Starting phenix.real_space_refine
on Wed Jul 30 23:17:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7osf_13049/07_2025/7osf_13049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7osf_13049/07_2025/7osf_13049.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7osf_13049/07_2025/7osf_13049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7osf_13049/07_2025/7osf_13049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7osf_13049/07_2025/7osf_13049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7osf_13049/07_2025/7osf_13049.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.004
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     Cu      1      5.60       5
     Mg      1      5.21       5
     S      45      5.16       5
     C    8200      2.51       5
     N    2249      2.21       5
     O    2329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12826
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3077
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 16, 'TRANS': 375}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2375
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 12, 'TRANS': 295}
    Chain: "C"
      Number of atoms: 2367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2367
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 12, 'TRANS': 294}
    Chain: "D"
      Number of atoms: 2015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2015
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 8, 'TRANS': 258}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1896
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 8, 'TRANS': 239}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1092
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CU': 1, ' MG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  11839  SG  CYS H  45      45.459  41.805  48.159  1.00122.68           S
  ATOM  11862  SG  CYS H  48      43.354  42.911  45.783  1.00122.45           S
  ATOM  12043  SG  CYS H  72      46.189  43.837  44.237  1.00129.62           S

  Time building chain proxies: 8.38, per 1000 atoms: 0.65
  Number of scatterers: 12826
  At special positions: 0
  Unit cell: (80.352, 90.72, 194.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     Cu      1     28.99
     S      45     16.00
     Mg      1     11.99
     O    2329      8.00
     N    2249      7.00
     C    8200      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.78
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN H 201 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H  72 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H  48 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H  45 "


  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2996

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 13 sheets defined
      43.7% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.662A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   TRP A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 3.511A  pdb=" N   MET A 390 " --> pdb=" O   ARG A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 405
      removed outlier: 3.656A  pdb=" N   TRP A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLN A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 50
    Processing helix  chain 'B' and resid 69 through 74
      removed outlier: 3.512A  pdb=" N   ARG B  74 " --> pdb=" O   PRO B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 102
      removed outlier: 3.657A  pdb=" N   LEU B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ARG B 100 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU B 101 " --> pdb=" O   HIS B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 116
      removed outlier: 4.247A  pdb=" N   ASP B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLU B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 162 through 178
      removed outlier: 3.844A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG B 177 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 219
    Processing helix  chain 'B' and resid 234 through 239
      removed outlier: 3.570A  pdb=" N   ARG B 239 " --> pdb=" O   SER B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 297
      removed outlier: 3.529A  pdb=" N   TYR B 293 " --> pdb=" O   ASP B 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 51
      removed outlier: 3.868A  pdb=" N   MET C  46 " --> pdb=" O   LYS C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 74
      removed outlier: 3.600A  pdb=" N   ARG C  74 " --> pdb=" O   PRO C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 102
    Processing helix  chain 'C' and resid 108 through 113
      removed outlier: 3.546A  pdb=" N   LEU C 113 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 129
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 160 through 177
      removed outlier: 3.851A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 218
    Processing helix  chain 'C' and resid 233 through 241
      removed outlier: 3.564A  pdb=" N   GLN C 238 " --> pdb=" O   ASP C 234 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   ARG C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   THR C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 273
      removed outlier: 3.531A  pdb=" N   LEU C 267 " --> pdb=" O   HIS C 263 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLN C 270 " --> pdb=" O   VAL C 266 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU C 271 " --> pdb=" O   LEU C 267 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU C 272 " --> pdb=" O   LEU C 268 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY C 273 " --> pdb=" O   ARG C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 299
      removed outlier: 3.504A  pdb=" N   GLY C 299 " --> pdb=" O   MET C 295 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 4.166A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.536A  pdb=" N   PHE D  28 " --> pdb=" O   ILE D  24 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.661A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
    Processing helix  chain 'D' and resid 78 through 83
    Processing helix  chain 'D' and resid 85 through 91
