Starting phenix.real_space_refine
on Tue Jul 29 22:14:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o11_12686/07_2025/7o11_12686.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o11_12686/07_2025/7o11_12686.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o11_12686/07_2025/7o11_12686.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o11_12686/07_2025/7o11_12686.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o11_12686/07_2025/7o11_12686.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o11_12686/07_2025/7o11_12686.cif"
  }
  resolution = 3.7
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      37      5.16       5
     C    7466      2.51       5
     N    2038      2.21       5
     O    2109      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11651
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3140
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 16, 'TRANS': 385}
    Chain: "B"
      Number of atoms: 2303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2303
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 12, 'TRANS': 286}
    Chain: "C"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2295
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 12, 'TRANS': 285}
    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: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 7.32, per 1000 atoms: 0.63
  Number of scatterers: 11651
  At special positions: 0
  Unit cell: (87.21, 163.134, 137.484, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      37     16.00
     Mg      1     11.99
     O    2109      8.00
     N    2038      7.00
     C    7466      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: 2.50
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2722

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      45.4% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.735A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   TRP A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
    Processing helix  chain 'A' and resid 392 through 405
      removed outlier: 3.625A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 50
      removed outlier: 4.041A  pdb=" N   SER B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS B  47 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU B  50 " --> pdb=" O   MET B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 74
      removed outlier: 3.679A  pdb=" N   ARG B  73 " --> pdb=" O   ASP B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 102
      removed outlier: 3.607A  pdb=" N   LEU B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 116
      removed outlier: 4.465A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL B 116 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 160 through 178
      removed outlier: 3.540A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 219
      removed outlier: 3.584A  pdb=" N   GLU B 218 " --> pdb=" O   GLN B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 243
      removed outlier: 3.634A  pdb=" N   THR B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 275
      removed outlier: 3.569A  pdb=" N   GLY B 273 " --> pdb=" O   ARG B 269 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLU B 274 " --> pdb=" O   GLN B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.560A  pdb=" N   LEU B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 50
      removed outlier: 4.052A  pdb=" N   SER C  45 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU C  50 " --> pdb=" O   MET C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 74
      No H-bonds generated for 'chain 'C' and resid 72 through 74'
    Processing helix  chain 'C' and resid 91 through 103
    Processing helix  chain 'C' and resid 107 through 113
      removed outlier: 3.960A  pdb=" N   GLU C 111 " --> pdb=" O   THR C 107 " (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: 3.530A  pdb=" N   LEU C 169 " --> pdb=" O   GLN C 165 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ARG C 177 " --> pdb=" O   ARG C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 3.664A  pdb=" N   ALA C 193 " --> pdb=" O   GLY C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 219
    Processing helix  chain 'C' and resid 235 through 240
    Processing helix  chain 'C' and resid 265 through 272
      removed outlier: 3.726A  pdb=" N   ARG C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 299
      removed outlier: 3.651A  pdb=" N   LEU C 290 " --> pdb=" O   SER C 286 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA C 298 " --> pdb=" O   TYR C 294 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 4.083A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.622A  pdb=" N   ILE D  24 " --> pdb=" O   TRP D  20 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA D  36 " --> pdb=" O   ALA D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.569A  pdb=" N   ILE D  55 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU D  58 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
      removed outlier: 3.507A  pdb=" N   TYR D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 83
    Processing helix  chain 'D' and resid 85 through 91
      removed outlier: 3.876A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 4.072A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY D 119 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE D 127 " --> pdb=" O   ALA D 123 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 146
    Processing helix  chain 'D' and resid 146 through 167
      removed outlier: 3.633A  pdb=" N   THR D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 4.076A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU D 177 " --> pdb=" O   SER D 173 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 200
