Starting phenix.real_space_refine
on Sat Aug 23 04:31:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jia_36304/08_2025/8jia_36304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jia_36304/08_2025/8jia_36304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jia_36304/08_2025/8jia_36304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jia_36304/08_2025/8jia_36304.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jia_36304/08_2025/8jia_36304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jia_36304/08_2025/8jia_36304.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      49      5.16       5
     C    6045      2.51       5
     N    1697      2.21       5
     O    1790      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9587
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1581
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 9, 'TRANS': 217}
          Unresolved non-hydrogen bonds: 200
          Unresolved non-hydrogen angles: 246
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 13, 'ASP:plan': 5, 'GLU:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 133
    Chain: "B"
      Number of atoms: 1576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1576
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 9, 'TRANS': 215}
          Unresolved non-hydrogen bonds: 189
          Unresolved non-hydrogen angles: 235
          Unresolved non-hydrogen dihedrals: 150
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 8, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 122
    Chain: "E"
      Number of atoms: 1884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 1884
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 10, 'TRANS': 274}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 241
          Unresolved non-hydrogen angles: 310
          Unresolved non-hydrogen dihedrals: 198
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 8, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR%COO:plan': 1}
          Unresolved non-hydrogen planarities: 164
    Chain: "D"
      Number of atoms: 2227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2227
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 6, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 38
    Chain: "C"
      Number of atoms: 2257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2257
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 6, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.65, per 1000 atoms: 0.28
  Number of scatterers: 9587
  At special positions: 0
  Unit cell: (119.78, 106, 193.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     P       6     15.00
     O    1790      8.00
     N    1697      7.00
     C    6045      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  73 " - pdb=" SG  CYS D  78 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  73 " - pdb=" SG  CYS C  78 " 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: 0.98
  Conformation dependent library (CDL) restraints added in 413.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2476

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 6 sheets defined
      50.5% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 50
      removed outlier: 3.642A  pdb=" N   LEU A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 81
      removed outlier: 3.590A  pdb=" N   LEU A  79 " --> pdb=" O   HIS A  75 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 105
      removed outlier: 3.949A  pdb=" N   VAL A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ALA A 103 " --> pdb=" O   TYR A  99 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ALA A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 120
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 3.517A  pdb=" N   VAL A 127 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 123 through 128'
    Processing helix  chain 'A' and resid 141 through 154
      removed outlier: 3.625A  pdb=" N   GLN A 146 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ARG A 147 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL A 148 " --> pdb=" O   GLU A 144 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ALA A 149 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 187
      removed outlier: 3.657A  pdb=" N   MET A 179 " --> pdb=" O   SER A 175 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ASP A 180 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ARG A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 206
      removed outlier: 4.554A  pdb=" N   MET A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ARG A 206 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 201 through 206'
    Processing helix  chain 'B' and resid 38 through 41
    Processing helix  chain 'B' and resid 42 through 51
      removed outlier: 3.659A  pdb=" N   LEU B  50 " --> pdb=" O   PHE B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 103
      removed outlier: 3.682A  pdb=" N   VAL B 102 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 125
    Processing helix  chain 'B' and resid 141 through 153
      removed outlier: 3.875A  pdb=" N   GLN B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ARG B 147 " --> pdb=" O   GLY B 143 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ALA B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 187
      removed outlier: 4.015A  pdb=" N   ARG B 176 " --> pdb=" O   PRO B 172 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   ASP B 177 " --> pdb=" O   GLU B 173 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE B 178 " --> pdb=" O   THR B 174 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU B 182 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLU B 183 " --> pdb=" O   MET B 179 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 48 through 110
      removed outlier: 3.924A  pdb=" N   ALA E  54 " --> pdb=" O   LEU E  50 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLN E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR E  57 " --> pdb=" O   GLN E  53 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   LEU E  61 " --> pdb=" O   THR E  57 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   HIS E  62 " --> pdb=" O   THR E  58 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LEU E  66 " --> pdb=" O   HIS E  62 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASP E  67 " --> pdb=" O   SER E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 122
      removed outlier: 3.759A  pdb=" N   ILE E 122 " --> pdb=" O   MET E 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 127 through 195
