Starting phenix.real_space_refine
on Wed Mar  4 10:22:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7osh_13051/03_2026/7osh_13051.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7osh_13051/03_2026/7osh_13051.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7osh_13051/03_2026/7osh_13051.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7osh_13051/03_2026/7osh_13051.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7osh_13051/03_2026/7osh_13051.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7osh_13051/03_2026/7osh_13051.cif"
  }
  resolution = 3.8
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     Cu      1      5.60       5
     Mg      1      5.21       5
     S      45      5.16       5
     C    8200      2.51       5
     N    2249      2.21       5
     O    2329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12826
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3077
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 16, 'TRANS': 375}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2375
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 12, 'TRANS': 295}
    Chain: "C"
      Number of atoms: 2367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2367
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 12, 'TRANS': 294}
    Chain: "D"
      Number of atoms: 2015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2015
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 8, 'TRANS': 258}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1896
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 8, 'TRANS': 239}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1092
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CU': 1, ' MG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  11839  SG  CYS H  45      45.430  43.120  48.151  1.00133.21           S
  ATOM  11862  SG  CYS H  48      43.343  44.213  45.789  1.00130.17           S
  ATOM  12043  SG  CYS H  72      46.172  45.161  44.243  1.00137.89           S

  Time building chain proxies: 3.07, per 1000 atoms: 0.24
  Number of scatterers: 12826
  At special positions: 0
  Unit cell: (80.352, 92.016, 193.104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     Cu      1     28.99
     S      45     16.00
     Mg      1     11.99
     O    2329      8.00
     N    2249      7.00
     C    8200      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 638.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN H 201 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H  48 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H  72 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H  45 "


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

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 13 sheets defined
      44.6% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.535A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   TRP A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 3.507A  pdb=" N   MET A 390 " --> pdb=" O   ARG A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 405
      removed outlier: 3.645A  pdb=" N   TRP A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 50
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 90 through 102
      removed outlier: 3.851A  pdb=" N   ARG B 100 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU B 101 " --> pdb=" O   HIS B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 116
    Processing helix  chain 'B' and resid 130 through 141
      removed outlier: 3.595A  pdb=" N   GLN B 135 " --> pdb=" O   LYS B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 178
      removed outlier: 3.743A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 219
    Processing helix  chain 'B' and resid 233 through 244
      removed outlier: 4.406A  pdb=" N   ARG B 239 " --> pdb=" O   SER B 235 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ASP B 242 " --> pdb=" O   GLN B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 273
      removed outlier: 4.013A  pdb=" N   LEU B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.624A  pdb=" N   TYR B 293 " --> pdb=" O   ASP B 289 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 51
      removed outlier: 3.519A  pdb=" N   MET C  46 " --> pdb=" O   LYS C  42 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU C  50 " --> pdb=" O   MET C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 74
    Processing helix  chain 'C' and resid 90 through 103
    Processing helix  chain 'C' and resid 107 through 114
      removed outlier: 3.881A  pdb=" N   GLU C 111 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 129
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 160 through 177
      removed outlier: 3.616A  pdb=" N   GLN C 165 " --> pdb=" O   PRO C 161 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 218
    Processing helix  chain 'C' and resid 234 through 239
      removed outlier: 3.828A  pdb=" N   GLN C 238 " --> pdb=" O   ASP C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 273
      removed outlier: 3.644A  pdb=" N   LEU C 267 " --> pdb=" O   HIS C 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 299
      removed outlier: 3.568A  pdb=" N   ALA C 298 " --> pdb=" O   TYR C 294 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 4.155A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.524A  pdb=" N   GLY D  34 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA D  36 " --> pdb=" O   ALA D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.658A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
    Processing helix  chain 'D' and resid 78 through 83
    Processing helix  chain 'D' and resid 85 through 91
      removed outlier: 3.784A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU D  90 " --> pdb=" O   THR D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 4.108A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY D 119 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE D 127 " --> pdb=" O   ALA D 123 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 167