      removed outlier: 3.620A  pdb=" N   SER D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 215
      removed outlier: 3.504A  pdb=" N   LEU D 212 " --> pdb=" O   LEU D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 216 through 226
      removed outlier: 3.525A  pdb=" N   ASN D 225 " --> pdb=" O   TYR D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 245
      removed outlier: 3.769A  pdb=" N   LEU D 241 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA D 243 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 272
      removed outlier: 3.629A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE D 260 " --> pdb=" O   LEU D 256 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
      removed outlier: 3.511A  pdb=" N   ILE E   7 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 3 through 7'
    Processing helix  chain 'E' and resid 7 through 16
      removed outlier: 3.668A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.664A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.913A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
      removed outlier: 3.514A  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: 3.617A  pdb=" N   LEU E  89 " --> pdb=" O   GLY E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.680A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.162A  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: 3.689A  pdb=" N   LEU E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   TRP E 141 " --> pdb=" O   GLY E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
      removed outlier: 3.507A  pdb=" N   SER E 149 " --> pdb=" O   ARG E 145 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL E 168 " --> pdb=" O   LEU E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.631A  pdb=" N   ALA E 175 " --> pdb=" O   LYS E 171 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY E 176 " --> pdb=" O   SER E 172 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY E 180 " --> pdb=" O   GLY E 176 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL E 186 " --> pdb=" O   TRP E 182 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 199
      removed outlier: 3.528A  pdb=" N   LEU E 197 " --> pdb=" O   LEU E 193 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 213
      removed outlier: 3.633A  pdb=" N   LEU E 213 " --> pdb=" O   LEU E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 216 through 224
      removed outlier: 3.653A  pdb=" N   ILE E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 3.972A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE E 260 " --> pdb=" O   LEU E 256 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER E 263 " --> pdb=" O   TRP E 259 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40
      removed outlier: 8.120A  pdb=" N   ARG A  44 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   TRP A  45 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 3.542A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   LEU A 252 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   TYR A 228 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ASN A 254 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE A 251 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   TYR A 291 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   MET A 253 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 6.822A  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: 6.207A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   THR A 221 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.517A  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: 6.417A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.479A  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: 7.542A  pdb=" N   SER A 322 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ILE A 298 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5
      removed outlier: 3.607A  pdb=" N   VAL B   4 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11
      removed outlier: 7.401A  pdb=" N   GLN B  11 " --> pdb=" O   HIS B  20 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   HIS B  20 " --> pdb=" O   GLN B  11 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 153
      removed outlier: 3.669A  pdb=" N   LEU B 150 " --> pdb=" O   SER B 180 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL B  31 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   ALA B 199 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   GLY B  33 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 246 through 248
      removed outlier: 4.120A  pdb=" N   SER B 246 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLU B 256 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.558A  pdb=" N   GLN C  59 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 11
      removed outlier: 5.714A  pdb=" N   VAL C   9 " --> pdb=" O   ASP C  21 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 79
      removed outlier: 6.994A  pdb=" N   LEU C 150 " --> pdb=" O   ILE C 182 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   CYS C 184 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   LEU C 152 " --> pdb=" O   CYS C 184 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ALA C 198 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL C 209 " --> pdb=" O   ALA C 198 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE C 200 " --> pdb=" O   GLN C 207 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 254 through 259
      removed outlier: 3.507A  pdb=" N   SER C 228 " --> pdb=" O   ASP C 279 " (cutoff:3.500A)

    469 hydrogen bonds defined for protein.
    1332 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: 3.30

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3104
        1.33 -     1.45: 2076
