Starting phenix.real_space_refine
on Wed Mar  4 16:47:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m67_30115/03_2026/6m67_30115.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m67_30115/03_2026/6m67_30115.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m67_30115/03_2026/6m67_30115.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m67_30115/03_2026/6m67_30115.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m67_30115/03_2026/6m67_30115.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m67_30115/03_2026/6m67_30115.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.024 sd=   0.201
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      70      5.16       5
     C    9975      2.51       5
     N    2303      2.21       5
     O    2590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  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: 14938
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2134
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 11, 'TRANS': 253}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 2.09, per 1000 atoms: 0.14
  Number of scatterers: 14938
  At special positions: 0
  Unit cell: (112.042, 112.042, 117.327, 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      70     16.00
     O    2590      8.00
     N    2303      7.00
     C    9975      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 265 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 265 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 265 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  66 " - pdb=" SG  CYS D 265 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  66 " - pdb=" SG  CYS E 265 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  66 " - pdb=" SG  CYS F 265 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  66 " - pdb=" SG  CYS G 265 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  84 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  84 " - pdb=" SG  CYS C 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  84 " - pdb=" SG  CYS D 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  84 " - pdb=" SG  CYS F 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  84 " - pdb=" SG  CYS G 246 " distance=2.03

  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: 1.11
  Conformation dependent library (CDL) restraints added in 709.6 milliseconds
  

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3612

  Finding SS restraints...
    Secondary structure from input PDB file:
      126 helices and 7 sheets defined
      72.9% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 59
      removed outlier: 4.020A  pdb=" N   ILE A  41 " --> pdb=" O   MET A  37 " (cutoff:3.500A)
      Proline residue:  A  46  - end of helix
      removed outlier: 3.739A  pdb=" N   SER A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 87
    Processing helix  chain 'A' and resid 103 through 107
      removed outlier: 4.528A  pdb=" N   HIS A 106 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS A 107 " --> pdb=" O   TRP A 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 103 through 107'
    Processing helix  chain 'A' and resid 108 through 131
      removed outlier: 3.766A  pdb=" N   LEU A 115 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      Proline residue:  A 123  - end of helix
    Processing helix  chain 'A' and resid 131 through 156
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 198 through 203
      removed outlier: 3.682A  pdb=" N   LYS A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 209
      No H-bonds generated for 'chain 'A' and resid 207 through 209'
    Processing helix  chain 'A' and resid 210 through 238
      removed outlier: 4.788A  pdb=" N   CYS A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ARG A 217 " --> pdb=" O   TYR A 213 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 221 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   SER A 236 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 238 " --> pdb=" O   TYR A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 256
      removed outlier: 4.100A  pdb=" N   ASN A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 274
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 287 through 293
    Processing helix  chain 'A' and resid 294 through 300
      removed outlier: 5.063A  pdb=" N   VAL A 297 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      Proline residue:  A 298  - end of helix
      No H-bonds generated for 'chain 'A' and resid 294 through 300'
    Processing helix  chain 'A' and resid 311 through 316
      removed outlier: 3.925A  pdb=" N   ASP A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 320
    Processing helix  chain 'A' and resid 329 through 336
      removed outlier: 4.076A  pdb=" N   GLU A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 59
      removed outlier: 4.019A  pdb=" N   ILE B  41 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      Proline residue:  B  46  - end of helix
      removed outlier: 3.738A  pdb=" N   SER B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 87
    Processing helix  chain 'B' and resid 103 through 107
      removed outlier: 4.528A  pdb=" N   HIS B 106 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS B 107 " --> pdb=" O   TRP B 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 103 through 107'
