Starting phenix.real_space_refine
on Wed Mar  4 18:32:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zg8_11196/03_2026/6zg8_11196.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zg8_11196/03_2026/6zg8_11196.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zg8_11196/03_2026/6zg8_11196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zg8_11196/03_2026/6zg8_11196.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zg8_11196/03_2026/6zg8_11196.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zg8_11196/03_2026/6zg8_11196.cif"
  }
  resolution = 3.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4996      2.51       5
     N    1257      2.21       5
     O    1417      1.98       5
     H    7965      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15672
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "G"
      Number of atoms: 4300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 4300
          Classifications: {'peptide': 272}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 266}
    Chain: "H"
      Number of atoms: 1961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1961
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 4, 'TRANS': 128}
    Chain: "I"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 764
          Classifications: {'peptide': 47}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 46}
    Chain: "K"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1078
          Classifications: {'peptide': 74}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 1096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1096
          Classifications: {'peptide': 75}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "M"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1079
          Classifications: {'peptide': 74}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "N"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1079
          Classifications: {'peptide': 74}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "O"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1079
          Classifications: {'peptide': 74}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "P"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1079
          Classifications: {'peptide': 74}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "Q"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1078
          Classifications: {'peptide': 74}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1079
          Classifications: {'peptide': 74}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 2.79, per 1000 atoms: 0.18
  Number of scatterers: 15672
  At special positions: 0
  Unit cell: (67.072, 74.408, 187.592, 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      37     16.00
     O    1417      8.00
     N    1257      7.00
     C    4996      6.00
     H    7965      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 434.6 milliseconds
  

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1868

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 3 sheets defined
      77.5% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'G' and resid 2 through 55
      removed outlier: 3.643A  pdb=" N   LYS G  39 " --> pdb=" O   GLU G  35 " (cutoff:3.500A)
      Proline residue:  G  40  - end of helix
      removed outlier: 3.607A  pdb=" N   VAL G  43 " --> pdb=" O   LYS G  39 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LEU G  51 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   TYR G  52 " --> pdb=" O   SER G  48 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 99
      removed outlier: 3.769A  pdb=" N   ALA G  99 " --> pdb=" O   ASN G  95 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 109 through 116
      removed outlier: 3.745A  pdb=" N   ARG G 113 " --> pdb=" O   GLY G 109 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 137 through 151
      removed outlier: 3.698A  pdb=" N   ALA G 141 " --> pdb=" O   THR G 137 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER G 151 " --> pdb=" O   GLU G 147 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 180 through 185
    Processing helix  chain 'G' and resid 187 through 191
    Processing helix  chain 'G' and resid 199 through 272
      removed outlier: 3.548A  pdb=" N   LYS G 245 " --> pdb=" O   GLU G 241 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU G 248 " --> pdb=" O   ASP G 244 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 103
      No H-bonds generated for 'chain 'H' and resid 101 through 103'
    Processing helix  chain 'H' and resid 104 through 119
    Processing helix  chain 'H' and resid 124 through 146
    Processing helix  chain 'I' and resid 4 through 8
    Processing helix  chain 'I' and resid 10 through 25
    Processing helix  chain 'I' and resid 29 through 39
      removed outlier: 4.258A  pdb=" N   ASN I  33 " --> pdb=" O   GLU I  29 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR I  37 " --> pdb=" O   ASN I  33 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER I  38 " --> pdb=" O   ALA I  34 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 15
      removed outlier: 4.343A  pdb=" N   PHE K   8 " --> pdb=" O   THR K   4 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 17 through 39
      removed outlier: 3.997A  pdb=" N   SER K  21 " --> pdb=" O   GLY K  17 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE K  33 " --> pdb=" O   PHE K  29 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 42 through 73
      removed outlier: 3.943A  pdb=" N   LEU K  46 " --> pdb=" O   LEU K  42 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   CYS K  64 " --> pdb=" O   MET K  60 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU K  65 " --> pdb=" O   GLY K  61 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2 through 15
      removed outlier: 3.788A  pdb=" N   PHE L   8 " --> pdb=" O   THR L   4 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE L   9 " --> pdb=" O   ALA L   5 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 17 through 39
