9783/09_2026/6j99_9783.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6j99_9783/09_2026/6j99_9783.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6j99_9783/09_2026/6j99_9783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6j99_9783/09_2026/6j99_9783.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5830 atoms to isotropic.
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     289      5.49       5
     S      29      5.16       5
     C    8711      2.51       5
     N    2824      2.21       5
     O    3413      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 15266
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 698
          Classifications: {'peptide': 86}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 738
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 742
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 2935
          Classifications: {'DNA': 144}
          Link IDs: {'rna3p': 143}
    Chain: "J"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "L"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 603
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2665
          Classifications: {'peptide': 325}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
          Chain breaks: 1
  Time building chain proxies: 2.61, per 1000 atoms: 0.17
  Number of scatterers: 15266
  At special positions: 0
  Unit cell: (132.6, 137.8, 114.4, 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      29     16.00
     P     289     15.00
     O    3413      8.00
     N    2824      7.00
     C    8711      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 435.5 milliseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      62.3% alpha, 3.9% beta
      143 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 2.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 4.928A  pdb=" N   GLU A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   ARG A  53 " --> pdb=" O   ARG A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.508A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.841A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.794A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.649A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.347A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.793A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
      removed outlier: 3.973A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER D 120 " --> pdb=" O   THR D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 4.928A  pdb=" N   GLU E  50 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ARG E  53 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.507A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.840A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.749A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.852A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.651A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASN G  68 " --> pdb=" O   GLU G  64 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA G  69 " --> pdb=" O   LEU G  65 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'L' and resid 22 through 35
      removed outlier: 3.588A  pdb=" N   VAL L  26 " --> pdb=" O   THR L  22 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 32 through 46
      removed outlier: 3.548A  pdb=" N   ILE K  37 " --> pdb=" O   ALA K  33 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE K  38 " --> pdb=" O   ALA K  34 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 51 through 56
    Processing helix  chain 'K' and resid 67 through 90
    Processing helix  chain 'K' and resid 103 through 119
    Processing helix  chain 'K' and resid 121 through 127
      removed outlier: 3.625A  pdb=" N   LEU K 125 " --> pdb=" O   ASP K 121 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 140 through 151
      removed outlier: 4.054A  pdb=" N   VAL K 144 " --> pdb=" O   SER K 140 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 167 through 177
    Processing helix  chain 'K' and resid 188 through 209
    Processing helix  chain 'K' and resid 225 through 235
    Processing helix  chain 'K' and resid 241 through 245
      removed outlier: 4.552A  pdb=" N   ALA K 244 " --> pdb=" O   ASN K 241 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 246 through 258
    Processing helix  chain 'K' and resid 281 through 285
      removed outlier: 3.960A  pdb=" N   LEU K 284 " --> pdb=" O   SER K 281 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER K 285 " --> pdb=" O   ARG K 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 281 through 285'
    Processing helix  chain 'K' and resid 287 through 289
      No H-bonds generated for 'chain 'K' and resid 287 through 289'
    Processing helix  chain 'K' and resid 319 through 331
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.398A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.260A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.448A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.089A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.639A  pdb=" N   LEU L  69 " --> pdb=" O   LYS L   6 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 217 through 218
      removed outlier: 6.583A  pdb=" N   HIS K 182 " --> pdb=" O   THR K 217 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   PHE K 159 " --> pdb=" O   TYR K 183 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   VAL K 185 " --> pdb=" O   PHE K 159 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP K 161 " --> pdb=" O   VAL K 185 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   VAL K 160 " --> pdb=" O   PHE K 239 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   ILE K 238 " --> pdb=" O   VAL K 267 " (cutoff:3.500A)

    521 hydrogen bonds defined for protein.
    1542 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      366 hydrogen bonds
      728 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 2.78

  Time building geometry restraints manager: 1.20 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: 2782
        1.33 -     1.45: 5098
        1.45 -     1.57: 7638
        1.57 -     1.69: 577
        1.69 -     1.81: 50
  Bond restraints: 16145
  Sorted by residual:
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.435  1.488 -0.053 1.30e-02 5.92e+03 1.64e+01
