Starting phenix.real_space_refine
on Wed Mar  4 07:08:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o11_12686/03_2026/7o11_12686.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o11_12686/03_2026/7o11_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_12686/03_2026/7o11_12686.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o11_12686/03_2026/7o11_12686.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o11_12686/03_2026/7o11_12686.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o11_12686/03_2026/7o11_12686.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.49, per 1000 atoms: 0.21
  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: 0.80
  Conformation dependent library (CDL) restraints added in 600.7 milliseconds
  

  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: 0.44
  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: 1.95

  Time building geometry restraints manager: 1.07 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:                  0.010
  Normalize map: mean=0, sd=1:             1.870
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.720
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.290
-------------------------------------------------------------------------------
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 : 5.65
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.004   0.001   ARG A 242 
 TYR   0.019   0.002   TYR A 204 
 PHE   0.020   0.002   PHE E  64 
 TRP   0.023   0.002   TRP A  45 
 HIS   0.010   0.002   HIS A 163 

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

*********************** 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  : 0.417 
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: 0.9310 (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: 0.1022
  time to fit residues: 23.8296
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  : 0.449 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.2980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.057554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.046113 restraints weight = 54160.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.047602 restraints weight = 27115.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.048631 restraints weight = 17375.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.049353 restraints weight = 12692.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.049793 restraints weight = 10195.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1852

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= 0.119
  Angle     :  0.618  11.030  16116  Z= 0.313
  Chirality :  0.043   0.166   1861
  Planarity :  0.005   0.098   2063
  Dihedral  :  5.368  47.668   1644
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.56 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.74 (0.18), residues: 1498
  helix: -2.08 (0.16), residues: 663
  sheet: -3.16 (0.29), residues: 210
  loop : -2.50 (0.22), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 269 
 TYR   0.021   0.001   TYR C  13 
 PHE   0.011   0.001   PHE E 157 
 TRP   0.011   0.001   TRP A  98 
 HIS   0.004   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (11871)
  covalent geometry    : angle       0.61794 (16116)
  hydrogen bonds       : bond        0.03846 (  469)
  hydrogen bonds       : angle       5.05927 ( 1332)

*********************** 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
  138 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.7960 (pt) cc_final: 0.7650 (pp)
REVERT: A  231 MET cc_start: 0.8520 (mtt) cc_final: 0.8233 (mtp)
REVERT: A  305 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8811 (mtmt)
REVERT: B    2 ASN cc_start: 0.8405 (m110) cc_final: 0.7983 (m-40)
REVERT: B   46 MET cc_start: 0.8998 (ttp) cc_final: 0.8727 (ttm)
REVERT: B  263 HIS cc_start: 0.8605 (m90) cc_final: 0.8339 (m90)
REVERT: C  133 MET cc_start: 0.9080 (mtm) cc_final: 0.8696 (mtm)
REVERT: D   11 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8128 (mm-30)
REVERT: D   75 TYR cc_start: 0.9287 (p90) cc_final: 0.8941 (p90)
REVERT: D   82 ASP cc_start: 0.8996 (t0) cc_final: 0.8712 (t0)
REVERT: D   83 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8652 (mm-30)
REVERT: D  203 LYS cc_start: 0.9028 (mttt) cc_final: 0.8599 (pptt)
REVERT: D  216 ASN cc_start: 0.8642 (t0) cc_final: 0.7542 (t0)
REVERT: E   20 TRP cc_start: 0.8793 (m100) cc_final: 0.8486 (m-10)
REVERT: E  187 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8801 (pp)
REVERT: E  211 TRP cc_start: 0.7685 (m-10) cc_final: 0.6828 (t60)
  outliers start: 15
  outliers final: 6
  residues processed: 134
  average time/residue: 0.1047
  time to fit residues: 20.4836
Evaluate side-chains
  105 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Chi-restraints excluded: chain E residue  218 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 96 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 135 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 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  97 HIS
** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.054590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.043328 restraints weight = 56155.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.044716 restraints weight = 28695.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.045667 restraints weight = 18538.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.046282 restraints weight = 13760.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.046756 restraints weight = 11248.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11871  Z= 0.250
  Angle     :  0.689   8.793  16116  Z= 0.343
  Chirality :  0.045   0.166   1861
  Planarity :  0.004   0.099   2063
  Dihedral  :  5.197  44.499   1643
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.34 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.21), residues: 1498
  helix: -0.31 (0.20), residues: 660
  sheet: -2.79 (0.31), residues: 207
  loop : -2.19 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 171 
 TYR   0.020   0.002   TYR C  13 
 PHE   0.016   0.002   PHE E 204 
 TRP   0.011   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 (11871)
  covalent geometry    : angle       0.68906 (16116)
  hydrogen bonds       : bond        0.03527 (  469)
  hydrogen bonds       : angle       4.62445 ( 1332)