        1.45 -     1.57: 6625
        1.57 -     1.69: 2
        1.69 -     1.81: 64
  Bond restraints: 11871
  Sorted by residual:
  bond pdb=" CA  ILE E  51 "
       pdb=" C   ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.525  1.593 -0.068 2.10e-02 2.27e+03 1.04e+01
  bond pdb=" CA  ILE E  51 "
       pdb=" CB  ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.540  1.608 -0.068 2.70e-02 1.37e+03 6.32e+00
  bond pdb=" CA  ILE D  51 "
       pdb=" C   ILE D  51 "
    ideal  model  delta    sigma   weight residual
    1.523  1.543 -0.020 9.20e-03 1.18e+04 4.74e+00
  bond pdb=" C   LEU B 188 "
       pdb=" N   PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.333  1.356 -0.023 1.17e-02 7.31e+03 3.92e+00
  bond pdb=" C   ILE D  51 "
       pdb=" N   PRO D  52 "
    ideal  model  delta    sigma   weight residual
    1.337  1.358 -0.021 1.11e-02 8.12e+03 3.74e+00
  ... (remaining 11866 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.78: 15879
        3.78 -     7.55: 199
        7.55 -    11.33: 30
       11.33 -    15.10: 6
       15.10 -    18.88: 2
  Bond angle restraints: 16116
  Sorted by residual:
  angle pdb=" CA  LEU A 356 "
        pdb=" CB  LEU A 356 "
        pdb=" CG  LEU A 356 "
      ideal   model   delta    sigma   weight residual
     116.30  135.18  -18.88 3.50e+00 8.16e-02 2.91e+01
  angle pdb=" C   GLU B  81 "
        pdb=" N   ASN B  82 "
        pdb=" CA  ASN B  82 "
      ideal   model   delta    sigma   weight residual
     121.54  131.34   -9.80 1.91e+00 2.74e-01 2.63e+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  133.89  -17.59 3.50e+00 8.16e-02 2.53e+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  130.75   -9.21 1.91e+00 2.74e-01 2.32e+01
  angle pdb=" CA  GLU D 201 "
        pdb=" CB  GLU D 201 "
        pdb=" CG  GLU D 201 "
      ideal   model   delta    sigma   weight residual
     114.10  123.57   -9.47 2.00e+00 2.50e-01 2.24e+01
  ... (remaining 16111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 6215
       17.22 -    34.44: 643
       34.44 -    51.65: 132
       51.65 -    68.87: 23
       68.87 -    86.09: 8
  Dihedral angle restraints: 7021
    sinusoidal: 2752
      harmonic: 4269
  Sorted by residual:
  dihedral pdb=" CA  GLU B 276 "
           pdb=" C   GLU B 276 "
           pdb=" N   PRO B 277 "
           pdb=" CA  PRO B 277 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -123.38  -56.62     0      5.00e+00 4.00e-02 1.28e+02
  dihedral pdb=" CA  ILE B 230 "
           pdb=" C   ILE B 230 "
           pdb=" N   SER B 231 "
           pdb=" CA  SER B 231 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.13   25.87     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  LEU D  73 "
           pdb=" C   LEU D  73 "
           pdb=" N   ALA D  74 "
           pdb=" CA  ALA D  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.83  -22.17     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 7018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 1672
       0.100 -    0.200: 169
       0.200 -    0.300: 17
       0.300 -    0.400: 2
       0.400 -    0.500: 1
  Chirality restraints: 1861
  Sorted by residual:
  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   -2.13   -0.50 2.00e-01 2.50e+01 6.25e+00
  chirality pdb=" CB  VAL C 187 "
            pdb=" CA  VAL C 187 "
            pdb=" CG1 VAL C 187 "
            pdb=" CG2 VAL C 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  ASP A 182 "
            pdb=" N   ASP A 182 "
            pdb=" C   ASP A 182 "
            pdb=" CB  ASP A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.41e+00
  ... (remaining 1858 not shown)

  Planarity restraints: 2063
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 276 "   -0.064 5.00e-02 4.00e+02   9.62e-02 1.48e+01
        pdb=" N   PRO B 277 "    0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO B 277 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 277 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  30 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   VAL D  30 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL D  30 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LEU D  31 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  66 "    0.050 5.00e-02 4.00e+02   7.42e-02 8.80e+00
        pdb=" N   PRO D  67 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "    0.042 5.00e-02 4.00e+02
  ... (remaining 2060 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 116
        2.55 -     3.14: 7928
        3.14 -     3.72: 18612
        3.72 -     4.31: 26243
        4.31 -     4.90: 42841
  Nonbonded interactions: 95740
  Sorted by model distance:
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     1.960 2.170
  nonbonded pdb=" OD1 ASP A 363 "
            pdb="MG    MG A 501 "
     model   vdw
     2.156 2.170
  nonbonded pdb=" OD1 ASN A 361 "
            pdb="MG    MG A 501 "
     model   vdw
     2.321 2.170
  nonbonded pdb=" OG  SER C 286 "
            pdb=" OE1 GLU C 288 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   SER B  90 "
            pdb=" OG1 THR B  94 "
     model   vdw
     2.340 3.040
  ... (remaining 95735 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 299)
  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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     27.730
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  11871  Z= 0.274
  Angle     :  1.107  18.875  16116  Z= 0.570
  Chirality :  0.063   0.500   1861
  Planarity :  0.007   0.096   2063
  Dihedral  : 14.722  86.089   4299
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.40 %
    Favored  : 89.87 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -5.78 (0.15), residues: 1498
  helix: -4.54 (0.07), residues: 654