      removed outlier: 3.778A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU D  90 " --> pdb=" O   THR D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 4.159A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLY D 119 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE D 127 " --> pdb=" O   ALA D 123 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 167
      removed outlier: 3.531A  pdb=" N   SER D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.788A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 200
      removed outlier: 3.513A  pdb=" N   LEU D 194 " --> pdb=" O   ASP D 190 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 215
    Processing helix  chain 'D' and resid 216 through 226
    Processing helix  chain 'D' and resid 236 through 244
      removed outlier: 3.844A  pdb=" N   LEU D 241 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA D 243 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 273
      removed outlier: 3.613A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE D 260 " --> pdb=" O   LEU D 256 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ARG D 273 " --> pdb=" O   ALA D 269 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
    Processing helix  chain 'E' and resid 7 through 16
      removed outlier: 3.755A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.630A  pdb=" N   ILE E  24 " --> pdb=" O   TRP E  20 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.572A  pdb=" N   ALA E  56 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE E  64 " --> pdb=" O   SER E  60 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   MET E  66 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
      removed outlier: 3.506A  pdb=" N   TYR E  75 " --> pdb=" O   LEU E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 84
    Processing helix  chain 'E' and resid 85 through 91
      removed outlier: 3.605A  pdb=" N   LEU E  89 " --> pdb=" O   GLY E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.508A  pdb=" N   ILE E 100 " --> pdb=" O   GLY E  96 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU E 101 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 124 through 129
    Processing helix  chain 'E' and resid 135 through 143
      removed outlier: 3.788A  pdb=" N   LEU E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   TRP E 141 " --> pdb=" O   GLY E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
      removed outlier: 3.512A  pdb=" N   PHE E 157 " --> pdb=" O   LEU E 153 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL E 168 " --> pdb=" O   LEU E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.553A  pdb=" N   ALA E 175 " --> pdb=" O   LYS E 171 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY E 180 " --> pdb=" O   GLY E 176 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 200
      removed outlier: 3.593A  pdb=" N   LEU E 196 " --> pdb=" O   VAL E 192 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU E 197 " --> pdb=" O   LEU E 193 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 213
      removed outlier: 4.515A  pdb=" N   TRP E 211 " --> pdb=" O   GLU E 207 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 216 through 224
      removed outlier: 3.513A  pdb=" N   ILE E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 4.158A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER E 263 " --> pdb=" O   TRP E 259 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 51 through 55
      removed outlier: 3.800A  pdb=" N   ASP H  54 " --> pdb=" O   ILE H  51 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 73 through 82
    Processing helix  chain 'H' and resid 139 through 150
    Processing helix  chain 'H' and resid 160 through 172
      removed outlier: 3.683A  pdb=" N   GLN H 165 " --> pdb=" O   GLN H 161 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLU H 166 " --> pdb=" O   ALA H 162 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.602A  pdb=" N   GLY A 131 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   LEU A 252 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   TYR A 228 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ASN A 254 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ILE A 251 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   TYR A 291 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   MET A 253 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   GLN A 332 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73
      removed outlier: 6.226A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   THR A 221 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL A 266 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91
      removed outlier: 6.586A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   VAL A 142 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217
      removed outlier: 6.317A  pdb=" N   LEU A 216 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   SER A 322 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ILE A 298 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 23
      removed outlier: 5.933A  pdb=" N   VAL B   9 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ASN B  23 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   GLN B   7 " --> pdb=" O   ASN B  23 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLN B  59 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.650A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   ASP B 153 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LEU B  79 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   LEU B 150 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   CYS B 184 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   LEU B 152 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   VAL B  31 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   ALA B 199 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   GLY B  33 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 228
    Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 26
      removed outlier: 5.583A  pdb=" N   LEU C  22 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79
