Starting phenix.real_space_refine
on Tue Mar  3 19:42:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjl_33231/03_2026/7xjl_33231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjl_33231/03_2026/7xjl_33231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjl_33231/03_2026/7xjl_33231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjl_33231/03_2026/7xjl_33231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjl_33231/03_2026/7xjl_33231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjl_33231/03_2026/7xjl_33231.cif"
  }
  resolution = 3.5
  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=  -0.001 sd=   0.090
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5453      2.51       5
     N    1456      2.21       5
     O    1564      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 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: 8527
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 109
          Classifications: {'peptide': 14}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 12}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1750
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 81
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "C"
      Number of atoms: 2471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2471
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 160
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 98
    Chain: "D"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 353
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1712
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "F"
      Number of atoms: 2132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2132
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 55
          Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 44
  Time building chain proxies: 1.95, per 1000 atoms: 0.23
  Number of scatterers: 8527
  At special positions: 0
  Unit cell: (92.395, 119.57, 118.483, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1564      8.00
     N    1456      7.00
     C    5453      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  98 " - pdb=" SG  CYS F 175 " distance=2.03

  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: 0.70
  Conformation dependent library (CDL) restraints added in 356.1 milliseconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      39.5% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 12
    Processing helix  chain 'B' and resid 6 through 32
      removed outlier: 3.757A  pdb=" N   ARG B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.557A  pdb=" N   MET B  53 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 99
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 3.512A  pdb=" N   LEU B 134 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ARG B 135 " --> pdb=" O   ARG B 132 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 131 through 135'
    Processing helix  chain 'B' and resid 145 through 156
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.895A  pdb=" N   TYR B 163 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 168
    Processing helix  chain 'B' and resid 183 through 203
    Processing helix  chain 'B' and resid 222 through 243
      removed outlier: 4.139A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 26
      removed outlier: 3.654A  pdb=" N   ALA C  26 " --> pdb=" O   ARG C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 12 through 24
      removed outlier: 3.731A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.534A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
      removed outlier: 3.767A  pdb=" N   ASP D  48 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 48'
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.563A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.508A  pdb=" N   ASP E  90 " --> pdb=" O   ARG E  87 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing helix  chain 'F' and resid 24 through 53
      Proline residue:  F  29  - end of helix
    Processing helix  chain 'F' and resid 58 through 88
      Proline residue:  F  80  - end of helix
      removed outlier: 4.786A  pdb=" N   ILE F  85 " --> pdb=" O   PHE F  81 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   TYR F  86 " --> pdb=" O   GLN F  82 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 129
      removed outlier: 4.163A  pdb=" N   LEU F  97 " --> pdb=" O   PHE F  93 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   CYS F  98 " --> pdb=" O   GLY F  94 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS F  99 " --> pdb=" O   SER F  95 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   HIS F 102 " --> pdb=" O   CYS F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 131 through 136
      removed outlier: 3.807A  pdb=" N   GLU F 135 " --> pdb=" O   HIS F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 138 through 158
    Processing helix  chain 'F' and resid 159 through 163
    Processing helix  chain 'F' and resid 180 through 196
      removed outlier: 3.793A  pdb=" N   ALA F 186 " --> pdb=" O   PRO F 182 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 215
    Processing helix  chain 'F' and resid 225 through 261
      removed outlier: 3.811A  pdb=" N   TRP F 249 " --> pdb=" O   PHE F 245 " (cutoff:3.500A)
      Proline residue:  F 251  - end of helix
    Processing helix  chain 'F' and resid 267 through 293
      removed outlier: 3.863A  pdb=" N   SER F 285 " --> pdb=" O   SER F 281 " (cutoff:3.500A)
      Proline residue:  F 289  - end of helix
    Processing helix  chain 'F' and resid 296 through 307
      removed outlier: 4.032A  pdb=" N   THR F 305 " --> pdb=" O   LYS F 301 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE F 306 " --> pdb=" O   GLY F 302 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS F 307 " --> pdb=" O   PHE F 303 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76
      removed outlier: 4.848A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ARG B  35 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 4.112A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LEU C 336 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.665A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 105
      removed outlier: 3.740A  pdb=" N   GLY C 115 " --> pdb=" O   THR C 102 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA C 113 " --> pdb=" O   ALA C 104 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 148 through 151
      removed outlier: 5.947A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191
      removed outlier: 3.660A  pdb=" N   GLY C 202 " --> pdb=" O   SER C 189 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.703A  pdb=" N   SER C 245 " --> pdb=" O   THR C 249 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   THR C 249 " --> pdb=" O   SER C 245 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C 252 " --> pdb=" O   MET C 262 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 4.016A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.849A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.279A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.613A  pdb=" N   ILE E 177 " --> pdb=" O   TRP E 164 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LEU E 166 " --> pdb=" O   LEU E 175 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   LEU E 175 " --> pdb=" O   LEU E 166 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 164 through 169

    469 hydrogen bonds defined for protein.