      removed outlier: 3.738A  pdb=" N   SER L  21 " --> pdb=" O   GLY L  17 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 42 through 74
      removed outlier: 3.748A  pdb=" N   GLY L  61 " --> pdb=" O   SER L  57 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE L  63 " --> pdb=" O   ALA L  59 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   CYS L  64 " --> pdb=" O   MET L  60 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   LEU L  65 " --> pdb=" O   GLY L  61 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 2 through 15
    Processing helix  chain 'M' and resid 18 through 39
      removed outlier: 3.708A  pdb=" N   ILE M  33 " --> pdb=" O   PHE M  29 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 42 through 73
      removed outlier: 3.991A  pdb=" N   MET M  60 " --> pdb=" O   LEU M  56 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY M  61 " --> pdb=" O   SER M  57 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2 through 15
    Processing helix  chain 'N' and resid 18 through 38
      removed outlier: 3.513A  pdb=" N   ILE N  33 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 39 through 41
      No H-bonds generated for 'chain 'N' and resid 39 through 41'
    Processing helix  chain 'N' and resid 42 through 73
      removed outlier: 4.340A  pdb=" N   MET N  60 " --> pdb=" O   LEU N  56 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLY N  61 " --> pdb=" O   SER N  57 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 2 through 15
    Processing helix  chain 'O' and resid 17 through 39
      removed outlier: 3.831A  pdb=" N   SER O  21 " --> pdb=" O   GLY O  17 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE O  33 " --> pdb=" O   PHE O  29 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 42 through 73
      removed outlier: 4.732A  pdb=" N   MET O  60 " --> pdb=" O   LEU O  56 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLY O  61 " --> pdb=" O   SER O  57 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 15
      removed outlier: 3.993A  pdb=" N   PHE P   8 " --> pdb=" O   THR P   4 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA P  11 " --> pdb=" O   LYS P   7 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 17 through 39
      removed outlier: 3.914A  pdb=" N   SER P  21 " --> pdb=" O   GLY P  17 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE P  33 " --> pdb=" O   PHE P  29 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 42 through 74
      removed outlier: 4.989A  pdb=" N   MET P  60 " --> pdb=" O   LEU P  56 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLY P  61 " --> pdb=" O   SER P  57 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 2 through 16
      removed outlier: 3.647A  pdb=" N   THR Q  15 " --> pdb=" O   ALA Q  11 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL Q  16 " --> pdb=" O   GLY Q  12 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 17 through 39
      removed outlier: 4.097A  pdb=" N   SER Q  21 " --> pdb=" O   GLY Q  17 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASN Q  39 " --> pdb=" O   GLY Q  35 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 42 through 71
      removed outlier: 4.813A  pdb=" N   MET Q  60 " --> pdb=" O   LEU Q  56 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLY Q  61 " --> pdb=" O   SER Q  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 2 through 15
    Processing helix  chain 'R' and resid 17 through 39
      removed outlier: 4.195A  pdb=" N   SER R  21 " --> pdb=" O   GLY R  17 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ILE R  33 " --> pdb=" O   PHE R  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 74
      removed outlier: 5.443A  pdb=" N   MET R  60 " --> pdb=" O   LEU R  56 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLY R  61 " --> pdb=" O   SER R  57 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179
      removed outlier: 5.300A  pdb=" N   ASN G 163 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   HIS G  66 " --> pdb=" O   LYS G 104 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   ILE G 106 " --> pdb=" O   HIS G  66 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ILE G  68 " --> pdb=" O   ILE G 106 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   VAL G 108 " --> pdb=" O   ILE G  68 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   GLY G  70 " --> pdb=" O   VAL G 108 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   LEU G 125 " --> pdb=" O   VAL G 103 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   ILE G 105 " --> pdb=" O   LEU G 125 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   THR G 127 " --> pdb=" O   ILE G 105 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   GLY G 107 " --> pdb=" O   THR G 127 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   LYS G 129 " --> pdb=" O   GLY G 107 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   THR G 127 " --> pdb=" O   VAL I  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 26 through 31
      removed outlier: 5.030A  pdb=" N   PHE H  18 " --> pdb=" O   SER H  30 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   SER H  17 " --> pdb=" O   VAL H  90 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   LEU H  92 " --> pdb=" O   SER H  17 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   THR H  19 " --> pdb=" O   LEU H  92 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   ALA H  94 " --> pdb=" O   THR H  19 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   ALA H  21 " --> pdb=" O   ALA H  94 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 44 through 47
      removed outlier: 6.933A  pdb=" N   HIS H  66 " --> pdb=" O   ARG H  34 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL H  36 " --> pdb=" O   VAL H  64 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   VAL H  64 " --> pdb=" O   VAL H  36 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   VAL H  38 " --> pdb=" O   LEU H  62 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   LEU H  62 " --> pdb=" O   VAL H  38 " (cutoff:3.500A)

    648 hydrogen bonds defined for protein.