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.435  1.487 -0.052 1.30e-02 5.92e+03 1.62e+01
  bond pdb=" C3'  DG J  92 "
       pdb=" O3'  DG J  92 "
    ideal  model  delta    sigma   weight residual
    1.435  1.388  0.047 1.30e-02 5.92e+03 1.30e+01
  bond pdb=" C3'  DC I  56 "
       pdb=" O3'  DC I  56 "
    ideal  model  delta    sigma   weight residual
    1.435  1.388  0.047 1.30e-02 5.92e+03 1.28e+01
  bond pdb=" C3'  DG J 136 "
       pdb=" C2'  DG J 136 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.24e+01
  ... (remaining 16140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 22046
        2.38 -     4.76: 925
        4.76 -     7.14: 62
        7.14 -     9.52: 18
        9.52 -    11.90: 4
  Bond angle restraints: 23055
  Sorted by residual:
  angle pdb=" O4'  DA I  39 "
        pdb=" C4'  DA I  39 "
        pdb=" C3'  DA I  39 "
      ideal   model   delta    sigma   weight residual
     106.00  102.08    3.92 6.00e-01 2.78e+00 4.28e+01
  angle pdb=" O4'  DC I 109 "
        pdb=" C4'  DC I 109 "
        pdb=" C3'  DC I 109 "
      ideal   model   delta    sigma   weight residual
     106.00  102.20    3.80 6.00e-01 2.78e+00 4.00e+01
  angle pdb=" C   LEU K 299 "
        pdb=" N   LYS K 300 "
        pdb=" CA  LYS K 300 "
      ideal   model   delta    sigma   weight residual
     121.70  132.86  -11.16 1.80e+00 3.09e-01 3.84e+01
  angle pdb=" O4'  DC I 140 "
        pdb=" C4'  DC I 140 "
        pdb=" C3'  DC I 140 "
      ideal   model   delta    sigma   weight residual
     106.00  102.29    3.71 6.00e-01 2.78e+00 3.82e+01
  angle pdb=" O4'  DG I  83 "
        pdb=" C4'  DG I  83 "
        pdb=" C3'  DG I  83 "
      ideal   model   delta    sigma   weight residual
     106.00  102.34    3.66 6.00e-01 2.78e+00 3.72e+01
  ... (remaining 23050 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.05: 7058
       30.05 -    60.09: 1830
       60.09 -    90.14: 85
       90.14 -   120.18: 1
      120.18 -   150.23: 2
  Dihedral angle restraints: 8976
    sinusoidal: 5583
      harmonic: 3393
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.87  -34.13     0      5.00e+00 4.00e-02 4.66e+01
  dihedral pdb=" CA  SER K 304 "
           pdb=" C   SER K 304 "
           pdb=" N   TRP K 305 "
           pdb=" CA  TRP K 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.77   31.23     0      5.00e+00 4.00e-02 3.90e+01
  dihedral pdb=" CA  ARG L  74 "
           pdb=" C   ARG L  74 "
           pdb=" N   GLY L  75 "
           pdb=" CA  GLY L  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.47   29.53     0      5.00e+00 4.00e-02 3.49e+01
  ... (remaining 8973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1813
       0.052 -    0.104: 644
       0.104 -    0.156: 127
       0.156 -    0.208: 19
       0.208 -    0.260: 4
  Chirality restraints: 2607
  Sorted by residual:
  chirality pdb=" P    DT J  83 "
            pdb=" OP1  DT J  83 "
            pdb=" OP2  DT J  83 "
            pdb=" O5'  DT J  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.60   -0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" C1'  DG J  82 "
            pdb=" O4'  DG J  82 "
            pdb=" C2'  DG J  82 "
            pdb=" N9   DG J  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.18    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C3'  DT J  15 "
            pdb=" C4'  DT J  15 "
            pdb=" O3'  DT J  15 "
            pdb=" C2'  DT J  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.51   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 2604 not shown)

  Planarity restraints: 1920
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E  45 "    0.014 2.00e-02 2.50e+03   2.87e-02 8.22e+00
        pdb=" C   THR E  45 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   THR E  45 "    0.019 2.00e-02 2.50e+03
        pdb=" N   VAL E  46 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  50 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.05e+00
        pdb=" C   GLU A  50 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLU A  50 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ILE A  51 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU E  50 "   -0.014 2.00e-02 2.50e+03   2.83e-02 8.01e+00
        pdb=" C   GLU E  50 "    0.049 2.00e-02 2.50e+03
        pdb=" O   GLU E  50 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE E  51 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1917 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1901
        2.74 -     3.28: 14252
        3.28 -     3.82: 32196
        3.82 -     4.36: 36012
        4.36 -     4.90: 51791
  Nonbonded interactions: 136152
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 123 "
            pdb=" NE2 HIS E 113 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD1 ASN K 242 "
            pdb=" OG  SER K 269 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O2   DC I  95 "
            pdb=" N2   DG J  53 "
     model   vdw
     2.260 2.496
  nonbonded pdb=" OH  TYR D  37 "
            pdb=" OP1  DG J 122 "
     model   vdw
     2.271 3.040
  ... (remaining 136147 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 13 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 28 through 120)
  selection = (chain 'H' and resid 28 through 120)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.930
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5182
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      :  0.008   0.065  16146  Z= 0.689
  Angle     :  1.078  11.900  23055  Z= 0.838
  Chirality :  0.054   0.260   2607
  Planarity :  0.007   0.066   1920
  Dihedral  : 27.095 150.230   6782
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -2.88 (0.21), residues: 1143
  helix: -1.35 (0.16), residues: 694
  sheet: -3.97 (0.63), residues: 37
  loop : -2.49 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K  80 
 TYR   0.041   0.004   TYR G  39 
 PHE   0.027   0.004   PHE K 245 
 TRP   0.024   0.004   TRP K 228 
 HIS   0.019   0.003   HIS C  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00838 /  0.69 (16145)
  covalent geometry    : angle       1.07810 /  0.84 (23055)
  hydrogen bonds       : bond        0.12316 /  8.33 (  887)
  hydrogen bonds       : angle       5.58243 /  3.97 ( 2270)
  Misc. bond           : bond        0.00203 /  0.14 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 379
