Starting phenix.real_space_refine
on Tue Nov 18 01:10:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zx1_60536/11_2025/8zx1_60536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zx1_60536/11_2025/8zx1_60536.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zx1_60536/11_2025/8zx1_60536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zx1_60536/11_2025/8zx1_60536.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zx1_60536/11_2025/8zx1_60536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zx1_60536/11_2025/8zx1_60536.map"
  }
  resolution = 3.5
  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=   0.004 sd=   0.044
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: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    6381      2.51       5
     N    1644      2.21       5
     O    1761      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9846
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 360, 2876
          Classifications: {'peptide': 360}
          Link IDs: {'PTRANS': 14, 'TRANS': 345}
    Chain: "B"
      Number of atoms: 2172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2172
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 15, 'TRANS': 257}
    Chain: "C"
      Number of atoms: 1936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1936
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 9, 'TRANS': 239}
    Chain: "D"
      Number of atoms: 2862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2862
          Classifications: {'peptide': 358}
          Link IDs: {'PTRANS': 13, 'TRANS': 344}
  Time building chain proxies: 2.35, per 1000 atoms: 0.24
  Number of scatterers: 9846
  At special positions: 0
  Unit cell: (85.36, 96.03, 132.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1761      8.00
     N    1644      7.00
     C    6381      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: 0.78
  Conformation dependent library (CDL) restraints added in 415.6 milliseconds
  

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2332

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 9 sheets defined
      51.9% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 65
    Processing helix  chain 'A' and resid 105 through 117
      removed outlier: 5.049A  pdb=" N   GLY A 113 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   LEU A 114 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 135
      removed outlier: 3.639A  pdb=" N   ILE A 124 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
      Proline residue:  A 126  - end of helix
      removed outlier: 3.700A  pdb=" N   VAL A 135 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 163
    Processing helix  chain 'A' and resid 179 through 198
      removed outlier: 3.684A  pdb=" N   ASN A 188 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 215
      removed outlier: 3.553A  pdb=" N   ALA A 211 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   MET A 214 " --> pdb=" O   GLU A 210 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER A 215 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 238
      removed outlier: 3.606A  pdb=" N   GLU A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 248
    Processing helix  chain 'A' and resid 295 through 297
      No H-bonds generated for 'chain 'A' and resid 295 through 297'
    Processing helix  chain 'B' and resid 8 through 23
      removed outlier: 4.247A  pdb=" N   ILE B  12 " --> pdb=" O   GLN B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 32
      removed outlier: 3.510A  pdb=" N   MET B  29 " --> pdb=" O   LEU B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 55
      removed outlier: 3.848A  pdb=" N   THR B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ARG B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 50 through 55'
    Processing helix  chain 'B' and resid 58 through 91
      removed outlier: 4.029A  pdb=" N   VAL B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU B  65 " --> pdb=" O   TYR B  61 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET B  71 " --> pdb=" O   HIS B  67 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA B  75 " --> pdb=" O   MET B  71 " (cutoff:3.500A)
      Proline residue:  B  85  - end of helix
    Processing helix  chain 'B' and resid 97 through 104
    Processing helix  chain 'B' and resid 105 through 111
      Proline residue:  B 108  - end of helix
    Processing helix  chain 'B' and resid 112 through 124
      removed outlier: 3.585A  pdb=" N   TYR B 118 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B 122 " --> pdb=" O   TYR B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 137
    Processing helix  chain 'B' and resid 149 through 162
      removed outlier: 3.526A  pdb=" N   VAL B 153 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 175
      removed outlier: 3.556A  pdb=" N   VAL B 166 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   MET B 167 " --> pdb=" O   PRO B 163 " (cutoff:3.500A)
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 177 through 188
      removed outlier: 3.513A  pdb=" N   LEU B 181 " --> pdb=" O   ASP B 177 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG B 185 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 198
    Processing helix  chain 'B' and resid 198 through 203
    Processing helix  chain 'B' and resid 203 through 219
      removed outlier: 3.580A  pdb=" N   VAL B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      Proline residue:  B 217  - end of helix
    Processing helix  chain 'B' and resid 221 through 229
      removed outlier: 4.495A  pdb=" N   SER B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 246
    Processing helix  chain 'B' and resid 249 through 279
      removed outlier: 3.795A  pdb=" N   THR B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU B 260 " --> pdb=" O   THR B 256 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   VAL B 263 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   MET B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL B 270 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 30
      removed outlier: 3.906A  pdb=" N   PHE C  10 " --> pdb=" O   LEU C   6 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   MET C  11 " --> pdb=" O   ARG C   7 " (cutoff:3.500A)
      Proline residue:  C  21  - end of helix
      removed outlier: 3.693A  pdb=" N   PHE C  30 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 52
      removed outlier: 3.589A  pdb=" N   SER C  48 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 88
    Processing helix  chain 'C' and resid 92 through 105
    Processing helix  chain 'C' and resid 107 through 123
    Processing helix  chain 'C' and resid 127 through 152
      Proline residue:  C 141  - end of helix
    Processing helix  chain 'C' and resid 156 through 165
      removed outlier: 4.263A  pdb=" N   GLU C 160 " --> pdb=" O   VAL C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 176
