Starting phenix.real_space_refine
on Sun Apr  5 16:04:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o10_12685/04_2026/7o10_12685.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o10_12685/04_2026/7o10_12685.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o10_12685/04_2026/7o10_12685.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o10_12685/04_2026/7o10_12685.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o10_12685/04_2026/7o10_12685.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o10_12685/04_2026/7o10_12685.cif"
  }
  resolution = 3.6
  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 43 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/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: 2.68, per 1000 atoms: 0.23
  Number of scatterers: 11651
  At special positions: 0
  Unit cell: (86.184, 168.264, 138.51, 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: 0.74
  Conformation dependent library (CDL) restraints added in 512.8 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:
      58 helices and 12 sheets defined
      47.1% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 344 through 348
      removed outlier: 4.243A  pdb=" N   GLY A 347 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.560A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.267A  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: 3.559A  pdb=" N   GLN A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 50
      removed outlier: 3.907A  pdb=" N   SER B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS B  47 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU B  50 " --> pdb=" O   MET B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
    Processing helix  chain 'B' and resid 69 through 74
      removed outlier: 3.532A  pdb=" N   ARG B  74 " --> pdb=" O   PRO B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 102
    Processing helix  chain 'B' and resid 106 through 116
      removed outlier: 4.589A  pdb=" N   ASP B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 160 through 177
      removed outlier: 3.601A  pdb=" N   GLN B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP B 166 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG B 177 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 192
      removed outlier: 4.293A  pdb=" N   VAL B 191 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLU B 192 " --> pdb=" O   LEU B 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 187 through 192'
    Processing helix  chain 'B' and resid 211 through 219
    Processing helix  chain 'B' and resid 264 through 270
    Processing helix  chain 'B' and resid 270 through 275
      removed outlier: 3.843A  pdb=" N   GLU B 274 " --> pdb=" O   GLN B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.718A  pdb=" N   GLU B 296 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 51
      removed outlier: 4.015A  pdb=" N   SER C  45 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 74
      removed outlier: 3.723A  pdb=" N   ARG C  73 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG C  74 " --> pdb=" O   PRO C  70 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 69 through 74'
    Processing helix  chain 'C' and resid 90 through 103
      removed outlier: 3.684A  pdb=" N   THR C  94 " --> pdb=" O   SER C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 114
      removed outlier: 3.894A  pdb=" N   GLU C 111 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU C 113 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 129
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 160 through 177
      removed outlier: 3.566A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 4.164A  pdb=" N   ALA C 193 " --> pdb=" O   GLY C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 219
    Processing helix  chain 'C' and resid 233 through 241
      removed outlier: 3.510A  pdb=" N   ARG C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
      removed outlier: 3.574A  pdb=" N   LEU C 268 " --> pdb=" O   LYS C 264 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ARG C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLN C 270 " --> pdb=" O   VAL C 266 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU C 271 " --> pdb=" O   LEU C 267 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLY C 273 " --> pdb=" O   ARG C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 298
      removed outlier: 3.542A  pdb=" N   LEU C 290 " --> pdb=" O   SER C 286 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU C 296 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 3.588A  pdb=" N   ILE D   7 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.516A  pdb=" N   ILE D  24 " --> pdb=" O   TRP D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.513A  pdb=" N   ILE D  55 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU D  58 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
      removed outlier: 3.540A  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: 3.731A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 4.113A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.564A  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: 3.584A  pdb=" N   THR D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.596A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 201
      removed outlier: 3.548A  pdb=" N   SER D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 215
    Processing helix  chain 'D' and resid 216 through 226
      removed outlier: 3.546A  pdb=" N   ASN D 225 " --> pdb=" O   TYR D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 236 through 244
      removed outlier: 3.764A  pdb=" N   LEU D 241 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 272
      removed outlier: 3.696A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
      removed outlier: 3.651A  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: 3.560A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.515A  pdb=" N   ILE E  24 " --> pdb=" O   TRP E  20 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.530A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   MET E  66 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
      removed outlier: 3.534A  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
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.808A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.197A  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: 3.827A  pdb=" N   LEU E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   TRP E 141 " --> pdb=" O   GLY E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.792A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 199
    Processing helix  chain 'E' and resid 211 through 215
    Processing helix  chain 'E' and resid 216 through 224
      removed outlier: 3.725A  pdb=" N   ILE E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 4.066A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
      removed outlier: 3.549A  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: 8.081A  pdb=" N   ARG A  44 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   TRP A  45 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53
      removed outlier: 3.637A  pdb=" N   GLN A  73 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ILE A 199 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A 266 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.517A  pdb=" N   GLY A 131 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   LEU A 252 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   TYR A 228 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ASN A 254 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ILE A 251 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   TYR A 291 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   MET A 253 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLN A 332 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91
      removed outlier: 6.578A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.452A  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: 7.577A  pdb=" N   SER A 322 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE A 298 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 11
      removed outlier: 5.740A  pdb=" N   VAL B   9 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.626A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ASP B 153 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   LEU B  79 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LEU B 150 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   CYS B 184 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU B 152 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 248
      removed outlier: 3.535A  pdb=" N   ALA B 259 " --> pdb=" O   VAL B 223 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG B 224 " --> pdb=" O   HIS B 283 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 24
      removed outlier: 5.592A  pdb=" N   LEU C  22 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLN C  59 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79
      removed outlier: 6.931A  pdb=" N   LEU C 150 " --> pdb=" O   ILE C 182 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   CYS C 184 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 6.505A  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: 6.198A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA C 198 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   VAL C 209 " --> pdb=" O   ALA C 198 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   ILE C 200 " --> pdb=" O   GLN C 207 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 254 through 255
      removed outlier: 3.590A  pdb=" N   ILE C 255 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 254 through 255
      removed outlier: 3.590A  pdb=" N   ILE C 255 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1359 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: 1.64