    Processing helix  chain 'B' and resid 108 through 131
      removed outlier: 3.766A  pdb=" N   LEU B 115 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      Proline residue:  B 123  - end of helix
    Processing helix  chain 'B' and resid 131 through 156
    Processing helix  chain 'B' and resid 195 through 197
      No H-bonds generated for 'chain 'B' and resid 195 through 197'
    Processing helix  chain 'B' and resid 198 through 203
      removed outlier: 3.682A  pdb=" N   LYS B 203 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 209
      No H-bonds generated for 'chain 'B' and resid 207 through 209'
    Processing helix  chain 'B' and resid 210 through 238
      removed outlier: 4.788A  pdb=" N   CYS B 216 " --> pdb=" O   LYS B 212 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ARG B 217 " --> pdb=" O   TYR B 213 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU B 218 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 221 " --> pdb=" O   ARG B 217 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE B 223 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE B 235 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   SER B 236 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B 238 " --> pdb=" O   TYR B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 256
      removed outlier: 4.099A  pdb=" N   ASN B 255 " --> pdb=" O   GLY B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 274
    Processing helix  chain 'B' and resid 275 through 277
      No H-bonds generated for 'chain 'B' and resid 275 through 277'
    Processing helix  chain 'B' and resid 278 through 286
    Processing helix  chain 'B' and resid 287 through 293
    Processing helix  chain 'B' and resid 294 through 300
      removed outlier: 5.063A  pdb=" N   VAL B 297 " --> pdb=" O   THR B 294 " (cutoff:3.500A)
      Proline residue:  B 298  - end of helix
      No H-bonds generated for 'chain 'B' and resid 294 through 300'
    Processing helix  chain 'B' and resid 311 through 316
      removed outlier: 3.925A  pdb=" N   ASP B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 320
    Processing helix  chain 'B' and resid 329 through 336
      removed outlier: 4.076A  pdb=" N   GLU B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 59
      removed outlier: 4.019A  pdb=" N   ILE C  41 " --> pdb=" O   MET C  37 " (cutoff:3.500A)
      Proline residue:  C  46  - end of helix
      removed outlier: 3.738A  pdb=" N   SER C  59 " --> pdb=" O   ALA C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 87
    Processing helix  chain 'C' and resid 103 through 107
      removed outlier: 4.528A  pdb=" N   HIS C 106 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS C 107 " --> pdb=" O   TRP C 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 103 through 107'
    Processing helix  chain 'C' and resid 108 through 131
      removed outlier: 3.765A  pdb=" N   LEU C 115 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      Proline residue:  C 123  - end of helix
    Processing helix  chain 'C' and resid 131 through 156
    Processing helix  chain 'C' and resid 195 through 197
      No H-bonds generated for 'chain 'C' and resid 195 through 197'
    Processing helix  chain 'C' and resid 198 through 203
      removed outlier: 3.682A  pdb=" N   LYS C 203 " --> pdb=" O   TYR C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 209
      No H-bonds generated for 'chain 'C' and resid 207 through 209'
    Processing helix  chain 'C' and resid 210 through 238
      removed outlier: 4.788A  pdb=" N   CYS C 216 " --> pdb=" O   LYS C 212 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ARG C 217 " --> pdb=" O   TYR C 213 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU C 218 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU C 221 " --> pdb=" O   ARG C 217 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE C 223 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE C 235 " --> pdb=" O   LEU C 231 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   SER C 236 " --> pdb=" O   GLY C 232 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER C 238 " --> pdb=" O   TYR C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 256
      removed outlier: 4.100A  pdb=" N   ASN C 255 " --> pdb=" O   GLY C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 274
    Processing helix  chain 'C' and resid 275 through 277
      No H-bonds generated for 'chain 'C' and resid 275 through 277'
    Processing helix  chain 'C' and resid 278 through 286
    Processing helix  chain 'C' and resid 287 through 293
    Processing helix  chain 'C' and resid 294 through 300
      removed outlier: 5.063A  pdb=" N   VAL C 297 " --> pdb=" O   THR C 294 " (cutoff:3.500A)
      Proline residue:  C 298  - end of helix
      No H-bonds generated for 'chain 'C' and resid 294 through 300'
    Processing helix  chain 'C' and resid 311 through 316
      removed outlier: 3.925A  pdb=" N   ASP C 316 " --> pdb=" O   LEU C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 317 through 320
    Processing helix  chain 'C' and resid 329 through 336
      removed outlier: 4.076A  pdb=" N   GLU C 336 " --> pdb=" O   ASN C 332 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 59
      removed outlier: 4.019A  pdb=" N   ILE D  41 " --> pdb=" O   MET D  37 " (cutoff:3.500A)
      Proline residue:  D  46  - end of helix