      removed outlier: 6.752A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   PHE C  35 " --> pdb=" O   LEU C 201 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ALA C 202 " --> pdb=" O   LEU C 206 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   LEU C 206 " --> pdb=" O   ALA C 202 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 249 through 251
      removed outlier: 6.890A  pdb=" N   SER C 254 " --> pdb=" O   LEU C 250 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70
    Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 121
      removed outlier: 3.552A  pdb=" N   VAL H 121 " --> pdb=" O   ARG H 152 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG H 152 " --> pdb=" O   VAL H 121 " (cutoff:3.500A)

    502 hydrogen bonds defined for protein.
    1425 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.95

  Time building geometry restraints manager: 3.39 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: 4117
        1.34 -     1.46: 2180
        1.46 -     1.57: 6691
        1.57 -     1.69: 2
        1.69 -     1.81: 77
  Bond restraints: 13067
  Sorted by residual:
  bond pdb=" CA  ILE E  51 "
       pdb=" C   ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.525  1.587 -0.062 2.10e-02 2.27e+03 8.70e+00
  bond pdb=" CA  ILE E  51 "
       pdb=" CB  ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.540  1.597 -0.057 2.70e-02 1.37e+03 4.39e+00
  bond pdb=" C   LEU E 209 "
       pdb=" N   PRO E 210 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.027 1.36e-02 5.41e+03 4.05e+00
  bond pdb=" CB  GLN A 232 "
       pdb=" CG  GLN A 232 "
    ideal  model  delta    sigma   weight residual
    1.520  1.460  0.060 3.00e-02 1.11e+03 4.04e+00
  bond pdb=" CB  VAL A 407 "
       pdb=" CG2 VAL A 407 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.67e+00
  ... (remaining 13062 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.32: 17372
        3.32 -     6.65: 299
        6.65 -     9.97: 48
        9.97 -    13.30: 6
       13.30 -    16.62: 1
  Bond angle restraints: 17726
  Sorted by residual:
  angle pdb=" C   VAL C 260 "
        pdb=" N   ASN C 261 "
        pdb=" CA  ASN C 261 "
      ideal   model   delta    sigma   weight residual
     121.54  133.17  -11.63 1.91e+00 2.74e-01 3.71e+01
  angle pdb=" C   GLU H  64 "
        pdb=" N   LYS H  65 "
        pdb=" CA  LYS H  65 "
      ideal   model   delta    sigma   weight residual
     125.02  133.56   -8.54 1.76e+00 3.23e-01 2.35e+01
  angle pdb=" C   GLU H 138 "
        pdb=" N   GLU H 139 "
        pdb=" CA  GLU H 139 "
      ideal   model   delta    sigma   weight residual
     121.54  130.66   -9.12 1.91e+00 2.74e-01 2.28e+01
  angle pdb=" CA  LEU A  35 "
        pdb=" CB  LEU A  35 "
        pdb=" CG  LEU A  35 "
      ideal   model   delta    sigma   weight residual
     116.30  132.92  -16.62 3.50e+00 8.16e-02 2.26e+01
  angle pdb=" C   GLN A 247 "
        pdb=" N   ASN A 248 "
        pdb=" CA  ASN A 248 "
      ideal   model   delta    sigma   weight residual
     121.54  130.57   -9.03 1.91e+00 2.74e-01 2.23e+01
  ... (remaining 17721 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.86: 6649
       14.86 -    29.72: 818
       29.72 -    44.57: 221
       44.57 -    59.43: 32
       59.43 -    74.29: 16
  Dihedral angle restraints: 7736
    sinusoidal: 3041
      harmonic: 4695
  Sorted by residual:
  dihedral pdb=" CA  VAL B 266 "
           pdb=" C   VAL B 266 "
           pdb=" N   LEU B 267 "
           pdb=" CA  LEU B 267 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -121.50  -58.50     0      5.00e+00 4.00e-02 1.37e+02
  dihedral pdb=" CA  HIS B 263 "
           pdb=" C   HIS B 263 "
           pdb=" N   LYS B 264 "
           pdb=" CA  LYS B 264 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.64  -48.36     0      5.00e+00 4.00e-02 9.35e+01
  dihedral pdb=" CA  ASP H 108 "
           pdb=" C   ASP H 108 "
           pdb=" N   GLY H 109 "
           pdb=" CA  GLY H 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.17   30.83     0      5.00e+00 4.00e-02 3.80e+01
  ... (remaining 7733 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1787
       0.092 -    0.184: 209
       0.184 -    0.276: 27
       0.276 -    0.368: 5
       0.368 -    0.460: 2
  Chirality restraints: 2030
  Sorted by residual:
  chirality pdb=" CG  LEU B 265 "
            pdb=" CB  LEU B 265 "
            pdb=" CD1 LEU B 265 "
            pdb=" CD2 LEU B 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.13   -0.46 2.00e-01 2.50e+01 5.29e+00
  chirality pdb=" CB  VAL A 413 "
            pdb=" CA  VAL A 413 "
            pdb=" CG1 VAL A 413 "
            pdb=" CG2 VAL A 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.41 2.00e-01 2.50e+01 4.20e+00
  chirality pdb=" CB  THR A 297 "
            pdb=" CA  THR A 297 "
            pdb=" OG1 THR A 297 "
            pdb=" CG2 THR A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.25    0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 2027 not shown)

  Planarity restraints: 2276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 209 "   -0.063 5.00e-02 4.00e+02   9.40e-02 1.41e+01
        pdb=" N   PRO E 210 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO E 210 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO E 210 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 192 "    0.016 2.00e-02 2.50e+03   3.10e-02 9.63e+00
        pdb=" C   VAL E 192 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   VAL E 192 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU E 193 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  66 "    0.051 5.00e-02 4.00e+02   7.56e-02 9.14e+00
        pdb=" N   PRO D  67 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "    0.043 5.00e-02 4.00e+02
  ... (remaining 2273 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 107
        2.56 -     3.15: 9202
        3.15 -     3.73: 19932
        3.73 -     4.32: 28121
        4.32 -     4.90: 46425
  Nonbonded interactions: 103787
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU H  76 "
            pdb="ZN    ZN H 201 "
     model   vdw