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.5261 (mt) cc_final: 0.4331 (mt)
REVERT: A   93 GLN cc_start: 0.4178 (tt0) cc_final: 0.3781 (tt0)
REVERT: A  116 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7230 (ptm160)
REVERT: A  120 MET cc_start: 0.1644 (mtt) cc_final: 0.1187 (mtt)
REVERT: B  100 PHE cc_start: 0.7406 (m-80) cc_final: 0.7028 (m-10)
REVERT: C   57 TYR cc_start: 0.8736 (t80) cc_final: 0.8125 (t80)
REVERT: C   75 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7572 (mmmt)
REVERT: D   90 GLU cc_start: 0.7424 (mp0) cc_final: 0.7197 (mp0)
REVERT: D  106 HIS cc_start: 0.7983 (m-70) cc_final: 0.7284 (m-70)
REVERT: G   68 ASN cc_start: 0.8396 (m-40) cc_final: 0.8053 (m-40)
REVERT: G   72 ASP cc_start: 0.9244 (m-30) cc_final: 0.8828 (m-30)
REVERT: G  115 LEU cc_start: 0.6386 (mt) cc_final: 0.5938 (tt)
REVERT: H   90 GLU cc_start: 0.6324 (mp0) cc_final: 0.5990 (mt-10)
REVERT: H  100 PRO cc_start: 0.4871 (Cg_endo) cc_final: 0.4583 (Cg_exo)
REVERT: L    1 MET cc_start: 0.2615 (ttp) cc_final: 0.1890 (ttt)
REVERT: L    6 LYS cc_start: 0.8999 (tttt) cc_final: 0.8755 (tptt)
REVERT: L   71 LEU cc_start: 0.8587 (mp) cc_final: 0.7861 (mt)
REVERT: K   53 LEU cc_start: 0.5821 (tp) cc_final: 0.5536 (pp)
REVERT: K   66 LYS cc_start: 0.7634 (mppt) cc_final: 0.7181 (pttt)
REVERT: K   96 MET cc_start: -0.0461 (ttp) cc_final: -0.1124 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 379
  average time/residue: 0.1617
  time to fit residues: 82.1114
Evaluate side-chains
  235 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    0.3980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    7.9990
   overall best weight:    3.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  18 HIS
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
D  79 HIS
D  81 ASN
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
G  38 ASN
L   2 GLN
K 126 ASN
K 213 HIS
K 234 ASN
K 251 HIS
K 252 GLN
** K 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.187109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.161878 restraints weight = 55102.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.165334 restraints weight = 33200.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.167434 restraints weight = 23208.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.168743 restraints weight = 18411.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.169483 restraints weight = 15966.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.4486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5809
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.149  16146  Z= 0.274
  Angle     :  0.941  17.359  23055  Z= 0.513
  Chirality :  0.060   0.620   2607
  Planarity :  0.007   0.067   1920
  Dihedral  : 32.592 149.090   4447
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 20.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  4.61 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.23), residues: 1143
  helix: -0.19 (0.18), residues: 701
  sheet: -3.22 (0.63), residues: 45
  loop : -2.29 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG E 129 
 TYR   0.015   0.002   TYR B  88 
 PHE   0.054   0.004   PHE E  67 
 TRP   0.014   0.002   TRP K 305 
 HIS   0.006   0.002   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.27 (16145)
  covalent geometry    : angle       0.94062 /  0.51 (23055)
  hydrogen bonds       : bond        0.07055 /  4.70 (  887)
  hydrogen bonds       : angle       4.69571 /  3.35 ( 2270)
  Misc. bond           : bond        0.00204 /  0.14 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 310
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8161 (tp30) cc_final: 0.7832 (tp30)
REVERT: A   62 ILE cc_start: 0.6444 (mt) cc_final: 0.5856 (mt)
REVERT: A   93 GLN cc_start: 0.4784 (tt0) cc_final: 0.4452 (tt0)
REVERT: B   88 TYR cc_start: 0.8259 (m-80) cc_final: 0.7805 (m-80)
REVERT: B  100 PHE cc_start: 0.7887 (m-80) cc_final: 0.7610 (m-10)
REVERT: C   61 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7604 (tp30)
REVERT: C   75 LYS cc_start: 0.7798 (mmtp) cc_final: 0.7597 (mmmt)
REVERT: D   81 ASN cc_start: 0.7743 (m-40) cc_final: 0.7475 (m-40)
REVERT: D   82 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8412 (mmtt)
REVERT: D  106 HIS cc_start: 0.7649 (m-70) cc_final: 0.6801 (m-70)
REVERT: D  112 THR cc_start: 0.8739 (m) cc_final: 0.8383 (m)
REVERT: D  118 TYR cc_start: 0.8529 (t80) cc_final: 0.7767 (t80)
REVERT: E   55 GLN cc_start: 0.7557 (pp30) cc_final: 0.7300 (pp30)
REVERT: F   84 MET cc_start: 0.6780 (mmp) cc_final: 0.6417 (mmp)
REVERT: G   99 ARG cc_start: 0.7182 (mmp80) cc_final: 0.6704 (mmt180)
REVERT: H   52 SER cc_start: 0.6004 (m) cc_final: 0.5625 (m)
REVERT: H   76 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.7861 (ttt-90)
REVERT: H   98 LEU cc_start: 0.8001 (tp) cc_final: 0.7772 (tp)
REVERT: L    1 MET cc_start: 0.1233 (ttp) cc_final: 0.0109 (ttt)
REVERT: L   24 GLU cc_start: 0.8382 (tt0) cc_final: 0.7864 (mm-30)
REVERT: K   55 MET cc_start: 0.7419 (mmp) cc_final: 0.7215 (tmm)
REVERT: K   66 LYS cc_start: 0.7840 (mppt) cc_final: 0.7327 (pttt)
REVERT: K   96 MET cc_start: 0.0089 (ttp) cc_final: -0.0828 (tpt)
REVERT: K  147 MET cc_start: 0.6774 (mtm) cc_final: 0.6524 (ttp)
REVERT: K  153 MET cc_start: 0.3058 (ttt) cc_final: 0.2614 (tmm)
REVERT: K  179 CYS cc_start: 0.3349 (m) cc_final: 0.2009 (m)
REVERT: K  205 TRP cc_start: 0.7358 (m100) cc_final: 0.7152 (m100)
  outliers start: 4
  outliers final: 4
  residues processed: 313
  average time/residue: 0.1453
  time to fit residues: 62.8180
Evaluate side-chains
  245 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 241
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 133 optimal weight:    0.8980
   chunk 99 optimal weight:   40.0000
   chunk 44 optimal weight:    7.9990
   chunk 112 optimal weight:    4.9990
   chunk 87 optimal weight:   40.0000
   chunk 93 optimal weight:   10.0000
   chunk 92 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    4.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
F  25 ASN
G  31 HIS
G  38 ASN
G  82 HIS
G  89 ASN
G  94 ASN
L   2 GLN
K  35 HIS
K 181 HIS
K 241 ASN