*********************** 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
  125 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8628 (mpp) cc_final: 0.8216 (mpp)
REVERT: A  305 LYS cc_start: 0.9207 (mmtt) cc_final: 0.8848 (mtmt)
REVERT: B    2 ASN cc_start: 0.8504 (m110) cc_final: 0.8064 (m-40)
REVERT: B   50 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9120 (mt)
REVERT: B   86 TYR cc_start: 0.9192 (m-80) cc_final: 0.8898 (m-80)
REVERT: B  113 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9380 (mm)
REVERT: B  263 HIS cc_start: 0.8643 (m90) cc_final: 0.8373 (m90)
REVERT: C   61 LYS cc_start: 0.8743 (mttm) cc_final: 0.8340 (mmmt)
REVERT: C  133 MET cc_start: 0.9084 (mtm) cc_final: 0.8803 (mtm)
REVERT: D   82 ASP cc_start: 0.9030 (t0) cc_final: 0.8750 (t0)
REVERT: D   83 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8649 (mm-30)
REVERT: D  203 LYS cc_start: 0.9089 (mttt) cc_final: 0.8688 (pptt)
REVERT: D  216 ASN cc_start: 0.8668 (t0) cc_final: 0.8030 (t0)
REVERT: D  219 ASP cc_start: 0.8916 (m-30) cc_final: 0.8673 (m-30)
REVERT: E   20 TRP cc_start: 0.8867 (m100) cc_final: 0.8664 (m-10)
REVERT: E  187 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8779 (pp)
  outliers start: 26
  outliers final: 17
  residues processed: 119
  average time/residue: 0.0985
  time to fit residues: 17.6213
Evaluate side-chains
  108 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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   50 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  181 ILE
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   20 TRP
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  102 LEU
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 118 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 144 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 49 optimal weight:    0.4980
   chunk 25 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 135 optimal weight:    0.4980
   chunk 5 optimal weight:    0.4980
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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**
A 301 ASN
A 324 ASN
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 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.056089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.044800 restraints weight = 55239.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.046251 restraints weight = 27511.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.047241 restraints weight = 17627.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.047942 restraints weight = 12965.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.048312 restraints weight = 10435.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2635

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= 0.121
  Angle     :  0.589   9.106  16116  Z= 0.289
  Chirality :  0.042   0.161   1861
  Planarity :  0.004   0.097   2063
  Dihedral  :  4.944  43.412   1643
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.16 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.22), residues: 1498
  helix:  0.29 (0.21), residues: 666
  sheet: -2.70 (0.31), residues: 214
  loop : -2.06 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 248 
 TYR   0.021   0.001   TYR C  13 
 PHE   0.012   0.001   PHE E  64 
 TRP   0.009   0.001   TRP A  98 
 HIS   0.011   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (11871)
  covalent geometry    : angle       0.58930 (16116)
  hydrogen bonds       : bond        0.02944 (  469)
  hydrogen bonds       : angle       4.18795 ( 1332)