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3678
        1.34 -     1.46: 1830
        1.46 -     1.57: 6297
        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  1.597 -0.072 2.10e-02 2.27e+03 1.16e+01
  bond pdb=" CB  THR E 218 "
       pdb=" CG2 THR E 218 "
    ideal  model  delta    sigma   weight residual
    1.521  1.440  0.081 3.30e-02 9.18e+02 6.07e+00
  bond pdb=" CA  ILE E  51 "
       pdb=" CB  ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.540  1.600 -0.060 2.70e-02 1.37e+03 4.98e+00
  bond pdb=" C   LEU C 188 "
       pdb=" N   PRO C 189 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.77e+00
  bond pdb=" C   ILE E  51 "
       pdb=" N   PRO E  52 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.026 1.25e-02 6.40e+03 4.35e+00
  ... (remaining 11866 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.65: 15854
        3.65 -     7.30: 229
        7.30 -    10.95: 29
       10.95 -    14.61: 2
       14.61 -    18.26: 2
  Bond angle restraints: 16116
  Sorted by residual:
  angle pdb=" CA  LEU A  35 "
        pdb=" CB  LEU A  35 "
        pdb=" CG  LEU A  35 "
      ideal   model   delta    sigma   weight residual
     116.30  134.56  -18.26 3.50e+00 8.16e-02 2.72e+01
  angle pdb=" CA  THR A 188 "
        pdb=" CB  THR A 188 "
        pdb=" CG2 THR A 188 "
      ideal   model   delta    sigma   weight residual
     110.50  119.05   -8.55 1.70e+00 3.46e-01 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  130.57   -9.03 1.91e+00 2.74e-01 2.24e+01
  angle pdb=" CA  LEU E 112 "
        pdb=" CB  LEU E 112 "
        pdb=" CG  LEU E 112 "
      ideal   model   delta    sigma   weight residual
     116.30  132.30  -16.00 3.50e+00 8.16e-02 2.09e+01
  angle pdb=" C   ARG A 181 "
        pdb=" N   ASP A 182 "
        pdb=" CA  ASP A 182 "
      ideal   model   delta    sigma   weight residual
     121.54  130.21   -8.67 1.91e+00 2.74e-01 2.06e+01
  ... (remaining 16111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 6161
       16.82 -    33.63: 678
       33.63 -    50.45: 160
       50.45 -    67.26: 15
       67.26 -    84.07: 7
  Dihedral angle restraints: 7021
    sinusoidal: 2752
      harmonic: 4269
  Sorted by residual:
  dihedral pdb=" CA  VAL C  83 "
           pdb=" C   VAL C  83 "
           pdb=" N   THR C  84 "
           pdb=" CA  THR C  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.81   26.19     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  TRP C 240 "
           pdb=" C   TRP C 240 "
           pdb=" N   THR C 241 "
           pdb=" CA  THR C 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.56   23.44     0      5.00e+00 4.00e-02 2.20e+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 -157.42  -22.58     0      5.00e+00 4.00e-02 2.04e+01
  ... (remaining 7018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1690
       0.103 -    0.205: 149
       0.205 -    0.308: 17
       0.308 -    0.410: 2
       0.410 -    0.513: 3
  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   -2.12   -0.51 2.00e-01 2.50e+01 6.57e+00
  chirality pdb=" CB  ILE B 230 "
            pdb=" CA  ILE B 230 "
            pdb=" CG1 ILE B 230 "
            pdb=" CG2 ILE B 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CB  VAL C 260 "
            pdb=" CA  VAL C 260 "
            pdb=" CG1 VAL C 260 "
            pdb=" CG2 VAL C 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.21   -0.42 2.00e-01 2.50e+01 4.33e+00
  ... (remaining 1858 not shown)

