Starting phenix.real_space_refine
on Wed Mar  4 06:23:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zye_11560/03_2026/6zye_11560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zye_11560/03_2026/6zye_11560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zye_11560/03_2026/6zye_11560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zye_11560/03_2026/6zye_11560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zye_11560/03_2026/6zye_11560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zye_11560/03_2026/6zye_11560.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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      49      5.16       5
     C    7392      2.51       5
     N    1995      2.21       5
     O    2156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11592
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "E"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1656
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 7, 'TRANS': 214}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'UNK:plan-1': 36}
          Unresolved non-hydrogen planarities: 36
  Restraints were copied for chains:
    C, A, B, D, F, G
  Time building chain proxies: 1.44, per 1000 atoms: 0.12
  Number of scatterers: 11592
  At special positions: 0
  Unit cell: (97.842, 98.9055, 108.477, 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      49     16.00
     O    2156      8.00
     N    1995      7.00
     C    7392      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: 0.77
  Conformation dependent library (CDL) restraints added in 492.7 milliseconds
  

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2912

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 22 sheets defined
      54.4% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'E' and resid -35 through -16
    Processing helix  chain 'E' and resid 150 through 160
      removed outlier: 3.839A  pdb=" N   GLY E 157 " --> pdb=" O   GLY E 153 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET E 158 " --> pdb=" O   LEU E 154 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY E 160 " --> pdb=" O   VAL E 156 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 176
    Processing helix  chain 'E' and resid 219 through 224
      removed outlier: 3.662A  pdb=" N   ILE E 224 " --> pdb=" O   PHE E 221 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 229 through 232
    Processing helix  chain 'E' and resid 244 through 249
      removed outlier: 3.524A  pdb=" N   ALA E 248 " --> pdb=" O   TYR E 245 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ALA E 249 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 264
    Processing helix  chain 'E' and resid 298 through 320
    Processing helix  chain 'C' and resid -34 through -16
    Processing helix  chain 'C' and resid 150 through 160
      removed outlier: 3.839A  pdb=" N   GLY C 157 " --> pdb=" O   GLY C 153 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   MET C 158 " --> pdb=" O   LEU C 154 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY C 160 " --> pdb=" O   VAL C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 176
    Processing helix  chain 'C' and resid 219 through 224
      removed outlier: 3.662A  pdb=" N   ILE C 224 " --> pdb=" O   PHE C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 232
    Processing helix  chain 'C' and resid 244 through 249
      removed outlier: 3.524A  pdb=" N   ALA C 248 " --> pdb=" O   TYR C 245 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ALA C 249 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 264
    Processing helix  chain 'C' and resid 298 through 320
    Processing helix  chain 'A' and resid -34 through -16
    Processing helix  chain 'A' and resid 150 through 160
      removed outlier: 3.839A  pdb=" N   GLY A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY A 160 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 176
    Processing helix  chain 'A' and resid 219 through 224
      removed outlier: 3.661A  pdb=" N   ILE A 224 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 232
    Processing helix  chain 'A' and resid 244 through 249
      removed outlier: 3.525A  pdb=" N   ALA A 248 " --> pdb=" O   TYR A 245 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ALA A 249 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 264
    Processing helix  chain 'A' and resid 298 through 320
    Processing helix  chain 'B' and resid -34 through -16
    Processing helix  chain 'B' and resid 150 through 160
      removed outlier: 3.839A  pdb=" N   GLY B 157 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET B 158 " --> pdb=" O   LEU B 154 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY B 160 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 176
    Processing helix  chain 'B' and resid 219 through 224
      removed outlier: 3.662A  pdb=" N   ILE B 224 " --> pdb=" O   PHE B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 232
    Processing helix  chain 'B' and resid 244 through 249
      removed outlier: 3.524A  pdb=" N   ALA B 248 " --> pdb=" O   TYR B 245 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ALA B 249 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 264
    Processing helix  chain 'B' and resid 298 through 320
    Processing helix  chain 'D' and resid -34 through -16
    Processing helix  chain 'D' and resid 150 through 160
      removed outlier: 3.839A  pdb=" N   GLY D 157 " --> pdb=" O   GLY D 153 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   MET D 158 " --> pdb=" O   LEU D 154 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY D 160 " --> pdb=" O   VAL D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 176
    Processing helix  chain 'D' and resid 219 through 224
      removed outlier: 3.661A  pdb=" N   ILE D 224 " --> pdb=" O   PHE D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 229 through 232
    Processing helix  chain 'D' and resid 244 through 249
      removed outlier: 3.525A  pdb=" N   ALA D 248 " --> pdb=" O   TYR D 245 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ALA D 249 " --> pdb=" O   GLU D 246 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 264
    Processing helix  chain 'D' and resid 298 through 320
    Processing helix  chain 'F' and resid -34 through -16
    Processing helix  chain 'F' and resid 150 through 160
      removed outlier: 3.839A  pdb=" N   GLY F 157 " --> pdb=" O   GLY F 153 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   MET F 158 " --> pdb=" O   LEU F 154 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY F 160 " --> pdb=" O   VAL F 156 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 160 through 176
    Processing helix  chain 'F' and resid 219 through 224
      removed outlier: 3.663A  pdb=" N   ILE F 224 " --> pdb=" O   PHE F 221 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 229 through 232
    Processing helix  chain 'F' and resid 244 through 249
      removed outlier: 3.524A  pdb=" N   ALA F 248 " --> pdb=" O   TYR F 245 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ALA F 249 " --> pdb=" O   GLU F 246 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 250 through 264
    Processing helix  chain 'F' and resid 298 through 320
    Processing helix  chain 'G' and resid -34 through -16
    Processing helix  chain 'G' and resid 150 through 160
      removed outlier: 3.839A  pdb=" N   GLY G 157 " --> pdb=" O   GLY G 153 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET G 158 " --> pdb=" O   LEU G 154 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY G 160 " --> pdb=" O   VAL G 156 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 160 through 176
    Processing helix  chain 'G' and resid 219 through 224