*********************** 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
  122 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8805 (mtmt)
REVERT: B    2 ASN cc_start: 0.8398 (m110) cc_final: 0.8041 (m-40)
REVERT: B  263 HIS cc_start: 0.8614 (m90) cc_final: 0.8338 (m90)
REVERT: C   61 LYS cc_start: 0.8777 (mttm) cc_final: 0.8377 (mmmt)
REVERT: D   75 TYR cc_start: 0.9274 (p90) cc_final: 0.9032 (p90)
REVERT: D   82 ASP cc_start: 0.9003 (t0) cc_final: 0.8660 (t0)
REVERT: D   83 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8541 (mm-30)
REVERT: D  201 GLU cc_start: 0.8431 (pm20) cc_final: 0.8191 (pm20)
REVERT: D  203 LYS cc_start: 0.9071 (mttt) cc_final: 0.8669 (pptt)
REVERT: D  216 ASN cc_start: 0.8637 (t0) cc_final: 0.7889 (t0)
REVERT: D  219 ASP cc_start: 0.8901 (m-30) cc_final: 0.8612 (m-30)
REVERT: E   10 LYS cc_start: 0.9282 (tmtt) cc_final: 0.8844 (tttp)
REVERT: E  187 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8811 (pp)
REVERT: E  211 TRP cc_start: 0.7764 (m-10) cc_final: 0.6798 (t60)
  outliers start: 20
  outliers final: 10
  residues processed: 117
  average time/residue: 0.0911
  time to fit residues: 16.3137
Evaluate side-chains
  108 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  223 VAL
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  213 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 139 optimal weight:    0.9990
   chunk 137 optimal weight:    5.9990
   chunk 49 optimal weight:    0.5980
   chunk 126 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 29 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.056594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.045300 restraints weight = 55206.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.046772 restraints weight = 27552.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.047614 restraints weight = 17640.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.048390 restraints weight = 13466.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.048849 restraints weight = 10719.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  11871  Z= 0.112
  Angle     :  0.582  10.054  16116  Z= 0.282
  Chirality :  0.042   0.297   1861
  Planarity :  0.004   0.095   2063
  Dihedral  :  4.754  42.741   1643
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.22), residues: 1498
  helix:  0.69 (0.22), residues: 662
  sheet: -2.58 (0.32), residues: 214
  loop : -1.97 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 248 
 TYR   0.025   0.001   TYR C  13 
 PHE   0.011   0.001   PHE E  64 
 TRP   0.009   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (11871)
  covalent geometry    : angle       0.58244 (16116)
  hydrogen bonds       : bond        0.02740 (  469)
  hydrogen bonds       : angle       3.97769 ( 1332)

*********************** 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  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8695 (mpp) cc_final: 0.7895 (mpp)
REVERT: A  238 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.8947 (p)
REVERT: A  299 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7703 (mp0)
REVERT: A  305 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8810 (mtmt)
REVERT: B    2 ASN cc_start: 0.8344 (m110) cc_final: 0.7995 (m-40)
REVERT: B   46 MET cc_start: 0.8749 (ttp) cc_final: 0.8502 (tpp)
REVERT: B   86 TYR cc_start: 0.9110 (m-80) cc_final: 0.8807 (m-80)
REVERT: B  263 HIS cc_start: 0.8628 (m90) cc_final: 0.8374 (m170)
REVERT: C   61 LYS cc_start: 0.8805 (mttm) cc_final: 0.8429 (mmmt)
REVERT: D   82 ASP cc_start: 0.9006 (t0) cc_final: 0.8643 (t0)
REVERT: D   83 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8490 (mm-30)
REVERT: D  201 GLU cc_start: 0.8390 (pm20) cc_final: 0.8157 (pm20)
REVERT: D  203 LYS cc_start: 0.9075 (mttt) cc_final: 0.8661 (pptt)
REVERT: D  216 ASN cc_start: 0.8668 (t0) cc_final: 0.7841 (t0)
REVERT: D  219 ASP cc_start: 0.8882 (m-30) cc_final: 0.8560 (m-30)
REVERT: E  187 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8805 (pp)
REVERT: E  211 TRP cc_start: 0.7664 (m-10) cc_final: 0.6740 (t60)
REVERT: E  216 ASN cc_start: 0.8685 (t0) cc_final: 0.8443 (t0)
  outliers start: 28
  outliers final: 16
  residues processed: 124
  average time/residue: 0.0896
  time to fit residues: 17.0199
Evaluate side-chains
  115 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
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  299 GLU
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  223 VAL
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain D residue    4 VAL
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  102 LEU
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 98 optimal weight:    4.9990
   chunk 132 optimal weight:    0.8980
   chunk 137 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 136 optimal weight:    9.9990
   chunk 143 optimal weight:    3.9990
   chunk 107 optimal weight:    0.1980
   chunk 93 optimal weight:    0.8980
   chunk 97 optimal weight:    8.9990
   chunk 63 optimal weight:   20.0000
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.056935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.045669 restraints weight = 55168.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.047145 restraints weight = 27440.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.048178 restraints weight = 17548.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.048823 restraints weight = 12880.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.049330 restraints weight = 10419.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2936