      removed outlier: 3.854A  pdb=" N   LEU C 173 " --> pdb=" O   GLU C 169 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG C 174 " --> pdb=" O   PHE C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 199
      removed outlier: 3.726A  pdb=" N   LEU C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
      Proline residue:  C 183  - end of helix
      removed outlier: 3.642A  pdb=" N   MET C 197 " --> pdb=" O   PHE C 193 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP C 199 " --> pdb=" O   LEU C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 207
      removed outlier: 3.558A  pdb=" N   THR C 207 " --> pdb=" O   SER C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 225
      removed outlier: 4.188A  pdb=" N   LYS C 223 " --> pdb=" O   TYR C 219 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   VAL C 224 " --> pdb=" O   SER C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 253
      removed outlier: 3.645A  pdb=" N   THR C 235 " --> pdb=" O   ASN C 231 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET C 244 " --> pdb=" O   LEU C 240 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE C 246 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG C 253 " --> pdb=" O   GLN C 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 65
    Processing helix  chain 'D' and resid 105 through 117
      removed outlier: 4.798A  pdb=" N   GLY D 113 " --> pdb=" O   ASN D 109 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   LEU D 114 " --> pdb=" O   VAL D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 135
      removed outlier: 3.907A  pdb=" N   ILE D 124 " --> pdb=" O   PRO D 120 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   THR D 125 " --> pdb=" O   ALA D 121 " (cutoff:3.500A)
      Proline residue:  D 126  - end of helix
      removed outlier: 3.586A  pdb=" N   VAL D 135 " --> pdb=" O   ALA D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 163
    Processing helix  chain 'D' and resid 181 through 198
      removed outlier: 3.776A  pdb=" N   ASN D 188 " --> pdb=" O   LYS D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 215
      removed outlier: 3.632A  pdb=" N   ALA D 211 " --> pdb=" O   ASP D 207 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER D 215 " --> pdb=" O   ALA D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 238
    Processing helix  chain 'D' and resid 243 through 248
    Processing helix  chain 'D' and resid 295 through 297
      No H-bonds generated for 'chain 'D' and resid 295 through 297'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 41
      removed outlier: 6.183A  pdb=" N   VAL A  32 " --> pdb=" O   CYS A  26 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   CYS A  26 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   ARG A  24 " --> pdb=" O   PRO A  34 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   LEU A  36 " --> pdb=" O   GLY A  22 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLY A  22 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   LEU A  20 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   MET A  75 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   GLY A  22 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   ARG A  73 " --> pdb=" O   GLY A  22 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER A  71 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94
      removed outlier: 3.570A  pdb=" N   LEU A 169 " --> pdb=" O   THR A 200 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   PHE A  45 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   VAL A 219 " --> pdb=" O   PHE A  45 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   THR A  47 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   MET A 221 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   LEU A  49 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ILE A 218 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ASP A 229 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL A 220 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 278
      removed outlier: 3.520A  pdb=" N   ALA A 269 " --> pdb=" O   CYS A 276 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE A 278 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ARG A 268 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A 256 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 370 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303
      removed outlier: 3.741A  pdb=" N   ALA A 361 " --> pdb=" O   GLU A 302 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   VAL A 330 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   ARG A 320 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLU A 328 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   TYR A 322 " --> pdb=" O   THR A 326 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   THR A 326 " --> pdb=" O   TYR A 322 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 30 through 40
      removed outlier: 6.744A  pdb=" N   LYS D  25 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   ILE D  23 " --> pdb=" O   PRO D  34 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   LEU D  36 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA D  21 " --> pdb=" O   LEU D  36 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LEU D  38 " --> pdb=" O   GLN D  19 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   GLN D  19 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ILE D  23 " --> pdb=" O   SER D  71 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   SER D  71 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 91 through 94
      removed outlier: 6.572A  pdb=" N   ASN D  92 " --> pdb=" O   LEU D 170 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL D 204 " --> pdb=" O   LEU D 171 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE D  45 " --> pdb=" O   ARG D 217 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   VAL D 219 " --> pdb=" O   PHE D  45 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR D  47 " --> pdb=" O   VAL D 219 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   MET D 221 " --> pdb=" O   THR D  47 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LEU D  49 " --> pdb=" O   MET D 221 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLN D 228 " --> pdb=" O   VAL D 220 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ARG D 222 " --> pdb=" O   ILE D 226 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   ILE D 226 " --> pdb=" O   ARG D 222 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 274 through 279
      removed outlier: 3.860A  pdb=" N   CYS D 276 " --> pdb=" O   ALA D 269 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA D 269 " --> pdb=" O   CYS D 276 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   ARG D 266 " --> pdb=" O   ARG D 261 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   ARG D 261 " --> pdb=" O   ARG D 266 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ARG D 268 " --> pdb=" O   ILE D 259 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL D 370 " --> pdb=" O   LEU D 293 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 299 through 303