      removed outlier: 3.735A  pdb=" N   ILE E 132 " --> pdb=" O   PRO E 128 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ASP E 133 " --> pdb=" O   GLN E 129 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL E 140 " --> pdb=" O   SER E 136 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   HIS E 143 " --> pdb=" O   ARG E 139 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN E 186 " --> pdb=" O   ALA E 182 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU E 187 " --> pdb=" O   VAL E 183 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS E 189 " --> pdb=" O   ALA E 185 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLN E 195 " --> pdb=" O   GLN E 191 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 197 through 202
    Processing helix  chain 'E' and resid 320 through 325
    Processing helix  chain 'D' and resid 3 through 17
      removed outlier: 3.664A  pdb=" N   ASN D   8 " --> pdb=" O   GLY D   4 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLU D   9 " --> pdb=" O   PHE D   5 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL D  10 " --> pdb=" O   LEU D   6 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   LEU D  11 " --> pdb=" O   LEU D   7 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR D  12 " --> pdb=" O   ASN D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 50
      removed outlier: 3.516A  pdb=" N   THR D  21 " --> pdb=" O   ASN D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 85
      removed outlier: 3.925A  pdb=" N   ALA D  80 " --> pdb=" O   THR D  76 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   LEU D  81 " --> pdb=" O   ALA D  77 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLU D  83 " --> pdb=" O   LYS D  79 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE D  85 " --> pdb=" O   LEU D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 110
      removed outlier: 3.707A  pdb=" N   ASP D 104 " --> pdb=" O   GLN D 100 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ALA D 106 " --> pdb=" O   ALA D 102 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ILE D 107 " --> pdb=" O   TYR D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 122
      removed outlier: 4.409A  pdb=" N   PHE D 122 " --> pdb=" O   LYS D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 136 through 141
      removed outlier: 3.672A  pdb=" N   ASP D 140 " --> pdb=" O   HIS D 136 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   THR D 141 " --> pdb=" O   LYS D 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 136 through 141'
    Processing helix  chain 'D' and resid 157 through 163
    Processing helix  chain 'D' and resid 164 through 190
      removed outlier: 3.587A  pdb=" N   GLY D 183 " --> pdb=" O   VAL D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 196
      removed outlier: 3.762A  pdb=" N   VAL D 194 " --> pdb=" O   ASN D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 204
      removed outlier: 3.678A  pdb=" N   ILE D 203 " --> pdb=" O   ARG D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 244
      removed outlier: 4.481A  pdb=" N   GLN D 217 " --> pdb=" O   ARG D 213 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU D 218 " --> pdb=" O   TRP D 214 " (cutoff:3.500A)
      Proline residue:  D 219  - end of helix
      removed outlier: 3.839A  pdb=" N   GLU D 223 " --> pdb=" O   PRO D 219 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ALA D 224 " --> pdb=" O   PHE D 220 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA D 237 " --> pdb=" O   GLY D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 254
    Processing helix  chain 'D' and resid 264 through 271
      removed outlier: 3.747A  pdb=" N   ILE D 271 " --> pdb=" O   ASP D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 285
    Processing helix  chain 'D' and resid 288 through 293
      removed outlier: 3.517A  pdb=" N   ARG D 292 " --> pdb=" O   TYR D 288 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU D 293 " --> pdb=" O   LEU D 289 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 288 through 293'
    Processing helix  chain 'C' and resid 9 through 17
      removed outlier: 3.896A  pdb=" N   GLY C  13 " --> pdb=" O   GLU C   9 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ASN C  17 " --> pdb=" O   GLY C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 49
      removed outlier: 3.618A  pdb=" N   ILE C  22 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ALA C  23 " --> pdb=" O   THR C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 69
      removed outlier: 3.846A  pdb=" N   ASN C  69 " --> pdb=" O   ASP C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 86
      removed outlier: 3.827A  pdb=" N   LYS C  79 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LYS C  84 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE C  85 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 103
      removed outlier: 4.203A  pdb=" N   TYR C 103 " --> pdb=" O   GLN C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 110
    Processing helix  chain 'C' and resid 136 through 143
    Processing helix  chain 'C' and resid 161 through 199
    Processing helix  chain 'C' and resid 202 through 210
      removed outlier: 3.677A  pdb=" N   GLY C 210 " --> pdb=" O   MET C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 247
      removed outlier: 3.798A  pdb=" N   GLN C 217 " --> pdb=" O   ARG C 213 " (cutoff:3.500A)
      Proline residue:  C 219  - end of helix
      removed outlier: 4.220A  pdb=" N   PHE C 246 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 257
      removed outlier: 3.843A  pdb=" N   GLN C 256 " --> pdb=" O   ASN C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 287
      removed outlier: 4.081A  pdb=" N   ALA C 281 " --> pdb=" O   LEU C 277 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   THR C 286 " --> pdb=" O   MET C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 295
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 9
      removed outlier: 6.266A  pdb=" N   HIS A   7 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   ASP A  60 " --> pdb=" O   HIS A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86
      removed outlier: 5.659A  pdb=" N   GLY A  84 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ASP A 164 " --> pdb=" O   GLY A  84 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   VAL A  86 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   PHE A  34 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   LEU A 212 " --> pdb=" O   PHE A  34 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   VAL A 209 " --> pdb=" O   ASP A 220 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   ASP A 220 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   GLU A 211 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 9