      removed outlier: 3.662A  pdb=" N   ILE G 224 " --> pdb=" O   PHE G 221 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 229 through 232
    Processing helix  chain 'G' and resid 244 through 249
      removed outlier: 3.525A  pdb=" N   ALA G 248 " --> pdb=" O   TYR G 245 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ALA G 249 " --> pdb=" O   GLU G 246 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 250 through 264
    Processing helix  chain 'G' and resid 298 through 320
    Processing sheet with id=AA1, first strand: chain 'E' and resid 184 through 186
      removed outlier: 6.613A  pdb=" N   LYS E 205 " --> pdb=" O   ALA E 197 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 226 through 227
      removed outlier: 6.613A  pdb=" N   LYS D 205 " --> pdb=" O   ALA D 197 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 235 through 243
      removed outlier: 3.685A  pdb=" N   ARG E 235 " --> pdb=" O   THR E 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR E 239 " --> pdb=" O   VAL E 290 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 235 through 243
      removed outlier: 3.685A  pdb=" N   ARG E 235 " --> pdb=" O   THR E 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR E 239 " --> pdb=" O   VAL E 290 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER E 285 " --> pdb=" O   ALA E 282 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN E 280 " --> pdb=" O   ASN E 287 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   MET E 289 " --> pdb=" O   PHE E 278 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE E 278 " --> pdb=" O   MET E 289 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 328 through 332
      removed outlier: 8.444A  pdb=" N   GLN D 329 " --> pdb=" O   SER E 328 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   THR E 330 " --> pdb=" O   GLN D 329 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   LEU D 331 " --> pdb=" O   THR E 330 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   TYR E 332 " --> pdb=" O   LEU D 331 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   GLN G 329 " --> pdb=" O   SER C 328 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   THR C 330 " --> pdb=" O   GLN G 329 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   LEU G 331 " --> pdb=" O   THR C 330 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   TYR C 332 " --> pdb=" O   LEU G 331 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 186
      removed outlier: 6.612A  pdb=" N   LYS C 205 " --> pdb=" O   ALA C 197 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227
      removed outlier: 6.613A  pdb=" N   LYS G 205 " --> pdb=" O   ALA G 197 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243
      removed outlier: 3.685A  pdb=" N   ARG C 235 " --> pdb=" O   THR C 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR C 239 " --> pdb=" O   VAL C 290 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 235 through 243
      removed outlier: 3.685A  pdb=" N   ARG C 235 " --> pdb=" O   THR C 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR C 239 " --> pdb=" O   VAL C 290 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER C 285 " --> pdb=" O   ALA C 282 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN C 280 " --> pdb=" O   ASN C 287 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   MET C 289 " --> pdb=" O   PHE C 278 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE C 278 " --> pdb=" O   MET C 289 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 186
      removed outlier: 6.613A  pdb=" N   LYS A 205 " --> pdb=" O   ALA A 197 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 235 through 243
      removed outlier: 3.685A  pdb=" N   ARG A 235 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR A 239 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 235 through 243
      removed outlier: 3.685A  pdb=" N   ARG A 235 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR A 239 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER A 285 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN A 280 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   MET A 289 " --> pdb=" O   PHE A 278 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE A 278 " --> pdb=" O   MET A 289 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 184 through 186
      removed outlier: 6.613A  pdb=" N   LYS B 205 " --> pdb=" O   ALA B 197 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 235 through 243
      removed outlier: 3.686A  pdb=" N   ARG B 235 " --> pdb=" O   THR B 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR B 239 " --> pdb=" O   VAL B 290 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 235 through 243
      removed outlier: 3.686A  pdb=" N   ARG B 235 " --> pdb=" O   THR B 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR B 239 " --> pdb=" O   VAL B 290 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER B 285 " --> pdb=" O   ALA B 282 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN B 280 " --> pdb=" O   ASN B 287 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   MET B 289 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE B 278 " --> pdb=" O   MET B 289 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 235 through 243
      removed outlier: 3.686A  pdb=" N   ARG D 235 " --> pdb=" O   THR D 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR D 239 " --> pdb=" O   VAL D 290 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 235 through 243
      removed outlier: 3.686A  pdb=" N   ARG D 235 " --> pdb=" O   THR D 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR D 239 " --> pdb=" O   VAL D 290 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER D 285 " --> pdb=" O   ALA D 282 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN D 280 " --> pdb=" O   ASN D 287 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   MET D 289 " --> pdb=" O   PHE D 278 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   PHE D 278 " --> pdb=" O   MET D 289 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 184 through 186
      removed outlier: 6.613A  pdb=" N   LYS F 205 " --> pdb=" O   ALA F 197 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 235 through 243
      removed outlier: 3.686A  pdb=" N   ARG F 235 " --> pdb=" O   THR F 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR F 239 " --> pdb=" O   VAL F 290 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 235 through 243
      removed outlier: 3.686A  pdb=" N   ARG F 235 " --> pdb=" O   THR F 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR F 239 " --> pdb=" O   VAL F 290 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER F 285 " --> pdb=" O   ALA F 282 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN F 280 " --> pdb=" O   ASN F 287 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   MET F 289 " --> pdb=" O   PHE F 278 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE F 278 " --> pdb=" O   MET F 289 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 235 through 243
      removed outlier: 3.685A  pdb=" N   ARG G 235 " --> pdb=" O   THR G 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR G 239 " --> pdb=" O   VAL G 290 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'G' and resid 235 through 243
      removed outlier: 3.685A  pdb=" N   ARG G 235 " --> pdb=" O   THR G 294 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR G 239 " --> pdb=" O   VAL G 290 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER G 285 " --> pdb=" O   ALA G 282 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN G 280 " --> pdb=" O   ASN G 287 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   MET G 289 " --> pdb=" O   PHE G 278 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   PHE G 278 " --> pdb=" O   MET G 289 " (cutoff:3.500A)

    695 hydrogen bonds defined for protein.