      removed outlier: 3.519A  pdb=" N   SER D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.869A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 200
      removed outlier: 3.620A  pdb=" N   SER D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 215
    Processing helix  chain 'D' and resid 216 through 226
    Processing helix  chain 'D' and resid 236 through 244
      removed outlier: 3.993A  pdb=" N   LEU D 241 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA D 243 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 273
      removed outlier: 3.637A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE D 260 " --> pdb=" O   LEU D 256 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG D 273 " --> pdb=" O   ALA D 269 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
    Processing helix  chain 'E' and resid 7 through 16
      removed outlier: 3.756A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.644A  pdb=" N   ILE E  24 " --> pdb=" O   TRP E  20 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.648A  pdb=" N   ALA E  56 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   MET E  66 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
    Processing helix  chain 'E' and resid 78 through 84
    Processing helix  chain 'E' and resid 85 through 91
      removed outlier: 3.586A  pdb=" N   LEU E  89 " --> pdb=" O   GLY E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.549A  pdb=" N   LEU E 101 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.092A  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: 3.787A  pdb=" N   LEU E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   TRP E 141 " --> pdb=" O   GLY E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
      removed outlier: 3.501A  pdb=" N   PHE E 157 " --> pdb=" O   LEU E 153 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL E 168 " --> pdb=" O   LEU E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.535A  pdb=" N   ALA E 175 " --> pdb=" O   LYS E 171 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY E 180 " --> pdb=" O   GLY E 176 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 200
    Processing helix  chain 'E' and resid 207 through 213
      removed outlier: 4.044A  pdb=" N   TRP E 211 " --> pdb=" O   GLU E 207 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 216 through 224
      removed outlier: 3.516A  pdb=" N   ILE E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 4.233A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TRP E 253 " --> pdb=" O   ALA E 249 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER E 263 " --> pdb=" O   TRP E 259 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 51 through 55
      removed outlier: 3.803A  pdb=" N   ASP H  54 " --> pdb=" O   ILE H  51 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 73 through 82
    Processing helix  chain 'H' and resid 139 through 150
    Processing helix  chain 'H' and resid 160 through 172
      removed outlier: 3.681A  pdb=" N   GLN H 165 " --> pdb=" O   GLN H 161 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU H 166 " --> pdb=" O   ALA H 162 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40
      removed outlier: 7.937A  pdb=" N   ARG A  44 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53
      removed outlier: 3.797A  pdb=" N   GLN A  73 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ILE A 199 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   THR A 221 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.526A  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: 6.591A  pdb=" N   GLY A 131 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE A 251 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   TYR A 291 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   MET A 253 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 6.797A  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: 6.653A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   VAL A 142 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217
      removed outlier: 6.332A  pdb=" N   LEU A 216 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   SER A 322 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ILE A 298 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 25
      removed outlier: 5.368A  pdb=" N   HIS B  20 " --> pdb=" O   GLN B  11 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLN B  11 " --> pdb=" O   HIS B  20 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   LEU B  24 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   GLN B   7 " --> pdb=" O   LEU B  24 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN B  59 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.703A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   ASP B 153 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU B  79 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   LEU B 150 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   CYS B 184 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU B 152 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL B  31 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   ALA B 199 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   GLY B  33 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 251
      removed outlier: 6.692A  pdb=" N   SER B 254 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 26
      removed outlier: 3.791A  pdb=" N   VAL C   4 " --> pdb=" O   LEU C  26 " (cutoff:3.500A)
      removed outlier: 3.604A  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: 6.782A  pdb=" N   LEU C 150 " --> pdb=" O   ILE C 182 " (cutoff:3.500A)
      removed outlier: 8.193A  pdb=" N   CYS C 184 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU C 152 " --> pdb=" O   CYS C 184 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   PHE C  35 " --> pdb=" O   LEU C 201 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 228
      removed outlier: 3.676A  pdb=" N   SER C 254 " --> pdb=" O   LEU C 250 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70
    Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 121