  Planarity restraints: 2063
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 376 "   -0.022 2.00e-02 2.50e+03   4.31e-02 1.86e+01
        pdb=" C   VAL A 376 "    0.075 2.00e-02 2.50e+03
        pdb=" O   VAL A 376 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ASP A 377 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  30 "   -0.017 2.00e-02 2.50e+03   3.30e-02 1.09e+01
        pdb=" C   VAL D  30 "    0.057 2.00e-02 2.50e+03
        pdb=" O   VAL D  30 "   -0.021 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=" CA  ASP A 182 "    0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   ASP A 182 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASP A 182 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLY A 183 "    0.019 2.00e-02 2.50e+03
  ... (remaining 2060 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 102
        2.54 -     3.13: 7694
        3.13 -     3.72: 18541
        3.72 -     4.31: 26273
        4.31 -     4.90: 42946
  Nonbonded interactions: 95556
  Sorted by model distance:
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     1.946 2.170
  nonbonded pdb=" OD1 ASP A 359 "
            pdb="MG    MG A 501 "
     model   vdw
     2.018 2.170
  nonbonded pdb=" OD1 ASP A 363 "
            pdb="MG    MG A 501 "
     model   vdw
     2.184 2.170
  nonbonded pdb=" OD1 ASN A 361 "
            pdb="MG    MG A 501 "
     model   vdw
     2.292 2.170
  nonbonded pdb=" O   SER B  90 "
            pdb=" OG1 THR B  94 "
     model   vdw
     2.340 3.040
  ... (remaining 95551 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 2 through 299)
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through  \ 
274))
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.900
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
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   0.083  11871  Z= 0.271
  Angle     :  1.086  18.258  16116  Z= 0.570
  Chirality :  0.065   0.513   1861
  Planarity :  0.007   0.075   2063
  Dihedral  : 14.559  84.075   4299
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.78 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.64 (0.15), residues: 1498
  helix: -4.51 (0.08), residues: 639
  sheet: -3.63 (0.26), residues: 215
  loop : -2.70 (0.21), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 360 
 TYR   0.017   0.002   TYR A  52 
 PHE   0.015   0.002   PHE E  64 
 TRP   0.031   0.002   TRP C 240 
 HIS   0.009   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 (11871)
  covalent geometry    : angle       1.08588 (16116)
  hydrogen bonds       : bond        0.31494 (  483)
  hydrogen bonds       : angle      11.12987 ( 1359)

*********************** 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
  175 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8903 (mpp) cc_final: 0.8479 (mpp)
REVERT: A  231 MET cc_start: 0.9149 (mtt) cc_final: 0.8858 (mtt)
REVERT: A  256 ILE cc_start: 0.9218 (pt) cc_final: 0.8941 (pt)
REVERT: A  420 MET cc_start: 0.8848 (mmm) cc_final: 0.8646 (mmm)
REVERT: B   61 LYS cc_start: 0.8778 (mttp) cc_final: 0.8436 (mmmt)
REVERT: C   86 TYR cc_start: 0.8963 (m-80) cc_final: 0.8665 (m-10)
REVERT: C  287 LEU cc_start: 0.9380 (tp) cc_final: 0.8968 (tp)
REVERT: D   75 TYR cc_start: 0.9156 (p90) cc_final: 0.8910 (p90)
REVERT: D  139 LEU cc_start: 0.9176 (tp) cc_final: 0.8955 (tp)
REVERT: D  169 ASN cc_start: 0.8875 (p0) cc_final: 0.8326 (p0)
REVERT: D  219 ASP cc_start: 0.9034 (m-30) cc_final: 0.8745 (m-30)
REVERT: E    3 GLN cc_start: 0.8347 (mt0) cc_final: 0.8090 (mt0)
REVERT: E   82 ASP cc_start: 0.9165 (t0) cc_final: 0.8953 (t0)
REVERT: E  118 ILE cc_start: 0.8456 (mm) cc_final: 0.8175 (tt)
REVERT: E  171 LYS cc_start: 0.9232 (tttt) cc_final: 0.9016 (tttt)
REVERT: E  211 TRP cc_start: 0.8527 (m100) cc_final: 0.8163 (m-10)
REVERT: E  219 ASP cc_start: 0.8061 (m-30) cc_final: 0.7737 (m-30)
REVERT: E  221 TYR cc_start: 0.9022 (t80) cc_final: 0.8516 (t80)
  outliers start: 13
  outliers final: 7
  residues processed: 174
  average time/residue: 0.1268
  time to fit residues: 29.9123
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  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain E residue  112 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 122 ASN
A 123 ASN
A 141 GLN
A 145 ASN
A 160 ASN
A 175 ASN
A 176 HIS
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 417 HIS
B  11 GLN
B  20 HIS
B 176 GLN
B 283 HIS
C   2 ASN
C  75 GLN
C 135 GLN
C 214 GLN
C 283 HIS
D   6 ASN
D 205 ASN
D 225 ASN
E 108 HIS
E 225 ASN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.064578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.051959 restraints weight = 45938.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.053765 restraints weight = 20813.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.054982 restraints weight = 12594.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.055787 restraints weight = 9004.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056190 restraints weight = 7115.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2158