     1.976 2.230
  nonbonded pdb=" NE2 HIS A 207 "
            pdb="CU    CU A 502 "
     model   vdw
     2.000 2.320
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.111 2.170
  nonbonded pdb=" SD  MET H  50 "
            pdb="CU    CU A 502 "
     model   vdw
     2.130 2.600
  nonbonded pdb=" OD1 ASN A 361 "
            pdb="MG    MG A 501 "
     model   vdw
     2.163 2.170
  ... (remaining 103782 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 'B' and resid 2 through 308)
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through  \ 
274))
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.280
  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:             0.030
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     35.230
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.050
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
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      :  0.007   0.073  13070  Z= 0.334
  Angle     :  1.113  16.623  17726  Z= 0.588
  Chirality :  0.066   0.460   2030
  Planarity :  0.007   0.094   2276
  Dihedral  : 14.292  74.290   4740
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.93 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  9.16 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.56 (0.14), residues: 1645
  helix: -4.44 (0.08), residues: 696
  sheet: -2.91 (0.28), residues: 250
  loop : -2.94 (0.19), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E 211 
 HIS   0.015   0.003   HIS C  37 
 PHE   0.025   0.002   PHE E 204 
 TYR   0.012   0.002   TYR A 249 
 ARG   0.005   0.001   ARG A 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29947 (  502)
  hydrogen bonds       : angle      10.50904 ( 1425)
  metal coordination   : bond        0.04653 (    3)
  covalent geometry    : bond        0.00737 (13067)
  covalent geometry    : angle       1.11312 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 177
  time to evaluate  : 1.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.8955 (tp) cc_final: 0.8648 (tp)
REVERT: B   86 TYR cc_start: 0.8972 (m-80) cc_final: 0.8537 (m-10)
REVERT: B  196 ASN cc_start: 0.8851 (t0) cc_final: 0.8448 (m-40)
REVERT: B  279 ASP cc_start: 0.8613 (m-30) cc_final: 0.8258 (t0)
REVERT: B  283 HIS cc_start: 0.6550 (m-70) cc_final: 0.5737 (m-70)
REVERT: D   66 MET cc_start: 0.8978 (mmm) cc_final: 0.8643 (mmm)
REVERT: D   81 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8049 (mt-10)
REVERT: D   83 GLU cc_start: 0.9103 (pt0) cc_final: 0.8890 (pt0)
REVERT: D  135 GLU cc_start: 0.8932 (tp30) cc_final: 0.8588 (pm20)
REVERT: D  171 LYS cc_start: 0.9433 (ttmt) cc_final: 0.8894 (ttmm)
REVERT: D  190 ASP cc_start: 0.8229 (m-30) cc_final: 0.8013 (t0)
REVERT: D  238 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8839 (t)
REVERT: E   11 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8086 (mm-30)
REVERT: E   66 MET cc_start: 0.9157 (mmm) cc_final: 0.8835 (mmp)
REVERT: E   76 ASP cc_start: 0.9054 (p0) cc_final: 0.8745 (p0)
REVERT: H   65 LYS cc_start: 0.8851 (pttm) cc_final: 0.8319 (tmtt)
REVERT: H   94 TYR cc_start: 0.8941 (m-80) cc_final: 0.8197 (m-10)
REVERT: H  143 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9072 (mmtp)
  outliers start: 7
  outliers final: 1
  residues processed: 184
  average time/residue: 0.3563
  time to fit residues: 87.1348
Evaluate side-chains
  105 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain D residue  238 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:   30.0000
   chunk 123 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 127 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 95 optimal weight:    0.8980
   chunk 148 optimal weight:    0.7980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
A 174 HIS
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 HIS
A 179 ASN
A 190 ASN
A 212 ASN
A 241 ASN
A 301 ASN
A 324 ASN
A 417 HIS
B  20 HIS
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 HIS
B 176 GLN
C  25 ASN
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 GLN
C 261 ASN
C 270 GLN
D 225 ASN
E 108 HIS
E 225 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.059224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.047459 restraints weight = 49795.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.049205 restraints weight = 24792.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.050352 restraints weight = 15750.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13070  Z= 0.119
  Angle     :  0.617  11.441  17726  Z= 0.317
  Chirality :  0.042   0.197   2030
  Planarity :  0.005   0.055   2276
  Dihedral  :  5.243  40.985   1805
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.47 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 14.00 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.17), residues: 1645
  helix: -2.01 (0.15), residues: 702
  sheet: -2.65 (0.30), residues: 234
  loop : -2.37 (0.21), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 240 
 HIS   0.004   0.001   HIS H 149 
 PHE   0.010   0.001   PHE D 157 
 TYR   0.015   0.001   TYR C  13 
 ARG   0.006   0.000   ARG H  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  502)
  hydrogen bonds       : angle       4.94499 ( 1425)
  metal coordination   : bond        0.00341 (    3)
  covalent geometry    : bond        0.00256 (13067)
  covalent geometry    : angle       0.61678 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 1.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8818 (mp)
REVERT: A   89 LEU cc_start: 0.8922 (tp) cc_final: 0.8572 (tp)
REVERT: A  125 MET cc_start: 0.8323 (mpp) cc_final: 0.7895 (mpp)
REVERT: A  305 LYS cc_start: 0.9162 (mttt) cc_final: 0.8957 (mttp)
REVERT: D   82 ASP cc_start: 0.8772 (t0) cc_final: 0.8455 (m-30)
REVERT: D  190 ASP cc_start: 0.8447 (m-30) cc_final: 0.7747 (t0)
REVERT: D  219 ASP cc_start: 0.8018 (m-30) cc_final: 0.7813 (m-30)
REVERT: E  194 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8898 (tt)
REVERT: E  205 ASN cc_start: 0.8417 (t0) cc_final: 0.7569 (t0)
REVERT: H   50 MET cc_start: 0.8502 (ptt) cc_final: 0.8257 (ptt)
  outliers start: 12
  outliers final: 9
  residues processed: 123