    Processing sheet with id=AA9, first strand: chain 'D' and resid 319 through 322
      removed outlier: 4.270A  pdb=" N   GLU D 319 " --> pdb=" O   VAL D 330 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1365 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.23

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2168
        1.33 -     1.45: 2106
        1.45 -     1.58: 5656
        1.58 -     1.70: 0
        1.70 -     1.82: 111
  Bond restraints: 10041
  Sorted by residual:
  bond pdb=" N   PHE D  95 "
       pdb=" CA  PHE D  95 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.037 1.21e-02 6.83e+03 9.17e+00
  bond pdb=" N   VAL D 365 "
       pdb=" CA  VAL D 365 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.20e-02 6.94e+03 8.19e+00
  bond pdb=" N   SER D 367 "
       pdb=" CA  SER D 367 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.32e-02 5.74e+03 6.97e+00
  bond pdb=" N   GLU D 366 "
       pdb=" CA  GLU D 366 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.28e-02 6.10e+03 6.86e+00
  bond pdb=" N   ASP D 351 "
       pdb=" CA  ASP D 351 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.031 1.20e-02 6.94e+03 6.47e+00
  ... (remaining 10036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.94: 13569
        5.94 -    11.89: 41
       11.89 -    17.83: 4
       17.83 -    23.78: 1
       23.78 -    29.72: 1
  Bond angle restraints: 13616
  Sorted by residual:
  angle pdb=" C   ASN D 321 "
        pdb=" CA  ASN D 321 "
        pdb=" CB  ASN D 321 "
      ideal   model   delta    sigma   weight residual
     110.74   81.02   29.72 1.61e+00 3.86e-01 3.41e+02
  angle pdb=" N   TYR D 322 "
        pdb=" CA  TYR D 322 "
        pdb=" CB  TYR D 322 "
      ideal   model   delta    sigma   weight residual
     110.56   91.37   19.19 1.56e+00 4.11e-01 1.51e+02
  angle pdb=" N   TYR D 322 "
        pdb=" CA  TYR D 322 "
        pdb=" C   TYR D 322 "
      ideal   model   delta    sigma   weight residual
     110.42  100.18   10.24 1.55e+00 4.16e-01 4.37e+01
  angle pdb=" N   ASN D 321 "
        pdb=" CA  ASN D 321 "
        pdb=" C   ASN D 321 "
      ideal   model   delta    sigma   weight residual
     108.02   97.40   10.62 1.75e+00 3.27e-01 3.68e+01
  angle pdb=" CB  MET D 116 "
        pdb=" CG  MET D 116 "
        pdb=" SD  MET D 116 "
      ideal   model   delta    sigma   weight residual
     112.70   96.99   15.71 3.00e+00 1.11e-01 2.74e+01
  ... (remaining 13611 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 5442
       17.94 -    35.89: 506
       35.89 -    53.83: 77
       53.83 -    71.77: 17
       71.77 -    89.71: 8
  Dihedral angle restraints: 6050
    sinusoidal: 2450
      harmonic: 3600
  Sorted by residual:
  dihedral pdb=" C   ASN D 321 "
           pdb=" N   ASN D 321 "
           pdb=" CA  ASN D 321 "
           pdb=" CB  ASN D 321 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -83.26  -39.34     0      2.50e+00 1.60e-01 2.48e+02
  dihedral pdb=" N   TYR D 322 "
           pdb=" C   TYR D 322 "
           pdb=" CA  TYR D 322 "
           pdb=" CB  TYR D 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   95.21   27.59     0      2.50e+00 1.60e-01 1.22e+02
  dihedral pdb=" C   TYR D 322 "
           pdb=" N   TYR D 322 "
           pdb=" CA  TYR D 322 "
           pdb=" CB  TYR D 322 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.50  -12.10     0      2.50e+00 1.60e-01 2.34e+01
  ... (remaining 6047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 1540
       0.125 -    0.249: 50
       0.249 -    0.374: 5
       0.374 -    0.499: 0
       0.499 -    0.623: 2
  Chirality restraints: 1597
  Sorted by residual:
  chirality pdb=" CA  TYR D 322 "
            pdb=" N   TYR D 322 "
            pdb=" C   TYR D 322 "
            pdb=" CB  TYR D 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.13   -0.62 2.00e-01 2.50e+01 9.71e+00
  chirality pdb=" CA  ASN D 321 "
            pdb=" N   ASN D 321 "
            pdb=" C   ASN D 321 "
            pdb=" CB  ASN D 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.12   -0.61 2.00e-01 2.50e+01 9.34e+00
  chirality pdb=" CA  PHE B  43 "
            pdb=" N   PHE B  43 "
            pdb=" C   PHE B  43 "
            pdb=" CB  PHE B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.42e+00
  ... (remaining 1594 not shown)

  Planarity restraints: 1723
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 101 "    0.022 2.00e-02 2.50e+03   2.52e-02 1.11e+01
        pdb=" CG  PHE C 101 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 101 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 101 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 101 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 101 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 101 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 110 "   -0.025 2.00e-02 2.50e+03   2.06e-02 1.06e+01
        pdb=" CG  TRP B 110 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 110 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 110 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 110 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 110 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 110 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  33 "   -0.049 5.00e-02 4.00e+02   7.39e-02 8.74e+00
        pdb=" N   PRO D  34 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO D  34 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO D  34 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 1720 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 66
        2.52 -     3.11: 7631
        3.11 -     3.71: 15023
        3.71 -     4.30: 20424
        4.30 -     4.90: 33709
  Nonbonded interactions: 76853
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 105 "
            pdb=" OE1 GLU A 108 "
     model   vdw
     1.921 3.040
  nonbonded pdb=" OG  SER C 227 "
            pdb=" OE1 GLU C 229 "
     model   vdw
     1.973 3.040
  nonbonded pdb=" O   PHE D 344 "
            pdb=" CZ  PHE D 352 "
     model   vdw
     1.985 3.340
  nonbonded pdb=" OD2 ASP C 155 "
            pdb=" NH1 ARG C 157 "
     model   vdw
     2.150 3.120
  nonbonded pdb=" O   PHE D 344 "
            pdb=" CE1 PHE D 352 "
     model   vdw
     2.181 3.340
  ... (remaining 76848 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 'A' and resid 16 through 373)
  selection = chain 'D'
}

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:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.710
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5954
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.083  10041  Z= 0.301
  Angle     :  1.122  29.721  13616  Z= 0.610