      removed outlier: 3.523A  pdb=" N   VAL H 121 " --> pdb=" O   ARG H 152 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG H 152 " --> pdb=" O   VAL H 121 " (cutoff:3.500A)

    524 hydrogen bonds defined for protein.
    1491 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: 2.13

  Time building geometry restraints manager: 1.30 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: 4182
        1.34 -     1.46: 2340
        1.46 -     1.57: 6466
        1.57 -     1.69: 2
        1.69 -     1.81: 77
  Bond restraints: 13067
  Sorted by residual:
  bond pdb=" CA  ILE E  51 "
       pdb=" C   ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.525  1.586 -0.061 2.10e-02 2.27e+03 8.35e+00
  bond pdb=" CG1 ILE B 181 "
       pdb=" CD1 ILE B 181 "
    ideal  model  delta    sigma   weight residual
    1.513  1.416  0.097 3.90e-02 6.57e+02 6.24e+00
  bond pdb=" CB  VAL A 202 "
       pdb=" CG1 VAL A 202 "
    ideal  model  delta    sigma   weight residual
    1.521  1.445  0.076 3.30e-02 9.18e+02 5.34e+00
  bond pdb=" CB  GLN A 232 "
       pdb=" CG  GLN A 232 "
    ideal  model  delta    sigma   weight residual
    1.520  1.453  0.067 3.00e-02 1.11e+03 4.99e+00
  bond pdb=" CB  TYR A 291 "
       pdb=" CG  TYR A 291 "
    ideal  model  delta    sigma   weight residual
    1.512  1.465  0.047 2.20e-02 2.07e+03 4.61e+00
  ... (remaining 13062 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 17443
        3.47 -     6.94: 241
        6.94 -    10.41: 35
       10.41 -    13.88: 5
       13.88 -    17.34: 2
  Bond angle restraints: 17726
  Sorted by residual:
  angle pdb=" CA  LEU A 356 "
        pdb=" CB  LEU A 356 "
        pdb=" CG  LEU A 356 "
      ideal   model   delta    sigma   weight residual
     116.30  133.64  -17.34 3.50e+00 8.16e-02 2.46e+01
  angle pdb=" C   GLU H  64 "
        pdb=" N   LYS H  65 "
        pdb=" CA  LYS H  65 "
      ideal   model   delta    sigma   weight residual
     125.02  133.63   -8.61 1.76e+00 3.23e-01 2.39e+01
  angle pdb=" C   GLU B  81 "
        pdb=" N   ASN B  82 "
        pdb=" CA  ASN B  82 "
      ideal   model   delta    sigma   weight residual
     122.07  128.93   -6.86 1.43e+00 4.89e-01 2.30e+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  130.59   -9.05 1.91e+00 2.74e-01 2.24e+01
  angle pdb=" C   GLU H 138 "
        pdb=" N   GLU H 139 "
        pdb=" CA  GLU H 139 "
      ideal   model   delta    sigma   weight residual
     121.54  130.50   -8.96 1.91e+00 2.74e-01 2.20e+01
  ... (remaining 17721 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 6835
       16.98 -    33.97: 714
       33.97 -    50.95: 162
       50.95 -    67.93: 18
       67.93 -    84.92: 7
  Dihedral angle restraints: 7736
    sinusoidal: 3041
      harmonic: 4695
  Sorted by residual:
  dihedral pdb=" CA  ASP H 108 "
           pdb=" C   ASP H 108 "
           pdb=" N   GLY H 109 "
           pdb=" CA  GLY H 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.88   31.12     0      5.00e+00 4.00e-02 3.88e+01
  dihedral pdb=" CA  ARG C 233 "
           pdb=" C   ARG C 233 "
           pdb=" N   ASP C 234 "
           pdb=" CA  ASP C 234 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.70  -29.30     0      5.00e+00 4.00e-02 3.43e+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 -157.01  -22.99     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 7733 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1704
       0.082 -    0.164: 277
       0.164 -    0.245: 41
       0.245 -    0.327: 5
       0.327 -    0.409: 3
  Chirality restraints: 2030
  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   -2.22   -0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" CB  VAL A 202 "
            pdb=" CA  VAL A 202 "
            pdb=" CG1 VAL A 202 "
            pdb=" CG2 VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CA  ASN C 261 "
            pdb=" N   ASN C 261 "
            pdb=" C   ASN C 261 "
            pdb=" CB  ASN C 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 2027 not shown)

  Planarity restraints: 2276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 209 "   -0.064 5.00e-02 4.00e+02   9.64e-02 1.49e+01
        pdb=" N   PRO E 210 "    0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO E 210 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO E 210 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  66 "    0.050 5.00e-02 4.00e+02   7.48e-02 8.96e+00
        pdb=" N   PRO D  67 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E  66 "   -0.049 5.00e-02 4.00e+02   7.29e-02 8.51e+00
        pdb=" N   PRO E  67 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO E  67 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO E  67 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 2273 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 120
        2.56 -     3.14: 9266
        3.14 -     3.73: 20139
        3.73 -     4.31: 28354
        4.31 -     4.90: 46659
  Nonbonded interactions: 104538
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU H  76 "
            pdb="ZN    ZN H 201 "
     model   vdw
     1.971 2.230
  nonbonded pdb=" NE2 HIS A 207 "
            pdb="CU    CU A 502 "
     model   vdw
     2.002 2.320
  nonbonded pdb=" SD  MET H  50 "
            pdb="CU    CU A 502 "
     model   vdw
     2.113 2.600
  nonbonded pdb=" OD1 ASP A 359 "
            pdb="MG    MG A 501 "
     model   vdw
     2.129 2.170
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.157 2.170
  ... (remaining 104533 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 2 through 308)
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through  \ 
274))
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:             0.020
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.140
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
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      :  0.008   0.097  13070  Z= 0.376
  Angle     :  1.089  17.345  17726  Z= 0.575
  Chirality :  0.065   0.409   2030
  Planarity :  0.007   0.096   2276
  Dihedral  : 14.372  84.915   4740
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 10.05 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -5.50 (0.14), residues: 1645