      removed outlier: 3.590A  pdb=" N   ARG B  62 " --> pdb=" O   THR B   4 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP B   6 " --> pdb=" O   ASP B  60 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ASP B  60 " --> pdb=" O   ASP B   6 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   VAL B   8 " --> pdb=" O   SER B  58 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   SER B  58 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86
      removed outlier: 5.788A  pdb=" N   GLY B  84 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 60
    Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 94
      removed outlier: 7.134A  pdb=" N   LYS C 129 " --> pdb=" O   LYS C  92 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1203 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: 1.36

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3169
        1.34 -     1.46: 1871
        1.46 -     1.58: 4586
        1.58 -     1.70: 7
        1.70 -     1.82: 91
  Bond restraints: 9724
  Sorted by residual:
  bond pdb=" CA  ASN D  17 "
       pdb=" CB  ASN D  17 "
    ideal  model  delta    sigma   weight residual
    1.522  1.551 -0.029 1.27e-02 6.20e+03 5.26e+00
  bond pdb=" CA  ILE A  23 "
       pdb=" CB  ILE A  23 "
    ideal  model  delta    sigma   weight residual
    1.539  1.558 -0.020 1.19e-02 7.06e+03 2.73e+00
  bond pdb=" C   VAL B  76 "
       pdb=" N   PRO B  77 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.020 1.25e-02 6.40e+03 2.58e+00
  bond pdb=" CB  GLN B  95 "
       pdb=" CG  GLN B  95 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 3.00e-02 1.11e+03 2.50e+00
  bond pdb=" C   VAL A 120 "
       pdb=" N   PRO A 121 "
    ideal  model  delta    sigma   weight residual
    1.334  1.347 -0.013 8.40e-03 1.42e+04 2.37e+00
  ... (remaining 9719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.79: 12888
        2.79 -     5.58: 278
        5.58 -     8.37: 63
        8.37 -    11.16: 14
       11.16 -    13.94: 4
  Bond angle restraints: 13247
  Sorted by residual:
  angle pdb=" N   VAL E 304 "
        pdb=" CA  VAL E 304 "
        pdb=" C   VAL E 304 "
      ideal   model   delta    sigma   weight residual
     113.71  108.30    5.41 9.50e-01 1.11e+00 3.24e+01
  angle pdb=" CB  MET D 225 "
        pdb=" CG  MET D 225 "
        pdb=" SD  MET D 225 "
      ideal   model   delta    sigma   weight residual
     112.70  126.64  -13.94 3.00e+00 1.11e-01 2.16e+01
  angle pdb=" C   ASP B  89 "
        pdb=" N   PHE B  90 "
        pdb=" CA  PHE B  90 "
      ideal   model   delta    sigma   weight residual
     121.54  130.09   -8.55 1.91e+00 2.74e-01 2.00e+01
  angle pdb=" N   ILE A 185 "
        pdb=" CA  ILE A 185 "
        pdb=" C   ILE A 185 "
      ideal   model   delta    sigma   weight residual
     112.35  106.08    6.27 1.41e+00 5.03e-01 1.98e+01
  angle pdb=" N   VAL D 242 "
        pdb=" CA  VAL D 242 "
        pdb=" C   VAL D 242 "
      ideal   model   delta    sigma   weight residual
     113.39  106.88    6.51 1.47e+00 4.63e-01 1.96e+01
  ... (remaining 13242 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.12: 5412
       16.12 -    32.23: 363
       32.23 -    48.35: 79
       48.35 -    64.47: 24
       64.47 -    80.58: 7
  Dihedral angle restraints: 5885
    sinusoidal: 2067
      harmonic: 3818
  Sorted by residual:
  dihedral pdb=" CA  LYS C 262 "
           pdb=" C   LYS C 262 "
           pdb=" N   VAL C 263 "
           pdb=" CA  VAL C 263 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.21   28.79     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  MET D 206 "
           pdb=" C   MET D 206 "
           pdb=" N   ARG D 207 "
           pdb=" CA  ARG D 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.78   21.22     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  ILE C  85 "
           pdb=" C   ILE C  85 "
           pdb=" N   GLU C  86 "
           pdb=" CA  GLU C  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.82   19.18     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5882 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1137
       0.053 -    0.106: 377
       0.106 -    0.159: 82
       0.159 -    0.212: 20
       0.212 -    0.265: 5
  Chirality restraints: 1621
  Sorted by residual:
  chirality pdb=" CG  LEU D 239 "
            pdb=" CB  LEU D 239 "
            pdb=" CD1 LEU D 239 "
            pdb=" CD2 LEU D 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CB  VAL B  76 "
            pdb=" CA  VAL B  76 "
            pdb=" CG1 VAL B  76 "
            pdb=" CG2 VAL B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CB  THR A 167 "
            pdb=" CA  THR A 167 "
            pdb=" OG1 THR A 167 "
            pdb=" CG2 THR A 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1618 not shown)

  Planarity restraints: 1710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 110 "   -0.049 5.00e-02 4.00e+02   7.42e-02 8.81e+00
        pdb=" N   PRO C 111 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO C 111 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C 111 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D  57 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.40e+00
        pdb=" CD  GLU D  57 "   -0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLU D  57 "    0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU D  57 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 223 "    0.009 2.00e-02 2.50e+03   1.83e-02 3.37e+00
        pdb=" CD  GLU C 223 "   -0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 223 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 223 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1707 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 2958
        2.82 -     3.34: 9285
        3.34 -     3.86: 15527
        3.86 -     4.38: 17074
        4.38 -     4.90: 28606
  Nonbonded interactions: 73450
  Sorted by model distance:
  nonbonded pdb=" O   LEU E  47 "
            pdb=" OG1 THR E 363 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   ARG C 213 "
            pdb=" OG1 THR C 216 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   ILE C 268 "
            pdb=" OG1 THR C 272 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   GLU C   9 "
            pdb=" OG1 THR C  12 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" NH1 ARG C  99 "
            pdb=" OD1 ASP C 120 "
     model   vdw
     2.356 3.120
  ... (remaining 73445 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 6 through 12 or (resid 13 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 14 through 19 or (resid 20 through 2 \ 
2 and (name N or name CA or name C or name O or name CB )) or resid 23 or (resid \ 