    1920 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.47

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7811
        1.03 -     1.23: 186
        1.23 -     1.42: 3159
        1.42 -     1.62: 4567
        1.62 -     1.81: 64
  Bond restraints: 15787
  Sorted by residual:
  bond pdb=" CA  M3L N  43 "
       pdb=" HA  M3L N  43 "
    ideal  model  delta    sigma   weight residual
    0.970  1.134 -0.164 2.00e-02 2.50e+03 6.71e+01
  bond pdb=" CA  M3L P  43 "
       pdb=" HA  M3L P  43 "
    ideal  model  delta    sigma   weight residual
    0.970  1.134 -0.164 2.00e-02 2.50e+03 6.69e+01
  bond pdb=" CA  M3L Q  43 "
       pdb=" HA  M3L Q  43 "
    ideal  model  delta    sigma   weight residual
    0.970  1.133 -0.163 2.00e-02 2.50e+03 6.65e+01
  bond pdb=" CA  M3L M  43 "
       pdb=" HA  M3L M  43 "
    ideal  model  delta    sigma   weight residual
    0.970  1.133 -0.163 2.00e-02 2.50e+03 6.64e+01
  bond pdb=" CA  M3L O  43 "
       pdb=" HA  M3L O  43 "
    ideal  model  delta    sigma   weight residual
    0.970  1.133 -0.163 2.00e-02 2.50e+03 6.62e+01
  ... (remaining 15782 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 28081
        1.71 -     3.41: 432
        3.41 -     5.12: 45
        5.12 -     6.82: 7
        6.82 -     8.53: 2
  Bond angle restraints: 28567
  Sorted by residual:
  angle pdb=" N   THR H  40 "
        pdb=" CA  THR H  40 "
        pdb=" C   THR H  40 "
      ideal   model   delta    sigma   weight residual
     111.71  116.82   -5.11 1.34e+00 5.57e-01 1.46e+01
  angle pdb=" C   GLY L  53 "
        pdb=" N   PHE L  54 "
        pdb=" CA  PHE L  54 "
      ideal   model   delta    sigma   weight residual
     120.31  115.33    4.98 1.52e+00 4.33e-01 1.07e+01
  angle pdb=" N   ILE G 169 "
        pdb=" CA  ILE G 169 "
        pdb=" C   ILE G 169 "
      ideal   model   delta    sigma   weight residual
     112.96  109.81    3.15 1.00e+00 1.00e+00 9.89e+00
  angle pdb=" N   PHE L  54 "
        pdb=" CA  PHE L  54 "
        pdb=" CB  PHE L  54 "
      ideal   model   delta    sigma   weight residual
     110.28  114.74   -4.46 1.55e+00 4.16e-01 8.27e+00
  angle pdb=" N   GLU K  58 "
        pdb=" CA  GLU K  58 "
        pdb=" CB  GLU K  58 "
      ideal   model   delta    sigma   weight residual
     110.22  114.51   -4.29 1.54e+00 4.22e-01 7.76e+00
  ... (remaining 28562 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 6483
       17.90 -    35.81: 570
       35.81 -    53.71: 234
       53.71 -    71.61: 73
       71.61 -    89.51: 14
  Dihedral angle restraints: 7374
    sinusoidal: 3943
      harmonic: 3431
  Sorted by residual:
  dihedral pdb=" CA  LEU R  56 "
           pdb=" C   LEU R  56 "
           pdb=" N   SER R  57 "
           pdb=" CA  SER R  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.66   22.34     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  ILE I  44 "
           pdb=" C   ILE I  44 "
           pdb=" N   VAL I  45 "
           pdb=" CA  VAL I  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.30   19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ALA H  21 "
           pdb=" C   ALA H  21 "
           pdb=" N   SER H  22 "
           pdb=" CA  SER H  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.36   19.64     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 7371 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 824
       0.035 -    0.070: 313
       0.070 -    0.105: 72
       0.105 -    0.140: 38
       0.140 -    0.175: 4
  Chirality restraints: 1251
  Sorted by residual:
  chirality pdb=" CG  LEU R  56 "
            pdb=" CB  LEU R  56 "
            pdb=" CD1 LEU R  56 "
            pdb=" CD2 LEU R  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  MET K  60 "
            pdb=" N   MET K  60 "
            pdb=" C   MET K  60 "
            pdb=" CB  MET K  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" CA  M3L M  43 "
            pdb=" N   M3L M  43 "
            pdb=" C   M3L M  43 "
            pdb=" CB  M3L M  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.87e-01
  ... (remaining 1248 not shown)

  Planarity restraints: 2335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU L  52 "    0.009 2.00e-02 2.50e+03   1.90e-02 3.61e+00
        pdb=" C   LEU L  52 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   LEU L  52 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLY L  53 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE K  54 "   -0.013 2.00e-02 2.50e+03   1.04e-02 3.22e+00
        pdb=" CG  PHE K  54 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE K  54 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE K  54 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE K  54 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE K  54 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE K  54 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD1 PHE K  54 "    0.002 2.00e-02 2.50e+03