  helix: -4.39 (0.08), residues: 697
  sheet: -2.98 (0.29), residues: 235
  loop : -2.90 (0.19), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 378 
 TYR   0.014   0.002   TYR C  13 
 PHE   0.018   0.003   PHE D 157 
 TRP   0.031   0.003   TRP E 211 
 HIS   0.013   0.002   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00839 (13067)
  covalent geometry    : angle       1.08863 (17726)
  hydrogen bonds       : bond        0.29413 (  524)
  hydrogen bonds       : angle      10.58048 ( 1491)
  metal coordination   : bond        0.05108 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8644 (mtt) cc_final: 0.8102 (mpp)
REVERT: A  235 LYS cc_start: 0.9403 (mmtt) cc_final: 0.9166 (mmmm)
REVERT: B   47 LYS cc_start: 0.9295 (mttm) cc_final: 0.8987 (mtpp)
REVERT: B  133 MET cc_start: 0.9101 (ttm) cc_final: 0.8872 (mtm)
REVERT: C   37 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6290 (t-90)
REVERT: C   61 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8658 (mmmm)
REVERT: C   86 TYR cc_start: 0.8995 (m-80) cc_final: 0.8697 (m-10)
REVERT: C  181 ILE cc_start: 0.9376 (mt) cc_final: 0.9144 (mm)
REVERT: C  283 HIS cc_start: 0.7721 (m90) cc_final: 0.7275 (m90)
REVERT: C  304 GLN cc_start: 0.8583 (mp10) cc_final: 0.8208 (pt0)
REVERT: D  132 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7426 (pm20)
REVERT: E    3 GLN cc_start: 0.8501 (mt0) cc_final: 0.7910 (mt0)
REVERT: E   10 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8800 (tmtt)
REVERT: H   65 LYS cc_start: 0.8715 (pttm) cc_final: 0.7839 (pttt)
REVERT: H   77 MET cc_start: 0.9564 (ttp) cc_final: 0.9337 (ttm)
REVERT: H   87 ARG cc_start: 0.9178 (mmm160) cc_final: 0.8893 (mmm160)
REVERT: H   90 ASP cc_start: 0.8695 (t0) cc_final: 0.8067 (p0)
REVERT: H   92 LYS cc_start: 0.9377 (tttp) cc_final: 0.9037 (ttmm)
REVERT: H   98 MET cc_start: 0.8958 (mmm) cc_final: 0.8662 (mmm)
REVERT: H  155 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8692 (mmm-85)
  outliers start: 8
  outliers final: 1
  residues processed: 147
  average time/residue: 0.1647
  time to fit residues: 32.2970
Evaluate side-chains
  94 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   37 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:   10.0000
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 179 ASN
A 190 ASN
A 212 ASN
A 241 ASN
A 301 ASN
A 324 ASN
B  20 HIS
B  37 HIS
B  38 ASN
B 176 GLN
C  25 ASN
C 194 HIS
C 238 GLN
C 270 GLN
D 225 ASN
E 108 HIS
E 205 ASN
E 225 ASN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.054298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.043890 restraints weight = 53759.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.045587 restraints weight = 26063.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.046730 restraints weight = 16210.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.047437 restraints weight = 11778.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.047996 restraints weight = 9486.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13070  Z= 0.129
  Angle     :  0.600  10.159  17726  Z= 0.310
  Chirality :  0.042   0.168   2030
  Planarity :  0.005   0.058   2276
  Dihedral  :  5.137  35.583   1806
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.73 %
    Favored  : 86.00 %
  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: -3.37 (0.18), residues: 1645
  helix: -1.82 (0.16), residues: 714
  sheet: -2.69 (0.30), residues: 233
  loop : -2.36 (0.21), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 248 
 TYR   0.011   0.001   TYR B  86 
 PHE   0.011   0.001   PHE D 157 
 TRP   0.011   0.001   TRP D 253 
 HIS   0.003   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (13067)
  covalent geometry    : angle       0.60015 (17726)
  hydrogen bonds       : bond        0.03483 (  524)
  hydrogen bonds       : angle       4.98584 ( 1491)
  metal coordination   : bond        0.00227 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7154 (mtt) cc_final: 0.6791 (mpp)
REVERT: A  125 MET cc_start: 0.8507 (mtt) cc_final: 0.8238 (mpp)
REVERT: A  420 MET cc_start: 0.8782 (mmm) cc_final: 0.8303 (mmm)
REVERT: B   46 MET cc_start: 0.9349 (mmp) cc_final: 0.9131 (mmt)
REVERT: C   37 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6593 (t-90)
REVERT: C   61 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8823 (mmmm)
REVERT: C  181 ILE cc_start: 0.9276 (mt) cc_final: 0.9042 (mm)
REVERT: C  283 HIS cc_start: 0.7462 (m90) cc_final: 0.7093 (m90)
REVERT: D   88 MET cc_start: 0.8266 (tpp) cc_final: 0.8040 (tpp)
REVERT: E    3 GLN cc_start: 0.8551 (mt0) cc_final: 0.8066 (mt0)
REVERT: H   65 LYS cc_start: 0.8448 (pttm) cc_final: 0.7577 (pttt)
REVERT: H   87 ARG cc_start: 0.9063 (mmm160) cc_final: 0.8844 (mmm160)
REVERT: H   90 ASP cc_start: 0.8507 (t0) cc_final: 0.7845 (p0)
REVERT: H  155 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8463 (tpp80)
  outliers start: 17
  outliers final: 5
  residues processed: 131
  average time/residue: 0.1075
  time to fit residues: 20.8015
Evaluate side-chains
  96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   63 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 157 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 132 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 95 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9990
   chunk 134 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0170
   chunk 86 optimal weight:    6.9990
   chunk 144 optimal weight:    4.9990
   overall best weight:    0.9624

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
B  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.055026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.044601 restraints weight = 54090.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.046330 restraints weight = 25803.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.047503 restraints weight = 15948.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.048213 restraints weight = 11514.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.048752 restraints weight = 9255.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13070  Z= 0.107