    1320 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: 1.46

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2759
        1.34 -     1.46: 2106
        1.46 -     1.58: 3777
        1.58 -     1.70: 0
        1.70 -     1.81: 74
  Bond restraints: 8716
  Sorted by residual:
  bond pdb=" CA  GLU C 130 "
       pdb=" CB  GLU C 130 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.69e-02 3.50e+03 1.02e+00
  bond pdb=" CG1 ILE F  64 "
       pdb=" CD1 ILE F  64 "
    ideal  model  delta    sigma   weight residual
    1.513  1.479  0.034 3.90e-02 6.57e+02 7.81e-01
  bond pdb=" CB  ASP F  71 "
       pdb=" CG  ASP F  71 "
    ideal  model  delta    sigma   weight residual
    1.516  1.495  0.021 2.50e-02 1.60e+03 7.28e-01
  bond pdb=" CB  LYS A  11 "
       pdb=" CG  LYS A  11 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.17e-01
  bond pdb=" CA  ASN C 313 "
       pdb=" C   ASN C 313 "
    ideal  model  delta    sigma   weight residual
    1.524  1.533 -0.009 1.23e-02 6.61e+03 5.93e-01
  ... (remaining 8711 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 11558
        1.55 -     3.10: 257
        3.10 -     4.65: 44
        4.65 -     6.21: 13
        6.21 -     7.76: 5
  Bond angle restraints: 11877
  Sorted by residual:
  angle pdb=" C   ARG E 179 "
        pdb=" N   MET E 180 "
        pdb=" CA  MET E 180 "
      ideal   model   delta    sigma   weight residual
     121.54  128.88   -7.34 1.91e+00 2.74e-01 1.48e+01
  angle pdb=" CA  GLU C 130 "
        pdb=" CB  GLU C 130 "
        pdb=" CG  GLU C 130 "
      ideal   model   delta    sigma   weight residual
     114.10  121.06   -6.96 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" C   ARG C 129 "
        pdb=" N   GLU C 130 "
        pdb=" CA  GLU C 130 "
      ideal   model   delta    sigma   weight residual
     121.54  126.46   -4.92 1.91e+00 2.74e-01 6.63e+00
  angle pdb=" CB  LYS A  11 "
        pdb=" CG  LYS A  11 "
        pdb=" CD  LYS A  11 "
      ideal   model   delta    sigma   weight residual
     111.30  116.88   -5.58 2.30e+00 1.89e-01 5.88e+00
  angle pdb=" CA  LYS B  73 "
        pdb=" CB  LYS B  73 "
        pdb=" CG  LYS B  73 "
      ideal   model   delta    sigma   weight residual
     114.10  118.95   -4.85 2.00e+00 2.50e-01 5.87e+00
  ... (remaining 11872 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4611
       17.69 -    35.38: 390
       35.38 -    53.06: 69
       53.06 -    70.75: 10
       70.75 -    88.44: 5
  Dihedral angle restraints: 5085
    sinusoidal: 1795
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  LYS B  73 "
           pdb=" C   LYS B  73 "
           pdb=" N   PHE B  74 "
           pdb=" CA  PHE B  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.15   27.85     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" CA  GLY B 181 "
           pdb=" C   GLY B 181 "
           pdb=" N   ASP B 182 "
           pdb=" CA  ASP B 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.46   16.54     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CB  GLU C 138 "
           pdb=" CG  GLU C 138 "
           pdb=" CD  GLU C 138 "
           pdb=" OE1 GLU C 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.44   88.44     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 5082 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 889
       0.032 -    0.064: 324
       0.064 -    0.095: 104
       0.095 -    0.127: 57
       0.127 -    0.159: 8
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  GLU C 130 "
            pdb=" N   GLU C 130 "
            pdb=" C   GLU C 130 "
            pdb=" CB  GLU C 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CG  LEU F  72 "
            pdb=" CB  LEU F  72 "
            pdb=" CD1 LEU F  72 "
            pdb=" CD2 LEU F  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.59e-01
  chirality pdb=" CA  THR F  87 "
            pdb=" N   THR F  87 "
            pdb=" C   THR F  87 "
            pdb=" CB  THR F  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.17e-01
  ... (remaining 1379 not shown)

  Planarity restraints: 1504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 332 "   -0.015 2.00e-02 2.50e+03   1.49e-02 5.54e+00
        pdb=" CG  TRP C 332 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 332 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 332 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 332 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 332 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 332 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 332 "   -0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 332 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A   3 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.79e+00
        pdb=" N   PRO A   4 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A   4 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A   4 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  69 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.45e+00
        pdb=" C   VAL F  69 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   VAL F  69 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA F  70 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1501 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 266
        2.71 -     3.26: 8531
        3.26 -     3.81: 14009
        3.81 -     4.35: 16871
        4.35 -     4.90: 28921
  Nonbonded interactions: 68598
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 161 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   GLN C  75 "