    1980 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: 1.69

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3843
        1.34 -     1.46: 3054
        1.46 -     1.58: 4835
        1.58 -     1.70: 0
        1.70 -     1.82: 91
  Bond restraints: 11823
  Sorted by residual:
  bond pdb=" CG  LEU D 214 "
       pdb=" CD2 LEU D 214 "
    ideal  model  delta    sigma   weight residual
    1.521  1.443  0.078 3.30e-02 9.18e+02 5.61e+00
  bond pdb=" CG  LEU F 214 "
       pdb=" CD2 LEU F 214 "
    ideal  model  delta    sigma   weight residual
    1.521  1.443  0.078 3.30e-02 9.18e+02 5.54e+00
  bond pdb=" CG  LEU C 214 "
       pdb=" CD2 LEU C 214 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.51e+00
  bond pdb=" CG  LEU B 214 "
       pdb=" CD2 LEU B 214 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.50e+00
  bond pdb=" CB  VAL D 196 "
       pdb=" CG2 VAL D 196 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.49e+00
  ... (remaining 11818 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 14709
        1.68 -     3.37: 1171
        3.37 -     5.05: 151
        5.05 -     6.74: 48
        6.74 -     8.42: 14
  Bond angle restraints: 16093
  Sorted by residual:
  angle pdb=" N   LYS G 161 "
        pdb=" CA  LYS G 161 "
        pdb=" C   LYS G 161 "
      ideal   model   delta    sigma   weight residual
     111.28  118.59   -7.31 1.09e+00 8.42e-01 4.50e+01
  angle pdb=" N   LYS C 161 "
        pdb=" CA  LYS C 161 "
        pdb=" C   LYS C 161 "
      ideal   model   delta    sigma   weight residual
     111.28  118.56   -7.28 1.09e+00 8.42e-01 4.47e+01
  angle pdb=" N   LYS F 161 "
        pdb=" CA  LYS F 161 "
        pdb=" C   LYS F 161 "
      ideal   model   delta    sigma   weight residual
     111.28  118.56   -7.28 1.09e+00 8.42e-01 4.46e+01
  angle pdb=" N   LYS E 161 "
        pdb=" CA  LYS E 161 "
        pdb=" C   LYS E 161 "
      ideal   model   delta    sigma   weight residual
     111.28  118.55   -7.27 1.09e+00 8.42e-01 4.45e+01
  angle pdb=" N   LYS A 161 "
        pdb=" CA  LYS A 161 "
        pdb=" C   LYS A 161 "
      ideal   model   delta    sigma   weight residual
     111.28  118.54   -7.26 1.09e+00 8.42e-01 4.44e+01
  ... (remaining 16088 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 6405
       17.39 -    34.78: 476
       34.78 -    52.16: 56
       52.16 -    69.55: 14
       69.55 -    86.94: 7
  Dihedral angle restraints: 6958
    sinusoidal: 2457
      harmonic: 4501
  Sorted by residual:
  dihedral pdb=" CA  PHE D 326 "
           pdb=" C   PHE D 326 "
           pdb=" N   PRO D 327 "
           pdb=" CA  PRO D 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  PHE B 326 "
           pdb=" C   PHE B 326 "
           pdb=" N   PRO B 327 "
           pdb=" CA  PRO B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.49   19.51     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  PHE G 326 "
           pdb=" C   PHE G 326 "
           pdb=" N   PRO G 327 "
           pdb=" CA  PRO G 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.50   19.50     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 6955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1071
       0.049 -    0.097: 541
       0.097 -    0.146: 181
       0.146 -    0.194: 55
       0.194 -    0.243: 7
  Chirality restraints: 1855
  Sorted by residual:
  chirality pdb=" CA  LYS G 161 "
            pdb=" N   LYS G 161 "
            pdb=" C   LYS G 161 "
            pdb=" CB  LYS G 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  LYS A 161 "
            pdb=" N   LYS A 161 "
            pdb=" C   LYS A 161 "
            pdb=" CB  LYS A 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  LYS F 161 "
            pdb=" N   LYS F 161 "
            pdb=" C   LYS F 161 "
            pdb=" CB  LYS F 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1852 not shown)

  Planarity restraints: 2079
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 160 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.75e+00
        pdb=" C   GLY A 160 "    0.045 2.00e-02 2.50e+03
        pdb=" O   GLY A 160 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS A 161 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 160 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.74e+00
        pdb=" C   GLY B 160 "    0.045 2.00e-02 2.50e+03
        pdb=" O   GLY B 160 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS B 161 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D 160 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.70e+00
        pdb=" C   GLY D 160 "    0.045 2.00e-02 2.50e+03
        pdb=" O   GLY D 160 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS D 161 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2076 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2766
        2.77 -     3.30: 12298
        3.30 -     3.84: 18947
        3.84 -     4.37: 22630
        4.37 -     4.90: 38197
  Nonbonded interactions: 94838
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 162 "
            pdb=" O   SER B 222 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   ILE B 268 "
            pdb=" NZ  LYS B 295 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   ILE C 268 "
            pdb=" NZ  LYS C 295 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   ARG C 202 "
            pdb=" ND2 ASN C 218 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   ARG F 202 "
            pdb=" ND2 ASN F 218 "
     model   vdw
     2.290 3.120
  ... (remaining 94833 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'C'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'G'
}

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:             0.520
  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:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.310
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
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      :  0.016   0.082  11823  Z= 0.694
  Angle     :  1.047   8.425  16093  Z= 0.605
  Chirality :  0.064   0.243   1855
  Planarity :  0.006   0.040   2079
  Dihedral  : 13.053  86.940   4046
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 17.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.22), residues: 1288
  helix: -1.24 (0.21), residues: 490
  sheet: -4.36 (0.29), residues: 161
  loop : -2.20 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 236 
 TYR   0.020   0.003   TYR C 277 
 PHE   0.022   0.003   PHE G 281 
 TRP   0.011   0.002   TRP B 184 
 HIS   0.006   0.002   HIS D 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.01571 (11823)
  covalent geometry    : angle       1.04673 (16093)
  hydrogen bonds       : bond        0.18411 (  639)