  sheet: -3.49 (0.28), residues: 199
  loop : -2.94 (0.20), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  45 
 HIS   0.010   0.002   HIS A 163 
 PHE   0.020   0.002   PHE E  64 
 TYR   0.019   0.002   TYR A 204 
 ARG   0.004   0.001   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29520 (  469)
  hydrogen bonds       : angle      10.87004 ( 1332)
  covalent geometry    : bond        0.00593 (11871)
  covalent geometry    : angle       1.10749 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.8011 (pt) cc_final: 0.7765 (pp)
REVERT: A  106 ASP cc_start: 0.7100 (m-30) cc_final: 0.6653 (m-30)
REVERT: A  125 MET cc_start: 0.9202 (mpp) cc_final: 0.8972 (mpp)
REVERT: A  235 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9298 (tppp)
REVERT: A  305 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8647 (mtmt)
REVERT: B    2 ASN cc_start: 0.8674 (m110) cc_final: 0.7991 (m-40)
REVERT: B   46 MET cc_start: 0.9111 (ttp) cc_final: 0.8536 (ttp)
REVERT: B   86 TYR cc_start: 0.9025 (m-80) cc_final: 0.8815 (m-10)
REVERT: B  131 LYS cc_start: 0.9598 (tptt) cc_final: 0.9309 (tppt)
REVERT: B  263 HIS cc_start: 0.8689 (m90) cc_final: 0.8440 (m90)
REVERT: B  281 GLU cc_start: 0.8886 (pt0) cc_final: 0.8433 (pm20)
REVERT: C  133 MET cc_start: 0.9103 (mtm) cc_final: 0.8635 (mtm)
REVERT: D    9 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8331 (mtm180)
REVERT: D   11 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7709 (mm-30)
REVERT: D   66 MET cc_start: 0.9056 (mmm) cc_final: 0.8800 (mmp)
REVERT: D  201 GLU cc_start: 0.8077 (pm20) cc_final: 0.7869 (pm20)
REVERT: D  203 LYS cc_start: 0.9039 (mttt) cc_final: 0.8516 (pptt)
REVERT: D  216 ASN cc_start: 0.8789 (t0) cc_final: 0.8188 (t0)
REVERT: E    3 GLN cc_start: 0.8360 (mt0) cc_final: 0.8053 (mt0)
REVERT: E   20 TRP cc_start: 0.8844 (m100) cc_final: 0.8348 (m-10)
REVERT: E   81 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7660 (mt-10)
REVERT: E  138 MET cc_start: 0.7566 (tpt) cc_final: 0.7179 (tmm)
  outliers start: 9
  outliers final: 2
  residues processed: 162
  average time/residue: 0.2476
  time to fit residues: 57.2581
Evaluate side-chains
  103 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain B residue  191 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    4.9990
   chunk 112 optimal weight:    0.7980
   chunk 62 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0000
   chunk 75 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 116 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   chunk 134 optimal weight:    4.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 179 ASN
A 190 ASN
A 212 ASN
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 341 GLN
A 417 HIS
B  20 HIS
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 214 GLN
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
C  97 HIS
C 214 GLN
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 205 ASN
E 108 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.056843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.045378 restraints weight = 54361.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.046840 restraints weight = 27425.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.047836 restraints weight = 17674.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11871  Z= 0.148
  Angle     :  0.631  10.866  16116  Z= 0.321
  Chirality :  0.043   0.166   1861
  Planarity :  0.005   0.099   2063
  Dihedral  :  5.387  47.352   1644
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.97 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -3.65 (0.18), residues: 1498
  helix: -1.99 (0.16), residues: 664
  sheet: -3.13 (0.30), residues: 198
  loop : -2.50 (0.22), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.004   0.001   HIS B  37 
 PHE   0.012   0.001   PHE E 157 
 TYR   0.020   0.002   TYR C  13 
 ARG   0.005   0.000   ARG B 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  469)
  hydrogen bonds       : angle       5.05330 ( 1332)
  covalent geometry    : bond        0.00318 (11871)
  covalent geometry    : angle       0.63122 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 MET cc_start: 0.8524 (mtt) cc_final: 0.8212 (mtp)
REVERT: A  305 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8814 (mtmt)
REVERT: B    2 ASN cc_start: 0.8497 (m110) cc_final: 0.8080 (m-40)
REVERT: B  263 HIS cc_start: 0.8661 (m90) cc_final: 0.8407 (m90)
REVERT: C  133 MET cc_start: 0.9118 (mtm) cc_final: 0.8718 (mtm)
REVERT: D   11 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8162 (mm-30)
REVERT: D   82 ASP cc_start: 0.9044 (t0) cc_final: 0.8772 (t0)
REVERT: D   83 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8690 (mm-30)
REVERT: D  203 LYS cc_start: 0.9057 (mttt) cc_final: 0.8612 (pptt)
REVERT: D  216 ASN cc_start: 0.8637 (t0) cc_final: 0.7557 (t0)
REVERT: D  219 ASP cc_start: 0.8844 (m-30) cc_final: 0.8601 (m-30)
REVERT: E   20 TRP cc_start: 0.8802 (m100) cc_final: 0.8481 (m-10)
REVERT: E  138 MET cc_start: 0.7424 (tpt) cc_final: 0.7217 (tmm)
REVERT: E  187 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8785 (pp)
REVERT: E  211 TRP cc_start: 0.7726 (m-10) cc_final: 0.6819 (t60)
  outliers start: 14
  outliers final: 6
  residues processed: 129
  average time/residue: 0.2339
  time to fit residues: 43.9028
Evaluate side-chains
  103 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 132 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 HIS
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
A 324 ASN
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.057046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.045665 restraints weight = 54740.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.047133 restraints weight = 27494.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.048143 restraints weight = 17638.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11871  Z= 0.118