        pdb=" HD2 PHE K  54 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 PHE K  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE2 PHE K  54 "   -0.000 2.00e-02 2.50e+03
        pdb=" HZ  PHE K  54 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET L  66 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.07e+00
        pdb=" C   MET L  66 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   MET L  66 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL L  67 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2332 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 1674
        2.23 -     2.82: 35594
        2.82 -     3.41: 44457
        3.41 -     4.01: 58870
        4.01 -     4.60: 91524
  Nonbonded interactions: 232119
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP G  74 "
            pdb=" H   ASP G 110 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" OE1 GLN L  45 "
            pdb=" H   GLN L  45 "
     model   vdw
     1.644 2.450
  nonbonded pdb=" OD1 ASP Q   3 "
            pdb=" H   THR Q   4 "
     model   vdw
     1.660 2.450
  nonbonded pdb=" O   SER G 180 "
            pdb=" H   THR G 183 "
     model   vdw
     1.675 2.450
  nonbonded pdb=" HG1 THR G 137 "
            pdb=" O   GLY I  39 "
     model   vdw
     1.684 2.450
  ... (remaining 232114 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 'K'
  selection = (chain 'L' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ 
 name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ 
 or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ 
me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ 
 HM33)) or resid 44 through 74))
  selection = (chain 'M' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ 
 name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ 
 or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ 
me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ 
 HM33)) or resid 44 through 74))
  selection = (chain 'N' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ 
 name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ 
 or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ 
me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ 
 HM33)) or resid 44 through 74))
  selection = (chain 'O' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ 
 name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ 
 or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ 
me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ 
 HM33)) or resid 44 through 74))
  selection = (chain 'P' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ 
 name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ 
 or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ 
me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ 
 HM33)) or resid 44 through 74))
  selection = chain 'Q'
  selection = (chain 'R' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ 
 name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ 
 or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ 
me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ 
 HM33)) or resid 44 through 74))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     15.340
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
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      :  0.006   0.081   7822  Z= 0.268
  Angle     :  0.687   8.530  10565  Z= 0.383
  Chirality :  0.042   0.175   1251
  Planarity :  0.004   0.039   1321
  Dihedral  : 14.972  89.513   2712
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.27), residues: 999
  helix:  0.95 (0.19), residues: 736
  sheet: -0.79 (0.61), residues: 77
  loop : -1.94 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG G 252 
 TYR   0.016   0.002   TYR G  44 
 PHE   0.028   0.002   PHE K  54 
 TRP   0.004   0.001   TRP I   4 
 HIS   0.004   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 ( 7822)
  covalent geometry    : angle       0.68702 (10565)
  hydrogen bonds       : bond        0.10628 (  648)
  hydrogen bonds       : angle       5.01347 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   41 THR cc_start: 0.8295 (p) cc_final: 0.7961 (m)
REVERT: Q   70 LEU cc_start: 0.8055 (mt) cc_final: 0.7835 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1664
  time to fit residues: 36.2951
Evaluate side-chains
  132 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN
P  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.128558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.105266 restraints weight = 30758.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.72
r_work: 0.3167 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7822  Z= 0.151
  Angle     :  0.540   5.687  10565  Z= 0.292