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= 0.120
  Angle     :  0.612   9.423  16116  Z= 0.312
  Chirality :  0.043   0.267   1861
  Planarity :  0.005   0.044   2063
  Dihedral  :  5.246  24.189   1651
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.44 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.51 (0.19), residues: 1498
  helix: -1.97 (0.16), residues: 659
  sheet: -3.19 (0.29), residues: 204
  loop : -2.25 (0.23), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 117 
 TYR   0.017   0.001   TYR E 268 
 PHE   0.012   0.001   PHE D  64 
 TRP   0.014   0.001   TRP C 240 
 HIS   0.003   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (11871)
  covalent geometry    : angle       0.61152 (16116)
  hydrogen bonds       : bond        0.03690 (  483)
  hydrogen bonds       : angle       5.02426 ( 1359)

*********************** 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
  150 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8639 (mpp) cc_final: 0.8203 (mpp)
REVERT: A  231 MET cc_start: 0.9129 (mtt) cc_final: 0.8693 (mtt)
REVERT: A  233 SER cc_start: 0.8970 (m) cc_final: 0.8328 (t)
REVERT: A  297 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.7748 (p)
REVERT: A  400 TRP cc_start: 0.8490 (t60) cc_final: 0.8234 (t60)
REVERT: B   61 LYS cc_start: 0.8829 (mttp) cc_final: 0.8549 (mmmt)
REVERT: C   78 TYR cc_start: 0.8672 (t80) cc_final: 0.8399 (t80)
REVERT: C  287 LEU cc_start: 0.9422 (tp) cc_final: 0.8987 (tp)
REVERT: D  117 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8701 (tt)
REVERT: D  135 GLU cc_start: 0.7171 (tp30) cc_final: 0.6915 (tp30)
REVERT: D  171 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8763 (ttmm)
REVERT: D  219 ASP cc_start: 0.9012 (m-30) cc_final: 0.8683 (m-30)
REVERT: E    3 GLN cc_start: 0.8343 (mt0) cc_final: 0.7958 (mt0)
REVERT: E   20 TRP cc_start: 0.8457 (m100) cc_final: 0.7875 (m-10)
REVERT: E   82 ASP cc_start: 0.9104 (t0) cc_final: 0.8880 (t0)
REVERT: E   95 LEU cc_start: 0.9090 (mt) cc_final: 0.8855 (mt)
REVERT: E  221 TYR cc_start: 0.9055 (t80) cc_final: 0.8741 (t80)
  outliers start: 23
  outliers final: 11
  residues processed: 147
  average time/residue: 0.0971
  time to fit residues: 21.3808
Evaluate side-chains
  116 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  203 LYS
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  283 HIS
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain E residue  100 ILE
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:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   chunk 135 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.063757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.050765 restraints weight = 46938.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.052542 restraints weight = 21698.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.053767 restraints weight = 13315.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.054550 restraints weight = 9545.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.055059 restraints weight = 7619.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2599

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= 0.149
  Angle     :  0.596  10.103  16116  Z= 0.298
  Chirality :  0.043   0.246   1861
  Planarity :  0.004   0.043   2063
  Dihedral  :  4.892  26.711   1645
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.58 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.21), residues: 1498
  helix: -0.35 (0.20), residues: 658
  sheet: -2.80 (0.31), residues: 208
  loop : -2.03 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 225 
 TYR   0.015   0.001   TYR B  86 
 PHE   0.010   0.001   PHE E 157 
 TRP   0.015   0.001   TRP C 240 
 HIS   0.013   0.001   HIS C 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11871)
  covalent geometry    : angle       0.59638 (16116)
  hydrogen bonds       : bond        0.03273 (  483)
  hydrogen bonds       : angle       4.38143 ( 1359)

*********************** 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
  139 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8681 (mpp) cc_final: 0.8241 (mpp)
REVERT: A  390 MET cc_start: 0.8537 (tpp) cc_final: 0.8229 (tpp)
REVERT: A  400 TRP cc_start: 0.8645 (t60) cc_final: 0.8294 (t60)
REVERT: A  420 MET cc_start: 0.8700 (mmm) cc_final: 0.8304 (tpp)
REVERT: B   61 LYS cc_start: 0.8815 (mttp) cc_final: 0.8533 (mmmt)
REVERT: C   78 TYR cc_start: 0.8727 (t80) cc_final: 0.8400 (t80)
REVERT: C  287 LEU cc_start: 0.9431 (tp) cc_final: 0.8981 (tp)
REVERT: D  117 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8646 (tt)
REVERT: D  171 LYS cc_start: 0.9003 (ttpp) cc_final: 0.8697 (ttmt)
REVERT: D  219 ASP cc_start: 0.8998 (m-30) cc_final: 0.8692 (m-30)
REVERT: E   20 TRP cc_start: 0.8530 (m100) cc_final: 0.7927 (m-10)
REVERT: E   83 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8688 (mt-10)
REVERT: E  219 ASP cc_start: 0.8601 (m-30) cc_final: 0.7992 (m-30)
REVERT: E  221 TYR cc_start: 0.9154 (t80) cc_final: 0.8846 (t80)
  outliers start: 27
  outliers final: 16
  residues processed: 136
  average time/residue: 0.0970
  time to fit residues: 19.4110
Evaluate side-chains
  116 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  224 ILE
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:    0.1980
   chunk 144 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 28 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 135 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 270 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.064246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.051377 restraints weight = 46895.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.053175 restraints weight = 21657.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.054421 restraints weight = 13203.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.055196 restraints weight = 9449.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.055743 restraints weight = 7545.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2837