  hydrogen bonds       : angle       8.26066 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 366
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  189 ASP cc_start: 0.7123 (m-30) cc_final: 0.6848 (m-30)
REVERT: E  215 TYR cc_start: 0.8494 (m-80) cc_final: 0.8195 (m-80)
REVERT: E  312 LYS cc_start: 0.8416 (mttt) cc_final: 0.7858 (mttm)
REVERT: C  164 LEU cc_start: 0.7669 (mt) cc_final: 0.7403 (mm)
REVERT: C  165 SER cc_start: 0.8766 (m) cc_final: 0.8432 (p)
REVERT: C  215 TYR cc_start: 0.8449 (m-80) cc_final: 0.8159 (m-10)
REVERT: C  312 LYS cc_start: 0.8310 (mttt) cc_final: 0.7563 (mmtt)
REVERT: A  312 LYS cc_start: 0.8316 (mttt) cc_final: 0.7638 (mttm)
REVERT: B  158 MET cc_start: 0.5287 (mtm) cc_final: 0.4792 (ttm)
REVERT: B  312 LYS cc_start: 0.8431 (mttt) cc_final: 0.7862 (mmtt)
REVERT: B  313 ILE cc_start: 0.9290 (mt) cc_final: 0.9077 (mt)
REVERT: D  179 PHE cc_start: 0.8182 (p90) cc_final: 0.7753 (p90)
REVERT: D  312 LYS cc_start: 0.8357 (mttt) cc_final: 0.7525 (mttm)
REVERT: F  260 GLU cc_start: 0.6707 (tp30) cc_final: 0.6462 (tp30)
REVERT: F  291 TYR cc_start: 0.8027 (t80) cc_final: 0.7794 (t80)
REVERT: F  312 LYS cc_start: 0.8257 (mttt) cc_final: 0.7423 (mttm)
REVERT: G  312 LYS cc_start: 0.8322 (mttt) cc_final: 0.7673 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 366
  average time/residue: 0.1355
  time to fit residues: 65.6991
Evaluate side-chains
  200 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:   30.0000
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:   20.0000
   chunk 149 optimal weight:    5.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
E 228 ASN
** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 320 HIS
** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 280 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.101335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.081021 restraints weight = 33600.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.082740 restraints weight = 21034.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.083602 restraints weight = 15301.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.084477 restraints weight = 12648.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.084823 restraints weight = 10982.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11823  Z= 0.161
  Angle     :  0.632   6.383  16093  Z= 0.327
  Chirality :  0.046   0.149   1855
  Planarity :  0.004   0.027   2079
  Dihedral  :  5.168  17.971   1666
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.50 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.24), residues: 1288
  helix:  1.30 (0.23), residues: 504
  sheet: -3.13 (0.34), residues: 189
  loop : -1.75 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 212 
 TYR   0.016   0.002   TYR B 174 
 PHE   0.016   0.001   PHE A 168 
 TRP   0.016   0.002   TRP B 201 
 HIS   0.001   0.001   HIS F 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (11823)
  covalent geometry    : angle       0.63221 (16093)
  hydrogen bonds       : bond        0.04365 (  639)
  hydrogen bonds       : angle       5.11579 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 333
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  205 LYS cc_start: 0.8973 (tmmt) cc_final: 0.8750 (ttmm)
REVERT: E  215 TYR cc_start: 0.8390 (m-80) cc_final: 0.7707 (m-80)
REVERT: E  228 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8511 (m110)
REVERT: E  312 LYS cc_start: 0.8996 (mttt) cc_final: 0.8602 (mttm)
REVERT: C  189 ASP cc_start: 0.7360 (m-30) cc_final: 0.7050 (m-30)
REVERT: C  210 ASP cc_start: 0.8304 (m-30) cc_final: 0.7921 (m-30)
REVERT: C  215 TYR cc_start: 0.8289 (m-80) cc_final: 0.7968 (m-80)
REVERT: C  279 ASN cc_start: 0.8598 (p0) cc_final: 0.8266 (p0)
REVERT: C  287 ASN cc_start: 0.8939 (m-40) cc_final: 0.8688 (m-40)
REVERT: C  312 LYS cc_start: 0.8866 (mttt) cc_final: 0.8559 (mttp)
REVERT: B  172 MET cc_start: 0.7162 (tpt) cc_final: 0.6580 (tpt)
REVERT: B  210 ASP cc_start: 0.8122 (m-30) cc_final: 0.7864 (m-30)
REVERT: B  312 LYS cc_start: 0.8907 (mttt) cc_final: 0.8596 (mttm)
REVERT: D  210 ASP cc_start: 0.8124 (m-30) cc_final: 0.7892 (m-30)
REVERT: D  236 ARG cc_start: 0.8073 (ttp-170) cc_final: 0.7801 (ttp80)
REVERT: D  312 LYS cc_start: 0.8893 (mttt) cc_final: 0.8611 (mttm)
REVERT: F  291 TYR cc_start: 0.8193 (t80) cc_final: 0.7842 (t80)
REVERT: F  308 ASP cc_start: 0.8375 (p0) cc_final: 0.8138 (p0)
REVERT: F  312 LYS cc_start: 0.8976 (mttt) cc_final: 0.8432 (mttm)
REVERT: G  201 TRP cc_start: 0.6063 (m100) cc_final: 0.5715 (m-10)
REVERT: G  291 TYR cc_start: 0.8306 (t80) cc_final: 0.8081 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 334
  average time/residue: 0.1343
  time to fit residues: 59.1146
Evaluate side-chains
  198 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 87 optimal weight:   10.0000
   chunk 126 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 80 optimal weight:    5.9990
   chunk 128 optimal weight:    7.9990
   chunk 34 optimal weight:    8.9990
   chunk 78 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
E 228 ASN
E 320 HIS
C 228 ASN
C 280 GLN
C 320 HIS
A 264 ASN
A 318 GLN
A 320 HIS
B 280 GLN
D 228 ASN
D 280 GLN
D 320 HIS
F 264 ASN
F 280 GLN
F 320 HIS
** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 264 ASN
G 280 GLN
** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 320 HIS

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.093916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.072908 restraints weight = 34192.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.074544 restraints weight = 20887.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.075621 restraints weight = 15120.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.076106 restraints weight = 12245.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.076641 restraints weight = 10940.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054  11823  Z= 0.316
  Angle     :  0.806   8.719  16093  Z= 0.418
  Chirality :  0.051   0.157   1855
  Planarity :  0.005   0.055   2079
  Dihedral  :  5.756  19.360   1666
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  5.39 %
    Favored  : 94.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.23), residues: 1288
  helix:  0.84 (0.23), residues: 497
  sheet: -2.45 (0.28), residues: 259
  loop : -1.69 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 231 
 TYR   0.020   0.003   TYR B 277 
 PHE   0.018   0.002   PHE G 209 
 TRP   0.013   0.002   TRP E 201 
 HIS   0.004   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00696 (11823)
  covalent geometry    : angle       0.80609 (16093)
  hydrogen bonds       : bond        0.04413 (  639)