 24 and (name N or name CA or name C or name O or name CB )) or resid 25 or (res \ 
id 26 and (name N or name CA or name C or name O or name CB )) or resid 27 or (r \ 
esid 28 through 29 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 30 through 65 or (resid 66 through 70 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 71 through 88 or (resid 89 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 90 through 92 or (resid 93 through 100 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 101 through 1 \ 
24 or (resid 125 and (name N or name CA or name C or name O or name CB )) or res \ 
id 126 through 133 or (resid 134 through 136 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 137 through 138 or (resid 139 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 140 through 172 or (resid 173 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 174 through 217 o \ 
r (resid 218 through 219 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 220 through 225 or resid 301))
  selection = (chain 'B' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ 
 or name O or name CB )) or (resid 30 through 32 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 33 through 34 or (resid 35 through 36 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 37 through 44 or (res \ 
id 45 and (name N or name CA or name C or name O or name CB )) or resid 46 throu \ 
gh 50 or (resid 51 through 55 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 56 through 59 or (resid 60 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 61 through 68 or (resid 69 through 70 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 71 or (resid 72 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 73 or (resid 74 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 75 through 77 or (resid \ 
 78 and (name N or name CA or name C or name O or name CB )) or resid 79 through \ 
 94 or (resid 95 through 100 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 101 through 128 or (resid 129 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 130 through 137 or (resid 138 through 139 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 140 through 156 or (r \ 
esid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 t \ 
hrough 175 or (resid 176 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 177 through 179 or (resid 180 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 181 through 192 or (resid 193 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 194 through 198 or (resid 199 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 200 through 213 or (r \ 
esid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 t \ 
hrough 218 or (resid 219 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 220 or (resid 221 through 223 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 224 or (resid 225 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 301))
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 13 through 15 or (resid 16 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 17 through 108 or (resid 109 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 110 through 133 or \ 
 (resid 134 through 135 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 136 or (resid 137 and (name N or name CA or name C or name O or name C \ 
B )) or resid 138 through 152 or (resid 153 through 155 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 156 through 219 or (resid 220 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 221 through 291 or (re \ 
sid 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or \ 
 (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 
5))
  selection = (chain 'D' and (resid 1 through 115 or (resid 116 through 117 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 118 through 143 or (resid 144 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 145 through 196  \ 
or (resid 197 and (name N or name CA or name C or name O or name CB )) or resid  \ 
198 through 199 or (resid 200 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 201 through 295))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.610
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.600
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
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      :  0.005   0.076   9726  Z= 0.220
  Angle     :  1.062  13.944  13251  Z= 0.546
  Chirality :  0.056   0.265   1621
  Planarity :  0.006   0.074   1710
  Dihedral  : 12.520  80.584   3403
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.15 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.99 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.20 (0.20), residues: 1315
  helix: -1.72 (0.18), residues: 585
  sheet: -2.20 (0.66), residues: 54
  loop : -2.50 (0.21), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 187 
 TYR   0.028   0.002   TYR C 255 
 PHE   0.019   0.002   PHE D 110 
 TRP   0.006   0.001   TRP C 274 
 HIS   0.016   0.002   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 9724)
  covalent geometry    : angle       1.06159 (13247)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.79358 (    4)
  hydrogen bonds       : bond        0.17955 (  410)
  hydrogen bonds       : angle       6.65607 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 181
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 CYS cc_start: 0.8601 (t) cc_final: 0.8396 (t)
REVERT: B  205 MET cc_start: 0.8013 (mmp) cc_final: 0.7464 (mmp)
REVERT: E   52 ARG cc_start: 0.8165 (tpm170) cc_final: 0.7459 (tpp-160)
REVERT: E  305 MET cc_start: 0.8275 (tmm) cc_final: 0.7915 (tmm)
REVERT: E  358 MET cc_start: 0.6550 (mpp) cc_final: 0.6061 (mpp)
REVERT: D  157 GLU cc_start: 0.7976 (pm20) cc_final: 0.7702 (pm20)
REVERT: D  160 ASP cc_start: 0.8499 (m-30) cc_final: 0.7963 (t0)
REVERT: D  217 GLN cc_start: 0.8793 (pm20) cc_final: 0.8478 (pm20)
REVERT: D  252 ASN cc_start: 0.8506 (m110) cc_final: 0.7096 (m-40)
REVERT: D  282 MET cc_start: 0.8482 (ppp) cc_final: 0.8203 (ppp)
REVERT: C  230 MET cc_start: 0.9007 (tpt) cc_final: 0.8682 (tpp)
REVERT: C  255 TYR cc_start: 0.8152 (t80) cc_final: 0.7500 (t80)
REVERT: C  262 LYS cc_start: 0.8854 (mmpt) cc_final: 0.8587 (mmtt)
REVERT: C  278 LEU cc_start: 0.9308 (tp) cc_final: 0.9107 (tt)
  outliers start: 3
  outliers final: 1
  residues processed: 182
  average time/residue: 0.0891
  time to fit residues: 23.4142
Evaluate side-chains
  143 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.2980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.2980
   chunk 66 optimal weight:    1.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0870
   chunk 55 optimal weight:    9.9990
   chunk 129 optimal weight:    2.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
B 186 ASN
E  48 ASN