  average time/residue: 0.2909
  time to fit residues: 52.3730
Evaluate side-chains
  98 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  194 LEU
Chi-restraints excluded: chain E residue  260 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 96 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 115 optimal weight:   10.0000
   chunk 158 optimal weight:   20.0000
   chunk 128 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 154 optimal weight:    1.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
A  53 GLN
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
C  20 HIS
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 169 ASN
H  96 HIS
H 149 HIS
H 172 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.054072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.042434 restraints weight = 51482.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.044103 restraints weight = 25549.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.045195 restraints weight = 16368.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  13070  Z= 0.287
  Angle     :  0.731   7.591  17726  Z= 0.371
  Chirality :  0.046   0.176   2030
  Planarity :  0.004   0.047   2276
  Dihedral  :  5.346  51.520   1804
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.46 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.20), residues: 1645
  helix: -0.31 (0.19), residues: 699
  sheet: -2.57 (0.29), residues: 260
  loop : -2.22 (0.22), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP E  20 
 HIS   0.007   0.001   HIS H 149 
 PHE   0.019   0.002   PHE H  71 
 TYR   0.016   0.002   TYR E 221 
 ARG   0.006   0.001   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  502)
  hydrogen bonds       : angle       4.63086 ( 1425)
  metal coordination   : bond        0.00356 (    3)
  covalent geometry    : bond        0.00624 (13067)
  covalent geometry    : angle       0.73141 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 1.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.9008 (tp) cc_final: 0.8672 (tp)
REVERT: A  125 MET cc_start: 0.8617 (mpp) cc_final: 0.8097 (mpp)
REVERT: A  305 LYS cc_start: 0.9189 (mttt) cc_final: 0.8753 (mttt)
REVERT: B   57 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7241 (tm-30)
REVERT: B  264 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7450 (pttp)
REVERT: D   81 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7783 (mt-10)
REVERT: D   88 MET cc_start: 0.8179 (tpp) cc_final: 0.7909 (tpp)
REVERT: E   11 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8198 (tp30)
REVERT: H   65 LYS cc_start: 0.8585 (tmtt) cc_final: 0.8054 (tptp)
REVERT: H  138 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7586 (tm-30)
  outliers start: 25
  outliers final: 12
  residues processed: 111
  average time/residue: 0.2569
  time to fit residues: 42.1377
Evaluate side-chains
  96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 1.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  426 LYS
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain H residue   85 GLU
Chi-restraints excluded: chain H residue  110 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 37 optimal weight:    0.0060
   chunk 88 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 135 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 129 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    2.5602

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 261 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.054911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.043344 restraints weight = 50452.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.045034 restraints weight = 25004.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.046164 restraints weight = 15947.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13070  Z= 0.175
  Angle     :  0.607   9.187  17726  Z= 0.308
  Chirality :  0.044   0.277   2030
  Planarity :  0.004   0.040   2276
  Dihedral  :  5.005  47.293   1804
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.24 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.21), residues: 1645
  helix:  0.50 (0.20), residues: 702
  sheet: -2.28 (0.29), residues: 273
  loop : -2.10 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  20 
 HIS   0.003   0.001   HIS E 108 
 PHE   0.014   0.001   PHE D 157 
 TYR   0.015   0.001   TYR C 293 
 ARG   0.003   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03063 (  502)
  hydrogen bonds       : angle       4.22166 ( 1425)
  metal coordination   : bond        0.00212 (    3)
  covalent geometry    : bond        0.00389 (13067)
  covalent geometry    : angle       0.60669 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.8990 (tp) cc_final: 0.8668 (tp)
REVERT: A  125 MET cc_start: 0.8617 (mpp) cc_final: 0.7978 (mpp)
REVERT: A  305 LYS cc_start: 0.9197 (mttt) cc_final: 0.8775 (mttt)
REVERT: B   57 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6995 (tm-30)
REVERT: C  295 MET cc_start: 0.9067 (tpp) cc_final: 0.8829 (mpp)
REVERT: D   81 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7661 (mt-10)
REVERT: D   88 MET cc_start: 0.8191 (tpp) cc_final: 0.7952 (tpp)
REVERT: E   11 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8134 (tp30)
REVERT: H   65 LYS cc_start: 0.8553 (tmtt) cc_final: 0.8208 (tptp)
REVERT: H  138 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7329 (tm-30)
REVERT: H  140 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8612 (mp10)
  outliers start: 22
  outliers final: 13
  residues processed: 110
  average time/residue: 0.2559
  time to fit residues: 41.5284
Evaluate side-chains
  101 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  426 LYS
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain H residue   85 GLU
Chi-restraints excluded: chain H residue  124 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 118 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 124 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 104 optimal weight:    8.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 169 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.053827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.042553 restraints weight = 51150.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.044169 restraints weight = 26186.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.045221 restraints weight = 17063.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.4212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  13070  Z= 0.293