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= 0.105
  Angle     :  0.578  10.411  16116  Z= 0.278
  Chirality :  0.042   0.171   1861
  Planarity :  0.004   0.094   2063
  Dihedral  :  4.631  42.185   1643
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.71 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.23), residues: 1498
  helix:  1.05 (0.22), residues: 656
  sheet: -2.32 (0.34), residues: 219
  loop : -1.95 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 248 
 TYR   0.028   0.001   TYR C  13 
 PHE   0.011   0.001   PHE E 157 
 TRP   0.009   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (11871)
  covalent geometry    : angle       0.57787 (16116)
  hydrogen bonds       : bond        0.02597 (  469)
  hydrogen bonds       : angle       3.78860 ( 1332)

*********************** 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
  130 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8690 (mpp) cc_final: 0.8005 (mpp)
REVERT: A  238 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.8931 (p)
REVERT: A  305 LYS cc_start: 0.9124 (mmtt) cc_final: 0.8774 (mtmt)
REVERT: B    2 ASN cc_start: 0.8360 (m110) cc_final: 0.8032 (m-40)
REVERT: B   46 MET cc_start: 0.8777 (ttp) cc_final: 0.8505 (tpp)
REVERT: B  263 HIS cc_start: 0.8566 (m90) cc_final: 0.8336 (m170)
REVERT: C   61 LYS cc_start: 0.8805 (mttm) cc_final: 0.8388 (mmmt)
REVERT: D   82 ASP cc_start: 0.8976 (t0) cc_final: 0.8621 (t0)
REVERT: D   83 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8689 (mm-30)
REVERT: D  201 GLU cc_start: 0.8388 (pm20) cc_final: 0.8168 (pm20)
REVERT: D  203 LYS cc_start: 0.8984 (mttt) cc_final: 0.8621 (pptt)
REVERT: D  216 ASN cc_start: 0.8664 (t0) cc_final: 0.7811 (t0)
REVERT: D  219 ASP cc_start: 0.8867 (m-30) cc_final: 0.8535 (m-30)
REVERT: E   66 MET cc_start: 0.9106 (tpp) cc_final: 0.8874 (mmp)
REVERT: E  138 MET cc_start: 0.8757 (tmm) cc_final: 0.8381 (tmm)
REVERT: E  211 TRP cc_start: 0.7577 (m-10) cc_final: 0.6778 (t60)
REVERT: E  213 LEU cc_start: 0.8571 (mm) cc_final: 0.8215 (mm)
  outliers start: 26
  outliers final: 17
  residues processed: 125
  average time/residue: 0.0897
  time to fit residues: 17.2040
Evaluate side-chains
  114 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
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  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  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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 142 optimal weight:    0.0020
   chunk 16 optimal weight:    7.9990
   chunk 90 optimal weight:    0.0980
   chunk 10 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 93 optimal weight:    0.2980
   chunk 5 optimal weight:   20.0000
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.7990

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.056965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.045827 restraints weight = 55014.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.047269 restraints weight = 27539.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.048296 restraints weight = 17594.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.049017 restraints weight = 12825.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.049426 restraints weight = 10292.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3079

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= 0.110
  Angle     :  0.582  10.692  16116  Z= 0.281
  Chirality :  0.042   0.176   1861
  Planarity :  0.004   0.093   2063
  Dihedral  :  4.574  41.836   1643
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.12 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.23), residues: 1498
  helix:  1.25 (0.22), residues: 657
  sheet: -2.25 (0.33), residues: 229
  loop : -1.93 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 248 
 TYR   0.030   0.001   TYR C  13 
 PHE   0.012   0.001   PHE E 157 
 TRP   0.009   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (11871)
  covalent geometry    : angle       0.58173 (16116)
  hydrogen bonds       : bond        0.02602 (  469)
  hydrogen bonds       : angle       3.69549 ( 1332)