E 100 GLN
E 104 ASN
E 117 HIS
D 100 GLN
D 101 GLN
D 112 GLN
C 180 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.073265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.058738 restraints weight = 52209.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.060124 restraints weight = 31813.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.061099 restraints weight = 22436.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.061755 restraints weight = 17425.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.062167 restraints weight = 14629.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9726  Z= 0.117
  Angle     :  0.592   7.462  13251  Z= 0.304
  Chirality :  0.040   0.130   1621
  Planarity :  0.004   0.046   1710
  Dihedral  :  7.740  88.120   1478
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.78 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.67 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.95 (0.22), residues: 1315
  helix: -0.28 (0.20), residues: 632
  sheet: -2.96 (0.56), residues: 63
  loop : -2.20 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 187 
 TYR   0.008   0.001   TYR C 294 
 PHE   0.016   0.001   PHE A  87 
 TRP   0.004   0.001   TRP D 214 
 HIS   0.005   0.001   HIS E 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9724)
  covalent geometry    : angle       0.59237 (13247)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       0.47944 (    4)
  hydrogen bonds       : bond        0.03925 (  410)
  hydrogen bonds       : angle       4.43618 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8719 (m-10) cc_final: 0.8394 (m-10)
REVERT: A  187 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8025 (mtm-85)
REVERT: B  205 MET cc_start: 0.7876 (mmp) cc_final: 0.7506 (mmp)
REVERT: E   52 ARG cc_start: 0.8270 (tpm170) cc_final: 0.7475 (tpm170)
REVERT: E  305 MET cc_start: 0.8464 (tmm) cc_final: 0.8129 (tmm)
REVERT: D  160 ASP cc_start: 0.8452 (m-30) cc_final: 0.7997 (t0)
REVERT: D  217 GLN cc_start: 0.8785 (pm20) cc_final: 0.8576 (pm20)
REVERT: D  223 GLU cc_start: 0.8599 (pm20) cc_final: 0.8317 (pm20)
REVERT: D  248 GLU cc_start: 0.7552 (tp30) cc_final: 0.7255 (tp30)
REVERT: D  252 ASN cc_start: 0.8355 (m110) cc_final: 0.6987 (m110)
REVERT: D  282 MET cc_start: 0.8405 (ppp) cc_final: 0.7995 (ppp)
REVERT: C  278 LEU cc_start: 0.9329 (tp) cc_final: 0.9101 (tt)
  outliers start: 11
  outliers final: 5
  residues processed: 164
  average time/residue: 0.0821
  time to fit residues: 19.2355
Evaluate side-chains
  139 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 44 optimal weight:    0.0770
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 88 optimal weight:    0.1980
   chunk 27 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.5740

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

Flipped N/Q/H residues before XYZ refinement:
E 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.072152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.057840 restraints weight = 52238.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.059235 restraints weight = 31566.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.060157 restraints weight = 22086.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.060836 restraints weight = 17153.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.061323 restraints weight = 14264.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9726  Z= 0.112
  Angle     :  0.573  10.915  13251  Z= 0.289
  Chirality :  0.040   0.137   1621
  Planarity :  0.003   0.047   1710
  Dihedral  :  7.249  84.930   1476
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.69 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 14.62 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.23), residues: 1315
  helix:  0.36 (0.21), residues: 628
  sheet: -2.30 (0.63), residues: 62
  loop : -2.07 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 187 
 TYR   0.009   0.001   TYR C 294 
 PHE   0.016   0.001   PHE A  87 
 TRP   0.005   0.001   TRP C 274 
 HIS   0.003   0.001   HIS E 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9724)
  covalent geometry    : angle       0.57289 (13247)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.33752 (    4)
  hydrogen bonds       : bond        0.03565 (  410)
  hydrogen bonds       : angle       4.14572 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8664 (m-10) cc_final: 0.8378 (m-10)
REVERT: B  205 MET cc_start: 0.7947 (mmp) cc_final: 0.7678 (mmm)
REVERT: E   52 ARG cc_start: 0.8329 (tpm170) cc_final: 0.7596 (tpm170)
REVERT: E  305 MET cc_start: 0.8486 (tmm) cc_final: 0.8165 (tmm)
REVERT: D  100 GLN cc_start: 0.8701 (tp40) cc_final: 0.8175 (tp40)
REVERT: D  160 ASP cc_start: 0.8460 (m-30) cc_final: 0.7981 (t0)
REVERT: D  171 ASN cc_start: 0.8155 (p0) cc_final: 0.7824 (p0)
REVERT: D  248 GLU cc_start: 0.7628 (tp30) cc_final: 0.7215 (tp30)
REVERT: D  252 ASN cc_start: 0.8549 (m110) cc_final: 0.7222 (m110)
REVERT: D  282 MET cc_start: 0.8473 (ppp) cc_final: 0.7991 (ppp)
REVERT: C   20 MET cc_start: 0.8820 (ttt) cc_final: 0.8400 (ttt)
  outliers start: 9
  outliers final: 4
  residues processed: 154
  average time/residue: 0.0875
  time to fit residues: 19.5344
Evaluate side-chains
  135 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 120 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0670
   chunk 101 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0000
   chunk 74 optimal weight:    1.9990
   chunk 128 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 119 optimal weight:    0.5980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.4122

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

Flipped N/Q/H residues before XYZ refinement:
E 189 HIS
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.072776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.057838 restraints weight = 53366.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.059229 restraints weight = 32207.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.060195 restraints weight = 22738.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.060857 restraints weight = 17727.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.061334 restraints weight = 14880.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9726  Z= 0.102
  Angle     :  0.553   8.535  13251  Z= 0.277
  Chirality :  0.040   0.137   1621
  Planarity :  0.003   0.050   1710
  Dihedral  :  6.871  78.717   1476
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.08 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.04 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.24), residues: 1315
  helix:  0.72 (0.22), residues: 628
  sheet: -2.19 (0.65), residues: 62