  Chirality :  0.063   0.623   1597
  Planarity :  0.006   0.074   1723
  Dihedral  : 13.958  89.713   3718
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  3.69 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.17 %
  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: -0.25 (0.24), residues: 1232
  helix:  0.94 (0.22), residues: 556
  sheet:  0.25 (0.38), residues: 207
  loop : -1.74 (0.26), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.031   0.002   ARG A 143 
 TYR   0.027   0.003   TYR B 118 
 PHE   0.058   0.003   PHE C 101 
 TRP   0.056   0.003   TRP B 110 
 HIS   0.006   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00660 (10041)
  covalent geometry    : angle       1.12218 (13616)
  hydrogen bonds       : bond        0.23787 (  466)
  hydrogen bonds       : angle       6.91471 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 307
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASN cc_start: 0.6382 (m-40) cc_final: 0.6012 (t0)
REVERT: A   93 THR cc_start: 0.6767 (m) cc_final: 0.6427 (p)
REVERT: A  117 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7532 (mm110)
REVERT: A  118 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7794 (mmmt)
REVERT: A  120 PRO cc_start: 0.5406 (Cg_exo) cc_final: 0.5102 (Cg_endo)
REVERT: A  136 GLN cc_start: 0.6005 (mp-120) cc_final: 0.5699 (mp-120)
REVERT: A  207 ASP cc_start: 0.6237 (t0) cc_final: 0.5805 (t70)
REVERT: A  210 GLU cc_start: 0.7127 (tt0) cc_final: 0.6655 (tt0)
REVERT: A  240 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7773 (mtmm)
REVERT: A  252 ASN cc_start: 0.5793 (m-40) cc_final: 0.5341 (m-40)
REVERT: A  319 GLU cc_start: 0.6261 (tp30) cc_final: 0.5506 (mp0)
REVERT: A  340 MET cc_start: 0.5808 (mpp) cc_final: 0.5347 (mpp)
REVERT: A  344 PHE cc_start: 0.6396 (p90) cc_final: 0.5666 (p90)
REVERT: B  170 TYR cc_start: 0.6288 (t80) cc_final: 0.5781 (t80)
REVERT: B  191 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7669 (ttmt)
REVERT: B  219 MET cc_start: 0.6929 (mtp) cc_final: 0.6670 (mtp)
REVERT: C  120 MET cc_start: 0.7243 (tmm) cc_final: 0.7009 (tmm)
REVERT: C  126 LEU cc_start: 0.7175 (mm) cc_final: 0.6932 (mm)
REVERT: C  238 LEU cc_start: 0.5780 (mm) cc_final: 0.5528 (mm)
REVERT: D  107 PHE cc_start: 0.7502 (t80) cc_final: 0.7094 (t80)
REVERT: D  172 ASP cc_start: 0.5930 (t70) cc_final: 0.5548 (t0)
REVERT: D  205 THR cc_start: 0.7261 (m) cc_final: 0.7049 (m)
REVERT: D  207 ASP cc_start: 0.7391 (t0) cc_final: 0.6866 (t70)
REVERT: D  214 MET cc_start: 0.6098 (mtt) cc_final: 0.5501 (mtt)
REVERT: D  238 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6819 (mp0)
REVERT: D  241 ASN cc_start: 0.6993 (p0) cc_final: 0.6653 (p0)
REVERT: D  250 GLU cc_start: 0.6292 (mp0) cc_final: 0.6065 (mt-10)
REVERT: D  253 MET cc_start: 0.7057 (tpt) cc_final: 0.6776 (tpp)
REVERT: D  294 LEU cc_start: 0.7889 (mt) cc_final: 0.7628 (mt)
REVERT: D  319 GLU cc_start: 0.6526 (tm-30) cc_final: 0.6301 (tm-30)
REVERT: D  330 VAL cc_start: 0.5718 (p) cc_final: 0.5409 (p)
REVERT: D  360 MET cc_start: 0.3275 (mmp) cc_final: 0.2967 (mmp)
  outliers start: 11
  outliers final: 4
  residues processed: 317
  average time/residue: 0.0944
  time to fit residues: 42.0925
Evaluate side-chains
  283 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 279
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain D residue  353 ASP
Chi-restraints excluded: chain D residue  366 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  42 ASN
C  28 ASN
D 252 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.171964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.143191 restraints weight = 14640.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.147754 restraints weight = 7694.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.150683 restraints weight = 4900.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.152864 restraints weight = 3609.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.154037 restraints weight = 2866.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.104  10041  Z= 0.302
  Angle     :  0.827  10.249  13616  Z= 0.431
  Chirality :  0.051   0.172   1597
  Planarity :  0.006   0.056   1723
  Dihedral  :  5.742  63.528   1347
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 13.18 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.34 (0.24), residues: 1232
  helix:  0.76 (0.21), residues: 598
  sheet:  0.23 (0.38), residues: 209
  loop : -1.87 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  38 
 TYR   0.019   0.002   TYR B 118 
 PHE   0.034   0.003   PHE A  45 
 TRP   0.024   0.002   TRP B 110 
 HIS   0.006   0.002   HIS C  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00697 (10041)
  covalent geometry    : angle       0.82656 (13616)
  hydrogen bonds       : bond        0.07560 (  466)
  hydrogen bonds       : angle       5.26272 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 293
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 THR cc_start: 0.7055 (m) cc_final: 0.6555 (p)
REVERT: A  136 GLN cc_start: 0.6684 (mp-120) cc_final: 0.6403 (mp-120)
REVERT: A  187 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7036 (mm-40)
REVERT: A  252 ASN cc_start: 0.7316 (m-40) cc_final: 0.6663 (m-40)
REVERT: A  294 LEU cc_start: 0.8632 (tp) cc_final: 0.8319 (mm)
REVERT: A  297 GLU cc_start: 0.6807 (tp30) cc_final: 0.6527 (tm-30)
REVERT: A  320 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6944 (mtm180)
REVERT: A  344 PHE cc_start: 0.6652 (p90) cc_final: 0.6146 (p90)
REVERT: B  102 LEU cc_start: 0.7495 (tp) cc_final: 0.7252 (tt)
REVERT: B  164 PHE cc_start: 0.8425 (m-80) cc_final: 0.8195 (m-10)
REVERT: B  170 TYR cc_start: 0.7209 (t80) cc_final: 0.6502 (t80)
REVERT: B  191 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7810 (ttmt)
REVERT: B  204 MET cc_start: 0.7102 (tpp) cc_final: 0.6839 (tpp)
REVERT: C   49 LEU cc_start: 0.8273 (tt) cc_final: 0.7996 (tt)
REVERT: C  242 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6961 (mm)
REVERT: D  154 GLN cc_start: 0.7828 (tp40) cc_final: 0.7506 (tp40)
REVERT: D  172 ASP cc_start: 0.6417 (t70) cc_final: 0.6092 (t70)
REVERT: D  187 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7355 (mm-40)
REVERT: D  222 ARG cc_start: 0.7901 (ttt180) cc_final: 0.7328 (ttp-170)
REVERT: D  243 PHE cc_start: 0.6721 (t80) cc_final: 0.6333 (t80)
REVERT: D  319 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6138 (tm-30)
REVERT: D  328 GLU cc_start: 0.6995 (pp20) cc_final: 0.6585 (pp20)
  outliers start: 48
  outliers final: 30
  residues processed: 318
  average time/residue: 0.0919
  time to fit residues: 40.7880
Evaluate side-chains
  311 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 279
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  320 ARG
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   26 CYS
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  130 GLU
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  353 ASP