  Angle     :  0.556  10.116  17726  Z= 0.279
  Chirality :  0.042   0.164   2030
  Planarity :  0.004   0.049   2276
  Dihedral  :  4.708  33.645   1806
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.26 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.20), residues: 1645
  helix: -0.21 (0.19), residues: 714
  sheet: -2.39 (0.30), residues: 258
  loop : -2.07 (0.22), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  66 
 TYR   0.014   0.001   TYR H 118 
 PHE   0.010   0.001   PHE D 157 
 TRP   0.007   0.001   TRP E 211 
 HIS   0.004   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (13067)
  covalent geometry    : angle       0.55605 (17726)
  hydrogen bonds       : bond        0.02889 (  524)
  hydrogen bonds       : angle       4.35905 ( 1491)
  metal coordination   : bond        0.00164 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7251 (mtt) cc_final: 0.6783 (mpp)
REVERT: A  125 MET cc_start: 0.8531 (mtt) cc_final: 0.8320 (mpp)
REVERT: A  214 ASN cc_start: 0.7921 (t0) cc_final: 0.7587 (t0)
REVERT: A  305 LYS cc_start: 0.8903 (pttt) cc_final: 0.8592 (pttp)
REVERT: A  420 MET cc_start: 0.8750 (mmm) cc_final: 0.8475 (mmm)
REVERT: B  133 MET cc_start: 0.8636 (mtp) cc_final: 0.8365 (mtp)
REVERT: C   37 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.6610 (t-90)
REVERT: C   61 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8874 (mmmm)
REVERT: C  181 ILE cc_start: 0.9335 (mt) cc_final: 0.9121 (mm)
REVERT: C  283 HIS cc_start: 0.7348 (m90) cc_final: 0.7064 (m90)
REVERT: E    3 GLN cc_start: 0.8490 (mt0) cc_final: 0.8055 (mt0)
REVERT: H   51 ILE cc_start: 0.9490 (mm) cc_final: 0.9254 (mm)
REVERT: H   64 GLU cc_start: 0.7889 (tt0) cc_final: 0.7469 (tp30)
REVERT: H   90 ASP cc_start: 0.8457 (t0) cc_final: 0.7587 (p0)
REVERT: H  155 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8381 (mmm-85)
  outliers start: 14
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1134
  time to fit residues: 20.1804
Evaluate side-chains
  105 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain H residue   54 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0060
   chunk 13 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 119 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   chunk 99 optimal weight:    5.9990
   chunk 143 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 148 optimal weight:    7.9990
   overall best weight:    4.2004

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
B  11 GLN
B  38 ASN
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 283 HIS
H 172 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.052018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.041555 restraints weight = 55057.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.043153 restraints weight = 27296.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.044234 restraints weight = 17400.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.044969 restraints weight = 12839.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.045270 restraints weight = 10399.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  13070  Z= 0.262
  Angle     :  0.668   8.236  17726  Z= 0.335
  Chirality :  0.044   0.155   2030
  Planarity :  0.004   0.041   2276
  Dihedral  :  4.864  36.397   1806
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.16 %
    Favored  : 81.31 %
  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: -1.47 (0.21), residues: 1645
  helix:  0.50 (0.20), residues: 721
  sheet: -2.40 (0.30), residues: 253
  loop : -1.99 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  17 
 TYR   0.018   0.002   TYR B  86 
 PHE   0.019   0.002   PHE D 157 
 TRP   0.013   0.001   TRP E 211 
 HIS   0.011   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 (13067)
  covalent geometry    : angle       0.66781 (17726)
  hydrogen bonds       : bond        0.03253 (  524)
  hydrogen bonds       : angle       4.44402 ( 1491)
  metal coordination   : bond        0.00327 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 91
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8669 (mtt) cc_final: 0.8368 (mpp)
REVERT: A  214 ASN cc_start: 0.8189 (t0) cc_final: 0.7944 (t0)
REVERT: A  420 MET cc_start: 0.8751 (mmm) cc_final: 0.8307 (mmm)
REVERT: C   61 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8817 (mmmm)
REVERT: C  283 HIS cc_start: 0.7799 (m-70) cc_final: 0.7534 (m90)
REVERT: E    3 GLN cc_start: 0.8667 (mt0) cc_final: 0.8163 (mt0)
REVERT: E   64 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8510 (t80)
REVERT: H   64 GLU cc_start: 0.8021 (tt0) cc_final: 0.7577 (tt0)
REVERT: H   90 ASP cc_start: 0.8507 (t0) cc_final: 0.7716 (p0)
REVERT: H  148 MET cc_start: 0.9092 (ptm) cc_final: 0.8715 (mtm)
  outliers start: 34
  outliers final: 17
  residues processed: 116
  average time/residue: 0.1144
  time to fit residues: 19.6768
Evaluate side-chains
  104 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain B residue   38 ASN
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  164 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain H residue   50 MET
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  126 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 151 optimal weight:    0.5980
   chunk 92 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 161 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   chunk 128 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
A 341 GLN
B  38 ASN
C  97 HIS
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.054158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.043695 restraints weight = 54435.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.045403 restraints weight = 26488.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.046545 restraints weight = 16540.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.047309 restraints weight = 12067.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.047810 restraints weight = 9644.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13070  Z= 0.101
  Angle     :  0.550   9.297  17726  Z= 0.277
  Chirality :  0.042   0.162   2030