  loop : -1.96 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 187 
 TYR   0.013   0.001   TYR C 294 
 PHE   0.009   0.001   PHE A  87 
 TRP   0.004   0.000   TRP C 274 
 HIS   0.002   0.001   HIS E 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9724)
  covalent geometry    : angle       0.55313 (13247)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       0.27900 (    4)
  hydrogen bonds       : bond        0.03401 (  410)
  hydrogen bonds       : angle       3.91775 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8641 (m-10) cc_final: 0.8426 (m-10)
REVERT: A  187 ARG cc_start: 0.8480 (mtm110) cc_final: 0.8213 (ptp-110)
REVERT: B  205 MET cc_start: 0.7937 (mmp) cc_final: 0.7676 (mmm)
REVERT: E   48 ASN cc_start: 0.8806 (t0) cc_final: 0.8398 (p0)
REVERT: E   52 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7676 (tpp-160)
REVERT: E  305 MET cc_start: 0.8515 (tmm) cc_final: 0.8246 (tmm)
REVERT: D   34 LEU cc_start: 0.9454 (tt) cc_final: 0.9236 (tt)
REVERT: D  160 ASP cc_start: 0.8461 (m-30) cc_final: 0.8009 (t0)
REVERT: D  223 GLU cc_start: 0.8571 (pm20) cc_final: 0.8326 (pm20)
REVERT: D  248 GLU cc_start: 0.7668 (tp30) cc_final: 0.7217 (tp30)
REVERT: D  252 ASN cc_start: 0.8594 (m110) cc_final: 0.7150 (m110)
REVERT: D  282 MET cc_start: 0.8459 (ppp) cc_final: 0.8169 (ppp)
  outliers start: 13
  outliers final: 6
  residues processed: 154
  average time/residue: 0.0889
  time to fit residues: 19.8032
Evaluate side-chains
  141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 57 optimal weight:    0.7980
   chunk 87 optimal weight:    0.0030
   chunk 52 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 129 optimal weight:    1.9990
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  17 ASN
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.070240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.055923 restraints weight = 52901.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.057309 restraints weight = 31306.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.058191 restraints weight = 21798.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.058822 restraints weight = 17078.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.059249 restraints weight = 14203.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9726  Z= 0.133
  Angle     :  0.574   6.941  13251  Z= 0.293
  Chirality :  0.040   0.168   1621
  Planarity :  0.003   0.043   1710
  Dihedral  :  6.527  69.258   1476
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.84 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 17.47 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.24), residues: 1315
  helix:  0.71 (0.22), residues: 647
  sheet: -1.78 (0.74), residues: 51
  loop : -1.92 (0.25), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 187 
 TYR   0.011   0.001   TYR C 294 
 PHE   0.015   0.001   PHE C 163 
 TRP   0.007   0.001   TRP C 274 
 HIS   0.003   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9724)
  covalent geometry    : angle       0.57374 (13247)
  SS BOND              : bond        0.00209 (    2)
  SS BOND              : angle       0.42846 (    4)
  hydrogen bonds       : bond        0.03414 (  410)
  hydrogen bonds       : angle       3.99217 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8677 (m-10) cc_final: 0.8421 (m-10)
REVERT: A   90 PHE cc_start: 0.9047 (m-80) cc_final: 0.8676 (m-80)
REVERT: A  187 ARG cc_start: 0.8535 (mtm110) cc_final: 0.8294 (ptp-110)
REVERT: B  205 MET cc_start: 0.7871 (mmp) cc_final: 0.7628 (mmm)
REVERT: E   46 LYS cc_start: 0.3545 (OUTLIER) cc_final: 0.3252 (pptt)
REVERT: E   52 ARG cc_start: 0.8364 (tpm170) cc_final: 0.7702 (tpp-160)
REVERT: E  305 MET cc_start: 0.8462 (tmm) cc_final: 0.8260 (tmm)
REVERT: D  160 ASP cc_start: 0.8470 (m-30) cc_final: 0.8044 (t0)
REVERT: D  180 GLN cc_start: 0.8941 (tp40) cc_final: 0.8734 (tp-100)
REVERT: D  223 GLU cc_start: 0.8547 (pm20) cc_final: 0.8287 (pm20)
REVERT: D  248 GLU cc_start: 0.7653 (tp30) cc_final: 0.7218 (tp30)
REVERT: D  252 ASN cc_start: 0.8637 (m110) cc_final: 0.7145 (m110)
REVERT: D  282 MET cc_start: 0.8350 (ppp) cc_final: 0.7858 (ppp)
REVERT: C   20 MET cc_start: 0.8714 (tpp) cc_final: 0.8502 (ttt)
REVERT: C  240 MET cc_start: 0.8590 (mmm) cc_final: 0.8333 (mmm)
  outliers start: 12
  outliers final: 7
  residues processed: 147
  average time/residue: 0.0816
  time to fit residues: 17.4050
Evaluate side-chains
  139 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 43 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
E  65 GLN
** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  17 ASN
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.068762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.053901 restraints weight = 54145.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.055216 restraints weight = 32616.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.056150 restraints weight = 22902.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.056661 restraints weight = 17828.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.057177 restraints weight = 15218.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9726  Z= 0.159
  Angle     :  0.609   7.203  13251  Z= 0.312
  Chirality :  0.041   0.158   1621
  Planarity :  0.004   0.050   1710
  Dihedral  :  6.349  63.897   1476
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.30 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.35 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.24), residues: 1315
  helix:  0.63 (0.21), residues: 662
  sheet: -1.42 (0.72), residues: 59
  loop : -1.93 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  55 
 TYR   0.026   0.001   TYR C 255 
 PHE   0.019   0.001   PHE C 163 
 TRP   0.009   0.001   TRP C 274 
 HIS   0.004   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9724)
  covalent geometry    : angle       0.60929 (13247)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.73828 (    4)
  hydrogen bonds       : bond        0.03594 (  410)
  hydrogen bonds       : angle       4.03363 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8770 (m-10) cc_final: 0.8398 (m-10)
REVERT: A   90 PHE cc_start: 0.9149 (m-80) cc_final: 0.8694 (m-80)
REVERT: A  196 THR cc_start: 0.9070 (p) cc_final: 0.8850 (t)
REVERT: B  205 MET cc_start: 0.8038 (mmp) cc_final: 0.7639 (mmm)
REVERT: E   46 LYS cc_start: 0.4030 (OUTLIER) cc_final: 0.3667 (pptt)
REVERT: E   52 ARG cc_start: 0.8489 (tpm170) cc_final: 0.7871 (tpp-160)
REVERT: E  141 MET cc_start: 0.9137 (tpp) cc_final: 0.8880 (tpt)
REVERT: D  160 ASP cc_start: 0.8408 (m-30) cc_final: 0.7999 (t0)
REVERT: D  180 GLN cc_start: 0.9035 (tp40) cc_final: 0.8755 (tp-100)
REVERT: D  223 GLU cc_start: 0.8637 (pm20) cc_final: 0.8096 (pm20)