  Angle     :  0.710   9.689  17726  Z= 0.354
  Chirality :  0.046   0.283   2030
  Planarity :  0.004   0.036   2276
  Dihedral  :  5.207  50.055   1804
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.80 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.21), residues: 1645
  helix:  0.88 (0.21), residues: 693
  sheet: -2.38 (0.29), residues: 273
  loop : -1.99 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  20 
 HIS   0.004   0.001   HIS H 110 
 PHE   0.017   0.002   PHE D 157 
 TYR   0.015   0.002   TYR C  13 
 ARG   0.006   0.001   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03410 (  502)
  hydrogen bonds       : angle       4.44955 ( 1425)
  metal coordination   : bond        0.00462 (    3)
  covalent geometry    : bond        0.00645 (13067)
  covalent geometry    : angle       0.70964 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 86
  time to evaluate  : 1.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7751 (mpp) cc_final: 0.7277 (mpp)
REVERT: A   89 LEU cc_start: 0.9073 (tp) cc_final: 0.8736 (tt)
REVERT: A  125 MET cc_start: 0.8615 (mpp) cc_final: 0.7941 (mpp)
REVERT: A  305 LYS cc_start: 0.9224 (mttt) cc_final: 0.8838 (mttt)
REVERT: B   57 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7152 (tm-30)
REVERT: B  264 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7840 (pttp)
REVERT: D   81 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7706 (mt-10)
REVERT: D   88 MET cc_start: 0.8203 (tpp) cc_final: 0.7981 (tpp)
REVERT: E   11 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8130 (tp30)
REVERT: H   65 LYS cc_start: 0.8592 (tmtt) cc_final: 0.7896 (tptp)
REVERT: H  161 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8594 (mm-40)
  outliers start: 38
  outliers final: 22
  residues processed: 119
  average time/residue: 0.2345
  time to fit residues: 42.3379
Evaluate side-chains
  106 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  426 LYS
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  151 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain H residue   85 GLU
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain H residue  141 ASP
Chi-restraints excluded: chain H residue  159 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 158 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 159 optimal weight:    0.9990
   chunk 94 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   chunk 93 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  97 HIS
** C 115 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 = 0.3031 r_free = 0.3031 target = 0.053773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.042395 restraints weight = 51329.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.043932 restraints weight = 27429.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.044918 restraints weight = 18146.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.4272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13070  Z= 0.102
  Angle     :  0.584  10.593  17726  Z= 0.291
  Chirality :  0.043   0.306   2030
  Planarity :  0.003   0.045   2276
  Dihedral  :  4.761  41.314   1804
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.14 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.22), residues: 1645
  helix:  1.17 (0.21), residues: 705
  sheet: -2.13 (0.30), residues: 277
  loop : -1.86 (0.24), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B  20 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.017   0.001   TYR C  13 
 ARG   0.004   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02637 (  502)
  hydrogen bonds       : angle       3.85269 ( 1425)
  metal coordination   : bond        0.00547 (    3)
  covalent geometry    : bond        0.00226 (13067)
  covalent geometry    : angle       0.58394 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 1.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.9031 (tp) cc_final: 0.8706 (tt)
REVERT: A  125 MET cc_start: 0.8601 (mpp) cc_final: 0.7746 (mpp)
REVERT: B    7 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8225 (mm110)
REVERT: C   61 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8721 (mmmm)
REVERT: C  295 MET cc_start: 0.9082 (tpp) cc_final: 0.8648 (mpp)
REVERT: D   66 MET cc_start: 0.8911 (mmp) cc_final: 0.8691 (mmm)
REVERT: D   81 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: D   88 MET cc_start: 0.8354 (tpp) cc_final: 0.8058 (tpp)
REVERT: D  148 ILE cc_start: 0.8699 (pt) cc_final: 0.8453 (mm)
REVERT: D  254 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8371 (tt)
REVERT: E   11 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8398 (tp30)
REVERT: E   81 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7181 (mt-10)
REVERT: H  161 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8509 (mm-40)
  outliers start: 23
  outliers final: 15
  residues processed: 110
  average time/residue: 0.2438
  time to fit residues: 40.4068
Evaluate side-chains
  102 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 1.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   85 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 104 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 133 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 127 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 148 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 GLN
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.055476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.044258 restraints weight = 50371.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.045942 restraints weight = 25318.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.047031 restraints weight = 16237.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13070  Z= 0.167
  Angle     :  0.611   8.815  17726  Z= 0.305
  Chirality :  0.043   0.318   2030