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= 0.116
  Angle     :  0.567  10.173  16116  Z= 0.281
  Chirality :  0.042   0.220   1861
  Planarity :  0.003   0.040   2063
  Dihedral  :  4.644  25.315   1645
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.30 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.22), residues: 1498
  helix:  0.33 (0.21), residues: 668
  sheet: -2.64 (0.32), residues: 209
  loop : -1.83 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 225 
 TYR   0.017   0.001   TYR E 268 
 PHE   0.009   0.001   PHE D  64 
 TRP   0.012   0.001   TRP C 240 
 HIS   0.003   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11871)
  covalent geometry    : angle       0.56744 (16116)
  hydrogen bonds       : bond        0.02963 (  483)
  hydrogen bonds       : angle       4.10126 ( 1359)

*********************** 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
  143 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8673 (mpp) cc_final: 0.8177 (mpp)
REVERT: A  233 SER cc_start: 0.8802 (m) cc_final: 0.8060 (t)
REVERT: A  420 MET cc_start: 0.8765 (mmm) cc_final: 0.8345 (tpp)
REVERT: B   34 LEU cc_start: 0.9530 (tt) cc_final: 0.9327 (tt)
REVERT: B   61 LYS cc_start: 0.8834 (mttp) cc_final: 0.8557 (mmmt)
REVERT: B   86 TYR cc_start: 0.8791 (m-80) cc_final: 0.8507 (m-80)
REVERT: B  183 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9261 (mm)
REVERT: C   78 TYR cc_start: 0.8794 (t80) cc_final: 0.8459 (t80)
REVERT: C  287 LEU cc_start: 0.9439 (tp) cc_final: 0.8981 (tp)
REVERT: D   63 THR cc_start: 0.9376 (m) cc_final: 0.9044 (m)
REVERT: D  117 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8691 (tt)
REVERT: D  171 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8781 (ttmm)
REVERT: D  219 ASP cc_start: 0.8992 (m-30) cc_final: 0.8600 (m-30)
REVERT: E   10 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8684 (tttp)
REVERT: E   20 TRP cc_start: 0.8562 (m100) cc_final: 0.7968 (m-10)
REVERT: E   83 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8617 (mt-10)
REVERT: E  147 MET cc_start: 0.8274 (mpp) cc_final: 0.8004 (mmt)
REVERT: E  171 LYS cc_start: 0.9073 (tttt) cc_final: 0.8814 (tttm)
REVERT: E  219 ASP cc_start: 0.8593 (m-30) cc_final: 0.8045 (m-30)
REVERT: E  221 TYR cc_start: 0.9143 (t80) cc_final: 0.8883 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 138
  average time/residue: 0.0901
  time to fit residues: 18.9231
Evaluate side-chains
  123 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain E residue   10 LYS
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  224 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 139 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 126 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 71 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0970
   chunk 54 optimal weight:    0.7980
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
** 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   7 GLN
C 245 HIS
E   6 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.062869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.050120 restraints weight = 46894.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.051864 restraints weight = 21921.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.053059 restraints weight = 13527.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.053817 restraints weight = 9796.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.054356 restraints weight = 7843.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11871  Z= 0.163
  Angle     :  0.589   9.779  16116  Z= 0.293
  Chirality :  0.043   0.234   1861
  Planarity :  0.003   0.039   2063
  Dihedral  :  4.632  26.532   1645
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.79 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.22), residues: 1498
  helix:  0.74 (0.21), residues: 668
  sheet: -2.22 (0.36), residues: 192
  loop : -1.89 (0.24), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 225 
 TYR   0.022   0.001   TYR D 268 
 PHE   0.017   0.001   PHE D  64 
 TRP   0.016   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (11871)
  covalent geometry    : angle       0.58892 (16116)
  hydrogen bonds       : bond        0.03028 (  483)
  hydrogen bonds       : angle       4.06007 ( 1359)