*********************** 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
  127 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8679 (mpp) cc_final: 0.7981 (mpp)
REVERT: A  142 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9099 (p)
REVERT: A  235 LYS cc_start: 0.9136 (tppp) cc_final: 0.8731 (tppt)
REVERT: A  305 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8735 (mtmt)
REVERT: B    2 ASN cc_start: 0.8312 (m110) cc_final: 0.8005 (m-40)
REVERT: B   46 MET cc_start: 0.8802 (ttp) cc_final: 0.8580 (tpp)
REVERT: B  263 HIS cc_start: 0.8496 (m90) cc_final: 0.8295 (m170)
REVERT: B  295 MET cc_start: 0.9292 (mmp) cc_final: 0.9066 (mmm)
REVERT: C   61 LYS cc_start: 0.8818 (mttm) cc_final: 0.8396 (mmmt)
REVERT: D   82 ASP cc_start: 0.8955 (t0) cc_final: 0.8589 (t0)
REVERT: D   83 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8718 (mm-30)
REVERT: D  201 GLU cc_start: 0.8421 (pm20) cc_final: 0.8221 (pm20)
REVERT: D  203 LYS cc_start: 0.8995 (mttt) cc_final: 0.8621 (pptt)
REVERT: D  216 ASN cc_start: 0.8655 (t0) cc_final: 0.7772 (t0)
REVERT: D  219 ASP cc_start: 0.8873 (m-30) cc_final: 0.8519 (m-30)
REVERT: E   66 MET cc_start: 0.9085 (tpp) cc_final: 0.8852 (mmp)
REVERT: E  138 MET cc_start: 0.8667 (tmm) cc_final: 0.8280 (tmm)
REVERT: E  187 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8791 (pp)
REVERT: E  211 TRP cc_start: 0.7536 (m-10) cc_final: 0.6559 (t60)
  outliers start: 29
  outliers final: 21
  residues processed: 121
  average time/residue: 0.0913
  time to fit residues: 16.7027
Evaluate side-chains
  119 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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   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  191 LEU
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  187 LEU
Chi-restraints excluded: chain E residue  218 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0970
   chunk 2 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 66 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 135 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.057234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.045992 restraints weight = 55033.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.047471 restraints weight = 27570.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.048494 restraints weight = 17723.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.049145 restraints weight = 13026.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.049631 restraints weight = 10532.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3184

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= 0.105
  Angle     :  0.582  11.323  16116  Z= 0.281
  Chirality :  0.042   0.224   1861
  Planarity :  0.004   0.093   2063
  Dihedral  :  4.513  41.341   1643
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.18 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.23), residues: 1498
  helix:  1.39 (0.22), residues: 659
  sheet: -2.22 (0.33), residues: 223
  loop : -1.88 (0.24), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 224 
 TYR   0.033   0.001   TYR C  13 
 PHE   0.011   0.001   PHE E 157 
 TRP   0.008   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (11871)
  covalent geometry    : angle       0.58154 (16116)
  hydrogen bonds       : bond        0.02531 (  469)
  hydrogen bonds       : angle       3.62014 ( 1332)