            pdb=" OG  SER C  98 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG  SER C 281 "
            pdb=" O   HIS D  44 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" NZ  LYS B  95 "
            pdb=" OD2 ASP C 228 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   ALA B  41 "
            pdb=" OG  SER B  44 "
     model   vdw
     2.252 3.040
  ... (remaining 68593 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.050
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8718  Z= 0.123
  Angle     :  0.607   7.758  11881  Z= 0.327
  Chirality :  0.041   0.159   1382
  Planarity :  0.004   0.055   1504
  Dihedral  : 13.569  88.438   2957
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.78 (0.25), residues: 1115
  helix:  2.17 (0.26), residues: 401
  sheet:  0.49 (0.31), residues: 272
  loop : -1.04 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 185 
 TYR   0.013   0.001   TYR B 191 
 PHE   0.020   0.002   PHE B  74 
 TRP   0.038   0.002   TRP C 332 
 HIS   0.008   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8716)
  covalent geometry    : angle       0.60680 (11877)
  SS BOND              : bond        0.00252 (    2)
  SS BOND              : angle       0.61594 (    4)
  hydrogen bonds       : bond        0.13436 (  462)
  hydrogen bonds       : angle       6.43891 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.8816 (t80) cc_final: 0.8449 (t80)
REVERT: B   73 LYS cc_start: 0.8376 (mmtm) cc_final: 0.7713 (pttm)
REVERT: B  122 LEU cc_start: 0.8967 (mt) cc_final: 0.8647 (mp)
REVERT: B  232 LYS cc_start: 0.8886 (tttp) cc_final: 0.8627 (tttp)
REVERT: C  289 TYR cc_start: 0.8566 (m-80) cc_final: 0.8236 (m-80)
REVERT: C  301 LYS cc_start: 0.8592 (mmpt) cc_final: 0.8138 (mmmt)
REVERT: E   96 CYS cc_start: 0.8086 (t) cc_final: 0.7407 (t)
REVERT: E   98 ARG cc_start: 0.8524 (ptm160) cc_final: 0.7856 (ptm160)
REVERT: E  190 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7514 (ptp90)
REVERT: E  192 SER cc_start: 0.7065 (t) cc_final: 0.6830 (t)
REVERT: E  218 MET cc_start: 0.7594 (tmm) cc_final: 0.6614 (tmm)
REVERT: F   55 GLN cc_start: 0.8187 (mp10) cc_final: 0.7974 (mp10)
REVERT: F  244 LEU cc_start: 0.8064 (tp) cc_final: 0.7850 (tt)
REVERT: F  305 THR cc_start: 0.7514 (m) cc_final: 0.7127 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.0849
  time to fit residues: 31.4434
Evaluate side-chains
  227 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 GLN
** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 340 ASN
E 182 ASN
** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 284 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.166129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.128208 restraints weight = 12885.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.132520 restraints weight = 6659.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.135377 restraints weight = 4422.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.137289 restraints weight = 3423.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138211 restraints weight = 2917.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8718  Z= 0.133
  Angle     :  0.588   8.699  11881  Z= 0.307
  Chirality :  0.044   0.225   1382
  Planarity :  0.004   0.054   1504
  Dihedral  :  4.040  29.650   1222
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.95 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.87 (0.25), residues: 1115
  helix:  2.24 (0.26), residues: 402
  sheet:  0.50 (0.31), residues: 268
  loop : -0.95 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 283 
 TYR   0.024   0.002   TYR F 213 
 PHE   0.020   0.002   PHE B  74 
 TRP   0.010   0.001   TRP F 260 
 HIS   0.004   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8716)
  covalent geometry    : angle       0.58793 (11877)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       1.30766 (    4)
  hydrogen bonds       : bond        0.03851 (  462)
  hydrogen bonds       : angle       5.12914 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 231
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A    9 TYR cc_start: 0.8917 (t80) cc_final: 0.8428 (t80)
REVERT: B   73 LYS cc_start: 0.8503 (mmtm) cc_final: 0.7718 (pttm)
REVERT: B  223 ASN cc_start: 0.8054 (p0) cc_final: 0.7563 (p0)
REVERT: C  176 GLN cc_start: 0.7775 (mt0) cc_final: 0.7455 (mt0)
REVERT: C  228 ASP cc_start: 0.8219 (p0) cc_final: 0.7016 (p0)
REVERT: C  246 ASP cc_start: 0.8223 (m-30) cc_final: 0.7921 (m-30)
REVERT: C  289 TYR cc_start: 0.8576 (m-80) cc_final: 0.8355 (m-80)
REVERT: C  301 LYS cc_start: 0.8418 (mmpt) cc_final: 0.8079 (mmmt)
REVERT: E   18 ARG cc_start: 0.6956 (tpt-90) cc_final: 0.6643 (tpt-90)
REVERT: E   96 CYS cc_start: 0.7990 (t) cc_final: 0.7659 (t)
REVERT: E   98 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7785 (ptm160)
REVERT: E  180 MET cc_start: 0.6916 (ptt) cc_final: 0.6460 (ptt)
REVERT: E  190 ARG cc_start: 0.8090 (ptp-170) cc_final: 0.7529 (ptp90)
REVERT: F   55 GLN cc_start: 0.8184 (mp10) cc_final: 0.7931 (mp10)
REVERT: F  129 TYR cc_start: 0.8374 (m-10) cc_final: 0.7788 (m-10)
  outliers start: 9
  outliers final: 6
  residues processed: 233
  average time/residue: 0.0884
  time to fit residues: 28.5269
Evaluate side-chains
  222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 216
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue  275 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0670
   chunk 75 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:   30.0000
   chunk 14 optimal weight:   10.0000
   chunk 8 optimal weight:    0.5980
   chunk 83 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0370