  Chirality :  0.038   0.139   1251
  Planarity :  0.003   0.031   1321
  Dihedral  :  6.720  56.618   1127
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  6.92 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.27), residues: 999
  helix:  1.50 (0.19), residues: 757
  sheet: -0.84 (0.56), residues: 89
  loop : -1.42 (0.51), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 252 
 TYR   0.012   0.001   TYR G  44 
 PHE   0.030   0.002   PHE L  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.003   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7822)
  covalent geometry    : angle       0.53955 (10565)
  hydrogen bonds       : bond        0.04317 (  648)
  hydrogen bonds       : angle       3.85627 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 149
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   23 MET cc_start: 0.6733 (mmp) cc_final: 0.6523 (mtt)
REVERT: G  156 ASP cc_start: 0.8236 (m-30) cc_final: 0.7987 (m-30)
REVERT: I   41 THR cc_start: 0.8389 (p) cc_final: 0.8020 (m)
REVERT: K   15 THR cc_start: 0.8982 (t) cc_final: 0.8730 (m)
REVERT: Q   70 LEU cc_start: 0.8123 (mt) cc_final: 0.7887 (mt)
  outliers start: 5
  outliers final: 3
  residues processed: 151
  average time/residue: 0.1733
  time to fit residues: 37.0941
Evaluate side-chains
  143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 140
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain Q residue   46 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.128127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.104852 restraints weight = 31006.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.75
r_work: 0.3161 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7822  Z= 0.171
  Angle     :  0.527   6.633  10565  Z= 0.287
  Chirality :  0.038   0.140   1251
  Planarity :  0.003   0.033   1321
  Dihedral  :  6.643  58.043   1127
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.66 %
    Favored  : 89.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.27), residues: 999
  helix:  1.78 (0.19), residues: 755
  sheet: -0.89 (0.56), residues: 89
  loop : -1.48 (0.50), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 252 
 TYR   0.012   0.001   TYR G 171 
 PHE   0.013   0.002   PHE L  29 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.003   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7822)
  covalent geometry    : angle       0.52736 (10565)
  hydrogen bonds       : bond        0.04254 (  648)
  hydrogen bonds       : angle       3.72568 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: G  156 ASP cc_start: 0.8164 (m-30) cc_final: 0.7896 (m-30)
REVERT: I   41 THR cc_start: 0.8366 (p) cc_final: 0.8008 (m)
REVERT: K   15 THR cc_start: 0.9013 (t) cc_final: 0.8771 (m)
REVERT: Q   54 PHE cc_start: 0.7943 (t80) cc_final: 0.7737 (t80)
REVERT: Q   70 LEU cc_start: 0.8118 (mt) cc_final: 0.7905 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 145
  average time/residue: 0.1779
  time to fit residues: 36.1986
Evaluate side-chains
  141 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain G residue  224 GLU
Chi-restraints excluded: chain K residue   54 PHE
Chi-restraints excluded: chain L residue   54 PHE
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain Q residue   46 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 91 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN
P  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.128563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.105431 restraints weight = 30662.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.72
r_work: 0.3168 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7822  Z= 0.166
  Angle     :  0.515   5.365  10565  Z= 0.280
  Chirality :  0.037   0.140   1251
  Planarity :  0.003   0.032   1321
  Dihedral  :  6.610  59.950   1127
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.75 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.27), residues: 999
  helix:  1.98 (0.19), residues: 750
  sheet: -0.87 (0.56), residues: 89
  loop : -1.37 (0.49), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G 252 
 TYR   0.015   0.001   TYR G 171 
 PHE   0.017   0.001   PHE M  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.002   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7822)
  covalent geometry    : angle       0.51516 (10565)
  hydrogen bonds       : bond        0.04096 (  648)
  hydrogen bonds       : angle       3.62114 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: G  156 ASP cc_start: 0.8141 (m-30) cc_final: 0.7880 (m-30)
REVERT: I   41 THR cc_start: 0.8356 (p) cc_final: 0.7988 (m)
REVERT: K   15 THR cc_start: 0.9023 (t) cc_final: 0.8790 (m)
REVERT: Q   70 LEU cc_start: 0.8102 (mt) cc_final: 0.7893 (mt)
  outliers start: 9
  outliers final: 8
  residues processed: 146
  average time/residue: 0.1628