K 315 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.172238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.143206 restraints weight = 55052.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.146266 restraints weight = 33168.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.148100 restraints weight = 23579.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.149252 restraints weight = 19139.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.149810 restraints weight = 16905.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.108  16146  Z= 0.317
  Angle     :  0.995  20.445  23055  Z= 0.552
  Chirality :  0.059   0.389   2607
  Planarity :  0.009   0.152   1920
  Dihedral  : 32.401 146.686   4447
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 23.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  5.81 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.23), residues: 1143
  helix: -0.18 (0.18), residues: 704
  sheet: -3.38 (0.61), residues: 55
  loop : -2.23 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.039   0.002   ARG F  92 
 TYR   0.025   0.003   TYR K 183 
 PHE   0.032   0.004   PHE A  78 
 TRP   0.013   0.002   TRP K 305 
 HIS   0.023   0.003   HIS K 182 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00633 /  0.32 (16145)
  covalent geometry    : angle       0.99504 /  0.55 (23055)
  hydrogen bonds       : bond        0.09551 /  6.25 (  887)
  hydrogen bonds       : angle       4.77799 /  3.42 ( 2270)
  Misc. bond           : bond        0.00036 /  0.02 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 328
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.7553 (mt) cc_final: 0.7013 (mt)
REVERT: A   93 GLN cc_start: 0.7219 (tt0) cc_final: 0.6932 (tt0)
REVERT: B   52 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7073 (mp0)
REVERT: B   88 TYR cc_start: 0.8434 (m-80) cc_final: 0.8076 (m-80)
REVERT: B   95 ARG cc_start: 0.8722 (ptp-110) cc_final: 0.8429 (ptp-110)
REVERT: C   75 LYS cc_start: 0.7550 (mmtp) cc_final: 0.7287 (mmmt)
REVERT: D   42 LEU cc_start: 0.8267 (tp) cc_final: 0.7916 (tp)
REVERT: D   92 GLN cc_start: 0.8452 (pt0) cc_final: 0.7363 (pm20)
REVERT: D  100 PRO cc_start: 0.8478 (Cg_endo) cc_final: 0.6877 (Cg_exo)
REVERT: D  106 HIS cc_start: 0.7581 (m-70) cc_final: 0.7259 (m-70)
REVERT: E   99 TYR cc_start: 0.8928 (t80) cc_final: 0.8662 (t80)
REVERT: E  105 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8510 (tm-30)
REVERT: E  106 ASP cc_start: 0.8487 (m-30) cc_final: 0.8205 (m-30)
REVERT: E  110 CYS cc_start: 0.7359 (m) cc_final: 0.7131 (m)
REVERT: E  123 ASP cc_start: 0.7548 (m-30) cc_final: 0.7191 (m-30)
REVERT: F   84 MET cc_start: 0.7607 (mmp) cc_final: 0.7108 (mmm)
REVERT: G   82 HIS cc_start: 0.8127 (m90) cc_final: 0.7817 (m90)
REVERT: G   84 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7683 (tm-30)
REVERT: G   94 ASN cc_start: 0.9286 (t0) cc_final: 0.9074 (t0)
REVERT: G  101 THR cc_start: 0.8937 (m) cc_final: 0.8593 (t)
REVERT: H  103 LEU cc_start: 0.7521 (pp) cc_final: 0.6896 (pp)
REVERT: L    1 MET cc_start: 0.1982 (ttp) cc_final: 0.1139 (ttt)
REVERT: L   24 GLU cc_start: 0.8205 (tt0) cc_final: 0.7620 (mm-30)
REVERT: L   62 GLN cc_start: 0.7635 (tp40) cc_final: 0.7399 (tp-100)
REVERT: K   66 LYS cc_start: 0.7955 (mppt) cc_final: 0.7445 (pttt)
REVERT: K   96 MET cc_start: 0.0912 (ttp) cc_final: -0.0473 (tpt)
REVERT: K  153 MET cc_start: 0.2293 (ttt) cc_final: 0.1988 (tmm)
REVERT: K  205 TRP cc_start: 0.7466 (m100) cc_final: 0.6788 (m100)
REVERT: K  241 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8446 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 331
  average time/residue: 0.1361
  time to fit residues: 63.4957
Evaluate side-chains
  268 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 266
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 88 optimal weight:   30.0000
   chunk 18 optimal weight:    0.0670
   chunk 41 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   chunk 102 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 101 optimal weight:   10.0000
   overall best weight:    0.7118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  79 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.175053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.146425 restraints weight = 54545.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.149683 restraints weight = 32260.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.151601 restraints weight = 22780.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.152719 restraints weight = 18461.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.153481 restraints weight = 16333.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.5915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  16146  Z= 0.161
  Angle     :  0.748   9.478  23055  Z= 0.418
  Chirality :  0.051   0.370   2607
  Planarity :  0.006   0.068   1920
  Dihedral  : 32.400 146.244   4447
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 18.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.85 (0.24), residues: 1143
  helix:  0.49 (0.19), residues: 698
  sheet: -2.95 (0.66), residues: 55
  loop : -2.10 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  92 
 TYR   0.028   0.002   TYR A  54 
 PHE   0.033   0.003   PHE G  25 
 TRP   0.008   0.001   TRP K 208 
 HIS   0.010   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.16 (16145)
  covalent geometry    : angle       0.74839 /  0.42 (23055)
  hydrogen bonds       : bond        0.05626 /  3.73 (  887)
  hydrogen bonds       : angle       4.18982 /  3.00 ( 2270)
  Misc. bond           : bond        0.00006 /  0.00 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 0.433 
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: A  115 LYS cc_start: 0.7396 (mptt) cc_final: 0.7118 (mmtm)
REVERT: B   88 TYR cc_start: 0.8349 (m-80) cc_final: 0.8134 (m-80)
REVERT: B   95 ARG cc_start: 0.8642 (ptp-110) cc_final: 0.8381 (ptp-110)
REVERT: D   42 LEU cc_start: 0.8169 (tp) cc_final: 0.7920 (tp)
REVERT: D   85 THR cc_start: 0.8709 (m) cc_final: 0.8264 (p)
REVERT: D   92 GLN cc_start: 0.8418 (pt0) cc_final: 0.7962 (pt0)
REVERT: D  103 LEU cc_start: 0.9317 (tp) cc_final: 0.8884 (tp)
REVERT: D  106 HIS cc_start: 0.7717 (m-70) cc_final: 0.7213 (m-70)
REVERT: D  119 THR cc_start: 0.8933 (p) cc_final: 0.8668 (p)
REVERT: E   99 TYR cc_start: 0.9141 (t80) cc_final: 0.8593 (t80)
REVERT: G   82 HIS cc_start: 0.8104 (m90) cc_final: 0.7766 (m-70)
REVERT: G   92 GLU cc_start: 0.8299 (tp30) cc_final: 0.8068 (tp30)