REVERT: D  248 GLU cc_start: 0.7771 (tp30) cc_final: 0.7351 (tp30)
REVERT: D  252 ASN cc_start: 0.8839 (m110) cc_final: 0.7283 (m110)
REVERT: D  282 MET cc_start: 0.8373 (ppp) cc_final: 0.7868 (ppp)
REVERT: C   20 MET cc_start: 0.8772 (tpp) cc_final: 0.8523 (ttt)
REVERT: C   54 ASP cc_start: 0.6697 (p0) cc_final: 0.6425 (p0)
  outliers start: 16
  outliers final: 11
  residues processed: 153
  average time/residue: 0.0670
  time to fit residues: 15.1990
Evaluate side-chains
  136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
E  65 GLN
** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  17 ASN
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.069120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.054306 restraints weight = 53649.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.055669 restraints weight = 32160.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.056607 restraints weight = 22474.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.057267 restraints weight = 17507.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.057669 restraints weight = 14595.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9726  Z= 0.132
  Angle     :  0.624  11.529  13251  Z= 0.312
  Chirality :  0.041   0.162   1621
  Planarity :  0.003   0.057   1710
  Dihedral  :  6.238  62.304   1476
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.07 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.00 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.24), residues: 1315
  helix:  0.73 (0.21), residues: 656
  sheet: -1.30 (0.70), residues: 61
  loop : -1.86 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 187 
 TYR   0.010   0.001   TYR C 294 
 PHE   0.013   0.001   PHE C 163 
 TRP   0.005   0.001   TRP C 274 
 HIS   0.002   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9724)
  covalent geometry    : angle       0.62369 (13247)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.58301 (    4)
  hydrogen bonds       : bond        0.03502 (  410)
  hydrogen bonds       : angle       3.94434 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8751 (m-80) cc_final: 0.8396 (m-10)
REVERT: A  187 ARG cc_start: 0.8820 (ptp-110) cc_final: 0.8591 (mtm110)
REVERT: B  205 MET cc_start: 0.8031 (mmp) cc_final: 0.7661 (mmm)
REVERT: E   46 LYS cc_start: 0.4222 (OUTLIER) cc_final: 0.3868 (pptt)
REVERT: E   52 ARG cc_start: 0.8482 (tpm170) cc_final: 0.7872 (tpp-160)
REVERT: E  141 MET cc_start: 0.9148 (tpp) cc_final: 0.8907 (tpt)
REVERT: D  160 ASP cc_start: 0.8337 (m-30) cc_final: 0.7902 (t0)
REVERT: D  223 GLU cc_start: 0.8633 (pm20) cc_final: 0.8094 (pm20)
REVERT: D  248 GLU cc_start: 0.7755 (tp30) cc_final: 0.7320 (tp30)
REVERT: D  252 ASN cc_start: 0.8854 (m110) cc_final: 0.7126 (m110)
REVERT: D  282 MET cc_start: 0.8400 (ppp) cc_final: 0.8065 (ppp)
  outliers start: 14
  outliers final: 9
  residues processed: 149
  average time/residue: 0.0714
  time to fit residues: 15.6306
Evaluate side-chains
  132 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 114 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 8 optimal weight:    0.1980
   chunk 67 optimal weight:    0.0980
   chunk 45 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 128 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
E 189 HIS
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.069473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.055289 restraints weight = 52592.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.056604 restraints weight = 31364.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.057575 restraints weight = 21940.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.058246 restraints weight = 16818.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.058697 restraints weight = 13948.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9726  Z= 0.116
  Angle     :  0.609   9.705  13251  Z= 0.305
  Chirality :  0.040   0.152   1621
  Planarity :  0.004   0.060   1710
  Dihedral  :  6.122  60.982   1476
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.46 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 20.55 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.25), residues: 1315
  helix:  0.80 (0.21), residues: 660
  sheet: -1.18 (0.71), residues: 61
  loop : -1.82 (0.27), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 243 
 TYR   0.017   0.001   TYR C 215 
 PHE   0.010   0.001   PHE B  46 
 TRP   0.007   0.001   TRP E 306 
 HIS   0.002   0.000   HIS E 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9724)
  covalent geometry    : angle       0.60871 (13247)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       0.47248 (    4)
  hydrogen bonds       : bond        0.03449 (  410)
  hydrogen bonds       : angle       3.85955 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6116 (mm)
REVERT: A   87 PHE cc_start: 0.8746 (m-80) cc_final: 0.8438 (m-10)
REVERT: B  205 MET cc_start: 0.7827 (mmp) cc_final: 0.7560 (mmm)
REVERT: E   46 LYS cc_start: 0.4138 (OUTLIER) cc_final: 0.3754 (pptt)
REVERT: E   48 ASN cc_start: 0.8786 (t0) cc_final: 0.8401 (p0)
REVERT: E   52 ARG cc_start: 0.8443 (tpm170) cc_final: 0.7807 (tpp-160)
REVERT: E  141 MET cc_start: 0.9045 (tpp) cc_final: 0.8828 (tpt)
REVERT: D  160 ASP cc_start: 0.8289 (m-30) cc_final: 0.7841 (t0)
REVERT: D  248 GLU cc_start: 0.7684 (tp30) cc_final: 0.7377 (tp30)
REVERT: D  252 ASN cc_start: 0.8832 (m110) cc_final: 0.7110 (m-40)
REVERT: D  282 MET cc_start: 0.8366 (ppp) cc_final: 0.8013 (ppp)
REVERT: C  268 ILE cc_start: 0.8476 (tt) cc_final: 0.8226 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 149
  average time/residue: 0.0717
  time to fit residues: 15.9057
Evaluate side-chains
  140 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain C residue  190 ASN
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 119 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 115 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
E  65 GLN
E  69 ASN
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 136 HIS
C 146 GLN
C 193 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.065082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.051152 restraints weight = 53895.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.052416 restraints weight = 31376.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.053097 restraints weight = 21789.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.053743 restraints weight = 17470.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.054093 restraints weight = 14564.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9726  Z= 0.239
  Angle     :  0.741   9.358  13251  Z= 0.380
  Chirality :  0.045   0.189   1621
  Planarity :  0.004   0.059   1710