  hydrogen bonds       : angle       5.48756 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 260
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  167 PHE cc_start: 0.7755 (t80) cc_final: 0.7521 (t80)
REVERT: E  198 GLU cc_start: 0.7819 (pp20) cc_final: 0.7031 (pp20)
REVERT: E  201 TRP cc_start: 0.6354 (m100) cc_final: 0.5667 (m-10)
REVERT: E  219 SER cc_start: 0.9276 (p) cc_final: 0.8922 (m)
REVERT: E  312 LYS cc_start: 0.9026 (mttt) cc_final: 0.8768 (mttm)
REVERT: C  179 PHE cc_start: 0.8715 (p90) cc_final: 0.8483 (p90)
REVERT: C  215 TYR cc_start: 0.8611 (m-80) cc_final: 0.8144 (m-10)
REVERT: C  260 GLU cc_start: 0.8587 (pp20) cc_final: 0.8361 (pp20)
REVERT: C  261 MET cc_start: 0.8683 (tmm) cc_final: 0.8323 (tmm)
REVERT: C  312 LYS cc_start: 0.8894 (mttt) cc_final: 0.8591 (mmtt)
REVERT: C  323 ASP cc_start: 0.8077 (t0) cc_final: 0.7848 (t0)
REVERT: A  260 GLU cc_start: 0.7646 (tp30) cc_final: 0.7318 (tp30)
REVERT: B  168 PHE cc_start: 0.8365 (m-80) cc_final: 0.8097 (m-10)
REVERT: B  245 TYR cc_start: 0.8210 (m-80) cc_final: 0.7985 (m-10)
REVERT: B  323 ASP cc_start: 0.7910 (t0) cc_final: 0.7406 (t0)
REVERT: D  179 PHE cc_start: 0.8784 (p90) cc_final: 0.8423 (p90)
REVERT: D  201 TRP cc_start: 0.6300 (m100) cc_final: 0.5987 (m-10)
REVERT: D  228 ASN cc_start: 0.9002 (m-40) cc_final: 0.8745 (m-40)
REVERT: D  231 ARG cc_start: 0.7691 (mtt-85) cc_final: 0.7432 (mtt180)
REVERT: D  312 LYS cc_start: 0.9073 (mttt) cc_final: 0.8804 (mmtt)
REVERT: F  179 PHE cc_start: 0.8840 (p90) cc_final: 0.8605 (p90)
REVERT: F  245 TYR cc_start: 0.8545 (m-80) cc_final: 0.8138 (m-10)
REVERT: F  261 MET cc_start: 0.8563 (tmm) cc_final: 0.8260 (tmm)
REVERT: F  312 LYS cc_start: 0.9131 (mttt) cc_final: 0.8700 (mmtt)
REVERT: G  168 PHE cc_start: 0.8332 (m-80) cc_final: 0.7820 (m-10)
REVERT: G  198 GLU cc_start: 0.8104 (tt0) cc_final: 0.7842 (tm-30)
REVERT: G  260 GLU cc_start: 0.7505 (tp30) cc_final: 0.7051 (tp30)
REVERT: G  306 GLN cc_start: 0.8553 (tt0) cc_final: 0.8112 (tt0)
REVERT: G  312 LYS cc_start: 0.9042 (mttt) cc_final: 0.8638 (mttm)
  outliers start: 1
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1224
  time to fit residues: 43.7419
Evaluate side-chains
  195 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 146 optimal weight:    0.9990
   chunk 48 optimal weight:   20.0000
   chunk 129 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:   40.0000
   chunk 97 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
C 228 ASN
B 318 GLN
D 280 GLN
F 280 GLN
F 318 GLN
G 228 ASN
G 280 GLN
** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.097458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.076739 restraints weight = 33353.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.078444 restraints weight = 20124.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.079547 restraints weight = 14410.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.080013 restraints weight = 11630.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.080572 restraints weight = 10420.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.5833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11823  Z= 0.143
  Angle     :  0.611   6.804  16093  Z= 0.316
  Chirality :  0.045   0.149   1855
  Planarity :  0.003   0.038   2079
  Dihedral  :  5.058  19.933   1666
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.23), residues: 1288
  helix:  1.77 (0.24), residues: 448
  sheet: -1.81 (0.26), residues: 343
  loop : -1.30 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 231 
 TYR   0.018   0.002   TYR B 277 
 PHE   0.014   0.001   PHE D 167 
 TRP   0.010   0.001   TRP G 299 
 HIS   0.001   0.001   HIS G 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (11823)
  covalent geometry    : angle       0.61082 (16093)
  hydrogen bonds       : bond        0.03752 (  639)
  hydrogen bonds       : angle       4.85155 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  158 MET cc_start: 0.5440 (mpp) cc_final: 0.4640 (tpt)
REVERT: E  198 GLU cc_start: 0.7642 (pp20) cc_final: 0.6915 (pp20)
REVERT: E  215 TYR cc_start: 0.8371 (m-80) cc_final: 0.7778 (m-80)
REVERT: E  219 SER cc_start: 0.9018 (p) cc_final: 0.8603 (m)
REVERT: E  312 LYS cc_start: 0.9114 (mttt) cc_final: 0.8695 (mttm)
REVERT: C  205 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8811 (ttmm)
REVERT: C  261 MET cc_start: 0.8560 (tmm) cc_final: 0.8318 (tmm)
REVERT: B  312 LYS cc_start: 0.9037 (mttt) cc_final: 0.8797 (mmtt)
REVERT: D  312 LYS cc_start: 0.9034 (mttt) cc_final: 0.8818 (mttm)
REVERT: F  245 TYR cc_start: 0.8407 (m-80) cc_final: 0.7899 (m-10)
REVERT: F  261 MET cc_start: 0.8451 (tmm) cc_final: 0.8159 (tmm)
REVERT: F  312 LYS cc_start: 0.9091 (mttt) cc_final: 0.8639 (mttm)
REVERT: G  306 GLN cc_start: 0.8531 (tt0) cc_final: 0.8126 (tt0)
REVERT: G  312 LYS cc_start: 0.9048 (mttt) cc_final: 0.8619 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1003
  time to fit residues: 37.5290
Evaluate side-chains
  204 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 127 optimal weight:    9.9990
   chunk 144 optimal weight:    9.9990
   chunk 22 optimal weight:   30.0000
   chunk 150 optimal weight:    0.9980
   chunk 89 optimal weight:   40.0000
   chunk 60 optimal weight:   10.0000
   chunk 147 optimal weight:    0.4980
   chunk 136 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 90 optimal weight:   30.0000
   chunk 139 optimal weight:    9.9990
   overall best weight:    4.4584

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

Flipped N/Q/H residues before XYZ refinement:
D 280 GLN
G 280 GLN
G 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.096473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.078002 restraints weight = 33402.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.079705 restraints weight = 19326.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.080733 restraints weight = 13392.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.081225 restraints weight = 10635.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.081358 restraints weight = 9393.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.6270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11823  Z= 0.201
  Angle     :  0.664   7.640  16093  Z= 0.343
  Chirality :  0.046   0.152   1855
  Planarity :  0.004   0.038   2079
  Dihedral  :  5.167  20.471   1666
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  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: -0.47 (0.23), residues: 1288
  helix:  1.75 (0.24), residues: 462
  sheet: -1.66 (0.26), residues: 343
  loop : -1.23 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 212 
 TYR   0.032   0.002   TYR A 245 
 PHE   0.015   0.002   PHE B 326 