  time to fit residues: 34.0742
Evaluate side-chains
  140 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain G residue  224 GLU
Chi-restraints excluded: chain K residue   54 PHE
Chi-restraints excluded: chain L residue   54 PHE
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain Q residue   46 LEU
Chi-restraints excluded: chain R residue    9 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0980
   chunk 94 optimal weight:    0.4980
   chunk 93 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.129318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106203 restraints weight = 30506.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.74
r_work: 0.3176 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7822  Z= 0.146
  Angle     :  0.504   5.537  10565  Z= 0.271
  Chirality :  0.037   0.141   1251
  Planarity :  0.003   0.032   1321
  Dihedral  :  6.546  59.252   1127
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.53 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.27), residues: 999
  helix:  2.16 (0.19), residues: 750
  sheet: -0.84 (0.56), residues: 89
  loop : -1.29 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 252 
 TYR   0.011   0.001   TYR G  44 
 PHE   0.018   0.001   PHE M  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.002   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7822)
  covalent geometry    : angle       0.50398 (10565)
  hydrogen bonds       : bond        0.03908 (  648)
  hydrogen bonds       : angle       3.53110 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: G  156 ASP cc_start: 0.8144 (m-30) cc_final: 0.7875 (m-30)
REVERT: I   41 THR cc_start: 0.8350 (p) cc_final: 0.7987 (m)
REVERT: K   15 THR cc_start: 0.9031 (t) cc_final: 0.8790 (m)
REVERT: K   60 MET cc_start: 0.7503 (mmm) cc_final: 0.7250 (mmp)
REVERT: L   49 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7943 (m-10)
REVERT: Q   70 LEU cc_start: 0.8095 (mt) cc_final: 0.7885 (mt)
  outliers start: 12
  outliers final: 8
  residues processed: 150
  average time/residue: 0.1546
  time to fit residues: 33.6327
Evaluate side-chains
  146 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain G residue  224 GLU
Chi-restraints excluded: chain K residue   54 PHE
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   54 PHE
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain Q residue   46 LEU
Chi-restraints excluded: chain R residue    9 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 255 GLN
N  39 ASN
P  45 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.128001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.105012 restraints weight = 30668.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.72
r_work: 0.3156 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7822  Z= 0.175
  Angle     :  0.525   5.944  10565  Z= 0.283
  Chirality :  0.037   0.140   1251
  Planarity :  0.003   0.032   1321
  Dihedral  :  6.572  58.452   1127
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.10 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.27), residues: 999
  helix:  2.15 (0.19), residues: 750
  sheet: -0.78 (0.56), residues: 89
  loop : -1.35 (0.49), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 252 
 TYR   0.012   0.001   TYR G 171 
 PHE   0.016   0.002   PHE M  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.002   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 7822)
  covalent geometry    : angle       0.52540 (10565)
  hydrogen bonds       : bond        0.04085 (  648)
  hydrogen bonds       : angle       3.53451 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: G  156 ASP cc_start: 0.8091 (m-30) cc_final: 0.7820 (m-30)
REVERT: I   41 THR cc_start: 0.8351 (p) cc_final: 0.7981 (m)
REVERT: K   15 THR cc_start: 0.9057 (t) cc_final: 0.8817 (m)
REVERT: K   60 MET cc_start: 0.7303 (mmm) cc_final: 0.7099 (mmp)
REVERT: L   49 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7902 (m-10)
REVERT: Q   70 LEU cc_start: 0.8117 (mt) cc_final: 0.7903 (mt)
  outliers start: 12
  outliers final: 10
  residues processed: 145
  average time/residue: 0.1615
  time to fit residues: 33.6402
Evaluate side-chains
  146 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  105 ILE
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain G residue  224 GLU
Chi-restraints excluded: chain K residue   54 PHE
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   54 PHE
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain Q residue   46 LEU
Chi-restraints excluded: chain R residue    9 ILE
Chi-restraints excluded: chain R residue   15 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.128308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.105316 restraints weight = 30617.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.72