  Planarity :  0.003   0.040   2276
  Dihedral  :  4.539  34.693   1806
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.13 %
    Favored  : 81.16 %
  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: -0.95 (0.21), residues: 1645
  helix:  1.05 (0.21), residues: 718
  sheet: -2.20 (0.29), residues: 273
  loop : -1.81 (0.24), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  66 
 TYR   0.015   0.001   TYR B  86 
 PHE   0.010   0.001   PHE D 157 
 TRP   0.007   0.001   TRP A  98 
 HIS   0.005   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (13067)
  covalent geometry    : angle       0.55014 (17726)
  hydrogen bonds       : bond        0.02557 (  524)
  hydrogen bonds       : angle       4.01566 ( 1491)
  metal coordination   : bond        0.00050 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7301 (mtt) cc_final: 0.6837 (mpp)
REVERT: A  125 MET cc_start: 0.8504 (mtt) cc_final: 0.8057 (mpp)
REVERT: A  214 ASN cc_start: 0.7941 (t0) cc_final: 0.7694 (t0)
REVERT: A  336 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8642 (m)
REVERT: A  420 MET cc_start: 0.8705 (mmm) cc_final: 0.8315 (mmm)
REVERT: C   61 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8956 (mmtm)
REVERT: C  181 ILE cc_start: 0.9292 (mt) cc_final: 0.8987 (mm)
REVERT: C  283 HIS cc_start: 0.7747 (m-70) cc_final: 0.7400 (m90)
REVERT: D   11 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8106 (mm-30)
REVERT: D  147 MET cc_start: 0.8655 (mtm) cc_final: 0.8190 (mpp)
REVERT: E    3 GLN cc_start: 0.8614 (mt0) cc_final: 0.8086 (mt0)
REVERT: E   64 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8540 (t80)
REVERT: H   51 ILE cc_start: 0.9563 (mm) cc_final: 0.9314 (mm)
REVERT: H   64 GLU cc_start: 0.8029 (tt0) cc_final: 0.7771 (tt0)
REVERT: H   87 ARG cc_start: 0.9142 (mmm160) cc_final: 0.8819 (mmm160)
REVERT: H   90 ASP cc_start: 0.8464 (t0) cc_final: 0.7693 (p0)
REVERT: H  148 MET cc_start: 0.8974 (ptm) cc_final: 0.8640 (mtm)
  outliers start: 23
  outliers final: 12
  residues processed: 120
  average time/residue: 0.0978
  time to fit residues: 18.0411
Evaluate side-chains
  106 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain H residue   63 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 129 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 145 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  96 HIS ** 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 = 0.3066 r_free = 0.3066 target = 0.052295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.041884 restraints weight = 54488.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.043500 restraints weight = 27025.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.044579 restraints weight = 17166.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.045258 restraints weight = 12640.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.045751 restraints weight = 10280.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13070  Z= 0.204
  Angle     :  0.610   8.503  17726  Z= 0.305
  Chirality :  0.043   0.180   2030
  Planarity :  0.003   0.035   2276
  Dihedral  :  4.654  37.813   1806
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.27 %
    Favored  : 80.42 %
  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: -0.77 (0.22), residues: 1645
  helix:  1.26 (0.21), residues: 723
  sheet: -2.23 (0.31), residues: 258
  loop : -1.79 (0.24), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  66 
 TYR   0.010   0.001   TYR H 118 
 PHE   0.016   0.001   PHE D 157 
 TRP   0.012   0.001   TRP E 211 
 HIS   0.006   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (13067)
  covalent geometry    : angle       0.61024 (17726)
  hydrogen bonds       : bond        0.02909 (  524)
  hydrogen bonds       : angle       4.17347 ( 1491)
  metal coordination   : bond        0.00221 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8640 (mtt) cc_final: 0.8100 (mpp)
REVERT: A  214 ASN cc_start: 0.8194 (t0) cc_final: 0.7954 (t0)
REVERT: A  231 MET cc_start: 0.7869 (mtm) cc_final: 0.7646 (mtm)
REVERT: A  420 MET cc_start: 0.8708 (mmm) cc_final: 0.8304 (mmm)
REVERT: B   86 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8632 (m-80)
REVERT: C   61 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8916 (mmtm)
REVERT: C  181 ILE cc_start: 0.9329 (mt) cc_final: 0.9089 (mm)
REVERT: C  283 HIS cc_start: 0.7785 (m-70) cc_final: 0.7440 (m90)
REVERT: D  147 MET cc_start: 0.8709 (mtm) cc_final: 0.8381 (mpp)
REVERT: E    3 GLN cc_start: 0.8628 (mt0) cc_final: 0.8104 (mt0)
REVERT: E   64 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8408 (t80)
REVERT: E   81 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7978 (mm-30)
REVERT: H   51 ILE cc_start: 0.9577 (mm) cc_final: 0.9299 (mm)
REVERT: H   90 ASP cc_start: 0.8483 (t0) cc_final: 0.7669 (p0)
  outliers start: 31
  outliers final: 21
  residues processed: 114
  average time/residue: 0.0999
  time to fit residues: 17.4431
Evaluate side-chains
  105 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   38 ASN
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  164 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain H residue   50 MET
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  110 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 135 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 115 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 77 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.053012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.042562 restraints weight = 54239.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.044198 restraints weight = 26735.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.045293 restraints weight = 16943.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.045983 restraints weight = 12465.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.046504 restraints weight = 10137.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13070  Z= 0.152
  Angle     :  0.576   8.866  17726  Z= 0.288
  Chirality :  0.042   0.154   2030
  Planarity :  0.003   0.035   2276
  Dihedral  :  4.426  19.693   1804