Chi-restraints excluded: chain D residue  366 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A  88 ASN
A 354 HIS
D  42 ASN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 241 ASN
D 335 ASN
D 354 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.173867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.145613 restraints weight = 14608.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.150215 restraints weight = 7644.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.153344 restraints weight = 4837.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.155347 restraints weight = 3495.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.156316 restraints weight = 2795.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  10041  Z= 0.178
  Angle     :  0.688   9.972  13616  Z= 0.354
  Chirality :  0.046   0.159   1597
  Planarity :  0.005   0.051   1723
  Dihedral  :  5.448  56.868   1347
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 16.50 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.21 (0.24), residues: 1232
  helix:  0.82 (0.22), residues: 601
  sheet:  0.37 (0.39), residues: 208
  loop : -1.79 (0.27), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 115 
 TYR   0.018   0.001   TYR C 148 
 PHE   0.051   0.002   PHE C 101 
 TRP   0.016   0.001   TRP B 136 
 HIS   0.008   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (10041)
  covalent geometry    : angle       0.68793 (13616)
  hydrogen bonds       : bond        0.05875 (  466)
  hydrogen bonds       : angle       4.89105 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 258
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 THR cc_start: 0.7054 (m) cc_final: 0.6778 (p)
REVERT: A  116 MET cc_start: 0.7506 (ttm) cc_final: 0.7232 (ttm)
REVERT: A  136 GLN cc_start: 0.6657 (mp-120) cc_final: 0.6357 (mp-120)
REVERT: A  187 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7040 (tp-100)
REVERT: A  240 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8095 (mtmm)
REVERT: A  297 GLU cc_start: 0.6686 (tp30) cc_final: 0.6293 (tm-30)
REVERT: A  320 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6795 (mtm180)
REVERT: B  102 LEU cc_start: 0.7517 (tp) cc_final: 0.7275 (tt)
REVERT: B  170 TYR cc_start: 0.7121 (t80) cc_final: 0.6444 (t80)
REVERT: B  191 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7661 (ttmt)
REVERT: B  215 MET cc_start: 0.5600 (tmm) cc_final: 0.5181 (tmm)
REVERT: B  217 PRO cc_start: 0.8011 (Cg_exo) cc_final: 0.7796 (Cg_endo)
REVERT: D  129 MET cc_start: 0.6732 (tpp) cc_final: 0.6476 (tpt)
REVERT: D  172 ASP cc_start: 0.6243 (t70) cc_final: 0.5881 (t70)
REVERT: D  214 MET cc_start: 0.6028 (mtt) cc_final: 0.5514 (mtt)
REVERT: D  217 ARG cc_start: 0.7364 (mtp-110) cc_final: 0.7033 (mtp-110)
  outliers start: 56
  outliers final: 39
  residues processed: 285
  average time/residue: 0.0956
  time to fit residues: 38.0088
Evaluate side-chains
  293 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 253
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  320 ARG
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain D residue   26 CYS
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   63 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  340 MET
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  366 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 114 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 4 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 111 optimal weight:   20.0000
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  42 ASN
A  88 ASN
A 354 HIS
B  27 ASN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 185 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.174341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.145943 restraints weight = 14747.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.150582 restraints weight = 7757.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.153726 restraints weight = 4902.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.155822 restraints weight = 3539.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.157050 restraints weight = 2820.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10041  Z= 0.163
  Angle     :  0.662  10.455  13616  Z= 0.340
  Chirality :  0.045   0.146   1597
  Planarity :  0.005   0.050   1723
  Dihedral  :  4.778  49.713   1340
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 18.34 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.07 (0.24), residues: 1232
  helix:  0.92 (0.22), residues: 597
  sheet:  0.63 (0.41), residues: 193
  loop : -1.70 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 320 
 TYR   0.027   0.001   TYR D 236 
 PHE   0.036   0.002   PHE C 101 
 TRP   0.014   0.001   TRP B 136 
 HIS   0.009   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (10041)
  covalent geometry    : angle       0.66245 (13616)
  hydrogen bonds       : bond        0.05373 (  466)
  hydrogen bonds       : angle       4.74141 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 268
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6281 (mp-120)
REVERT: A  136 GLN cc_start: 0.6613 (mp-120) cc_final: 0.6295 (mp-120)
REVERT: A  294 LEU cc_start: 0.8477 (tp) cc_final: 0.8165 (mm)
REVERT: A  320 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6814 (mtm180)
REVERT: A  344 PHE cc_start: 0.6580 (p90) cc_final: 0.6110 (p90)
REVERT: B   46 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6550 (ttm)
REVERT: B  102 LEU cc_start: 0.7553 (tp) cc_final: 0.7314 (tt)
REVERT: B  215 MET cc_start: 0.5589 (tmm) cc_final: 0.5278 (tmm)
REVERT: B  217 PRO cc_start: 0.7946 (Cg_exo) cc_final: 0.7718 (Cg_endo)
REVERT: C   49 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7830 (tt)
REVERT: D  109 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6577 (t0)
REVERT: D  129 MET cc_start: 0.6619 (tpp) cc_final: 0.6418 (tpt)
REVERT: D  147 GLN cc_start: 0.7248 (mp10) cc_final: 0.6970 (mp10)
REVERT: D  172 ASP cc_start: 0.6402 (t70) cc_final: 0.6024 (t70)
REVERT: D  214 MET cc_start: 0.6037 (mtt) cc_final: 0.5721 (mtt)
REVERT: D  217 ARG cc_start: 0.7378 (mtp-110) cc_final: 0.7017 (mtp-110)
  outliers start: 63
  outliers final: 44
  residues processed: 296
  average time/residue: 0.0968
  time to fit residues: 39.8837
Evaluate side-chains
  310 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 261
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 GLN
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  320 ARG
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain D residue   26 CYS
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   63 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  109 ASN
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  215 SER
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  340 MET
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  366 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 109 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   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  88 ASN
** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 GLN
B  27 ASN
** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.170875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.142231 restraints weight = 14715.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146734 restraints weight = 7758.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.149871 restraints weight = 4974.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.151734 restraints weight = 3602.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.153292 restraints weight = 2911.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  10041  Z= 0.237
  Angle     :  0.708  12.280  13616  Z= 0.367
  Chirality :  0.048   0.175   1597
  Planarity :  0.005   0.051   1723
  Dihedral  :  4.922  42.311   1340
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 20.74 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -0.34 (0.24), residues: 1232
  helix:  0.67 (0.22), residues: 603
  sheet:  0.42 (0.40), residues: 193
  loop : -1.78 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 300 
 TYR   0.031   0.002   TYR D 236 
 PHE   0.034   0.002   PHE C 101 
 TRP   0.014   0.002   TRP A 368 
 HIS   0.010   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 (10041)
  covalent geometry    : angle       0.70763 (13616)
  hydrogen bonds       : bond        0.06279 (  466)
  hydrogen bonds       : angle       4.90360 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 263
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.6457 (mp-120) cc_final: 0.6243 (mp-120)
REVERT: A  213 THR cc_start: 0.8017 (m) cc_final: 0.7702 (m)
REVERT: A  297 GLU cc_start: 0.6688 (tp30) cc_final: 0.6452 (tm-30)
REVERT: A  320 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6866 (mtm180)
REVERT: A  344 PHE cc_start: 0.6632 (p90) cc_final: 0.6166 (p90)
REVERT: B  102 LEU cc_start: 0.7661 (tp) cc_final: 0.7419 (tt)
REVERT: B  170 TYR cc_start: 0.7133 (t80) cc_final: 0.6420 (t80)
REVERT: B  215 MET cc_start: 0.5502 (tmm) cc_final: 0.5195 (tmm)
REVERT: C   49 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7878 (tt)
REVERT: D  109 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6643 (t0)
REVERT: D  172 ASP cc_start: 0.6339 (t70) cc_final: 0.5958 (t70)
REVERT: D  217 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6986 (mtp-110)
  outliers start: 67
  outliers final: 50
  residues processed: 290
  average time/residue: 0.0948
  time to fit residues: 38.5652
Evaluate side-chains
  309 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 256
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  320 ARG
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain D residue   26 CYS
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  109 ASN
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  215 SER
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  340 MET
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  352 PHE
Chi-restraints excluded: chain D residue  366 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0470
   chunk 42 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 33 optimal weight:    0.1980
   chunk 100 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0270
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.3536

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  88 ASN
** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.175235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146788 restraints weight = 15007.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.151501 restraints weight = 7913.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.154659 restraints weight = 5023.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.156579 restraints weight = 3637.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.158098 restraints weight = 2931.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6660
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10041  Z= 0.123
  Angle     :  0.630  11.693  13616  Z= 0.320
  Chirality :  0.044   0.146   1597
  Planarity :  0.005   0.050   1723
  Dihedral  :  4.480  36.442   1340
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 23.41 %
    Favored  : 72.26 %
  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:  0.10 (0.25), residues: 1232
  helix:  1.11 (0.23), residues: 589
  sheet:  0.53 (0.40), residues: 190
  loop : -1.54 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 183 
 TYR   0.024   0.001   TYR A 322 
 PHE   0.032   0.002   PHE C 101 
 TRP   0.020   0.001   TRP A 368 
 HIS   0.010   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10041)
  covalent geometry    : angle       0.62993 (13616)
  hydrogen bonds       : bond        0.04295 (  466)
  hydrogen bonds       : angle       4.58458 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 261
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.6630 (mp-120) cc_final: 0.6279 (mp-120)
REVERT: A  213 THR cc_start: 0.8075 (m) cc_final: 0.7733 (m)
REVERT: A  297 GLU cc_start: 0.6387 (tp30) cc_final: 0.6133 (tm-30)
REVERT: B   46 MET cc_start: 0.6499 (ttt) cc_final: 0.6176 (ttm)
REVERT: B  102 LEU cc_start: 0.7581 (tp) cc_final: 0.7358 (tt)
REVERT: B  165 MET cc_start: 0.7767 (tpp) cc_final: 0.7296 (tpt)
REVERT: C   49 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7805 (tt)
REVERT: C  117 VAL cc_start: 0.8398 (t) cc_final: 0.8128 (p)
REVERT: C  221 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.5781 (tmm)
REVERT: D  217 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.7102 (mtp-110)
REVERT: D  323 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7510 (mtmt)
REVERT: D  328 GLU cc_start: 0.7049 (pt0) cc_final: 0.6610 (pt0)
  outliers start: 47
  outliers final: 28
  residues processed: 284
  average time/residue: 0.0939
  time to fit residues: 37.1445
Evaluate side-chains
  289 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 259
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain B residue   79 CYS
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  215 SER
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  366 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 15 optimal weight:    0.4980
   chunk 1 optimal weight:    0.0770
   chunk 25 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.174327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.146003 restraints weight = 14875.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.150525 restraints weight = 7883.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.153678 restraints weight = 5035.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.155709 restraints weight = 3672.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.156952 restraints weight = 2937.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6678
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10041  Z= 0.128