*********************** 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
  122 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8693 (mpp) cc_final: 0.8056 (mpp)
REVERT: A  142 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9066 (p)
REVERT: A  235 LYS cc_start: 0.9124 (tppp) cc_final: 0.8734 (tppt)
REVERT: A  305 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8714 (mtmt)
REVERT: B    2 ASN cc_start: 0.8328 (m110) cc_final: 0.8041 (m-40)
REVERT: B   46 MET cc_start: 0.8799 (ttp) cc_final: 0.8571 (tpp)
REVERT: B   49 ILE cc_start: 0.9649 (mm) cc_final: 0.9416 (mm)
REVERT: B  263 HIS cc_start: 0.8466 (m90) cc_final: 0.8260 (m170)
REVERT: D   82 ASP cc_start: 0.8887 (t0) cc_final: 0.8454 (t0)
REVERT: D   83 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8727 (mm-30)
REVERT: D  203 LYS cc_start: 0.9024 (mttt) cc_final: 0.8628 (pptt)
REVERT: D  216 ASN cc_start: 0.8636 (t0) cc_final: 0.7704 (t0)
REVERT: D  219 ASP cc_start: 0.8858 (m-30) cc_final: 0.8498 (m-30)
REVERT: E   66 MET cc_start: 0.9073 (tpp) cc_final: 0.8840 (mmp)
REVERT: E  138 MET cc_start: 0.8687 (tmm) cc_final: 0.8275 (tmm)
REVERT: E  187 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8811 (pp)
REVERT: E  211 TRP cc_start: 0.7318 (m-10) cc_final: 0.6345 (t60)
  outliers start: 23
  outliers final: 20
  residues processed: 115
  average time/residue: 0.0950
  time to fit residues: 16.4633
Evaluate side-chains
  115 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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   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  187 LEU
Chi-restraints excluded: chain D residue  191 LEU
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  187 LEU
Chi-restraints excluded: chain E residue  218 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 126 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 139 optimal weight:    7.9990
   chunk 131 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 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 = 0.3202 r_free = 0.3202 target = 0.055765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.044577 restraints weight = 55527.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.046002 restraints weight = 27967.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.046875 restraints weight = 17973.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.047583 restraints weight = 13616.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.048049 restraints weight = 10995.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11871  Z= 0.229
  Angle     :  0.670  11.857  16116  Z= 0.328
  Chirality :  0.044   0.231   1861
  Planarity :  0.004   0.093   2063
  Dihedral  :  4.694  41.868   1643
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.34 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.23), residues: 1498
  helix:  1.39 (0.22), residues: 665
  sheet: -2.29 (0.33), residues: 224
  loop : -1.82 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 224 
 TYR   0.030   0.002   TYR C  13 
 PHE   0.018   0.001   PHE D  64 
 TRP   0.012   0.001   TRP E  37 
 HIS   0.004   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (11871)
  covalent geometry    : angle       0.67004 (16116)
  hydrogen bonds       : bond        0.02969 (  469)
  hydrogen bonds       : angle       3.92955 ( 1332)

*********************** 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
  126 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8715 (mpp) cc_final: 0.8057 (mpp)
REVERT: A  305 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8739 (mtmt)
REVERT: B    2 ASN cc_start: 0.8312 (m110) cc_final: 0.7975 (m-40)
REVERT: B   49 ILE cc_start: 0.9645 (mm) cc_final: 0.9407 (mm)
REVERT: B  263 HIS cc_start: 0.8611 (m90) cc_final: 0.8378 (m170)
REVERT: D   81 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7889 (mt-10)
REVERT: D   82 ASP cc_start: 0.8853 (t0) cc_final: 0.8404 (t0)
REVERT: D   83 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8582 (mm-30)
REVERT: D  203 LYS cc_start: 0.9059 (mttt) cc_final: 0.8666 (pptt)
REVERT: D  216 ASN cc_start: 0.8703 (t0) cc_final: 0.8127 (t0)
REVERT: E    3 GLN cc_start: 0.8602 (mt0) cc_final: 0.8267 (tt0)
REVERT: E   66 MET cc_start: 0.9117 (tpp) cc_final: 0.8888 (mmp)
REVERT: E  138 MET cc_start: 0.8684 (tmm) cc_final: 0.8306 (tmm)
REVERT: E  187 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8849 (pp)
REVERT: E  211 TRP cc_start: 0.7450 (m-10) cc_final: 0.6535 (t60)
  outliers start: 27
  outliers final: 18
  residues processed: 119
  average time/residue: 0.0958
  time to fit residues: 17.0689
Evaluate side-chains
  115 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 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  187 LEU
Chi-restraints excluded: chain E residue  218 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 139 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 147 optimal weight:    0.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3240 r_free = 0.3240 target = 0.057116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.045818 restraints weight = 55391.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.047306 restraints weight = 27574.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.048290 restraints weight = 17585.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.048930 restraints weight = 12935.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.049482 restraints weight = 10467.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3274