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
C 156 GLN
E 113 GLN
** F 252 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.166659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.128769 restraints weight = 12670.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.133116 restraints weight = 6640.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.136001 restraints weight = 4413.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.137594 restraints weight = 3408.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.138940 restraints weight = 2945.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8718  Z= 0.115
  Angle     :  0.568   8.123  11881  Z= 0.292
  Chirality :  0.042   0.187   1382
  Planarity :  0.004   0.045   1504
  Dihedral  :  4.014  29.147   1222
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.18 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.99 (0.25), residues: 1115
  helix:  2.33 (0.26), residues: 399
  sheet:  0.52 (0.32), residues: 262
  loop : -0.79 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 132 
 TYR   0.016   0.001   TYR F 164 
 PHE   0.029   0.001   PHE F 303 
 TRP   0.045   0.002   TRP F 260 
 HIS   0.003   0.001   HIS C 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8716)
  covalent geometry    : angle       0.56754 (11877)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       0.70997 (    4)
  hydrogen bonds       : bond        0.03480 (  462)
  hydrogen bonds       : angle       4.89466 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 232
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.8924 (t80) cc_final: 0.8551 (t80)
REVERT: B   73 LYS cc_start: 0.8490 (mmtm) cc_final: 0.7696 (pttm)
REVERT: C   86 THR cc_start: 0.9144 (p) cc_final: 0.8936 (p)
REVERT: C  101 MET cc_start: 0.8123 (mtm) cc_final: 0.7813 (ptp)
REVERT: C  176 GLN cc_start: 0.7783 (mt0) cc_final: 0.7533 (mt0)
REVERT: C  301 LYS cc_start: 0.8384 (mmpt) cc_final: 0.8113 (mmmt)
REVERT: E   96 CYS cc_start: 0.8068 (t) cc_final: 0.7760 (t)
REVERT: E   98 ARG cc_start: 0.8187 (ptm160) cc_final: 0.7600 (ptm-80)
REVERT: E  180 MET cc_start: 0.7005 (ptt) cc_final: 0.6531 (ptt)
REVERT: E  190 ARG cc_start: 0.8194 (ptp-170) cc_final: 0.7683 (ptp90)
REVERT: E  218 MET cc_start: 0.7989 (tmm) cc_final: 0.7407 (tmm)
REVERT: E  219 GLN cc_start: 0.8970 (pp30) cc_final: 0.8483 (pp30)
REVERT: F   55 GLN cc_start: 0.8213 (mp10) cc_final: 0.7901 (mp10)
REVERT: F  129 TYR cc_start: 0.8570 (m-10) cc_final: 0.7907 (m-10)
  outliers start: 16
  outliers final: 10
  residues processed: 237
  average time/residue: 0.0784
  time to fit residues: 26.2281
Evaluate side-chains
  223 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 213
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  113 GLN
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  275 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 17 optimal weight:    0.3980
   chunk 84 optimal weight:    0.0370
   chunk 36 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    0.5860

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 ASN
C  75 GLN
C 156 GLN
** F 252 HIS ** 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 = 0.4034 r_free = 0.4034 target = 0.166070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.127970 restraints weight = 12991.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.132352 restraints weight = 6784.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.135208 restraints weight = 4492.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.136873 restraints weight = 3464.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.138185 restraints weight = 2977.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8718  Z= 0.115
  Angle     :  0.561   9.326  11881  Z= 0.290
  Chirality :  0.042   0.170   1382
  Planarity :  0.004   0.049   1504
  Dihedral  :  3.963  28.768   1222
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.69 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.01 (0.25), residues: 1115
  helix:  2.36 (0.26), residues: 402
  sheet:  0.55 (0.32), residues: 268
  loop : -0.85 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 219 
 TYR   0.019   0.001   TYR F 164 
 PHE   0.029   0.001   PHE F 303 
 TRP   0.019   0.001   TRP F 260 
 HIS   0.009   0.001   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8716)
  covalent geometry    : angle       0.56092 (11877)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.65723 (    4)
  hydrogen bonds       : bond        0.03398 (  462)
  hydrogen bonds       : angle       4.75155 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 227
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.8946 (t80) cc_final: 0.8612 (t80)
REVERT: B   73 LYS cc_start: 0.8497 (mmtm) cc_final: 0.7703 (pttm)
REVERT: C   86 THR cc_start: 0.9175 (p) cc_final: 0.8970 (p)
REVERT: C  237 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.7034 (p0)
REVERT: C  298 ASP cc_start: 0.7643 (t0) cc_final: 0.7431 (t0)
REVERT: E   96 CYS cc_start: 0.8124 (t) cc_final: 0.7797 (t)
REVERT: E   98 ARG cc_start: 0.8153 (ptm160) cc_final: 0.7647 (ptm160)
REVERT: E  180 MET cc_start: 0.7130 (ptt) cc_final: 0.6641 (ptt)
REVERT: E  190 ARG cc_start: 0.8205 (ptp-170) cc_final: 0.7660 (ptp90)
REVERT: E  218 MET cc_start: 0.8038 (tmm) cc_final: 0.7213 (tmm)
REVERT: E  219 GLN cc_start: 0.8964 (pp30) cc_final: 0.8231 (pp30)
REVERT: F  129 TYR cc_start: 0.8663 (m-10) cc_final: 0.8006 (m-10)
REVERT: F  275 ILE cc_start: 0.9387 (mm) cc_final: 0.9035 (tp)
  outliers start: 17
  outliers final: 11
  residues processed: 232
  average time/residue: 0.0801