  Angle     :  0.591   9.424  16116  Z= 0.293
  Chirality :  0.042   0.169   1861
  Planarity :  0.004   0.097   2063
  Dihedral  :  4.975  44.013   1643
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 16.83 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -2.37 (0.21), residues: 1498
  helix: -0.44 (0.20), residues: 666
  sheet: -2.82 (0.31), residues: 205
  loop : -2.32 (0.23), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B  37 
 PHE   0.010   0.001   PHE E 157 
 TYR   0.020   0.001   TYR C  13 
 ARG   0.004   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03137 (  469)
  hydrogen bonds       : angle       4.37198 ( 1332)
  covalent geometry    : bond        0.00256 (11871)
  covalent geometry    : angle       0.59118 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8474 (mpp) cc_final: 0.8124 (mpp)
REVERT: A  231 MET cc_start: 0.8581 (mtt) cc_final: 0.8232 (mtp)
REVERT: A  305 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8762 (mtmt)
REVERT: B    2 ASN cc_start: 0.8478 (m110) cc_final: 0.8079 (m-40)
REVERT: B  263 HIS cc_start: 0.8656 (m90) cc_final: 0.8362 (m90)
REVERT: C   61 LYS cc_start: 0.8731 (mttm) cc_final: 0.8356 (mmmt)
REVERT: D   82 ASP cc_start: 0.9018 (t0) cc_final: 0.8714 (t0)
REVERT: D   83 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8584 (mm-30)
REVERT: D  203 LYS cc_start: 0.9138 (mttt) cc_final: 0.8711 (pptt)
REVERT: D  216 ASN cc_start: 0.8637 (t0) cc_final: 0.7560 (t0)
REVERT: E  187 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8803 (pp)
REVERT: E  211 TRP cc_start: 0.7741 (m-10) cc_final: 0.6838 (t60)
  outliers start: 13
  outliers final: 6
  residues processed: 116
  average time/residue: 0.2341
  time to fit residues: 40.8841
Evaluate side-chains
  100 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 127 optimal weight:    9.9990
   chunk 79 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 93 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:   10.0000
   chunk 116 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN
E   6 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.055663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.044372 restraints weight = 55391.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.045787 restraints weight = 27838.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.046734 restraints weight = 17984.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11871  Z= 0.176
  Angle     :  0.620   9.401  16116  Z= 0.304
  Chirality :  0.043   0.236   1861
  Planarity :  0.004   0.096   2063
  Dihedral  :  4.894  43.275   1643
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.08 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -1.66 (0.22), residues: 1498
  helix:  0.35 (0.21), residues: 665
  sheet: -2.64 (0.32), residues: 213
  loop : -2.10 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.004   0.001   HIS B 245 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.023   0.002   TYR C  13 
 ARG   0.005   0.000   ARG B 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03076 (  469)
  hydrogen bonds       : angle       4.18452 ( 1332)
  covalent geometry    : bond        0.00388 (11871)
  covalent geometry    : angle       0.61956 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 1.385 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8814 (mtmt)
REVERT: B    2 ASN cc_start: 0.8518 (m110) cc_final: 0.8135 (m-40)
REVERT: B   46 MET cc_start: 0.8854 (ttp) cc_final: 0.8633 (tpp)
REVERT: B  263 HIS cc_start: 0.8666 (m90) cc_final: 0.8365 (m90)
REVERT: C   61 LYS cc_start: 0.8825 (mttm) cc_final: 0.8387 (mmmt)
REVERT: D   75 TYR cc_start: 0.9268 (p90) cc_final: 0.8976 (p90)
REVERT: D   82 ASP cc_start: 0.9036 (t0) cc_final: 0.8697 (t0)
REVERT: D   83 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8602 (mm-30)
REVERT: D  201 GLU cc_start: 0.8485 (pm20) cc_final: 0.8262 (pm20)
REVERT: D  203 LYS cc_start: 0.9085 (mttt) cc_final: 0.8644 (pptt)
REVERT: D  216 ASN cc_start: 0.8725 (t0) cc_final: 0.8120 (t0)
REVERT: E  187 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8783 (pp)
REVERT: E  211 TRP cc_start: 0.7763 (m-10) cc_final: 0.6816 (t60)
  outliers start: 29
  outliers final: 19
  residues processed: 123
  average time/residue: 0.2139
  time to fit residues: 39.8067
Evaluate side-chains
  115 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  283 HIS
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  140 PHE
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  114 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 115 optimal weight:    3.9990
   chunk 118 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 128 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
C 261 ASN
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.056183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.044939 restraints weight = 55068.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.046377 restraints weight = 27739.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.047345 restraints weight = 17868.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11871  Z= 0.128
  Angle     :  0.581   9.890  16116  Z= 0.285
  Chirality :  0.042   0.164   1861
  Planarity :  0.004   0.095   2063
  Dihedral  :  4.755  42.743   1643
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.14 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -1.29 (0.22), residues: 1498
  helix:  0.69 (0.21), residues: 662
  sheet: -2.47 (0.32), residues: 216
  loop : -1.94 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.012   0.001   HIS B 283 
 PHE   0.010   0.001   PHE E 157 
 TYR   0.024   0.001   TYR C  13 