  Planarity :  0.003   0.045   2276
  Dihedral  :  4.809  45.728   1804
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.58 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.22), residues: 1645
  helix:  1.38 (0.21), residues: 701
  sheet: -2.05 (0.30), residues: 282
  loop : -1.79 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  20 
 HIS   0.002   0.001   HIS H 110 
 PHE   0.013   0.001   PHE D 157 
 TYR   0.017   0.001   TYR C  13 
 ARG   0.003   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02842 (  502)
  hydrogen bonds       : angle       3.96454 ( 1425)
  metal coordination   : bond        0.00667 (    3)
  covalent geometry    : bond        0.00376 (13067)
  covalent geometry    : angle       0.61096 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7916 (mpp) cc_final: 0.7303 (mpp)
REVERT: A   89 LEU cc_start: 0.9007 (tp) cc_final: 0.8676 (tt)
REVERT: A  125 MET cc_start: 0.8593 (mpp) cc_final: 0.7862 (mpp)
REVERT: B    7 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8272 (mm110)
REVERT: B  264 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7425 (pttp)
REVERT: C   61 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8779 (mmmm)
REVERT: C  295 MET cc_start: 0.9047 (tpp) cc_final: 0.8710 (mpp)
REVERT: D   88 MET cc_start: 0.8242 (tpp) cc_final: 0.7994 (tpp)
REVERT: E   11 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8171 (tp30)
REVERT: E   64 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8672 (t80)
REVERT: H  161 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8536 (mm-40)
  outliers start: 29
  outliers final: 20
  residues processed: 113
  average time/residue: 0.2553
  time to fit residues: 42.3798
Evaluate side-chains
  108 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  426 LYS
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   85 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 140 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 142 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 113 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.056933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.045760 restraints weight = 50315.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.047499 restraints weight = 25014.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.048635 restraints weight = 15879.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13070  Z= 0.106
  Angle     :  0.590  13.489  17726  Z= 0.291
  Chirality :  0.042   0.332   2030
  Planarity :  0.003   0.046   2276
  Dihedral  :  4.604  39.483   1804
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.48 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.22), residues: 1645
  helix:  1.50 (0.21), residues: 705
  sheet: -1.96 (0.31), residues: 282
  loop : -1.69 (0.24), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.004   0.001   HIS B  37 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.017   0.001   TYR C  13 
 ARG   0.007   0.000   ARG H  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02547 (  502)
  hydrogen bonds       : angle       3.73927 ( 1425)
  metal coordination   : bond        0.00492 (    3)
  covalent geometry    : bond        0.00240 (13067)
  covalent geometry    : angle       0.59049 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7879 (mpp) cc_final: 0.7271 (mpp)
REVERT: A   89 LEU cc_start: 0.8998 (tp) cc_final: 0.8679 (tt)
REVERT: A  125 MET cc_start: 0.8592 (mpp) cc_final: 0.7785 (mpp)
REVERT: B    7 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8184 (mm110)
REVERT: C   61 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8759 (mmmm)
REVERT: C  295 MET cc_start: 0.8992 (tpp) cc_final: 0.8581 (mpp)
REVERT: D   88 MET cc_start: 0.8233 (tpp) cc_final: 0.7983 (tpp)
REVERT: D  148 ILE cc_start: 0.8741 (pt) cc_final: 0.8512 (mm)
REVERT: D  254 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8360 (tt)
REVERT: E   11 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8194 (tp30)
REVERT: E   64 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8782 (t80)
REVERT: E   81 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7116 (mt-10)
REVERT: H   90 ASP cc_start: 0.8579 (t0) cc_final: 0.8306 (t0)
REVERT: H  105 LYS cc_start: 0.9391 (tptp) cc_final: 0.9148 (tptm)
REVERT: H  161 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8487 (mm-40)
  outliers start: 20
  outliers final: 15
  residues processed: 106
  average time/residue: 0.2434
  time to fit residues: 38.8250
Evaluate side-chains
  102 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain H residue   85 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 154 optimal weight:    5.9990
   chunk 144 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 114 optimal weight:    0.9980
   chunk 152 optimal weight:    9.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.055634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.044464 restraints weight = 50398.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.046147 restraints weight = 25334.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.047237 restraints weight = 16247.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.4524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13070  Z= 0.174
  Angle     :  0.630  11.823  17726  Z= 0.311
  Chirality :  0.044   0.313   2030
  Planarity :  0.003   0.045   2276
  Dihedral  :  4.738  43.455   1804
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.20 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.40 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.22), residues: 1645
  helix:  1.56 (0.21), residues: 706
  sheet: -1.96 (0.31), residues: 282
  loop : -1.63 (0.24), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D   5 
 HIS   0.002   0.001   HIS H  96 
 PHE   0.013   0.001   PHE D 157 
 TYR   0.017   0.001   TYR C  13 
 ARG   0.005   0.000   ARG H  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02825 (  502)
  hydrogen bonds       : angle       3.89386 ( 1425)
  metal coordination   : bond        0.00733 (    3)
  covalent geometry    : bond        0.00393 (13067)