*********************** 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
  136 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6879 (mmt) cc_final: 0.6666 (mmt)
REVERT: A  125 MET cc_start: 0.8730 (mpp) cc_final: 0.8226 (mpp)
REVERT: A  233 SER cc_start: 0.8756 (m) cc_final: 0.8013 (t)
REVERT: A  238 VAL cc_start: 0.9627 (OUTLIER) cc_final: 0.9416 (t)
REVERT: A  420 MET cc_start: 0.8811 (mmm) cc_final: 0.8395 (tpp)
REVERT: B   61 LYS cc_start: 0.8812 (mttp) cc_final: 0.8587 (mmmt)
REVERT: B  183 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9345 (mm)
REVERT: B  271 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7776 (tp)
REVERT: C   78 TYR cc_start: 0.8867 (t80) cc_final: 0.8632 (t80)
REVERT: D  117 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8760 (tt)
REVERT: D  219 ASP cc_start: 0.8963 (m-30) cc_final: 0.8742 (m-30)
REVERT: E   20 TRP cc_start: 0.8597 (m100) cc_final: 0.8071 (m-10)
REVERT: E   76 ASP cc_start: 0.8784 (p0) cc_final: 0.8563 (p0)
REVERT: E   83 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8834 (mt-10)
REVERT: E  171 LYS cc_start: 0.9138 (tttt) cc_final: 0.8924 (tttm)
REVERT: E  221 TYR cc_start: 0.9172 (t80) cc_final: 0.8967 (t80)
  outliers start: 35
  outliers final: 21
  residues processed: 132
  average time/residue: 0.1039
  time to fit residues: 20.2688
Evaluate side-chains
  120 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  192 GLU
Chi-restraints excluded: chain B residue  203 LYS
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  224 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 132 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 143 optimal weight:    9.9990
   chunk 107 optimal weight:    3.9990
   chunk 93 optimal weight:    7.9990
   chunk 97 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 207 GLN
C  97 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.061374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.048776 restraints weight = 47458.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.050488 restraints weight = 22065.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.051639 restraints weight = 13632.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.052404 restraints weight = 9883.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.052804 restraints weight = 7919.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11871  Z= 0.221
  Angle     :  0.652  11.326  16116  Z= 0.320
  Chirality :  0.044   0.165   1861
  Planarity :  0.004   0.039   2063
  Dihedral  :  4.788  28.712   1645
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.20 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.22), residues: 1498
  helix:  0.76 (0.21), residues: 673
  sheet: -2.14 (0.37), residues: 189
  loop : -1.88 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 225 
 TYR   0.018   0.001   TYR E 268 
 PHE   0.017   0.001   PHE D  64 
 TRP   0.014   0.001   TRP C 240 
 HIS   0.005   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (11871)
  covalent geometry    : angle       0.65239 (16116)
  hydrogen bonds       : bond        0.03215 (  483)
  hydrogen bonds       : angle       4.13561 ( 1359)

*********************** 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
  135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8809 (mpp) cc_final: 0.8265 (mpp)
REVERT: A  233 SER cc_start: 0.8777 (m) cc_final: 0.7985 (t)
REVERT: A  238 VAL cc_start: 0.9625 (OUTLIER) cc_final: 0.9407 (t)
REVERT: A  420 MET cc_start: 0.8850 (mmm) cc_final: 0.8498 (tpp)
REVERT: B   61 LYS cc_start: 0.8799 (mttp) cc_final: 0.8575 (mmmt)
REVERT: B  183 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9281 (mm)
REVERT: B  271 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7797 (tp)
REVERT: C   78 TYR cc_start: 0.8936 (t80) cc_final: 0.8727 (t80)
REVERT: C  223 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8842 (p)
REVERT: D  117 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8784 (tt)
REVERT: D  268 TYR cc_start: 0.8739 (t80) cc_final: 0.8535 (t80)
REVERT: E   20 TRP cc_start: 0.8612 (m100) cc_final: 0.8135 (m-10)
REVERT: E   83 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8788 (mt-10)
REVERT: E   88 MET cc_start: 0.8808 (tpp) cc_final: 0.8572 (tpt)
  outliers start: 43
  outliers final: 26
  residues processed: 130
  average time/residue: 0.0837
  time to fit residues: 16.8264
Evaluate side-chains
  119 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  192 GLU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  218 THR
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 116 optimal weight:    4.9990
   chunk 142 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 93 optimal weight:   20.0000
   chunk 5 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.062027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.049462 restraints weight = 47079.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.051182 restraints weight = 22024.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.052296 restraints weight = 13558.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.053102 restraints weight = 9861.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.053565 restraints weight = 7866.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11871  Z= 0.173
  Angle     :  0.616  10.750  16116  Z= 0.302
  Chirality :  0.043   0.154   1861
  Planarity :  0.003   0.038   2063
  Dihedral  :  4.657  28.043   1644
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.02 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.23), residues: 1498
  helix:  0.98 (0.21), residues: 672
  sheet: -2.20 (0.36), residues: 199
  loop : -1.71 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 225 
 TYR   0.009   0.001   TYR E 221 
 PHE   0.013   0.001   PHE D  64 
 TRP   0.011   0.001   TRP C 240 
 HIS   0.004   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (11871)
  covalent geometry    : angle       0.61598 (16116)
  hydrogen bonds       : bond        0.03050 (  483)
  hydrogen bonds       : angle       4.02581 ( 1359)