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.87 %
    Favored  : 80.04 %
  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: -0.58 (0.22), residues: 1645
  helix:  1.46 (0.21), residues: 724
  sheet: -2.19 (0.31), residues: 260
  loop : -1.71 (0.24), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG H  66 
 TYR   0.012   0.001   TYR B  13 
 PHE   0.013   0.001   PHE D 157 
 TRP   0.007   0.001   TRP E 211 
 HIS   0.007   0.001   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (13067)
  covalent geometry    : angle       0.57607 (17726)
  hydrogen bonds       : bond        0.02664 (  524)
  hydrogen bonds       : angle       4.02206 ( 1491)
  metal coordination   : bond        0.00110 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8556 (mtt) cc_final: 0.7990 (mpp)
REVERT: A  214 ASN cc_start: 0.8129 (t0) cc_final: 0.7889 (t0)
REVERT: A  231 MET cc_start: 0.7875 (mtm) cc_final: 0.7565 (mtm)
REVERT: A  420 MET cc_start: 0.8687 (mmm) cc_final: 0.8297 (mmm)
REVERT: B   86 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8581 (m-80)
REVERT: C   61 LYS cc_start: 0.9173 (mtpt) cc_final: 0.8911 (mmtm)
REVERT: C  181 ILE cc_start: 0.9309 (mt) cc_final: 0.8995 (mm)
REVERT: C  283 HIS cc_start: 0.7801 (m-70) cc_final: 0.7417 (m90)
REVERT: E    3 GLN cc_start: 0.8594 (mt0) cc_final: 0.8075 (mt0)
REVERT: E   64 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8401 (t80)
REVERT: H   51 ILE cc_start: 0.9567 (mm) cc_final: 0.9283 (mm)
REVERT: H   87 ARG cc_start: 0.9097 (mmm160) cc_final: 0.8677 (mmm160)
REVERT: H   90 ASP cc_start: 0.8435 (t0) cc_final: 0.7591 (p0)
  outliers start: 28
  outliers final: 20
  residues processed: 113
  average time/residue: 0.0916
  time to fit residues: 16.2072
Evaluate side-chains
  108 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   38 ASN
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain H residue   50 MET
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  110 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 124 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 131 optimal weight:    5.9990
   chunk 152 optimal weight:    0.9990
   chunk 67 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.053117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.042686 restraints weight = 54049.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.044305 restraints weight = 26705.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.045403 restraints weight = 17008.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.046147 restraints weight = 12491.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.046614 restraints weight = 10078.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13070  Z= 0.143
  Angle     :  0.578  10.536  17726  Z= 0.288
  Chirality :  0.042   0.197   2030
  Planarity :  0.003   0.035   2276
  Dihedral  :  4.352  18.965   1804
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.17 %
    Favored  : 79.67 %
  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: -0.42 (0.22), residues: 1645
  helix:  1.61 (0.21), residues: 723
  sheet: -2.15 (0.31), residues: 260
  loop : -1.64 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  66 
 TYR   0.012   0.001   TYR B  13 
 PHE   0.013   0.001   PHE D 157 
 TRP   0.008   0.001   TRP E 211 
 HIS   0.005   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (13067)
  covalent geometry    : angle       0.57823 (17726)
  hydrogen bonds       : bond        0.02595 (  524)
  hydrogen bonds       : angle       3.95022 ( 1491)
  metal coordination   : bond        0.00114 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8554 (mtt) cc_final: 0.8008 (mpp)
REVERT: A  214 ASN cc_start: 0.8094 (t0) cc_final: 0.7877 (t0)
REVERT: A  420 MET cc_start: 0.8687 (mmm) cc_final: 0.8296 (mmm)
REVERT: C   61 LYS cc_start: 0.9191 (mtpt) cc_final: 0.8919 (mmtm)
REVERT: C  181 ILE cc_start: 0.9313 (mt) cc_final: 0.9057 (mm)
REVERT: C  283 HIS cc_start: 0.7819 (m-70) cc_final: 0.7422 (m90)
REVERT: E    3 GLN cc_start: 0.8590 (mt0) cc_final: 0.8068 (mt0)
REVERT: E   64 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8370 (t80)
REVERT: H   51 ILE cc_start: 0.9570 (mm) cc_final: 0.9278 (mm)
REVERT: H   87 ARG cc_start: 0.9125 (mmm160) cc_final: 0.8659 (mmm160)
REVERT: H   90 ASP cc_start: 0.8422 (t0) cc_final: 0.7536 (p0)
  outliers start: 29
  outliers final: 22
  residues processed: 115
  average time/residue: 0.1005
  time to fit residues: 17.8464
Evaluate side-chains
  108 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   38 ASN
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain H residue   50 MET
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  110 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 66 optimal weight:   10.0000
   chunk 110 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 151 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 109 optimal weight:    0.9990
   chunk 131 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9980
   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**
B  88 GLN
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.053933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.043385 restraints weight = 54322.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.045061 restraints weight = 26807.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.046172 restraints weight = 16987.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.046917 restraints weight = 12507.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.047374 restraints weight = 10114.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13070  Z= 0.116
  Angle     :  0.569   9.176  17726  Z= 0.282
  Chirality :  0.042   0.180   2030
  Planarity :  0.003   0.035   2276
  Dihedral  :  4.246  18.195   1804
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 18.32 %
    Favored  : 79.97 %
  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: -0.27 (0.22), residues: 1645
  helix:  1.73 (0.21), residues: 722
  sheet: -2.03 (0.31), residues: 265
  loop : -1.55 (0.24), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  66 
 TYR   0.015   0.001   TYR B  86 