  Dihedral  :  6.739  63.444   1476
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.59 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.44 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.25), residues: 1315
  helix:  0.60 (0.21), residues: 652
  sheet: -1.51 (0.62), residues: 80
  loop : -1.89 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 187 
 TYR   0.012   0.002   TYR B  12 
 PHE   0.032   0.002   PHE C 163 
 TRP   0.016   0.002   TRP C 274 
 HIS   0.004   0.001   HIS A   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 9724)
  covalent geometry    : angle       0.74097 (13247)
  SS BOND              : bond        0.00315 (    2)
  SS BOND              : angle       0.87596 (    4)
  hydrogen bonds       : bond        0.04022 (  410)
  hydrogen bonds       : angle       4.27571 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8830 (m-80) cc_final: 0.8388 (m-10)
REVERT: A   90 PHE cc_start: 0.9195 (m-80) cc_final: 0.8734 (m-80)
REVERT: B  162 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8711 (pt)
REVERT: B  205 MET cc_start: 0.8315 (mmp) cc_final: 0.7937 (mmm)
REVERT: E   46 LYS cc_start: 0.4272 (OUTLIER) cc_final: 0.3826 (pptt)
REVERT: E  112 MET cc_start: 0.8772 (mpp) cc_final: 0.8429 (mpp)
REVERT: D  144 LYS cc_start: 0.8258 (pptt) cc_final: 0.7695 (mmmt)
REVERT: D  248 GLU cc_start: 0.7699 (tp30) cc_final: 0.7448 (tp30)
REVERT: D  282 MET cc_start: 0.8403 (ppp) cc_final: 0.8053 (ppp)
  outliers start: 18
  outliers final: 13
  residues processed: 143
  average time/residue: 0.0761
  time to fit residues: 16.0737
Evaluate side-chains
  134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain B residue   85 CYS
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 128 optimal weight:    0.9990
   chunk 127 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 44 optimal weight:    0.2980
   chunk 95 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E  69 ASN
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  69 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.067837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053176 restraints weight = 53874.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.054517 restraints weight = 31951.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.055461 restraints weight = 22188.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.056129 restraints weight = 17228.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.056586 restraints weight = 14298.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9726  Z= 0.137
  Angle     :  0.665  10.179  13251  Z= 0.332
  Chirality :  0.042   0.191   1621
  Planarity :  0.004   0.065   1710
  Dihedral  :  6.450  61.670   1476
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.77 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 22.20 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.25), residues: 1315
  helix:  0.60 (0.21), residues: 669
  sheet: -1.35 (0.69), residues: 64
  loop : -1.86 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 187 
 TYR   0.010   0.001   TYR C 215 
 PHE   0.013   0.001   PHE C 163 
 TRP   0.007   0.001   TRP D 214 
 HIS   0.004   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9724)
  covalent geometry    : angle       0.66459 (13247)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.64887 (    4)
  hydrogen bonds       : bond        0.03690 (  410)
  hydrogen bonds       : angle       4.06712 ( 1203)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 TYR cc_start: 0.6335 (m-80) cc_final: 0.6093 (m-10)
REVERT: A   20 LEU cc_start: 0.6503 (mt) cc_final: 0.6273 (mm)
REVERT: A   87 PHE cc_start: 0.8729 (m-80) cc_final: 0.8473 (m-10)
REVERT: B  162 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8608 (pt)
REVERT: B  179 MET cc_start: 0.9080 (mmm) cc_final: 0.8799 (mmm)
REVERT: B  205 MET cc_start: 0.8189 (mmp) cc_final: 0.7807 (mmm)
REVERT: B  212 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8298 (tt)
REVERT: E   46 LYS cc_start: 0.4556 (OUTLIER) cc_final: 0.4139 (pptt)
REVERT: E   52 ARG cc_start: 0.8596 (tpm170) cc_final: 0.8322 (tpm170)
REVERT: E  112 MET cc_start: 0.8691 (mpp) cc_final: 0.8338 (mpp)
REVERT: E  141 MET cc_start: 0.9085 (tpp) cc_final: 0.8840 (tpt)
REVERT: D  144 LYS cc_start: 0.8156 (pptt) cc_final: 0.7760 (mmmt)
REVERT: D  248 GLU cc_start: 0.7693 (tp30) cc_final: 0.7304 (tp30)
REVERT: D  252 ASN cc_start: 0.8857 (m110) cc_final: 0.6975 (m110)
REVERT: D  282 MET cc_start: 0.8388 (ppp) cc_final: 0.8009 (ppp)
  outliers start: 14
  outliers final: 11
  residues processed: 147
  average time/residue: 0.0795
  time to fit residues: 17.2329
Evaluate side-chains
  140 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   85 CYS
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain C residue   39 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 95 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 127 optimal weight:    0.0170
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
E  65 GLN
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 180 GLN
D 190 ASN
C  69 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.068193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.053618 restraints weight = 53683.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.054992 restraints weight = 32148.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.055895 restraints weight = 22309.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.056385 restraints weight = 17285.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.056922 restraints weight = 14738.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9726  Z= 0.130
  Angle     :  0.671   8.947  13251  Z= 0.334
  Chirality :  0.042   0.167   1621
  Planarity :  0.004   0.063   1710
  Dihedral  :  6.292  60.196   1476
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.38 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 22.42 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.25), residues: 1315
  helix:  0.72 (0.21), residues: 649
  sheet: -1.29 (0.67), residues: 70
  loop : -1.80 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 187 
 TYR   0.005   0.001   TYR D 255 
 PHE   0.011   0.001   PHE C 163 
 TRP   0.006   0.001   TRP D 214 
 HIS   0.005   0.001   HIS E 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9724)
  covalent geometry    : angle       0.67092 (13247)
  SS BOND              : bond        0.00226 (    2)
  SS BOND              : angle       0.58459 (    4)
  hydrogen bonds       : bond        0.03576 (  410)
  hydrogen bonds       : angle       3.99253 ( 1203)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1614.96 seconds
wall clock time: 28 minutes 36.69 seconds (1716.69 seconds total)