 TRP   0.008   0.002   TRP A 201 
 HIS   0.002   0.001   HIS C 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (11823)
  covalent geometry    : angle       0.66364 (16093)
  hydrogen bonds       : bond        0.03754 (  639)
  hydrogen bonds       : angle       4.86650 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  158 MET cc_start: 0.5361 (mpp) cc_final: 0.4565 (tpt)
REVERT: E  205 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8647 (ttmm)
REVERT: E  219 SER cc_start: 0.9060 (p) cc_final: 0.8688 (m)
REVERT: E  312 LYS cc_start: 0.9102 (mttt) cc_final: 0.8741 (mttm)
REVERT: E  333 MET cc_start: 0.7618 (mmm) cc_final: 0.7392 (mmm)
REVERT: C  205 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8666 (ttmm)
REVERT: A  198 GLU cc_start: 0.7746 (pp20) cc_final: 0.7352 (pp20)
REVERT: B  312 LYS cc_start: 0.9052 (mttt) cc_final: 0.8849 (mmtt)
REVERT: D  158 MET cc_start: 0.5772 (mpp) cc_final: 0.4930 (ttp)
REVERT: D  219 SER cc_start: 0.8969 (p) cc_final: 0.8606 (m)
REVERT: D  312 LYS cc_start: 0.8985 (mttt) cc_final: 0.8774 (mmtt)
REVERT: F  228 ASN cc_start: 0.8303 (m-40) cc_final: 0.8014 (m-40)
REVERT: F  261 MET cc_start: 0.8448 (tmm) cc_final: 0.8243 (tmm)
REVERT: F  312 LYS cc_start: 0.9109 (mttt) cc_final: 0.8676 (mmtt)
REVERT: G  306 GLN cc_start: 0.8566 (tt0) cc_final: 0.8183 (tt0)
REVERT: G  312 LYS cc_start: 0.9058 (mttt) cc_final: 0.8633 (mmtt)
REVERT: G  333 MET cc_start: 0.7895 (mmm) cc_final: 0.7684 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0990
  time to fit residues: 33.7193
Evaluate side-chains
  205 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 22 optimal weight:   30.0000
   chunk 66 optimal weight:   40.0000
   chunk 59 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 134 optimal weight:   50.0000
   chunk 102 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 135 optimal weight:   40.0000
   chunk 6 optimal weight:    3.9990
   chunk 138 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
D 280 GLN
F 280 GLN
G 280 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.097275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.076723 restraints weight = 33189.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.078449 restraints weight = 19524.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.079330 restraints weight = 13727.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.080206 restraints weight = 11227.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.080501 restraints weight = 9729.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.6511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11823  Z= 0.142
  Angle     :  0.590   6.970  16093  Z= 0.306
  Chirality :  0.044   0.147   1855
  Planarity :  0.003   0.024   2079
  Dihedral  :  4.908  20.005   1666
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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: -0.23 (0.23), residues: 1288
  helix:  1.95 (0.24), residues: 462
  sheet: -1.48 (0.26), residues: 343
  loop : -1.14 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 186 
 TYR   0.021   0.002   TYR G 277 
 PHE   0.013   0.002   PHE B 168 
 TRP   0.007   0.001   TRP E 302 
 HIS   0.002   0.001   HIS G 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (11823)
  covalent geometry    : angle       0.59023 (16093)
  hydrogen bonds       : bond        0.03534 (  639)
  hydrogen bonds       : angle       4.61869 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 257
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  198 GLU cc_start: 0.7609 (pp20) cc_final: 0.6991 (pp20)
REVERT: E  205 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8665 (ttmm)
REVERT: E  219 SER cc_start: 0.9002 (p) cc_final: 0.8606 (m)
REVERT: E  312 LYS cc_start: 0.9103 (mttt) cc_final: 0.8728 (mmtt)
REVERT: E  333 MET cc_start: 0.7774 (mmm) cc_final: 0.7560 (mmm)
REVERT: A  158 MET cc_start: 0.5481 (mtm) cc_final: 0.4757 (ttm)
REVERT: A  198 GLU cc_start: 0.7706 (pp20) cc_final: 0.7384 (pp20)
REVERT: B  158 MET cc_start: 0.4670 (ptp) cc_final: 0.3123 (tmm)
REVERT: B  219 SER cc_start: 0.9215 (p) cc_final: 0.8818 (m)
REVERT: B  312 LYS cc_start: 0.9048 (mttt) cc_final: 0.8842 (mmtt)
REVERT: D  158 MET cc_start: 0.5592 (mpp) cc_final: 0.5020 (ttp)
REVERT: D  161 LYS cc_start: 0.6415 (tppt) cc_final: 0.6014 (tppt)
REVERT: D  312 LYS cc_start: 0.9100 (mttt) cc_final: 0.8813 (mttm)
REVERT: F  158 MET cc_start: 0.5727 (mtm) cc_final: 0.5298 (mpp)
REVERT: F  312 LYS cc_start: 0.9113 (mttt) cc_final: 0.8667 (mmtt)
REVERT: G  312 LYS cc_start: 0.9135 (mttt) cc_final: 0.8758 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 257
  average time/residue: 0.1005
  time to fit residues: 37.0903
Evaluate side-chains
  205 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 149 optimal weight:    9.9990
   chunk 78 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 26 optimal weight:   40.0000
   chunk 31 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 110 optimal weight:   30.0000
   chunk 14 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
D 280 GLN
F 228 ASN
F 280 GLN
G 280 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.094586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.073966 restraints weight = 33296.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.075602 restraints weight = 20037.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.076693 restraints weight = 14467.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.077125 restraints weight = 11765.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.077628 restraints weight = 10597.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.6749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  11823  Z= 0.268
  Angle     :  0.716   8.093  16093  Z= 0.374
  Chirality :  0.047   0.162   1855
  Planarity :  0.004   0.027   2079
  Dihedral  :  5.324  20.030   1666
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  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: -0.47 (0.23), residues: 1288
  helix:  1.71 (0.23), residues: 462
  sheet: -1.54 (0.26), residues: 343
  loop : -1.29 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 235 
 TYR   0.029   0.002   TYR D 245 
 PHE   0.016   0.002   PHE B 326 
 TRP   0.013   0.002   TRP D 201 
 HIS   0.003   0.001   HIS D 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 (11823)
  covalent geometry    : angle       0.71551 (16093)
  hydrogen bonds       : bond        0.03936 (  639)
  hydrogen bonds       : angle       4.93829 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  158 MET cc_start: 0.5288 (ptp) cc_final: 0.5034 (ttp)
REVERT: E  205 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8712 (ttmm)