*********************** 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
  133 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 95
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8826 (mpp) cc_final: 0.8250 (mpp)
REVERT: A  233 SER cc_start: 0.8824 (m) cc_final: 0.8104 (t)
REVERT: A  420 MET cc_start: 0.8850 (mmm) cc_final: 0.8491 (tpp)
REVERT: B   61 LYS cc_start: 0.8803 (mttp) cc_final: 0.8597 (mmmt)
REVERT: B  183 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9260 (mm)
REVERT: B  271 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7836 (tp)
REVERT: D  117 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8781 (tt)
REVERT: E   11 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8437 (mt-10)
REVERT: E   20 TRP cc_start: 0.8596 (m100) cc_final: 0.8101 (m-10)
REVERT: E   76 ASP cc_start: 0.8755 (p0) cc_final: 0.8516 (p0)
REVERT: E   83 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8813 (mt-10)
REVERT: E   88 MET cc_start: 0.8840 (tpp) cc_final: 0.8552 (tpt)
REVERT: E  171 LYS cc_start: 0.9112 (tttt) cc_final: 0.8866 (tttm)
  outliers start: 38
  outliers final: 26
  residues processed: 125
  average time/residue: 0.0870
  time to fit residues: 17.1770
Evaluate side-chains
  120 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  192 GLU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  218 THR
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 121 optimal weight:    0.9980
   chunk 73 optimal weight:    0.2980
   chunk 123 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.061991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.049539 restraints weight = 47047.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.051253 restraints weight = 21511.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.052447 restraints weight = 13110.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.053240 restraints weight = 9386.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.053724 restraints weight = 7426.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11871  Z= 0.118
  Angle     :  0.587  10.687  16116  Z= 0.287
  Chirality :  0.042   0.155   1861
  Planarity :  0.003   0.037   2063
  Dihedral  :  4.442  26.044   1643
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.02 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.23), residues: 1498
  helix:  1.18 (0.21), residues: 672
  sheet: -2.09 (0.37), residues: 198
  loop : -1.71 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 225 
 TYR   0.019   0.001   TYR D 268 
 PHE   0.010   0.001   PHE E 157 
 TRP   0.012   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (11871)
  covalent geometry    : angle       0.58686 (16116)
  hydrogen bonds       : bond        0.02874 (  483)
  hydrogen bonds       : angle       3.86007 ( 1359)

*********************** 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
  137 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ARG cc_start: 0.8681 (ttm170) cc_final: 0.8408 (ttm-80)
REVERT: A  125 MET cc_start: 0.8828 (mpp) cc_final: 0.8270 (mpp)
REVERT: A  207 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7392 (t70)
REVERT: A  233 SER cc_start: 0.8939 (m) cc_final: 0.8244 (t)
REVERT: A  420 MET cc_start: 0.8860 (mmm) cc_final: 0.8505 (tpp)
REVERT: B   30 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8345 (mt-10)
REVERT: B   61 LYS cc_start: 0.8812 (mttp) cc_final: 0.8526 (mmmt)
REVERT: B  183 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9189 (mm)
REVERT: B  271 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7860 (tp)
REVERT: C  224 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8616 (tmm-80)
REVERT: E   11 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8271 (mt-10)
REVERT: E   20 TRP cc_start: 0.8550 (m100) cc_final: 0.7993 (m-10)
REVERT: E   64 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8496 (m-80)
REVERT: E   76 ASP cc_start: 0.8726 (p0) cc_final: 0.8478 (p0)
REVERT: E   83 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8850 (mt-10)
REVERT: E  219 ASP cc_start: 0.8582 (m-30) cc_final: 0.8060 (m-30)
REVERT: E  221 TYR cc_start: 0.9165 (t80) cc_final: 0.8868 (t80)
  outliers start: 34
  outliers final: 21
  residues processed: 130
  average time/residue: 0.1005
  time to fit residues: 19.5680
Evaluate side-chains
  122 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  207 HIS
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain D residue  218 THR
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 126 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 139 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.060586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.048127 restraints weight = 46790.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.049811 restraints weight = 22079.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.050968 restraints weight = 13711.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.051647 restraints weight = 9975.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.052178 restraints weight = 8074.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11871  Z= 0.198
  Angle     :  0.658  10.622  16116  Z= 0.321
  Chirality :  0.044   0.181   1861
  Planarity :  0.004   0.036   2063
  Dihedral  :  4.597  27.750   1643
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.26 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.23), residues: 1498
  helix:  1.12 (0.21), residues: 674
  sheet: -2.07 (0.36), residues: 204
  loop : -1.68 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 145 
 TYR   0.021   0.001   TYR D 221 
 PHE   0.014   0.001   PHE D  64 
 TRP   0.016   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (11871)
  covalent geometry    : angle       0.65834 (16116)
  hydrogen bonds       : bond        0.03174 (  483)
  hydrogen bonds       : angle       4.00717 ( 1359)