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= 0.122
  Angle     :  0.628  14.442  16116  Z= 0.301
  Chirality :  0.043   0.292   1861
  Planarity :  0.004   0.092   2063
  Dihedral  :  4.605  41.473   1643
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 21.00 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.23), residues: 1498
  helix:  1.45 (0.22), residues: 665
  sheet: -2.19 (0.34), residues: 228
  loop : -1.76 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 224 
 TYR   0.031   0.001   TYR C  13 
 PHE   0.012   0.001   PHE E 157 
 TRP   0.007   0.001   TRP A  98 
 HIS   0.004   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (11871)
  covalent geometry    : angle       0.62750 (16116)
  hydrogen bonds       : bond        0.02674 (  469)
  hydrogen bonds       : angle       3.76490 ( 1332)

********************** 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
  119 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8702 (mpp) cc_final: 0.8070 (mpp)
REVERT: A  305 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8742 (mtmt)
REVERT: B    2 ASN cc_start: 0.8248 (m110) cc_final: 0.7942 (m-40)
REVERT: B   46 MET cc_start: 0.8887 (ttp) cc_final: 0.8624 (tpp)
REVERT: B   49 ILE cc_start: 0.9642 (mm) cc_final: 0.9391 (mm)
REVERT: B  263 HIS cc_start: 0.8544 (m90) cc_final: 0.8340 (m170)
REVERT: C   61 LYS cc_start: 0.8839 (mttm) cc_final: 0.8396 (mmmt)
REVERT: D   82 ASP cc_start: 0.8847 (t0) cc_final: 0.8382 (t0)
REVERT: D   83 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8731 (mm-30)
REVERT: D  203 LYS cc_start: 0.8984 (mttt) cc_final: 0.8660 (pptt)
REVERT: D  216 ASN cc_start: 0.8710 (t0) cc_final: 0.7588 (t0)
REVERT: D  219 ASP cc_start: 0.8845 (m-30) cc_final: 0.8460 (m-30)
REVERT: E    3 GLN cc_start: 0.8505 (mt0) cc_final: 0.8202 (tt0)
REVERT: E   66 MET cc_start: 0.9078 (tpp) cc_final: 0.8855 (mmp)
REVERT: E  187 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8852 (pp)
REVERT: E  211 TRP cc_start: 0.7371 (m-10) cc_final: 0.6598 (t60)
  outliers start: 20
  outliers final: 17
  residues processed: 113
  average time/residue: 0.0992
  time to fit residues: 16.8074
Evaluate side-chains
  113 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   86 THR
Chi-restraints excluded: chain D residue  125 LEU
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  187 LEU
Chi-restraints excluded: chain E residue  218 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 140 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 112 optimal weight:    0.6980
   chunk 94 optimal weight:    8.9990
   chunk 117 optimal weight:    5.9990
   chunk 142 optimal weight:    3.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 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 = 0.3207 r_free = 0.3207 target = 0.056000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.044898 restraints weight = 55977.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.046339 restraints weight = 27985.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.047292 restraints weight = 17847.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.048004 restraints weight = 13134.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.048427 restraints weight = 10572.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11871  Z= 0.202
  Angle     :  0.665  13.517  16116  Z= 0.323
  Chirality :  0.045   0.347   1861
  Planarity :  0.004   0.092   2063
  Dihedral  :  4.688  41.787   1643
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.59 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.23), residues: 1498
  helix:  1.40 (0.22), residues: 668
  sheet: -2.26 (0.34), residues: 215
  loop : -1.76 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 224 
 TYR   0.030   0.002   TYR C  13 
 PHE   0.017   0.001   PHE D  64 
 TRP   0.011   0.001   TRP E  37 
 HIS   0.005   0.001   HIS B 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (11871)
  covalent geometry    : angle       0.66539 (16116)
  hydrogen bonds       : bond        0.02906 (  469)
  hydrogen bonds       : angle       3.94669 ( 1332)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1698.16 seconds
wall clock time: 30 minutes 23.86 seconds (1823.86 seconds total)