  Angle     :  0.616  11.382  13616  Z= 0.314
  Chirality :  0.044   0.135   1597
  Planarity :  0.004   0.049   1723
  Dihedral  :  4.346  30.951   1340
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 24.61 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.21 (0.25), residues: 1232
  helix:  1.24 (0.23), residues: 584
  sheet:  0.56 (0.40), residues: 190
  loop : -1.51 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 222 
 TYR   0.026   0.001   TYR D 236 
 PHE   0.035   0.002   PHE C 101 
 TRP   0.014   0.001   TRP A 368 
 HIS   0.006   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10041)
  covalent geometry    : angle       0.61581 (13616)
  hydrogen bonds       : bond        0.04361 (  466)
  hydrogen bonds       : angle       4.54317 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 265
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.6859 (mm-40) cc_final: 0.6612 (mp10)
REVERT: A  136 GLN cc_start: 0.6612 (mp-120) cc_final: 0.6226 (mp-120)
REVERT: A  201 PHE cc_start: 0.7363 (m-80) cc_final: 0.7108 (m-10)
REVERT: A  213 THR cc_start: 0.8022 (m) cc_final: 0.7768 (m)
REVERT: A  319 GLU cc_start: 0.6368 (tp30) cc_final: 0.6129 (tp30)
REVERT: B   46 MET cc_start: 0.6404 (ttt) cc_final: 0.6153 (ttm)
REVERT: B   81 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7865 (p)
REVERT: B  102 LEU cc_start: 0.7646 (tp) cc_final: 0.7436 (tt)
REVERT: B  204 MET cc_start: 0.7240 (tpp) cc_final: 0.6679 (tpp)
REVERT: B  215 MET cc_start: 0.5633 (tmm) cc_final: 0.5303 (tmm)
REVERT: C   49 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7794 (tt)
REVERT: D  217 ARG cc_start: 0.7326 (mtp-110) cc_final: 0.6696 (mtp-110)
REVERT: D  323 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7555 (mtmt)
REVERT: D  328 GLU cc_start: 0.7019 (pt0) cc_final: 0.6574 (pt0)
  outliers start: 50
  outliers final: 37
  residues processed: 289
  average time/residue: 0.0979
  time to fit residues: 39.4955
Evaluate side-chains
  304 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 265
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   79 CYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   26 CYS
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  215 SER
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  366 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 12 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 116 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
A 358 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.168740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.139803 restraints weight = 14804.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.144302 restraints weight = 7871.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.147421 restraints weight = 5067.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.149227 restraints weight = 3703.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.150653 restraints weight = 3024.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  10041  Z= 0.248
  Angle     :  0.723  11.422  13616  Z= 0.374
  Chirality :  0.048   0.174   1597
  Planarity :  0.005   0.050   1723
  Dihedral  :  4.738  31.066   1340
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 24.70 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -0.18 (0.24), residues: 1232
  helix:  0.73 (0.22), residues: 597
  sheet:  0.45 (0.40), residues: 193
  loop : -1.54 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 300 
 TYR   0.032   0.002   TYR D 236 
 PHE   0.038   0.002   PHE C 101 
 TRP   0.012   0.002   TRP A 368 
 HIS   0.007   0.002   HIS C  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 (10041)
  covalent geometry    : angle       0.72316 (13616)
  hydrogen bonds       : bond        0.06223 (  466)
  hydrogen bonds       : angle       4.91087 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 259
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.6953 (mm-40) cc_final: 0.6672 (mp10)
REVERT: A  136 GLN cc_start: 0.6487 (mp-120) cc_final: 0.6178 (mp-120)
REVERT: A  297 GLU cc_start: 0.6606 (tp30) cc_final: 0.6271 (tp30)
REVERT: A  319 GLU cc_start: 0.6370 (tp30) cc_final: 0.6140 (tp30)
REVERT: A  320 ARG cc_start: 0.7013 (mtm180) cc_final: 0.6381 (mtm180)
REVERT: B   27 ASN cc_start: 0.8261 (m-40) cc_final: 0.8020 (m-40)
REVERT: B   46 MET cc_start: 0.6673 (ttt) cc_final: 0.6399 (ttm)
REVERT: B  102 LEU cc_start: 0.7669 (tp) cc_final: 0.7450 (tt)
REVERT: B  170 TYR cc_start: 0.7123 (t80) cc_final: 0.6448 (t80)
REVERT: B  215 MET cc_start: 0.5581 (tmm) cc_final: 0.5284 (tmm)
REVERT: C   49 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7924 (tt)
REVERT: C  249 GLN cc_start: 0.7004 (tp-100) cc_final: 0.6702 (tp40)
REVERT: D  109 ASN cc_start: 0.7073 (OUTLIER) cc_final: 0.6528 (t0)
REVERT: D  217 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6785 (mtp-110)
  outliers start: 57
  outliers final: 42
  residues processed: 287
  average time/residue: 0.0946
  time to fit residues: 37.8297
Evaluate side-chains
  300 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 256
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain D residue   26 CYS
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  109 ASN
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  215 SER
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain D residue  340 MET
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  352 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0470
   chunk 82 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 91 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.9082

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.173673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.145171 restraints weight = 14552.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.149752 restraints weight = 7671.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.152858 restraints weight = 4868.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.154646 restraints weight = 3538.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.156171 restraints weight = 2877.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.4614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10041  Z= 0.142
  Angle     :  0.668  11.088  13616  Z= 0.336
  Chirality :  0.045   0.165   1597
  Planarity :  0.004   0.049   1723
  Dihedral  :  4.379  30.492   1337
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 26.64 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.06 (0.25), residues: 1232
  helix:  1.04 (0.22), residues: 596
  sheet:  0.44 (0.40), residues: 189
  loop : -1.49 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  61 
 TYR   0.028   0.001   TYR D 236 
 PHE   0.037   0.002   PHE C 101 
 TRP   0.014   0.001   TRP A 368 
 HIS   0.008   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10041)
  covalent geometry    : angle       0.66824 (13616)
  hydrogen bonds       : bond        0.04744 (  466)