  time to fit residues: 26.3950
Evaluate side-chains
  223 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 211
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  248 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   chunk 104 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0770
   overall best weight:    1.3742

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.162197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.123427 restraints weight = 13036.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.127667 restraints weight = 6909.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.130509 restraints weight = 4632.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.132327 restraints weight = 3607.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133216 restraints weight = 3090.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8718  Z= 0.150
  Angle     :  0.593  16.950  11881  Z= 0.300
  Chirality :  0.042   0.149   1382
  Planarity :  0.004   0.043   1504
  Dihedral  :  4.008  29.859   1222
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.03 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.99 (0.25), residues: 1115
  helix:  2.35 (0.26), residues: 400
  sheet:  0.50 (0.32), residues: 272
  loop : -0.84 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 219 
 TYR   0.018   0.002   TYR B 115 
 PHE   0.033   0.002   PHE F 303 
 TRP   0.051   0.002   TRP F 260 
 HIS   0.011   0.001   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8716)
  covalent geometry    : angle       0.59292 (11877)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.49442 (    4)
  hydrogen bonds       : bond        0.03545 (  462)
  hydrogen bonds       : angle       4.72517 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 233
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9049 (t80) cc_final: 0.8631 (t80)
REVERT: B   73 LYS cc_start: 0.8571 (mmtm) cc_final: 0.7794 (pttm)
REVERT: B  118 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8592 (tt)
REVERT: B  122 LEU cc_start: 0.8931 (mp) cc_final: 0.8667 (mp)
REVERT: C   78 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8571 (mmtp)
REVERT: C   86 THR cc_start: 0.9200 (p) cc_final: 0.8992 (p)
REVERT: C  101 MET cc_start: 0.8220 (mtm) cc_final: 0.7937 (ptp)
REVERT: C  118 ASP cc_start: 0.7968 (p0) cc_final: 0.7672 (p0)
REVERT: C  153 ASP cc_start: 0.7628 (m-30) cc_final: 0.7364 (m-30)
REVERT: C  155 ASN cc_start: 0.8777 (p0) cc_final: 0.7478 (t0)
REVERT: C  325 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7639 (ttp)
REVERT: E   18 ARG cc_start: 0.6949 (tpt-90) cc_final: 0.6570 (tpt-90)
REVERT: E   96 CYS cc_start: 0.8189 (t) cc_final: 0.7843 (t)
REVERT: E   98 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7636 (ptm160)
REVERT: E  180 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6875 (ptt)
REVERT: E  190 ARG cc_start: 0.8181 (ptp-170) cc_final: 0.7608 (ptp90)
REVERT: E  218 MET cc_start: 0.8071 (tmm) cc_final: 0.7684 (tmm)
REVERT: E  219 GLN cc_start: 0.9008 (pp30) cc_final: 0.8712 (pp30)
REVERT: F   55 GLN cc_start: 0.8175 (mp10) cc_final: 0.7958 (mp10)
REVERT: F  129 TYR cc_start: 0.8791 (m-80) cc_final: 0.8127 (m-10)
REVERT: F  176 HIS cc_start: 0.7647 (p90) cc_final: 0.7304 (p-80)
REVERT: F  237 MET cc_start: 0.8421 (mmm) cc_final: 0.7692 (mmt)
REVERT: F  275 ILE cc_start: 0.9419 (mm) cc_final: 0.9037 (tp)
  outliers start: 27
  outliers final: 17
  residues processed: 243
  average time/residue: 0.0847
  time to fit residues: 28.6062
Evaluate side-chains
  241 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 221
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  325 MET
Chi-restraints excluded: chain E residue   34 MET
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  248 CYS
Chi-restraints excluded: chain F residue  267 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:    0.0270
   chunk 23 optimal weight:   50.0000
   chunk 80 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   overall best weight:    1.9242

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

Flipped N/Q/H residues before XYZ refinement:
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.158897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.120008 restraints weight = 12970.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.124138 restraints weight = 6906.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.126836 restraints weight = 4656.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.128626 restraints weight = 3644.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.129505 restraints weight = 3130.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8718  Z= 0.185
  Angle     :  0.646  21.573  11881  Z= 0.321
  Chirality :  0.046   0.500   1382
  Planarity :  0.004   0.048   1504
  Dihedral  :  4.089  30.464   1222
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.42 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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:  0.83 (0.25), residues: 1115
  helix:  2.24 (0.26), residues: 395
  sheet:  0.37 (0.32), residues: 272
  loop : -0.88 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 185 
 TYR   0.026   0.002   TYR F 213 
 PHE   0.031   0.002   PHE F 303 
 TRP   0.029   0.002   TRP F 260 
 HIS   0.012   0.001   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 8716)
  covalent geometry    : angle       0.64558 (11877)
  SS BOND              : bond        0.00305 (    2)
  SS BOND              : angle       0.65629 (    4)
  hydrogen bonds       : bond        0.03720 (  462)