 ARG   0.004   0.000   ARG B 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02821 (  469)
  hydrogen bonds       : angle       3.97590 ( 1332)
  covalent geometry    : bond        0.00286 (11871)
  covalent geometry    : angle       0.58140 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8702 (mpp) cc_final: 0.7886 (mpp)
REVERT: A  238 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9028 (p)
REVERT: A  305 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8823 (mtmt)
REVERT: B    2 ASN cc_start: 0.8444 (m110) cc_final: 0.8098 (m-40)
REVERT: B   46 MET cc_start: 0.8830 (ttp) cc_final: 0.8619 (tpp)
REVERT: B  263 HIS cc_start: 0.8674 (m90) cc_final: 0.8433 (m170)
REVERT: C   61 LYS cc_start: 0.8815 (mttm) cc_final: 0.8359 (mmmt)
REVERT: D   82 ASP cc_start: 0.9034 (t0) cc_final: 0.8678 (t0)
REVERT: D   83 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8559 (mm-30)
REVERT: D  201 GLU cc_start: 0.8435 (pm20) cc_final: 0.8213 (pm20)
REVERT: D  203 LYS cc_start: 0.9084 (mttt) cc_final: 0.8655 (pptt)
REVERT: D  216 ASN cc_start: 0.8746 (t0) cc_final: 0.7844 (t0)
REVERT: E   10 LYS cc_start: 0.9257 (tmtt) cc_final: 0.8784 (tttp)
REVERT: E  187 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8782 (pp)
REVERT: E  211 TRP cc_start: 0.7657 (m-10) cc_final: 0.6815 (t60)
  outliers start: 28
  outliers final: 19
  residues processed: 124
  average time/residue: 0.2311
  time to fit residues: 42.1289
Evaluate side-chains
  117 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  140 PHE
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  255 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 129 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    2.1986

-------------------------------------------------------------------------------
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**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
C  37 HIS
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.055579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.044339 restraints weight = 56227.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.045776 restraints weight = 28095.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.046746 restraints weight = 18003.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11871  Z= 0.203
  Angle     :  0.638  11.565  16116  Z= 0.311
  Chirality :  0.044   0.231   1861
  Planarity :  0.004   0.095   2063
  Dihedral  :  4.795  42.724   1643
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.20 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -1.05 (0.23), residues: 1498
  helix:  0.98 (0.22), residues: 667
  sheet: -2.45 (0.34), residues: 215
  loop : -1.90 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  37 
 HIS   0.004   0.001   HIS B 186 
 PHE   0.013   0.001   PHE D  64 
 TYR   0.029   0.002   TYR C  13 
 ARG   0.004   0.000   ARG B 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02985 (  469)
  hydrogen bonds       : angle       4.03332 ( 1332)
  covalent geometry    : bond        0.00447 (11871)
  covalent geometry    : angle       0.63810 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 98
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8700 (mpp) cc_final: 0.8041 (mpp)
REVERT: A  238 VAL cc_start: 0.9446 (OUTLIER) cc_final: 0.9030 (p)
REVERT: A  305 LYS cc_start: 0.9191 (mmtt) cc_final: 0.8768 (mtmt)
REVERT: B    1 MET cc_start: 0.7457 (tpp) cc_final: 0.7249 (tmm)
REVERT: B  263 HIS cc_start: 0.8696 (m90) cc_final: 0.8411 (m90)
REVERT: C   61 LYS cc_start: 0.8845 (mttm) cc_final: 0.8395 (mmmt)
REVERT: D   82 ASP cc_start: 0.9054 (t0) cc_final: 0.8707 (t0)
REVERT: D  201 GLU cc_start: 0.8610 (pm20) cc_final: 0.8336 (pm20)
REVERT: D  203 LYS cc_start: 0.9110 (mttt) cc_final: 0.8681 (pptt)
REVERT: D  216 ASN cc_start: 0.8702 (t0) cc_final: 0.8081 (t0)
REVERT: E   10 LYS cc_start: 0.9312 (tmtt) cc_final: 0.8890 (tttp)
REVERT: E  187 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8812 (pp)
  outliers start: 34
  outliers final: 25
  residues processed: 122
  average time/residue: 0.2278
  time to fit residues: 41.3583
Evaluate side-chains
  121 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  140 PHE
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  255 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 33 optimal weight:    0.4980
   chunk 109 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0670
   chunk 112 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9990
   chunk 143 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 ASN
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
C  37 HIS
C 261 ASN
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.057145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.045891 restraints weight = 55351.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.047384 restraints weight = 27584.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.048363 restraints weight = 17640.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  11871  Z= 0.106
  Angle     :  0.580  11.439  16116  Z= 0.281
  Chirality :  0.042   0.171   1861
  Planarity :  0.004   0.094   2063
  Dihedral  :  4.621  41.890   1643
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.36 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -0.82 (0.23), residues: 1498
  helix:  1.22 (0.22), residues: 660
  sheet: -2.31 (0.33), residues: 221
  loop : -1.81 (0.25), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B 186 
 PHE   0.010   0.001   PHE E 157 
 TYR   0.029   0.001   TYR C  13 
 ARG   0.004   0.000   ARG B 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02692 (  469)
  hydrogen bonds       : angle       3.75815 ( 1332)
  covalent geometry    : bond        0.00241 (11871)
  covalent geometry    : angle       0.57978 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 1.300 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8663 (mpp) cc_final: 0.8007 (mpp)