  covalent geometry    : angle       0.63041 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 1.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7957 (mpp) cc_final: 0.7363 (mpp)
REVERT: A   89 LEU cc_start: 0.9024 (tp) cc_final: 0.8706 (tt)
REVERT: A  125 MET cc_start: 0.8589 (mpp) cc_final: 0.7807 (mpp)
REVERT: B    7 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8235 (mm110)
REVERT: B  264 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7298 (pttp)
REVERT: C   61 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8786 (mmmm)
REVERT: C  295 MET cc_start: 0.9042 (tpp) cc_final: 0.8713 (mpp)
REVERT: D   81 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7714 (mt-10)
REVERT: D   88 MET cc_start: 0.8244 (tpp) cc_final: 0.7997 (tpp)
REVERT: D  148 ILE cc_start: 0.8846 (pt) cc_final: 0.8552 (mm)
REVERT: E   11 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8181 (tp30)
REVERT: H  100 ARG cc_start: 0.8754 (ttp-110) cc_final: 0.8366 (ttp-110)
REVERT: H  105 LYS cc_start: 0.9358 (tptp) cc_final: 0.8785 (tptp)
REVERT: H  161 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8516 (mm-40)
  outliers start: 26
  outliers final: 21
  residues processed: 110
  average time/residue: 0.2707
  time to fit residues: 43.9984
Evaluate side-chains
  110 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   85 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 147 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 141 optimal weight:    0.9980
   chunk 154 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 73 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.056418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.045182 restraints weight = 50312.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.046901 restraints weight = 25273.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.048038 restraints weight = 16148.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.4581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13070  Z= 0.127
  Angle     :  0.614  11.963  17726  Z= 0.300
  Chirality :  0.043   0.308   2030
  Planarity :  0.003   0.045   2276
  Dihedral  :  4.665  40.970   1804
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.65 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.63 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.22), residues: 1645
  helix:  1.63 (0.21), residues: 708
  sheet: -1.93 (0.31), residues: 282
  loop : -1.64 (0.24), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B  20 
 PHE   0.013   0.001   PHE D 157 
 TYR   0.019   0.001   TYR C  13 
 ARG   0.005   0.000   ARG H  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02656 (  502)
  hydrogen bonds       : angle       3.79219 ( 1425)
  metal coordination   : bond        0.00566 (    3)
  covalent geometry    : bond        0.00289 (13067)
  covalent geometry    : angle       0.61385 (17726)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 1.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7933 (mpp) cc_final: 0.7304 (mpp)
REVERT: A   89 LEU cc_start: 0.8999 (tp) cc_final: 0.8681 (tt)
REVERT: A  125 MET cc_start: 0.8582 (mpp) cc_final: 0.7783 (mpp)
REVERT: B    7 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8314 (mm110)
REVERT: B  264 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7067 (pttp)
REVERT: C   61 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8789 (mmmm)
REVERT: C  295 MET cc_start: 0.9002 (tpp) cc_final: 0.8617 (mpp)
REVERT: D   81 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7618 (mt-10)
REVERT: D   88 MET cc_start: 0.8220 (tpp) cc_final: 0.7984 (tpp)
REVERT: D  148 ILE cc_start: 0.8716 (pt) cc_final: 0.8495 (mm)
REVERT: E   11 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8293 (tp30)
REVERT: E   64 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8806 (t80)
REVERT: E   81 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7050 (mt-10)
REVERT: H  100 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8273 (ttp-110)
REVERT: H  105 LYS cc_start: 0.9367 (tptp) cc_final: 0.8911 (tptp)
REVERT: H  161 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8480 (mm-40)
  outliers start: 25
  outliers final: 21
  residues processed: 109
  average time/residue: 0.2579
  time to fit residues: 41.8545
Evaluate side-chains
  109 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 1.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain B residue  264 LYS
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   85 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 123 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0060
   chunk 106 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 144 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 138 optimal weight:    0.9990
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.057305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.046043 restraints weight = 49787.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.047771 restraints weight = 25215.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.048910 restraints weight = 16185.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.4678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  13070  Z= 0.107
  Angle     :  0.602  11.954  17726  Z= 0.294
  Chirality :  0.042   0.308   2030
  Planarity :  0.003   0.045   2276
  Dihedral  :  4.518  39.131   1804
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.59 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 21.30 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.22), residues: 1645
  helix:  1.70 (0.21), residues: 707
  sheet: -1.95 (0.31), residues: 281
  loop : -1.61 (0.24), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B  20 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.020   0.001   TYR C  13 
 ARG   0.005   0.000   ARG H  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02522 (  502)
  hydrogen bonds       : angle       3.63989 ( 1425)
  metal coordination   : bond        0.00526 (    3)
  covalent geometry    : bond        0.00245 (13067)
  covalent geometry    : angle       0.60236 (17726)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3436.74 seconds
wall clock time: 61 minutes 6.68 seconds (3666.68 seconds total)