  hydrogen bonds       : angle       4.72548 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 223
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9123 (t80) cc_final: 0.8687 (t80)
REVERT: B   73 LYS cc_start: 0.8629 (mmtm) cc_final: 0.7878 (pttm)
REVERT: B  122 LEU cc_start: 0.9000 (mp) cc_final: 0.8798 (mp)
REVERT: C  101 MET cc_start: 0.8386 (mtm) cc_final: 0.8155 (ptp)
REVERT: C  153 ASP cc_start: 0.7675 (m-30) cc_final: 0.7397 (m-30)
REVERT: C  237 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7249 (p0)
REVERT: E   18 ARG cc_start: 0.6943 (tpt-90) cc_final: 0.6728 (mmm-85)
REVERT: E   96 CYS cc_start: 0.8219 (t) cc_final: 0.7908 (t)
REVERT: E   98 ARG cc_start: 0.8237 (ptm160) cc_final: 0.7784 (ptm160)
REVERT: E  180 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7030 (ptt)
REVERT: E  219 GLN cc_start: 0.9044 (pp30) cc_final: 0.8702 (pp30)
REVERT: F   55 GLN cc_start: 0.8229 (mp10) cc_final: 0.7950 (mp10)
REVERT: F  129 TYR cc_start: 0.8889 (m-80) cc_final: 0.8309 (m-10)
REVERT: F  185 ARG cc_start: 0.7148 (ttm110) cc_final: 0.6846 (ttm110)
REVERT: F  260 TRP cc_start: 0.7723 (m100) cc_final: 0.7195 (m100)
REVERT: F  288 ASN cc_start: 0.7542 (m110) cc_final: 0.7268 (m110)
  outliers start: 28
  outliers final: 21
  residues processed: 232
  average time/residue: 0.0830
  time to fit residues: 26.9564
Evaluate side-chains
  237 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 214
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   34 MET
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  248 CYS
Chi-restraints excluded: chain F residue  267 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 107 optimal weight:    0.1980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
** F 252 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 = 0.3972 r_free = 0.3972 target = 0.160932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.122544 restraints weight = 13019.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.126758 restraints weight = 6844.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.129559 restraints weight = 4570.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.131050 restraints weight = 3540.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.132373 restraints weight = 3067.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8718  Z= 0.133
  Angle     :  0.612  19.809  11881  Z= 0.305
  Chirality :  0.044   0.487   1382
  Planarity :  0.004   0.044   1504
  Dihedral  :  4.056  29.434   1222
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.00 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.96 (0.25), residues: 1115
  helix:  2.41 (0.26), residues: 388
  sheet:  0.51 (0.32), residues: 270
  loop : -0.86 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 185 
 TYR   0.020   0.001   TYR F 213 
 PHE   0.031   0.002   PHE F 303 
 TRP   0.019   0.001   TRP F 260 
 HIS   0.009   0.001   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8716)
  covalent geometry    : angle       0.61163 (11877)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       0.55463 (    4)
  hydrogen bonds       : bond        0.03477 (  462)
  hydrogen bonds       : angle       4.67895 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 227
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9056 (t80) cc_final: 0.8714 (t80)
REVERT: B   73 LYS cc_start: 0.8547 (mmtm) cc_final: 0.7826 (pttm)
REVERT: B  118 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8741 (tt)
REVERT: C   78 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8578 (mmtp)
REVERT: C  153 ASP cc_start: 0.7577 (m-30) cc_final: 0.7316 (m-30)
REVERT: C  155 ASN cc_start: 0.8784 (p0) cc_final: 0.7431 (t0)
REVERT: C  275 SER cc_start: 0.9231 (t) cc_final: 0.8690 (p)
REVERT: C  325 MET cc_start: 0.8035 (ttm) cc_final: 0.7588 (ttp)
REVERT: E   96 CYS cc_start: 0.8181 (t) cc_final: 0.7904 (t)
REVERT: E   98 ARG cc_start: 0.8292 (ptm160) cc_final: 0.7694 (ptm-80)
REVERT: E  180 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7023 (ptt)
REVERT: E  190 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7438 (ptp90)
REVERT: E  219 GLN cc_start: 0.9030 (pp30) cc_final: 0.8346 (pp30)
REVERT: F   55 GLN cc_start: 0.8315 (mp10) cc_final: 0.8015 (mp10)
REVERT: F  129 TYR cc_start: 0.8824 (m-80) cc_final: 0.8359 (m-10)
REVERT: F  176 HIS cc_start: 0.7595 (p90) cc_final: 0.7319 (p-80)
REVERT: F  185 ARG cc_start: 0.7237 (ttm110) cc_final: 0.6890 (ttm110)
REVERT: F  260 TRP cc_start: 0.7781 (m100) cc_final: 0.7160 (m100)
REVERT: F  275 ILE cc_start: 0.9418 (mm) cc_final: 0.9073 (tp)
  outliers start: 31
  outliers final: 17
  residues processed: 240
  average time/residue: 0.0819
  time to fit residues: 27.5411
Evaluate side-chains
  238 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 219
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   34 MET
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  248 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 8 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 38 optimal weight:    0.5980
   chunk 17 optimal weight:    7.9990
   chunk 86 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 237 ASN
D  44 HIS
** F 252 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 = 0.3966 r_free = 0.3966 target = 0.160138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.121738 restraints weight = 12938.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.125797 restraints weight = 6838.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.128535 restraints weight = 4595.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.130366 restraints weight = 3581.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.131273 restraints weight = 3063.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8718  Z= 0.145
  Angle     :  0.642  20.637  11881  Z= 0.315