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

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 93
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ARG cc_start: 0.8645 (ttm170) cc_final: 0.8290 (ttm-80)
REVERT: A  125 MET cc_start: 0.8823 (mpp) cc_final: 0.8299 (mpp)
REVERT: A  207 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7586 (t70)
REVERT: A  231 MET cc_start: 0.8910 (ptp) cc_final: 0.8525 (ptp)
REVERT: A  233 SER cc_start: 0.8961 (m) cc_final: 0.8207 (t)
REVERT: A  420 MET cc_start: 0.8858 (mmm) cc_final: 0.8501 (tpp)
REVERT: B   61 LYS cc_start: 0.8801 (mttp) cc_final: 0.8563 (mmmt)
REVERT: B  183 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9221 (mm)
REVERT: B  271 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7827 (tp)
REVERT: D  131 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8479 (m)
REVERT: E   20 TRP cc_start: 0.8594 (m100) cc_final: 0.8091 (m-10)
REVERT: E   64 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8646 (m-80)
REVERT: E   83 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8788 (mt-10)
REVERT: E  219 ASP cc_start: 0.8534 (m-30) cc_final: 0.8031 (m-30)
REVERT: E  221 TYR cc_start: 0.9181 (t80) cc_final: 0.8897 (t80)
  outliers start: 35
  outliers final: 25
  residues processed: 121
  average time/residue: 0.0903
  time to fit residues: 16.7563
Evaluate side-chains
  120 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  207 HIS
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  218 THR
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 118 optimal weight:    0.0470
   chunk 73 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 127 optimal weight:   10.0000
   chunk 98 optimal weight:    0.1980
   chunk 86 optimal weight:    0.9980
   chunk 139 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 147 optimal weight:    0.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**
C  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.062845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.050186 restraints weight = 46836.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.051965 restraints weight = 21469.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.053138 restraints weight = 13138.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.053954 restraints weight = 9455.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.054446 restraints weight = 7503.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11871  Z= 0.108
  Angle     :  0.608  11.165  16116  Z= 0.294
  Chirality :  0.043   0.170   1861
  Planarity :  0.003   0.037   2063
  Dihedral  :  4.414  25.734   1643
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.83 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.23), residues: 1498
  helix:  1.30 (0.22), residues: 672
  sheet: -1.78 (0.39), residues: 183
  loop : -1.72 (0.25), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E   9 
 TYR   0.018   0.001   TYR E 268 
 PHE   0.009   0.001   PHE E 146 
 TRP   0.018   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (11871)
  covalent geometry    : angle       0.60777 (16116)
  hydrogen bonds       : bond        0.02838 (  483)
  hydrogen bonds       : angle       3.77910 ( 1359)

********************** 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
  133 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8311 (ttm-80)
REVERT: A  125 MET cc_start: 0.8825 (mpp) cc_final: 0.8259 (mpp)
REVERT: A  207 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7360 (t70)
REVERT: A  233 SER cc_start: 0.8802 (m) cc_final: 0.8098 (t)
REVERT: A  390 MET cc_start: 0.8539 (tpp) cc_final: 0.8314 (mmm)
REVERT: A  420 MET cc_start: 0.8827 (mmm) cc_final: 0.8514 (tpp)
REVERT: B   30 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8214 (mt-10)
REVERT: B   61 LYS cc_start: 0.8817 (mttp) cc_final: 0.8530 (mmmt)
REVERT: B  183 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9176 (mm)
REVERT: B  271 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7831 (tp)
REVERT: C  224 ARG cc_start: 0.8884 (tmm-80) cc_final: 0.8506 (tmm-80)
REVERT: D  131 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8498 (m)
REVERT: E   20 TRP cc_start: 0.8499 (m100) cc_final: 0.7916 (m-10)
REVERT: E   64 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8396 (m-80)
REVERT: E   83 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8779 (mt-10)
REVERT: E  219 ASP cc_start: 0.8566 (m-30) cc_final: 0.8034 (m-30)
REVERT: E  221 TYR cc_start: 0.9155 (t80) cc_final: 0.8802 (t80)
  outliers start: 27
  outliers final: 21
  residues processed: 129
  average time/residue: 0.0915
  time to fit residues: 17.9324
Evaluate side-chains
  123 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  207 HIS
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  218 THR
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 140 optimal weight:    6.9990
   chunk 47 optimal weight:    0.2980
   chunk 112 optimal weight:    0.6980
   chunk 94 optimal weight:    8.9990
   chunk 117 optimal weight:    0.0670
   chunk 142 optimal weight:    1.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.062406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.049939 restraints weight = 47188.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.051692 restraints weight = 21762.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.052887 restraints weight = 13296.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.053629 restraints weight = 9500.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.054190 restraints weight = 7591.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11871  Z= 0.131
  Angle     :  0.616  10.813  16116  Z= 0.299
  Chirality :  0.043   0.209   1861
  Planarity :  0.003   0.035   2063
  Dihedral  :  4.429  26.079   1643
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.16 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.23), residues: 1498
  helix:  1.33 (0.21), residues: 672
  sheet: -1.75 (0.40), residues: 182
  loop : -1.67 (0.25), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E   9 
 TYR   0.023   0.001   TYR B 291 
 PHE   0.010   0.001   PHE E 157 
 TRP   0.017   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11871)
  covalent geometry    : angle       0.61590 (16116)
  hydrogen bonds       : bond        0.02908 (  483)
  hydrogen bonds       : angle       3.81066 ( 1359)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1720.68 seconds
wall clock time: 30 minutes 36.71 seconds (1836.71 seconds total)