r_work: 0.3171 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7822  Z= 0.159
  Angle     :  0.516   6.518  10565  Z= 0.277
  Chirality :  0.037   0.142   1251
  Planarity :  0.003   0.039   1321
  Dihedral  :  6.561  57.920   1127
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.62 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.27), residues: 999
  helix:  2.23 (0.19), residues: 750
  sheet: -0.77 (0.56), residues: 89
  loop : -1.32 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G 252 
 TYR   0.011   0.001   TYR G  44 
 PHE   0.017   0.002   PHE M  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.002   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7822)
  covalent geometry    : angle       0.51626 (10565)
  hydrogen bonds       : bond        0.03972 (  648)
  hydrogen bonds       : angle       3.49248 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: G  110 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6832 (t70)
REVERT: G  156 ASP cc_start: 0.8098 (m-30) cc_final: 0.7826 (m-30)
REVERT: I   41 THR cc_start: 0.8344 (p) cc_final: 0.7976 (m)
REVERT: K   15 THR cc_start: 0.9047 (t) cc_final: 0.8804 (m)
REVERT: K   60 MET cc_start: 0.7306 (mmm) cc_final: 0.7030 (mmp)
REVERT: L   49 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7903 (m-10)
REVERT: Q   70 LEU cc_start: 0.8111 (mt) cc_final: 0.7870 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 148
  average time/residue: 0.1565
  time to fit residues: 33.6733
Evaluate side-chains
  146 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain G residue  224 GLU
Chi-restraints excluded: chain K residue   54 PHE
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   54 PHE
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain Q residue   46 LEU
Chi-restraints excluded: chain R residue   15 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 34 optimal weight:    0.4980
   chunk 87 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN
P  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.128269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.105239 restraints weight = 30755.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.74
r_work: 0.3162 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7822  Z= 0.163
  Angle     :  0.520   6.842  10565  Z= 0.279
  Chirality :  0.038   0.183   1251
  Planarity :  0.003   0.043   1321
  Dihedral  :  6.574  57.376   1127
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.27 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.27), residues: 999
  helix:  2.24 (0.19), residues: 750
  sheet: -0.77 (0.56), residues: 89
  loop : -1.32 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 252 
 TYR   0.012   0.001   TYR G 171 
 PHE   0.019   0.002   PHE M  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.002   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7822)
  covalent geometry    : angle       0.51990 (10565)
  hydrogen bonds       : bond        0.03982 (  648)
  hydrogen bonds       : angle       3.47781 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: G  156 ASP cc_start: 0.8106 (m-30) cc_final: 0.7830 (m-30)
REVERT: I   41 THR cc_start: 0.8334 (p) cc_final: 0.7965 (m)
REVERT: K   15 THR cc_start: 0.9063 (t) cc_final: 0.8826 (m)
REVERT: K   60 MET cc_start: 0.7322 (mmm) cc_final: 0.7111 (mmp)
REVERT: L   49 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7909 (m-10)
REVERT: Q   70 LEU cc_start: 0.8112 (mt) cc_final: 0.7867 (mt)
  outliers start: 11
  outliers final: 8
  residues processed: 144
  average time/residue: 0.1569
  time to fit residues: 32.7469
Evaluate side-chains
  145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain G residue  224 GLU
Chi-restraints excluded: chain K residue   54 PHE
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   54 PHE
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain Q residue   46 LEU
Chi-restraints excluded: chain R residue   15 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 81 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.128293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.105347 restraints weight = 30648.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.73
r_work: 0.3167 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7822  Z= 0.168
  Angle     :  0.526   7.166  10565  Z= 0.283
  Chirality :  0.038   0.191   1251
  Planarity :  0.003   0.046   1321
  Dihedral  :  6.598  59.805   1127
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 15.27 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.27), residues: 999
  helix:  2.23 (0.19), residues: 750
  sheet: -0.79 (0.56), residues: 89
  loop : -1.33 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G 252 
 TYR   0.012   0.001   TYR G  44 
 PHE   0.017   0.002   PHE M  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.002   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7822)