  Chirality :  0.045   0.483   1382
  Planarity :  0.004   0.043   1504
  Dihedral  :  4.062  29.511   1222
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.16 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.92 (0.25), residues: 1115
  helix:  2.36 (0.26), residues: 388
  sheet:  0.59 (0.32), residues: 257
  loop : -0.90 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 185 
 TYR   0.020   0.001   TYR F 213 
 PHE   0.032   0.002   PHE F 303 
 TRP   0.022   0.001   TRP C 297 
 HIS   0.008   0.001   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8716)
  covalent geometry    : angle       0.64202 (11877)
  SS BOND              : bond        0.00318 (    2)
  SS BOND              : angle       0.56686 (    4)
  hydrogen bonds       : bond        0.03507 (  462)
  hydrogen bonds       : angle       4.71347 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 220
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9071 (t80) cc_final: 0.8689 (t80)
REVERT: B   73 LYS cc_start: 0.8586 (mmtm) cc_final: 0.7845 (pttm)
REVERT: B  146 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8026 (mm-40)
REVERT: C   78 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8583 (mmtp)
REVERT: C  153 ASP cc_start: 0.7593 (m-30) cc_final: 0.7330 (m-30)
REVERT: C  155 ASN cc_start: 0.8817 (p0) cc_final: 0.7420 (t0)
REVERT: C  275 SER cc_start: 0.9195 (t) cc_final: 0.8677 (p)
REVERT: C  276 VAL cc_start: 0.9232 (m) cc_final: 0.8948 (m)
REVERT: C  325 MET cc_start: 0.8071 (ttm) cc_final: 0.7612 (ttp)
REVERT: E   96 CYS cc_start: 0.8110 (t) cc_final: 0.7823 (t)
REVERT: E   98 ARG cc_start: 0.8220 (ptm160) cc_final: 0.7700 (ptm160)
REVERT: E  180 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7021 (ptt)
REVERT: E  190 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.7382 (ptp90)
REVERT: F  129 TYR cc_start: 0.8816 (m-80) cc_final: 0.8296 (m-10)
REVERT: F  176 HIS cc_start: 0.7601 (p90) cc_final: 0.7305 (p-80)
REVERT: F  260 TRP cc_start: 0.7854 (m100) cc_final: 0.6779 (m100)
REVERT: F  275 ILE cc_start: 0.9431 (mm) cc_final: 0.9089 (tp)
  outliers start: 28
  outliers final: 22
  residues processed: 231
  average time/residue: 0.0852
  time to fit residues: 27.3811
Evaluate side-chains
  237 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 214
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   34 MET
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  248 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 68 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   chunk 86 optimal weight:    0.5980
   chunk 107 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0020
   chunk 34 optimal weight:    2.9990
   chunk 74 optimal weight:   40.0000
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.4992

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.158570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.124464 restraints weight = 12990.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.125596 restraints weight = 5841.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.127345 restraints weight = 4373.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.127745 restraints weight = 3839.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.128544 restraints weight = 3630.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8718  Z= 0.163
  Angle     :  0.672  21.591  11881  Z= 0.327
  Chirality :  0.046   0.506   1382
  Planarity :  0.004   0.042   1504
  Dihedral  :  4.137  30.157   1222
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.81 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    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:  0.84 (0.25), residues: 1115
  helix:  2.23 (0.26), residues: 388
  sheet:  0.49 (0.32), residues: 259
  loop : -0.85 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 185 
 TYR   0.023   0.001   TYR F 213 
 PHE   0.033   0.002   PHE F 303 
 TRP   0.022   0.002   TRP C 297 
 HIS   0.008   0.001   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8716)
  covalent geometry    : angle       0.67222 (11877)
  SS BOND              : bond        0.00328 (    2)
  SS BOND              : angle       0.68614 (    4)
  hydrogen bonds       : bond        0.03616 (  462)
  hydrogen bonds       : angle       4.72648 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 220
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9110 (t80) cc_final: 0.8617 (t80)
REVERT: B   73 LYS cc_start: 0.8691 (mmtm) cc_final: 0.7861 (pttm)
REVERT: B  146 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7979 (mm-40)
REVERT: C  153 ASP cc_start: 0.7710 (m-30) cc_final: 0.7334 (m-30)
REVERT: C  220 GLN cc_start: 0.7939 (mt0) cc_final: 0.7695 (mt0)
REVERT: C  275 SER cc_start: 0.9209 (t) cc_final: 0.8723 (p)
REVERT: C  276 VAL cc_start: 0.9268 (m) cc_final: 0.8968 (m)
REVERT: C  325 MET cc_start: 0.8216 (ttm) cc_final: 0.7721 (ttp)
REVERT: E   96 CYS cc_start: 0.8150 (t) cc_final: 0.7841 (t)
REVERT: E   98 ARG cc_start: 0.8273 (ptm160) cc_final: 0.7735 (ptm160)
REVERT: E  143 VAL cc_start: 0.8317 (t) cc_final: 0.8077 (m)
REVERT: E  180 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7064 (ptt)
REVERT: E  190 ARG cc_start: 0.7788 (ptp-170) cc_final: 0.7270 (ptp90)
REVERT: E  219 GLN cc_start: 0.8939 (pp30) cc_final: 0.8630 (tm-30)
REVERT: F   55 GLN cc_start: 0.8242 (mp10) cc_final: 0.8030 (mp10)
REVERT: F  129 TYR cc_start: 0.8843 (m-80) cc_final: 0.8376 (m-10)