REVERT: G  101 THR cc_start: 0.8824 (m) cc_final: 0.8523 (t)
REVERT: H   70 ILE cc_start: 0.9001 (mm) cc_final: 0.8593 (mp)
REVERT: H   76 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8061 (ttm110)
REVERT: L    1 MET cc_start: 0.1539 (ttp) cc_final: 0.0702 (ttt)
REVERT: L   24 GLU cc_start: 0.8168 (tt0) cc_final: 0.7579 (mm-30)
REVERT: L   62 GLN cc_start: 0.7644 (tp40) cc_final: 0.7270 (tp40)
REVERT: K   66 LYS cc_start: 0.7962 (mppt) cc_final: 0.7445 (pttt)
REVERT: K   96 MET cc_start: 0.0619 (ttp) cc_final: -0.0448 (tpt)
REVERT: K  153 MET cc_start: 0.2271 (ttt) cc_final: 0.1845 (ttt)
REVERT: K  179 CYS cc_start: 0.2192 (m) cc_final: 0.0985 (m)
REVERT: K  205 TRP cc_start: 0.7387 (m100) cc_final: 0.6894 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 328
  average time/residue: 0.1301
  time to fit residues: 61.3701
Evaluate side-chains
  263 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 87 optimal weight:   50.0000
   chunk 59 optimal weight:    9.9990
   chunk 42 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 72 optimal weight:   40.0000
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
D 106 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 234 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.174625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.146646 restraints weight = 53018.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.149947 restraints weight = 30975.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.151981 restraints weight = 21604.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.153227 restraints weight = 17235.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.153856 restraints weight = 15039.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6398
moved from start:          0.6203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  16146  Z= 0.149
  Angle     :  0.717  11.617  23055  Z= 0.401
  Chirality :  0.050   0.363   2607
  Planarity :  0.005   0.061   1920
  Dihedral  : 32.147 144.945   4447
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.58 (0.25), residues: 1143
  helix:  0.69 (0.19), residues: 708
  sheet: -2.78 (0.68), residues: 55
  loop : -2.03 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  36 
 TYR   0.015   0.002   TYR B  72 
 PHE   0.030   0.002   PHE B 100 
 TRP   0.008   0.001   TRP K 208 
 HIS   0.004   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.15 (16145)
  covalent geometry    : angle       0.71750 /  0.40 (23055)
  hydrogen bonds       : bond        0.05260 /  3.49 (  887)
  hydrogen bonds       : angle       4.00761 /  2.88 ( 2270)
  Misc. bond           : bond        0.00003 /  0.00 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 0.464 
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: A  115 LYS cc_start: 0.7518 (mptt) cc_final: 0.7219 (mmtm)
REVERT: B   91 LYS cc_start: 0.8902 (tptt) cc_final: 0.8398 (tttm)
REVERT: B   95 ARG cc_start: 0.8647 (ptp-110) cc_final: 0.8360 (ptp-110)
REVERT: B  100 PHE cc_start: 0.8614 (m-10) cc_final: 0.8414 (m-10)
REVERT: D   85 THR cc_start: 0.8707 (m) cc_final: 0.8294 (p)
REVERT: D   92 GLN cc_start: 0.8476 (pt0) cc_final: 0.7991 (pt0)
REVERT: E   99 TYR cc_start: 0.8956 (t80) cc_final: 0.8506 (t80)
REVERT: E  105 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8226 (tm-30)
REVERT: E  106 ASP cc_start: 0.8090 (m-30) cc_final: 0.7490 (m-30)
REVERT: F   59 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8505 (mmmt)
REVERT: G   71 ARG cc_start: 0.8418 (mmp80) cc_final: 0.7499 (mmp80)
REVERT: G   75 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7831 (mmtt)
REVERT: G   79 ILE cc_start: 0.7449 (tt) cc_final: 0.6927 (tt)
REVERT: G   82 HIS cc_start: 0.8057 (m90) cc_final: 0.7486 (m90)
REVERT: G   84 GLN cc_start: 0.8207 (tp40) cc_final: 0.7392 (tm-30)
REVERT: G  101 THR cc_start: 0.8828 (m) cc_final: 0.8537 (t)
REVERT: H   76 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7977 (ttm110)
REVERT: L    1 MET cc_start: 0.1605 (ttp) cc_final: 0.0797 (ttt)
REVERT: L   24 GLU cc_start: 0.8170 (tt0) cc_final: 0.7560 (mm-30)
REVERT: L   62 GLN cc_start: 0.7796 (tp40) cc_final: 0.7453 (tp40)
REVERT: K   53 LEU cc_start: 0.5948 (tp) cc_final: 0.5548 (mt)
REVERT: K   66 LYS cc_start: 0.7925 (mppt) cc_final: 0.7442 (pttt)
REVERT: K   96 MET cc_start: 0.0508 (ttp) cc_final: -0.1101 (tpt)
REVERT: K  179 CYS cc_start: 0.2415 (m) cc_final: 0.1141 (m)
REVERT: K  205 TRP cc_start: 0.7220 (m100) cc_final: 0.6869 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1380
  time to fit residues: 64.1086
Evaluate side-chains
  270 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 130 optimal weight:   10.0000
   chunk 75 optimal weight:   20.0000
   chunk 31 optimal weight:    0.7980
   chunk 129 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 131 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 111 optimal weight:    0.8980
   chunk 80 optimal weight:   30.0000
   chunk 73 optimal weight:   30.0000
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
D  79 HIS
E  39 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 146 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 = 0.4595 r_free = 0.4595 target = 0.172701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.143596 restraints weight = 53631.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.146854 restraints weight = 31341.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.148841 restraints weight = 21984.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.149997 restraints weight = 17694.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.150613 restraints weight = 15621.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6495
moved from start:          0.6574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082  16146  Z= 0.155
  Angle     :  0.719   9.156  23055  Z= 0.399
  Chirality :  0.050   0.380   2607
  Planarity :  0.005   0.060   1920
  Dihedral  : 32.034 144.138   4447
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.90 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.44 (0.25), residues: 1143
  helix:  0.77 (0.19), residues: 708
  sheet: -2.72 (0.70), residues: 55
  loop : -1.91 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 129 
 TYR   0.020   0.002   TYR A  54 
 PHE   0.024   0.002   PHE B 100 
 TRP   0.007   0.001   TRP K 208 