REVERT: E  312 LYS cc_start: 0.9023 (mttt) cc_final: 0.8789 (mmtt)
REVERT: C  261 MET cc_start: 0.8658 (tmm) cc_final: 0.8419 (tmm)
REVERT: A  198 GLU cc_start: 0.7875 (pp20) cc_final: 0.7305 (pp20)
REVERT: B  158 MET cc_start: 0.4473 (ptp) cc_final: 0.2973 (tmm)
REVERT: B  219 SER cc_start: 0.9214 (p) cc_final: 0.8869 (m)
REVERT: B  312 LYS cc_start: 0.9047 (mttt) cc_final: 0.8754 (mmtt)
REVERT: D  161 LYS cc_start: 0.6731 (tppt) cc_final: 0.6340 (tppt)
REVERT: D  168 PHE cc_start: 0.8429 (m-80) cc_final: 0.7839 (m-10)
REVERT: D  212 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7417 (mtt180)
REVERT: D  312 LYS cc_start: 0.9050 (mttt) cc_final: 0.8806 (mttm)
REVERT: F  158 MET cc_start: 0.5766 (mtm) cc_final: 0.5343 (mpp)
REVERT: F  312 LYS cc_start: 0.9094 (mttt) cc_final: 0.8853 (mttt)
REVERT: G  201 TRP cc_start: 0.4661 (m-10) cc_final: 0.4419 (m-10)
REVERT: G  312 LYS cc_start: 0.9146 (mttt) cc_final: 0.8796 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.0978
  time to fit residues: 32.8111
Evaluate side-chains
  188 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 153 optimal weight:    4.9990
   chunk 117 optimal weight:    0.0020
   chunk 121 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9990
   chunk 23 optimal weight:   40.0000
   chunk 146 optimal weight:    4.9990
   chunk 46 optimal weight:   40.0000
   overall best weight:    1.4994

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

Flipped N/Q/H residues before XYZ refinement:
C 287 ASN
D 280 GLN
D 307 GLN
F 228 ASN
F 280 GLN
G 280 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.098939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.078264 restraints weight = 32865.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.080017 restraints weight = 19469.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.081132 restraints weight = 13848.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.081834 restraints weight = 11138.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.082100 restraints weight = 9827.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.6911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11823  Z= 0.119
  Angle     :  0.588   7.041  16093  Z= 0.306
  Chirality :  0.044   0.183   1855
  Planarity :  0.003   0.023   2079
  Dihedral  :  4.882  19.687   1666
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.72 %
    Favored  : 99.19 %
  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: -0.07 (0.23), residues: 1288
  helix:  2.09 (0.24), residues: 462
  sheet: -1.27 (0.26), residues: 343
  loop : -1.16 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 235 
 TYR   0.035   0.002   TYR B 245 
 PHE   0.015   0.001   PHE A 168 
 TRP   0.009   0.001   TRP E 302 
 HIS   0.003   0.001   HIS G 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (11823)
  covalent geometry    : angle       0.58802 (16093)
  hydrogen bonds       : bond        0.03430 (  639)
  hydrogen bonds       : angle       4.47994 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 257
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  158 MET cc_start: 0.5874 (ptp) cc_final: 0.5090 (ttp)
REVERT: E  198 GLU cc_start: 0.7591 (pp20) cc_final: 0.6863 (pp20)
REVERT: E  205 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8639 (ttmm)
REVERT: E  219 SER cc_start: 0.9120 (p) cc_final: 0.8619 (m)
REVERT: E  260 GLU cc_start: 0.8468 (pp20) cc_final: 0.7985 (pp20)
REVERT: E  312 LYS cc_start: 0.8990 (mttt) cc_final: 0.8657 (mmtt)
REVERT: C  261 MET cc_start: 0.8621 (tmm) cc_final: 0.8416 (tmm)
REVERT: A  158 MET cc_start: 0.5839 (mtm) cc_final: 0.4986 (ttm)
REVERT: A  198 GLU cc_start: 0.7787 (pp20) cc_final: 0.7368 (pp20)
REVERT: A  240 THR cc_start: 0.8337 (p) cc_final: 0.8093 (p)
REVERT: B  158 MET cc_start: 0.4902 (ptp) cc_final: 0.3557 (tmm)
REVERT: B  312 LYS cc_start: 0.9046 (mttt) cc_final: 0.8701 (mmtt)
REVERT: D  161 LYS cc_start: 0.6319 (tppt) cc_final: 0.6072 (tppt)
REVERT: D  165 SER cc_start: 0.8447 (p) cc_final: 0.8168 (p)
REVERT: D  168 PHE cc_start: 0.8278 (m-80) cc_final: 0.8050 (m-10)
REVERT: D  219 SER cc_start: 0.8986 (p) cc_final: 0.8676 (m)
REVERT: D  312 LYS cc_start: 0.9101 (mttt) cc_final: 0.8791 (mttm)
REVERT: F  158 MET cc_start: 0.5740 (mtm) cc_final: 0.5351 (mpp)
REVERT: F  291 TYR cc_start: 0.8177 (t80) cc_final: 0.7869 (t80)
REVERT: F  312 LYS cc_start: 0.9121 (mttt) cc_final: 0.8793 (mttt)
REVERT: G  158 MET cc_start: 0.5499 (mtm) cc_final: 0.5189 (mpp)
REVERT: G  312 LYS cc_start: 0.9182 (mttt) cc_final: 0.8775 (mttm)
  outliers start: 1
  outliers final: 0
  residues processed: 257
  average time/residue: 0.1066
  time to fit residues: 38.6768
Evaluate side-chains
  202 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 16 optimal weight:    0.0370
   chunk 41 optimal weight:    9.9990
   chunk 121 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   chunk 89 optimal weight:   40.0000
   chunk 59 optimal weight:    0.0970
   chunk 61 optimal weight:    7.9990
   chunk 147 optimal weight:    0.0970
   chunk 46 optimal weight:   40.0000
   chunk 29 optimal weight:    0.9990
   chunk 78 optimal weight:   20.0000
   overall best weight:    1.4458

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN
F 211 ASN
F 228 ASN
G 280 GLN
G 318 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.099479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.078623 restraints weight = 32654.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.080359 restraints weight = 19450.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.081495 restraints weight = 13900.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.082172 restraints weight = 11265.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.082373 restraints weight = 9954.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.7120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11823  Z= 0.116
  Angle     :  0.586   6.566  16093  Z= 0.306
  Chirality :  0.044   0.167   1855
  Planarity :  0.003   0.023   2079
  Dihedral  :  4.721  18.287   1666
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.54 %
    Favored  : 99.28 %
  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:  0.14 (0.23), residues: 1288
  helix:  2.41 (0.24), residues: 448
  sheet: -1.13 (0.27), residues: 343
  loop : -1.13 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 235 
 TYR   0.014   0.001   TYR G 277 
 PHE   0.015   0.001   PHE A 168 
 TRP   0.008   0.001   TRP D 201 
 HIS   0.002   0.000   HIS G 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11823)
  covalent geometry    : angle       0.58593 (16093)
  hydrogen bonds       : bond        0.03383 (  639)
  hydrogen bonds       : angle       4.40009 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 251