REVERT: A  142 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9131 (p)
REVERT: A  299 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7683 (mp0)
REVERT: A  305 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8767 (mtmt)
REVERT: B  263 HIS cc_start: 0.8588 (m90) cc_final: 0.8370 (m170)
REVERT: C   61 LYS cc_start: 0.8827 (mttm) cc_final: 0.8392 (mmmt)
REVERT: D    9 ARG cc_start: 0.8572 (ttm170) cc_final: 0.8283 (mtm180)
REVERT: D   82 ASP cc_start: 0.9007 (t0) cc_final: 0.8649 (t0)
REVERT: D   83 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8663 (mm-30)
REVERT: D  203 LYS cc_start: 0.9013 (mttt) cc_final: 0.8635 (pptt)
REVERT: D  216 ASN cc_start: 0.8725 (t0) cc_final: 0.7968 (t0)
REVERT: E  138 MET cc_start: 0.8710 (tmm) cc_final: 0.8353 (tmm)
REVERT: E  211 TRP cc_start: 0.7554 (m-10) cc_final: 0.6752 (t60)
REVERT: E  216 ASN cc_start: 0.8590 (t0) cc_final: 0.8071 (t0)
  outliers start: 29
  outliers final: 21
  residues processed: 128
  average time/residue: 0.2287
  time to fit residues: 43.1447
Evaluate side-chains
  121 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  140 PHE
Chi-restraints excluded: chain D residue  257 LEU
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  255 CYS
Chi-restraints excluded: chain E residue  257 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 125 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 35 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0370
   chunk 46 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.5062

-------------------------------------------------------------------------------
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**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
C 261 ASN
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.056751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.045525 restraints weight = 55839.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.047012 restraints weight = 27570.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.048034 restraints weight = 17504.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11871  Z= 0.153
  Angle     :  0.614  11.755  16116  Z= 0.299
  Chirality :  0.043   0.217   1861
  Planarity :  0.004   0.093   2063
  Dihedral  :  4.636  41.797   1643
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.67 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -0.69 (0.23), residues: 1498
  helix:  1.38 (0.22), residues: 664
  sheet: -2.25 (0.34), residues: 214
  loop : -1.85 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.005   0.001   HIS B 186 
 PHE   0.014   0.001   PHE E 146 
 TYR   0.031   0.001   TYR C  13 
 ARG   0.004   0.000   ARG C 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02763 (  469)
  hydrogen bonds       : angle       3.79062 ( 1332)
  covalent geometry    : bond        0.00344 (11871)
  covalent geometry    : angle       0.61390 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 1.316 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8684 (mpp) cc_final: 0.7990 (mpp)
REVERT: A  231 MET cc_start: 0.8952 (mtp) cc_final: 0.8613 (ptp)
REVERT: A  299 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8027 (mp0)
REVERT: A  305 LYS cc_start: 0.9196 (mmtt) cc_final: 0.8726 (mtmt)
REVERT: B   86 TYR cc_start: 0.9075 (m-80) cc_final: 0.8722 (m-80)
REVERT: B  263 HIS cc_start: 0.8654 (m90) cc_final: 0.8441 (m170)
REVERT: C   61 LYS cc_start: 0.8864 (mttm) cc_final: 0.8392 (mmmt)
REVERT: D   82 ASP cc_start: 0.9026 (t0) cc_final: 0.8671 (t0)
REVERT: D   83 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8739 (mm-30)
REVERT: D  203 LYS cc_start: 0.9075 (mttt) cc_final: 0.8681 (pptt)
REVERT: D  216 ASN cc_start: 0.8625 (t0) cc_final: 0.8286 (t0)
REVERT: E   10 LYS cc_start: 0.9256 (tmtt) cc_final: 0.8741 (tttp)
REVERT: E  138 MET cc_start: 0.8698 (tmm) cc_final: 0.8361 (tmm)
REVERT: E  187 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8828 (pp)
REVERT: E  211 TRP cc_start: 0.7681 (m-10) cc_final: 0.6760 (t60)
  outliers start: 28
  outliers final: 23
  residues processed: 123
  average time/residue: 0.2217
  time to fit residues: 40.6075
Evaluate side-chains
  122 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  140 PHE
Chi-restraints excluded: chain D residue  257 LEU
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  255 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 144 optimal weight:    0.1980
   chunk 84 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.056806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.045502 restraints weight = 55685.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.046979 restraints weight = 27986.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.047965 restraints weight = 17899.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11871  Z= 0.133
  Angle     :  0.609  13.041  16116  Z= 0.295
  Chirality :  0.043   0.231   1861
  Planarity :  0.004   0.093   2063
  Dihedral  :  4.613  41.734   1643
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 20.83 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -0.64 (0.23), residues: 1498
  helix:  1.40 (0.22), residues: 667
  sheet: -2.22 (0.34), residues: 224
  loop : -1.80 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.008   0.001   HIS A 207 
 PHE   0.011   0.001   PHE E 157 
 TYR   0.030   0.001   TYR C  13 
 ARG   0.004   0.000   ARG C 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02681 (  469)
  hydrogen bonds       : angle       3.73810 ( 1332)
  covalent geometry    : bond        0.00305 (11871)
  covalent geometry    : angle       0.60866 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8689 (mpp) cc_final: 0.8045 (mpp)