REVERT: F  176 HIS cc_start: 0.7611 (p90) cc_final: 0.7292 (p-80)
REVERT: F  237 MET cc_start: 0.8476 (mmm) cc_final: 0.7924 (mmt)
REVERT: F  260 TRP cc_start: 0.8024 (m100) cc_final: 0.7254 (m100)
REVERT: F  275 ILE cc_start: 0.9446 (mm) cc_final: 0.9097 (tp)
  outliers start: 28
  outliers final: 21
  residues processed: 233
  average time/residue: 0.0854
  time to fit residues: 27.7924
Evaluate side-chains
  238 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   34 MET
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  248 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 6 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 74 optimal weight:   40.0000
   chunk 67 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN
C 313 ASN
C 340 ASN
** F 252 HIS ** 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 = 0.3957 r_free = 0.3957 target = 0.159289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.124142 restraints weight = 12933.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.127528 restraints weight = 5928.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.128423 restraints weight = 4064.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.128945 restraints weight = 3652.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.128873 restraints weight = 3490.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8718  Z= 0.152
  Angle     :  0.674  21.359  11881  Z= 0.327
  Chirality :  0.046   0.496   1382
  Planarity :  0.004   0.042   1504
  Dihedral  :  4.124  29.649   1222
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.85 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.82 (0.25), residues: 1115
  helix:  2.19 (0.26), residues: 388
  sheet:  0.52 (0.33), residues: 258
  loop : -0.87 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 185 
 TYR   0.020   0.001   TYR F 213 
 PHE   0.042   0.002   PHE F 303 
 TRP   0.021   0.002   TRP C 297 
 HIS   0.007   0.001   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8716)
  covalent geometry    : angle       0.67373 (11877)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       0.52608 (    4)
  hydrogen bonds       : bond        0.03562 (  462)
  hydrogen bonds       : angle       4.71791 ( 1320)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 223
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9088 (t80) cc_final: 0.8608 (t80)
REVERT: B   73 LYS cc_start: 0.8648 (mmtm) cc_final: 0.7855 (pttm)
REVERT: B   95 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8612 (mmtm)
REVERT: C  153 ASP cc_start: 0.7708 (m-30) cc_final: 0.7342 (m-30)
REVERT: C  220 GLN cc_start: 0.7830 (mt0) cc_final: 0.7586 (mt0)
REVERT: C  246 ASP cc_start: 0.8258 (m-30) cc_final: 0.8010 (m-30)
REVERT: C  275 SER cc_start: 0.9195 (t) cc_final: 0.8706 (p)
REVERT: C  276 VAL cc_start: 0.9273 (m) cc_final: 0.8993 (m)
REVERT: E   96 CYS cc_start: 0.8166 (t) cc_final: 0.7864 (t)
REVERT: E   98 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7746 (ptm160)
REVERT: E  148 ARG cc_start: 0.8235 (mmt180) cc_final: 0.7050 (ttp-110)
REVERT: E  180 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7049 (ptt)
REVERT: E  190 ARG cc_start: 0.7743 (ptp-170) cc_final: 0.7238 (ptp90)
REVERT: F   55 GLN cc_start: 0.8229 (mp10) cc_final: 0.8005 (mp10)
REVERT: F  129 TYR cc_start: 0.8846 (m-80) cc_final: 0.8356 (m-10)
REVERT: F  176 HIS cc_start: 0.7566 (p90) cc_final: 0.7235 (p-80)
REVERT: F  237 MET cc_start: 0.8464 (mmm) cc_final: 0.7875 (mmt)
REVERT: F  260 TRP cc_start: 0.7996 (m100) cc_final: 0.7248 (m100)
REVERT: F  275 ILE cc_start: 0.9448 (mm) cc_final: 0.9105 (tp)
  outliers start: 26
  outliers final: 24
  residues processed: 234
  average time/residue: 0.0828
  time to fit residues: 27.0919
Evaluate side-chains
  241 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 216
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   34 MET
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  248 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 109 optimal weight:    0.3980
   chunk 49 optimal weight:    0.5980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.161373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.123147 restraints weight = 12840.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.127374 restraints weight = 6789.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.130164 restraints weight = 4531.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.131907 restraints weight = 3515.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.132854 restraints weight = 3003.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8718  Z= 0.126
  Angle     :  0.670  20.257  11881  Z= 0.322
  Chirality :  0.045   0.469   1382
  Planarity :  0.004   0.042   1504
  Dihedral  :  4.074  29.049   1222
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 22.08 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.86 (0.25), residues: 1115
  helix:  2.23 (0.26), residues: 387
  sheet:  0.50 (0.32), residues: 264
  loop : -0.83 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 185 
 TYR   0.018   0.001   TYR F 213 
 PHE   0.036   0.002   PHE F 303 
 TRP   0.016   0.001   TRP C 297 
 HIS   0.006   0.001   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8716)
  covalent geometry    : angle       0.67016 (11877)
  SS BOND              : bond        0.00269 (    2)
  SS BOND              : angle       0.49200 (    4)
  hydrogen bonds       : bond        0.03388 (  462)
  hydrogen bonds       : angle       4.66801 ( 1320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1636.67 seconds
wall clock time: 28 minutes 53.84 seconds (1733.84 seconds total)