 HIS   0.003   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.16 (16145)
  covalent geometry    : angle       0.71919 /  0.40 (23055)
  hydrogen bonds       : bond        0.05207 /  3.46 (  887)
  hydrogen bonds       : angle       3.95624 /  2.85 ( 2270)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 321
  time to evaluate  : 0.451 
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: A   93 GLN cc_start: 0.7387 (tt0) cc_final: 0.7150 (tt0)
REVERT: A  115 LYS cc_start: 0.7622 (mptt) cc_final: 0.7384 (mmtm)
REVERT: B  100 PHE cc_start: 0.8614 (m-10) cc_final: 0.8396 (m-10)
REVERT: C   57 TYR cc_start: 0.8629 (t80) cc_final: 0.8188 (t80)
REVERT: C   75 LYS cc_start: 0.7311 (mmtt) cc_final: 0.6970 (mmmt)
REVERT: D   85 THR cc_start: 0.8803 (m) cc_final: 0.8402 (p)
REVERT: D   88 SER cc_start: 0.8483 (p) cc_final: 0.8025 (m)
REVERT: D   92 GLN cc_start: 0.8560 (pt0) cc_final: 0.8006 (pt0)
REVERT: D  103 LEU cc_start: 0.9270 (tp) cc_final: 0.9067 (tp)
REVERT: D  106 HIS cc_start: 0.8026 (m90) cc_final: 0.7496 (m90)
REVERT: E   99 TYR cc_start: 0.8933 (t80) cc_final: 0.8434 (t80)
REVERT: E  131 ARG cc_start: 0.8565 (mmt90) cc_final: 0.8314 (tpp-160)
REVERT: F   59 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8629 (mmmt)
REVERT: F   71 THR cc_start: 0.7798 (p) cc_final: 0.7593 (p)
REVERT: G   71 ARG cc_start: 0.8458 (mmp80) cc_final: 0.8083 (mmp80)
REVERT: G   75 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7870 (mmtt)
REVERT: G   79 ILE cc_start: 0.7514 (tt) cc_final: 0.6998 (tt)
REVERT: G   82 HIS cc_start: 0.8134 (m90) cc_final: 0.7604 (m90)
REVERT: G  101 THR cc_start: 0.8799 (m) cc_final: 0.8498 (t)
REVERT: H   52 SER cc_start: 0.6477 (m) cc_final: 0.5908 (m)
REVERT: H   76 ARG cc_start: 0.8322 (ttm110) cc_final: 0.7639 (ttm110)
REVERT: L    1 MET cc_start: 0.1809 (ttp) cc_final: 0.1025 (ttt)
REVERT: L   24 GLU cc_start: 0.8147 (tt0) cc_final: 0.7508 (mm-30)
REVERT: L   62 GLN cc_start: 0.7891 (tp40) cc_final: 0.7573 (tp40)
REVERT: K   53 LEU cc_start: 0.6020 (tp) cc_final: 0.5619 (mt)
REVERT: K   66 LYS cc_start: 0.7923 (mppt) cc_final: 0.7399 (pttt)
REVERT: K   96 MET cc_start: 0.0746 (ttp) cc_final: -0.0030 (tpp)
REVERT: K  179 CYS cc_start: 0.3312 (m) cc_final: 0.2262 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 321
  average time/residue: 0.1351
  time to fit residues: 61.7171
Evaluate side-chains
  262 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 261
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 88 optimal weight:   30.0000
   chunk 30 optimal weight:    0.7980
   chunk 109 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 182 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.171869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.142588 restraints weight = 52934.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.145770 restraints weight = 31068.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.147700 restraints weight = 21946.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.148842 restraints weight = 17712.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.149388 restraints weight = 15667.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.6860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  16146  Z= 0.154
  Angle     :  0.726   9.656  23055  Z= 0.401
  Chirality :  0.050   0.390   2607
  Planarity :  0.005   0.060   1920
  Dihedral  : 31.946 143.515   4447
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.37 (0.25), residues: 1143
  helix:  0.79 (0.19), residues: 708
  sheet: -2.54 (0.73), residues: 53
  loop : -1.84 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B  55 
 TYR   0.021   0.002   TYR C  50 
 PHE   0.034   0.002   PHE G  25 
 TRP   0.015   0.002   TRP K 205 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.15 (16145)
  covalent geometry    : angle       0.72579 /  0.40 (23055)
  hydrogen bonds       : bond        0.05055 /  3.37 (  887)
  hydrogen bonds       : angle       3.94323 /  2.83 ( 2270)
  Misc. bond           : bond        0.00042 /  0.03 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 0.438 
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: A   51 ILE cc_start: 0.7577 (mt) cc_final: 0.7245 (mt)
REVERT: A   93 GLN cc_start: 0.7568 (tt0) cc_final: 0.7330 (tt0)
REVERT: A  115 LYS cc_start: 0.7707 (mptt) cc_final: 0.7443 (mmtm)
REVERT: B  100 PHE cc_start: 0.8570 (m-10) cc_final: 0.8296 (m-10)
REVERT: C   75 LYS cc_start: 0.7357 (mmtt) cc_final: 0.7074 (mmmt)
REVERT: D  103 LEU cc_start: 0.8867 (tp) cc_final: 0.8625 (tp)
REVERT: E   99 TYR cc_start: 0.8913 (t80) cc_final: 0.8487 (t80)
REVERT: F   68 ASP cc_start: 0.6670 (m-30) cc_final: 0.5674 (m-30)
REVERT: F   84 MET cc_start: 0.7775 (mmp) cc_final: 0.7482 (mmm)
REVERT: G   75 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7877 (mmtt)
REVERT: G   79 ILE cc_start: 0.7622 (tt) cc_final: 0.7057 (tt)
REVERT: G   82 HIS cc_start: 0.8076 (m90) cc_final: 0.7657 (m90)
REVERT: G  101 THR cc_start: 0.8795 (m) cc_final: 0.8480 (t)
REVERT: H   76 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7977 (ttm110)
REVERT: L    1 MET cc_start: 0.1580 (ttp) cc_final: 0.0751 (ttt)
REVERT: L   62 GLN cc_start: 0.7869 (tp40) cc_final: 0.7569 (tp40)
REVERT: K   46 GLU cc_start: 0.5311 (tp30) cc_final: 0.5080 (tp30)
REVERT: K   53 LEU cc_start: 0.6021 (tp) cc_final: 0.5618 (mt)
REVERT: K   66 LYS cc_start: 0.7933 (mppt) cc_final: 0.7410 (pttt)
REVERT: K   96 MET cc_start: 0.0753 (ttp) cc_final: -0.0093 (tpp)
REVERT: K  281 SER cc_start: 0.9054 (t) cc_final: 0.8652 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 317
  average time/residue: 0.1280
  time to fit residues: 58.8666
Evaluate side-chains
  254 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 137 optimal weight:    6.9990
   chunk 125 optimal weight:    2.9990
   chunk 87 optimal weight:   50.0000
   chunk 21 optimal weight:    0.6980
   chunk 70 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 47 optimal weight:    6.9990
   chunk 98 optimal weight:   30.0000
   overall best weight:    1.5984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN
** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.168051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.138443 restraints weight = 53143.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.141476 restraints weight = 31293.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.143209 restraints weight = 22184.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.144344 restraints weight = 18159.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.144877 restraints weight = 16131.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.7428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089  16146  Z= 0.171
  Angle     :  0.741   9.083  23055  Z= 0.408
  Chirality :  0.050   0.362   2607
  Planarity :  0.005   0.061   1920
  Dihedral  : 31.842 142.861   4447
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.30 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.30 (0.25), residues: 1143
  helix:  0.86 (0.19), residues: 711
  sheet: -2.52 (0.73), residues: 53
  loop : -1.87 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  55 
 TYR   0.025   0.002   TYR B  88 
 PHE   0.020   0.002   PHE G  25 
 TRP   0.025   0.002   TRP K 205 
 HIS   0.003   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.17 (16145)
  covalent geometry    : angle       0.74082 /  0.41 (23055)
  hydrogen bonds       : bond        0.05275 /  3.49 (  887)
  hydrogen bonds       : angle       3.96708 /  2.86 ( 2270)
  Misc. bond           : bond        0.00029 /  0.02 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 308
  time to evaluate  : 0.447 
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: A   90 MET cc_start: 0.8258 (ppp) cc_final: 0.7678 (ppp)
REVERT: B  100 PHE cc_start: 0.8544 (m-10) cc_final: 0.8242 (m-10)
REVERT: C   75 LYS cc_start: 0.7422 (mmtt) cc_final: 0.7155 (mmmt)
REVERT: D   76 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7576 (mtp180)
REVERT: D   83 ARG cc_start: 0.8395 (mmp80) cc_final: 0.8124 (mmp80)
REVERT: D   85 THR cc_start: 0.8855 (m) cc_final: 0.8370 (p)
REVERT: D   92 GLN cc_start: 0.7931 (pt0) cc_final: 0.7659 (pt0)
REVERT: D  103 LEU cc_start: 0.8783 (tp) cc_final: 0.8496 (tp)
REVERT: D  106 HIS cc_start: 0.7850 (m90) cc_final: 0.7423 (m-70)
REVERT: E   99 TYR cc_start: 0.8953 (t80) cc_final: 0.8542 (t80)
REVERT: F   84 MET cc_start: 0.7816 (mmp) cc_final: 0.7510 (mmm)
REVERT: G   71 ARG cc_start: 0.8517 (mmp80) cc_final: 0.7603 (mmp80)
REVERT: G   75 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7892 (mmtt)
REVERT: G   79 ILE cc_start: 0.7689 (tt) cc_final: 0.7303 (tt)
REVERT: G   84 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7594 (tm-30)
REVERT: G   97 LEU cc_start: 0.8649 (mp) cc_final: 0.8371 (mp)
REVERT: G  101 THR cc_start: 0.8745 (m) cc_final: 0.8454 (t)
REVERT: H   76 ARG cc_start: 0.8486 (ttm110) cc_final: 0.7867 (ttm110)
REVERT: L    1 MET cc_start: 0.1280 (ttp) cc_final: 0.0441 (ttt)
REVERT: L   62 GLN cc_start: 0.7927 (tp40) cc_final: 0.7629 (tp40)
REVERT: K   53 LEU cc_start: 0.6075 (tp) cc_final: 0.5635 (mt)
REVERT: K   66 LYS cc_start: 0.7933 (mppt) cc_final: 0.7395 (pttt)
REVERT: K   96 MET cc_start: 0.0648 (ttp) cc_final: -0.0194 (tpp)
REVERT: K  153 MET cc_start: 0.3746 (ppp) cc_final: 0.2770 (ppp)
REVERT: K  205 TRP cc_start: 0.7270 (m100) cc_final: 0.6743 (m100)
REVERT: K  281 SER cc_start: 0.9060 (t) cc_final: 0.8591 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 308
  average time/residue: 0.1314
  time to fit residues: 58.3315
Evaluate side-chains
  256 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 255
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:   20.0000
   chunk 76 optimal weight:   30.0000
   chunk 93 optimal weight:   30.0000
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 81 optimal weight:   20.0000
   chunk 74 optimal weight:   20.0000
   chunk 111 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.165382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.135282 restraints weight = 52659.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.138259 restraints weight = 31035.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.140055 restraints weight = 22003.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.141108 restraints weight = 17909.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.141606 restraints weight = 15936.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.7924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105  16146  Z= 0.181
  Angle     :  0.753   9.633  23055  Z= 0.416
  Chirality :  0.052   0.540   2607
  Planarity :  0.006   0.067   1920
  Dihedral  : 31.805 142.631   4447
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.38 (0.25), residues: 1143
  helix:  0.83 (0.19), residues: 712
  sheet: -2.57 (0.73), residues: 52
  loop : -1.99 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 131 
 TYR   0.026   0.002   TYR D  80 
 PHE   0.023   0.002   PHE B 100 
 TRP   0.017   0.001   TRP K 205 
 HIS   0.014   0.001   HIS G  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.18 (16145)
  covalent geometry    : angle       0.75262 /  0.42 (23055)
  hydrogen bonds       : bond        0.05400 /  3.55 (  887)
  hydrogen bonds       : angle       3.96767 /  2.88 ( 2270)
  Misc. bond           : bond        0.00014 /  0.01 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ILE cc_start: 0.7574 (mt) cc_final: 0.7272 (mt)
REVERT: A   90 MET cc_start: 0.8323 (ppp) cc_final: 0.7706 (ppp)
REVERT: A   93 GLN cc_start: 0.7889 (tt0) cc_final: 0.7686 (tt0)
REVERT: B  100 PHE cc_start: 0.8505 (m-10) cc_final: 0.8285 (m-10)
REVERT: C   75 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7370 (mmmt)
REVERT: D   83 ARG cc_start: 0.8470 (mmp80) cc_final: 0.8174 (mmp80)
REVERT: D   85 THR cc_start: 0.8909 (m) cc_final: 0.8438 (p)
REVERT: D  106 HIS cc_start: 0.7907 (m90) cc_final: 0.7282 (m-70)
REVERT: E   99 TYR cc_start: 0.9049 (t80) cc_final: 0.8408 (t80)
REVERT: E  110 CYS cc_start: 0.8023 (m) cc_final: 0.7297 (m)
REVERT: E  123 ASP cc_start: 0.7935 (m-30) cc_final: 0.7657 (t70)
REVERT: F   84 MET cc_start: 0.8008 (mmp) cc_final: 0.7684 (mmm)
REVERT: G   75 LYS cc_start: 0.8380 (mmtt) cc_final: 0.7814 (mmtt)
REVERT: G   84 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7318 (tm-30)
REVERT: G  101 THR cc_start: 0.8807 (m) cc_final: 0.8563 (t)
REVERT: H   76 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8031 (ttm110)
REVERT: L    1 MET cc_start: 0.1651 (ttp) cc_final: 0.0829 (ttt)
REVERT: L   62 GLN cc_start: 0.7928 (tp40) cc_final: 0.7639 (tp40)
REVERT: K   53 LEU cc_start: 0.6249 (tp) cc_final: 0.5838 (mt)