REVERT: A  142 VAL cc_start: 0.9451 (OUTLIER) cc_final: 0.9102 (p)
REVERT: A  305 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8717 (mtmt)
REVERT: B   86 TYR cc_start: 0.9030 (m-80) cc_final: 0.8673 (m-80)
REVERT: C   61 LYS cc_start: 0.8860 (mttm) cc_final: 0.8405 (mmmt)
REVERT: D   81 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8012 (mt-10)
REVERT: D   82 ASP cc_start: 0.8998 (t0) cc_final: 0.8626 (t0)
REVERT: D   83 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8683 (mm-30)
REVERT: D  203 LYS cc_start: 0.9038 (mttt) cc_final: 0.8681 (pptt)
REVERT: D  216 ASN cc_start: 0.8732 (t0) cc_final: 0.7992 (t0)
REVERT: E   10 LYS cc_start: 0.9243 (tmtt) cc_final: 0.8725 (tttp)
REVERT: E  187 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8830 (pp)
REVERT: E  211 TRP cc_start: 0.7604 (m-10) cc_final: 0.6701 (t60)
  outliers start: 26
  outliers final: 21
  residues processed: 120
  average time/residue: 0.2375
  time to fit residues: 42.1944
Evaluate side-chains
  122 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  140 PHE
Chi-restraints excluded: chain D residue  257 LEU
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  255 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 122 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0980
   chunk 72 optimal weight:    3.9990
   chunk 132 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   overall best weight:    1.8188

-------------------------------------------------------------------------------
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**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
C  37 HIS
C 261 ASN
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.056061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.044786 restraints weight = 56043.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.046236 restraints weight = 27883.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.047232 restraints weight = 17777.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11871  Z= 0.178
  Angle     :  0.635  13.154  16116  Z= 0.310
  Chirality :  0.043   0.215   1861
  Planarity :  0.004   0.093   2063
  Dihedral  :  4.686  41.601   1643
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.59 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -0.62 (0.23), residues: 1498
  helix:  1.44 (0.22), residues: 666
  sheet: -2.24 (0.34), residues: 224
  loop : -1.78 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  37 
 HIS   0.005   0.001   HIS B 186 
 PHE   0.024   0.001   PHE D  64 
 TYR   0.031   0.002   TYR C  13 
 ARG   0.005   0.000   ARG C 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02840 (  469)
  hydrogen bonds       : angle       3.86537 ( 1332)
  covalent geometry    : bond        0.00398 (11871)
  covalent geometry    : angle       0.63461 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 1.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8702 (mpp) cc_final: 0.8040 (mpp)
REVERT: A  305 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8717 (mtmt)
REVERT: B   86 TYR cc_start: 0.9081 (m-80) cc_final: 0.8716 (m-80)
REVERT: D   82 ASP cc_start: 0.9060 (t0) cc_final: 0.8659 (t0)
REVERT: D  203 LYS cc_start: 0.9077 (mttt) cc_final: 0.8692 (pptt)
REVERT: D  216 ASN cc_start: 0.8747 (t0) cc_final: 0.8018 (t0)
REVERT: E   10 LYS cc_start: 0.9271 (tmtt) cc_final: 0.8748 (tttp)
REVERT: E  138 MET cc_start: 0.8714 (tmm) cc_final: 0.8268 (tmm)
REVERT: E  187 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8849 (pp)
  outliers start: 30
  outliers final: 22
  residues processed: 121
  average time/residue: 0.2790
  time to fit residues: 50.6830
Evaluate side-chains
  120 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 1.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  140 PHE
Chi-restraints excluded: chain D residue  257 LEU
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  255 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 81 optimal weight:    0.0570
   chunk 89 optimal weight:    0.7980
   chunk 66 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0570
   chunk 10 optimal weight:    4.9990
   chunk 146 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   overall best weight:    0.5216

-------------------------------------------------------------------------------
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**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS
C  37 HIS
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.057691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.046358 restraints weight = 55007.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.047858 restraints weight = 27171.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.048862 restraints weight = 17324.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  11871  Z= 0.107
  Angle     :  0.611  14.243  16116  Z= 0.294
  Chirality :  0.043   0.229   1861
  Planarity :  0.004   0.093   2063
  Dihedral  :  4.568  41.240   1643
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 21.57 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

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: -0.52 (0.23), residues: 1498
  helix:  1.51 (0.22), residues: 659
  sheet: -2.01 (0.34), residues: 227
  loop : -1.76 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.011   0.001   HIS A 207 
 PHE   0.011   0.001   PHE E 157 
 TYR   0.031   0.001   TYR C  13 
 ARG   0.005   0.000   ARG C 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02555 (  469)
  hydrogen bonds       : angle       3.67258 ( 1332)
  covalent geometry    : bond        0.00244 (11871)
  covalent geometry    : angle       0.61058 (16116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3537.42 seconds
wall clock time: 64 minutes 24.28 seconds (3864.28 seconds total)