  covalent geometry    : angle       0.52594 (10565)
  hydrogen bonds       : bond        0.04020 (  648)
  hydrogen bonds       : angle       3.48535 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: G  110 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6839 (t70)
REVERT: G  156 ASP cc_start: 0.8114 (m-30) cc_final: 0.7839 (m-30)
REVERT: I   41 THR cc_start: 0.8331 (p) cc_final: 0.7968 (m)
REVERT: K   15 THR cc_start: 0.9075 (t) cc_final: 0.8824 (m)
REVERT: L   49 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7926 (m-10)
REVERT: L   51 ILE cc_start: 0.7960 (mm) cc_final: 0.7741 (mt)
REVERT: Q   70 LEU cc_start: 0.8111 (mt) cc_final: 0.7866 (mt)
  outliers start: 10
  outliers final: 7
  residues processed: 148
  average time/residue: 0.1605
  time to fit residues: 34.4431
Evaluate side-chains
  146 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain G residue  224 GLU
Chi-restraints excluded: chain K residue   54 PHE
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   54 PHE
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain Q residue   46 LEU
Chi-restraints excluded: chain R residue   15 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 48 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN
P  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.128485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.105623 restraints weight = 30504.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.73
r_work: 0.3166 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7822  Z= 0.155
  Angle     :  0.520   7.220  10565  Z= 0.277
  Chirality :  0.037   0.189   1251
  Planarity :  0.003   0.048   1321
  Dihedral  :  6.548  57.158   1127
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 16.06 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.27), residues: 999
  helix:  2.26 (0.19), residues: 751
  sheet: -0.77 (0.56), residues: 89
  loop : -1.27 (0.50), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G 252 
 TYR   0.012   0.001   TYR G  44 
 PHE   0.018   0.001   PHE M  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.001   0.001   HIS G  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7822)
  covalent geometry    : angle       0.51968 (10565)
  hydrogen bonds       : bond        0.03913 (  648)
  hydrogen bonds       : angle       3.45108 ( 1920)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: G  110 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6830 (t70)
REVERT: G  156 ASP cc_start: 0.8139 (m-30) cc_final: 0.7880 (m-30)
REVERT: I   41 THR cc_start: 0.8287 (p) cc_final: 0.7895 (m)
REVERT: K   15 THR cc_start: 0.9064 (t) cc_final: 0.8821 (m)
REVERT: L   49 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7919 (m-10)
REVERT: L   51 ILE cc_start: 0.7943 (mm) cc_final: 0.7740 (mt)
REVERT: Q   66 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6212 (ptp)
REVERT: Q   70 LEU cc_start: 0.8104 (mt) cc_final: 0.7862 (mt)
  outliers start: 10
  outliers final: 7
  residues processed: 145
  average time/residue: 0.1669
  time to fit residues: 34.6561
Evaluate side-chains
  147 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain G residue  224 GLU
Chi-restraints excluded: chain K residue   54 PHE
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   54 PHE
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain Q residue   46 LEU
Chi-restraints excluded: chain Q residue   66 MET
Chi-restraints excluded: chain R residue   15 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 88 optimal weight:    0.2980
   chunk 77 optimal weight:    1.9990
   chunk 75 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.128554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.105869 restraints weight = 30523.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.72
r_work: 0.3176 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7822  Z= 0.149
  Angle     :  0.516   6.738  10565  Z= 0.275
  Chirality :  0.037   0.167   1251
  Planarity :  0.003   0.048   1321
  Dihedral  :  6.499  55.422   1127
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.80 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.27), residues: 999
  helix:  2.32 (0.19), residues: 751
  sheet: -0.78 (0.56), residues: 89
  loop : -1.26 (0.50), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 252 
 TYR   0.012   0.001   TYR G  44 
 PHE   0.018   0.001   PHE K  54 
 TRP   0.003   0.001   TRP I   4 
 HIS   0.001   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7822)
  covalent geometry    : angle       0.51581 (10565)
  hydrogen bonds       : bond        0.03844 (  648)
  hydrogen bonds       : angle       3.42867 ( 1920)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3832.66 seconds
wall clock time: 65 minutes 40.84 seconds (3940.84 seconds total)