REVERT: K   66 LYS cc_start: 0.7940 (mppt) cc_final: 0.7415 (pttt)
REVERT: K   96 MET cc_start: 0.0574 (ttp) cc_final: -0.0085 (tpp)
REVERT: K  205 TRP cc_start: 0.7321 (m100) cc_final: 0.6890 (m100)
REVERT: K  281 SER cc_start: 0.9102 (t) cc_final: 0.8612 (m)
REVERT: K  291 MET cc_start: 0.5849 (pmm) cc_final: 0.5647 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 313
  average time/residue: 0.1260
  time to fit residues: 56.7518
Evaluate side-chains
  268 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 86 optimal weight:   50.0000
   chunk 30 optimal weight:    0.9990
   chunk 80 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9980
   chunk 133 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 8 optimal weight:    0.7980
   chunk 77 optimal weight:   20.0000
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 ASN
D  79 HIS
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.165321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.135455 restraints weight = 52169.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.138544 restraints weight = 30289.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.140380 restraints weight = 21194.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.141510 restraints weight = 17113.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.142037 restraints weight = 15106.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.8213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  16146  Z= 0.151
  Angle     :  0.750  10.122  23055  Z= 0.409
  Chirality :  0.050   0.362   2607
  Planarity :  0.005   0.051   1920
  Dihedral  : 31.725 142.074   4447
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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 (0.25), residues: 1143
  helix:  0.89 (0.19), residues: 705
  sheet: -2.18 (0.77), residues: 50
  loop : -1.87 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 134 
 TYR   0.018   0.002   TYR D  37 
 PHE   0.031   0.002   PHE K 326 
 TRP   0.021   0.001   TRP K 205 
 HIS   0.009   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.15 (16145)
  covalent geometry    : angle       0.74978 /  0.41 (23055)
  hydrogen bonds       : bond        0.04899 /  3.27 (  887)
  hydrogen bonds       : angle       3.89025 /  2.84 ( 2270)
  Misc. bond           : bond        0.00030 /  0.02 (    1)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 324
  time to evaluate  : 0.423 
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: A   51 ILE cc_start: 0.7558 (mt) cc_final: 0.7204 (mt)
REVERT: A   90 MET cc_start: 0.8398 (ppp) cc_final: 0.7946 (ppp)
REVERT: B   58 LEU cc_start: 0.8755 (tt) cc_final: 0.8501 (tt)
REVERT: B  100 PHE cc_start: 0.8460 (m-10) cc_final: 0.8157 (m-10)
REVERT: D   83 ARG cc_start: 0.8449 (mmp80) cc_final: 0.8040 (mmp80)
REVERT: D   85 THR cc_start: 0.8903 (m) cc_final: 0.8474 (p)
REVERT: D  103 LEU cc_start: 0.8793 (tp) cc_final: 0.8527 (tp)
REVERT: E   73 GLU cc_start: 0.6483 (tp30) cc_final: 0.6065 (tp30)
REVERT: E   99 TYR cc_start: 0.9094 (t80) cc_final: 0.8435 (t80)
REVERT: E  133 GLU cc_start: 0.6929 (pt0) cc_final: 0.6203 (pt0)
REVERT: F   84 MET cc_start: 0.8010 (mmp) cc_final: 0.7728 (mmm)
REVERT: G   75 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7979 (mmtt)
REVERT: G   79 ILE cc_start: 0.7707 (tt) cc_final: 0.7313 (tt)
REVERT: G   82 HIS cc_start: 0.8089 (m-70) cc_final: 0.7828 (m90)
REVERT: G   84 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7488 (tm-30)
REVERT: G   92 GLU cc_start: 0.8355 (tp30) cc_final: 0.8148 (tp30)
REVERT: G  101 THR cc_start: 0.8801 (m) cc_final: 0.8570 (t)
REVERT: H   76 ARG cc_start: 0.8506 (ttm110) cc_final: 0.8082 (ttm110)
REVERT: L    1 MET cc_start: 0.1309 (ttp) cc_final: 0.0459 (ttt)
REVERT: L   62 GLN cc_start: 0.7927 (tp40) cc_final: 0.7642 (tp40)
REVERT: K   53 LEU cc_start: 0.6189 (tp) cc_final: 0.5828 (mt)
REVERT: K   66 LYS cc_start: 0.7944 (mppt) cc_final: 0.7429 (pttt)
REVERT: K   96 MET cc_start: 0.0403 (ttp) cc_final: -0.0146 (tpp)
REVERT: K  205 TRP cc_start: 0.7084 (m100) cc_final: 0.6649 (m100)
REVERT: K  278 ARG cc_start: 0.6773 (tmt170) cc_final: 0.6521 (tmt170)
REVERT: K  281 SER cc_start: 0.9011 (t) cc_final: 0.8534 (m)
REVERT: K  291 MET cc_start: 0.5913 (pmm) cc_final: 0.5692 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 324
  average time/residue: 0.1305
  time to fit residues: 61.1739
Evaluate side-chains
  271 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9990
   chunk 98 optimal weight:   30.0000
   chunk 114 optimal weight:   20.0000
   chunk 125 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 ASN
D 106 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 213 HIS ** 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 = 0.4511 r_free = 0.4511 target = 0.164356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.134883 restraints weight = 51319.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.137931 restraints weight = 29848.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.139769 restraints weight = 20875.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.140903 restraints weight = 16805.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.141433 restraints weight = 14806.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.8442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16146  Z= 0.147
  Angle     :  0.725   9.300  23055  Z= 0.399
  Chirality :  0.049   0.361   2607
  Planarity :  0.005   0.057   1920
  Dihedral  : 31.620 141.643   4447
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.18 %
    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: -0.18 (0.25), residues: 1143
  helix:  0.99 (0.19), residues: 702
  sheet: -2.24 (0.77), residues: 52
  loop : -1.85 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG A 134 
 TYR   0.036   0.002   TYR D  80 
 PHE   0.018   0.001   PHE B 100 
 TRP   0.012   0.001   TRP K 205 
 HIS   0.008   0.001   HIS G  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.15 (16145)
  covalent geometry    : angle       0.72543 /  0.40 (23055)
  hydrogen bonds       : bond        0.04914 /  3.27 (  887)
  hydrogen bonds       : angle       3.84109 /  2.79 ( 2270)
  Misc. bond           : bond        0.00003 /  0.00 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2923.27 seconds
wall clock time: 51 minutes 6.24 seconds (3066.24 seconds total)