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  158 MET cc_start: 0.5608 (ptp) cc_final: 0.5080 (ttp)
REVERT: E  198 GLU cc_start: 0.7616 (pp20) cc_final: 0.6819 (pp20)
REVERT: E  219 SER cc_start: 0.9008 (p) cc_final: 0.8555 (m)
REVERT: E  312 LYS cc_start: 0.9020 (mttt) cc_final: 0.8758 (mmtt)
REVERT: A  158 MET cc_start: 0.6004 (mtm) cc_final: 0.5386 (ttm)
REVERT: A  198 GLU cc_start: 0.7658 (pp20) cc_final: 0.7231 (pp20)
REVERT: B  158 MET cc_start: 0.4870 (ptp) cc_final: 0.3532 (tmm)
REVERT: B  219 SER cc_start: 0.9087 (p) cc_final: 0.8584 (m)
REVERT: B  312 LYS cc_start: 0.9058 (mttt) cc_final: 0.8748 (mmtt)
REVERT: D  212 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7646 (mtt180)
REVERT: D  312 LYS cc_start: 0.9087 (mttt) cc_final: 0.8877 (mptt)
REVERT: F  158 MET cc_start: 0.5608 (mtm) cc_final: 0.5360 (mpp)
REVERT: F  291 TYR cc_start: 0.7945 (t80) cc_final: 0.7741 (t80)
REVERT: F  312 LYS cc_start: 0.9144 (mttt) cc_final: 0.8644 (mptt)
REVERT: G  312 LYS cc_start: 0.9132 (mttt) cc_final: 0.8878 (mttm)
  outliers start: 2
  outliers final: 0
  residues processed: 252
  average time/residue: 0.0950
  time to fit residues: 34.8618
Evaluate side-chains
  201 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 24 optimal weight:   40.0000
   chunk 30 optimal weight:    7.9990
   chunk 113 optimal weight:   40.0000
   chunk 112 optimal weight:   40.0000
   chunk 142 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 234 ASN
F 211 ASN
** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 211 ASN
G 280 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.098328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.077496 restraints weight = 33298.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.079217 restraints weight = 19863.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.080308 restraints weight = 14230.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.081003 restraints weight = 11544.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.081268 restraints weight = 10204.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.7166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11823  Z= 0.143
  Angle     :  0.614   6.938  16093  Z= 0.321
  Chirality :  0.044   0.178   1855
  Planarity :  0.003   0.024   2079
  Dihedral  :  4.807  18.188   1666
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.27 %
    Favored  : 99.64 %
  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:  0.13 (0.23), residues: 1288
  helix:  2.31 (0.24), residues: 455
  sheet: -1.06 (0.27), residues: 343
  loop : -1.14 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 231 
 TYR   0.021   0.002   TYR B 245 
 PHE   0.017   0.002   PHE B 175 
 TRP   0.007   0.001   TRP D 201 
 HIS   0.002   0.001   HIS G 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (11823)
  covalent geometry    : angle       0.61379 (16093)
  hydrogen bonds       : bond        0.03528 (  639)
  hydrogen bonds       : angle       4.48564 ( 1980)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 256
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  158 MET cc_start: 0.5614 (ptp) cc_final: 0.5115 (ttp)
REVERT: E  198 GLU cc_start: 0.7673 (pp20) cc_final: 0.7408 (pp20)
REVERT: E  219 SER cc_start: 0.9011 (p) cc_final: 0.8525 (m)
REVERT: E  312 LYS cc_start: 0.9058 (mttt) cc_final: 0.8708 (mmtt)
REVERT: C  261 MET cc_start: 0.8657 (tmm) cc_final: 0.8396 (tmm)
REVERT: A  158 MET cc_start: 0.5907 (mtm) cc_final: 0.5193 (ttm)
REVERT: A  198 GLU cc_start: 0.7704 (pp20) cc_final: 0.7240 (pp20)
REVERT: A  277 TYR cc_start: 0.8861 (m-80) cc_final: 0.8646 (m-10)
REVERT: B  158 MET cc_start: 0.5087 (ptp) cc_final: 0.3424 (tmm)
REVERT: B  180 SER cc_start: 0.6915 (p) cc_final: 0.6710 (t)
REVERT: B  219 SER cc_start: 0.9034 (p) cc_final: 0.8601 (m)
REVERT: B  220 LEU cc_start: 0.8768 (tp) cc_final: 0.8558 (tt)
REVERT: B  312 LYS cc_start: 0.9055 (mttt) cc_final: 0.8773 (mmtt)
REVERT: D  212 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7520 (mtt180)
REVERT: D  219 SER cc_start: 0.8966 (p) cc_final: 0.8595 (m)
REVERT: F  228 ASN cc_start: 0.8401 (m110) cc_final: 0.7934 (m-40)
REVERT: F  232 MET cc_start: 0.8203 (ptp) cc_final: 0.7885 (ptp)
REVERT: F  307 GLN cc_start: 0.8822 (tp40) cc_final: 0.8564 (tp40)
REVERT: F  312 LYS cc_start: 0.9112 (mttt) cc_final: 0.8652 (mptt)
REVERT: G  158 MET cc_start: 0.5395 (mpp) cc_final: 0.4872 (ptp)
REVERT: G  312 LYS cc_start: 0.9179 (mttt) cc_final: 0.8857 (mttm)
  outliers start: 1
  outliers final: 0
  residues processed: 257
  average time/residue: 0.0959
  time to fit residues: 36.0921
Evaluate side-chains
  209 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 128 optimal weight:    9.9990
   chunk 91 optimal weight:   40.0000
   chunk 99 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 48 optimal weight:    8.9990
   chunk 70 optimal weight:   20.0000
   chunk 148 optimal weight:    0.7980
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
C 211 ASN
C 234 ASN
D 280 GLN
F 211 ASN
** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 280 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.097318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.076672 restraints weight = 33499.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.078397 restraints weight = 19930.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.079495 restraints weight = 14213.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.080207 restraints weight = 11510.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.080598 restraints weight = 10106.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.7290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11823  Z= 0.165
  Angle     :  0.643  12.003  16093  Z= 0.336
  Chirality :  0.045   0.156   1855
  Planarity :  0.003   0.034   2079
  Dihedral  :  4.935  18.731   1666
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.27 %
    Favored  : 99.55 %
  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:  0.01 (0.23), residues: 1288
  helix:  2.04 (0.24), residues: 469
  sheet: -1.03 (0.27), residues: 343
  loop : -1.22 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 236 
 TYR   0.019   0.002   TYR C 245 
 PHE   0.017   0.002   PHE B 175 
 TRP   0.007   0.001   TRP F 201 
 HIS   0.002   0.001   HIS G 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (11823)
  covalent geometry    : angle       0.64317 (16093)
  hydrogen bonds       : bond        0.03596 (  639)
  hydrogen bonds       : angle       4.55477 ( 1980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1634.50 seconds
wall clock time: 29 minutes 4.42 seconds (1744.42 seconds total)