  hydrogen bonds       : angle       4.69095 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 264
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6598 (mp10)
REVERT: A  136 GLN cc_start: 0.6480 (mp-120) cc_final: 0.6122 (mp10)
REVERT: A  213 THR cc_start: 0.8031 (m) cc_final: 0.7672 (t)
REVERT: A  240 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8320 (mtmm)
REVERT: A  297 GLU cc_start: 0.6475 (tp30) cc_final: 0.6187 (tm-30)
REVERT: A  319 GLU cc_start: 0.6307 (tp30) cc_final: 0.6085 (tp30)
REVERT: A  320 ARG cc_start: 0.6958 (mtm180) cc_final: 0.6327 (mtm180)
REVERT: B   46 MET cc_start: 0.6372 (ttt) cc_final: 0.6075 (ttm)
REVERT: B   81 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7887 (p)
REVERT: B  102 LEU cc_start: 0.7631 (tp) cc_final: 0.7426 (tt)
REVERT: B  215 MET cc_start: 0.5620 (tmm) cc_final: 0.5265 (tmm)
REVERT: C  249 GLN cc_start: 0.6915 (tp-100) cc_final: 0.6643 (tp-100)
REVERT: D  109 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6496 (t0)
REVERT: D  147 GLN cc_start: 0.7469 (mp10) cc_final: 0.7047 (mp10)
REVERT: D  210 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7039 (mm-30)
REVERT: D  217 ARG cc_start: 0.7320 (mtp-110) cc_final: 0.6688 (mtp-110)
REVERT: D  323 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7678 (mtmt)
  outliers start: 39
  outliers final: 32
  residues processed: 283
  average time/residue: 0.0951
  time to fit residues: 37.3374
Evaluate side-chains
  294 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 260
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain D residue   26 CYS
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  109 ASN
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  215 SER
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain D residue  340 MET
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  352 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 115 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.174498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.146102 restraints weight = 14386.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.150502 restraints weight = 7618.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.153742 restraints weight = 4879.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.155561 restraints weight = 3534.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.156766 restraints weight = 2867.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10041  Z= 0.132
  Angle     :  0.673  11.615  13616  Z= 0.334
  Chirality :  0.045   0.177   1597
  Planarity :  0.004   0.049   1723
  Dihedral  :  4.272  30.477   1337
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 26.82 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.15 (0.25), residues: 1232
  helix:  1.13 (0.22), residues: 597
  sheet:  0.50 (0.40), residues: 190
  loop : -1.51 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 225 
 TYR   0.028   0.001   TYR D 236 
 PHE   0.051   0.002   PHE C 101 
 TRP   0.014   0.001   TRP A 368 
 HIS   0.008   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10041)
  covalent geometry    : angle       0.67259 (13616)
  hydrogen bonds       : bond        0.04388 (  466)
  hydrogen bonds       : angle       4.61009 ( 1365)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 263
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.6857 (mm-40) cc_final: 0.6603 (mp10)
REVERT: A  129 MET cc_start: 0.5416 (tpp) cc_final: 0.4915 (tpp)
REVERT: A  136 GLN cc_start: 0.6497 (mp-120) cc_final: 0.6145 (mp10)
REVERT: A  240 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8346 (mtmm)
REVERT: A  297 GLU cc_start: 0.6417 (tp30) cc_final: 0.6078 (tp30)
REVERT: A  320 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6366 (mtm180)
REVERT: B   46 MET cc_start: 0.6420 (ttt) cc_final: 0.6120 (ttm)
REVERT: B   81 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7845 (p)
REVERT: B  204 MET cc_start: 0.7280 (tpp) cc_final: 0.6873 (tpp)
REVERT: B  215 MET cc_start: 0.5593 (tmm) cc_final: 0.5318 (tmm)
REVERT: C  133 PHE cc_start: 0.7193 (m-80) cc_final: 0.6951 (t80)
REVERT: C  177 ILE cc_start: 0.6350 (mt) cc_final: 0.6143 (mt)
REVERT: C  249 GLN cc_start: 0.6918 (tp-100) cc_final: 0.6678 (tp40)
REVERT: D  109 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6431 (t0)
REVERT: D  214 MET cc_start: 0.6373 (mtt) cc_final: 0.6161 (mtt)
REVERT: D  323 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7852 (mtmt)
  outliers start: 40
  outliers final: 34
  residues processed: 281
  average time/residue: 0.0957
  time to fit residues: 37.5263
Evaluate side-chains
  297 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 261
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   26 CYS
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  109 ASN
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  158 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  294 LEU
Chi-restraints excluded: chain D residue  340 MET
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain D residue  352 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 116 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 93 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0970
   chunk 57 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 113 optimal weight:   10.0000
   overall best weight:    1.2380

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 187 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 = 0.4201 r_free = 0.4201 target = 0.173527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.144979 restraints weight = 14643.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.149488 restraints weight = 7708.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.152664 restraints weight = 4900.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.154735 restraints weight = 3547.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.155965 restraints weight = 2827.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.4847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10041  Z= 0.162
  Angle     :  0.700  11.647  13616  Z= 0.350
  Chirality :  0.045   0.159   1597
  Planarity :  0.005   0.049   1723
  Dihedral  :  4.390  31.122   1337
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 27.10 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.12 (0.25), residues: 1232
  helix:  1.08 (0.22), residues: 602
  sheet:  0.48 (0.40), residues: 190
  loop : -1.49 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 225 
 TYR   0.023   0.001   TYR D 236 
 PHE   0.056   0.002   PHE C  95 
 TRP   0.014   0.001   TRP A 368 
 HIS   0.008   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (10041)
  covalent geometry    : angle       0.70033 (13616)
  hydrogen bonds       : bond        0.04900 (  466)
  hydrogen bonds       : angle       4.67471 ( 1365)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1692.82 seconds
wall clock time: 29 minutes 54.43 seconds (1794.43 seconds total)