 PHE   0.011   0.001   PHE D 157 
 TRP   0.007   0.001   TRP A  98 
 HIS   0.004   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13067)
  covalent geometry    : angle       0.56927 (17726)
  hydrogen bonds       : bond        0.02457 (  524)
  hydrogen bonds       : angle       3.84424 ( 1491)
  metal coordination   : bond        0.00638 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7436 (mtt) cc_final: 0.6707 (mpp)
REVERT: A  125 MET cc_start: 0.8553 (mtt) cc_final: 0.7997 (mpp)
REVERT: A  420 MET cc_start: 0.8636 (mmm) cc_final: 0.8285 (mmm)
REVERT: C   61 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8955 (mmtm)
REVERT: C  181 ILE cc_start: 0.9321 (mt) cc_final: 0.9071 (mm)
REVERT: C  283 HIS cc_start: 0.7786 (m-70) cc_final: 0.7400 (m90)
REVERT: E    3 GLN cc_start: 0.8583 (mt0) cc_final: 0.8069 (mt0)
REVERT: E   64 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8381 (t80)
REVERT: H   51 ILE cc_start: 0.9557 (mm) cc_final: 0.9290 (mm)
REVERT: H   87 ARG cc_start: 0.9126 (mmm160) cc_final: 0.8667 (mmm160)
REVERT: H   90 ASP cc_start: 0.8378 (t0) cc_final: 0.7498 (p0)
  outliers start: 23
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0942
  time to fit residues: 16.3604
Evaluate side-chains
  110 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain H residue   50 MET
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  110 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 156 optimal weight:   10.0000
   chunk 134 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 162 optimal weight:    3.9990
   chunk 158 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 119 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.052301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.041831 restraints weight = 55258.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.043424 restraints weight = 27475.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.044503 restraints weight = 17537.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.045221 restraints weight = 12926.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.045731 restraints weight = 10480.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13070  Z= 0.217
  Angle     :  0.636   9.823  17726  Z= 0.315
  Chirality :  0.044   0.176   2030
  Planarity :  0.003   0.034   2276
  Dihedral  :  4.434  20.863   1804
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.17 %
    Favored  : 79.97 %
  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: -0.30 (0.22), residues: 1645
  helix:  1.67 (0.21), residues: 720
  sheet: -1.97 (0.31), residues: 276
  loop : -1.53 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  66 
 TYR   0.023   0.002   TYR B  86 
 PHE   0.016   0.001   PHE D 157 
 TRP   0.013   0.001   TRP E 211 
 HIS   0.005   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (13067)
  covalent geometry    : angle       0.63570 (17726)
  hydrogen bonds       : bond        0.02841 (  524)
  hydrogen bonds       : angle       4.10057 ( 1491)
  metal coordination   : bond        0.00838 (    3)

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

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8605 (mtt) cc_final: 0.8122 (mpp)
REVERT: A  420 MET cc_start: 0.8679 (mmm) cc_final: 0.8281 (mmm)
REVERT: C   61 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8947 (mmtm)
REVERT: C  181 ILE cc_start: 0.9326 (mt) cc_final: 0.9072 (mm)
REVERT: C  283 HIS cc_start: 0.7852 (m-70) cc_final: 0.7554 (m90)
REVERT: D  147 MET cc_start: 0.8748 (mtm) cc_final: 0.8389 (mpp)
REVERT: E   64 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8363 (t80)
REVERT: H   51 ILE cc_start: 0.9569 (mm) cc_final: 0.9267 (mm)
REVERT: H   90 ASP cc_start: 0.8570 (t0) cc_final: 0.7546 (p0)
  outliers start: 25
  outliers final: 21
  residues processed: 107
  average time/residue: 0.1025
  time to fit residues: 17.0492
Evaluate side-chains
  103 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain H residue   50 MET
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  110 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 161 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   chunk 131 optimal weight:    7.9990
   chunk 95 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0970
   chunk 137 optimal weight:   10.0000
   chunk 151 optimal weight:    0.0570
   chunk 91 optimal weight:    3.9990
   chunk 142 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    3.2302

-------------------------------------------------------------------------------
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**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.052229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.041776 restraints weight = 54857.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.043391 restraints weight = 27285.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.044434 restraints weight = 17384.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.045196 restraints weight = 12808.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.045656 restraints weight = 10327.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13070  Z= 0.205
  Angle     :  0.628   9.236  17726  Z= 0.313
  Chirality :  0.043   0.164   2030
  Planarity :  0.003   0.035   2276
  Dihedral  :  4.492  21.128   1804
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.09 %
    Favored  : 79.90 %
  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: -0.28 (0.22), residues: 1645
  helix:  1.69 (0.21), residues: 719
  sheet: -2.03 (0.31), residues: 278
  loop : -1.48 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  87 
 TYR   0.021   0.001   TYR B  86 
 PHE   0.015   0.001   PHE D 157 
 TRP   0.012   0.001   TRP E 211 
 HIS   0.005   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (13067)
  covalent geometry    : angle       0.62825 (17726)
  hydrogen bonds       : bond        0.02857 (  524)
  hydrogen bonds       : angle       4.10841 ( 1491)
  metal coordination   : bond        0.00761 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1610.79 seconds
wall clock time: 28 minutes 47.23 seconds (1727.23 seconds total)