      removed outlier: 3.739A  pdb=" N   SER D  59 " --> pdb=" O   ALA D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 87
    Processing helix  chain 'D' and resid 103 through 107
      removed outlier: 4.528A  pdb=" N   HIS D 106 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS D 107 " --> pdb=" O   TRP D 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 103 through 107'
    Processing helix  chain 'D' and resid 108 through 131
      removed outlier: 3.766A  pdb=" N   LEU D 115 " --> pdb=" O   TYR D 111 " (cutoff:3.500A)
      Proline residue:  D 123  - end of helix
    Processing helix  chain 'D' and resid 131 through 156
    Processing helix  chain 'D' and resid 195 through 197
      No H-bonds generated for 'chain 'D' and resid 195 through 197'
    Processing helix  chain 'D' and resid 198 through 203
      removed outlier: 3.681A  pdb=" N   LYS D 203 " --> pdb=" O   TYR D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 209
      No H-bonds generated for 'chain 'D' and resid 207 through 209'
    Processing helix  chain 'D' and resid 210 through 238
      removed outlier: 4.787A  pdb=" N   CYS D 216 " --> pdb=" O   LYS D 212 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ARG D 217 " --> pdb=" O   TYR D 213 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU D 218 " --> pdb=" O   ILE D 214 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU D 221 " --> pdb=" O   ARG D 217 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE D 223 " --> pdb=" O   LEU D 219 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE D 235 " --> pdb=" O   LEU D 231 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   SER D 236 " --> pdb=" O   GLY D 232 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER D 238 " --> pdb=" O   TYR D 234 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 256
      removed outlier: 4.100A  pdb=" N   ASN D 255 " --> pdb=" O   GLY D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 274
    Processing helix  chain 'D' and resid 275 through 277
      No H-bonds generated for 'chain 'D' and resid 275 through 277'
    Processing helix  chain 'D' and resid 278 through 286
    Processing helix  chain 'D' and resid 287 through 293
    Processing helix  chain 'D' and resid 294 through 300
      removed outlier: 5.064A  pdb=" N   VAL D 297 " --> pdb=" O   THR D 294 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      No H-bonds generated for 'chain 'D' and resid 294 through 300'
    Processing helix  chain 'D' and resid 311 through 316
      removed outlier: 3.925A  pdb=" N   ASP D 316 " --> pdb=" O   LEU D 312 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 317 through 320
    Processing helix  chain 'D' and resid 329 through 336
      removed outlier: 4.076A  pdb=" N   GLU D 336 " --> pdb=" O   ASN D 332 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 36 through 59
      removed outlier: 4.019A  pdb=" N   ILE E  41 " --> pdb=" O   MET E  37 " (cutoff:3.500A)
      Proline residue:  E  46  - end of helix
      removed outlier: 3.739A  pdb=" N   SER E  59 " --> pdb=" O   ALA E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 87
    Processing helix  chain 'E' and resid 103 through 107
      removed outlier: 4.529A  pdb=" N   HIS E 106 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS E 107 " --> pdb=" O   TRP E 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 103 through 107'
    Processing helix  chain 'E' and resid 108 through 131
      removed outlier: 3.766A  pdb=" N   LEU E 115 " --> pdb=" O   TYR E 111 " (cutoff:3.500A)
      Proline residue:  E 123  - end of helix
    Processing helix  chain 'E' and resid 131 through 156
    Processing helix  chain 'E' and resid 195 through 197
      No H-bonds generated for 'chain 'E' and resid 195 through 197'
    Processing helix  chain 'E' and resid 198 through 203
      removed outlier: 3.682A  pdb=" N   LYS E 203 " --> pdb=" O   TYR E 199 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 209
      No H-bonds generated for 'chain 'E' and resid 207 through 209'
    Processing helix  chain 'E' and resid 210 through 238
      removed outlier: 4.788A  pdb=" N   CYS E 216 " --> pdb=" O   LYS E 212 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ARG E 217 " --> pdb=" O   TYR E 213 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU E 218 " --> pdb=" O   ILE E 214 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU E 221 " --> pdb=" O   ARG E 217 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE E 223 " --> pdb=" O   LEU E 219 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE E 235 " --> pdb=" O   LEU E 231 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   SER E 236 " --> pdb=" O   GLY E 232 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER E 238 " --> pdb=" O   TYR E 234 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 256
      removed outlier: 4.099A  pdb=" N   ASN E 255 " --> pdb=" O   GLY E 251 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 274
    Processing helix  chain 'E' and resid 275 through 277
      No H-bonds generated for 'chain 'E' and resid 275 through 277'
    Processing helix  chain 'E' and resid 278 through 286
    Processing helix  chain 'E' and resid 287 through 293
    Processing helix  chain 'E' and resid 294 through 300
      removed outlier: 5.064A  pdb=" N   VAL E 297 " --> pdb=" O   THR E 294 " (cutoff:3.500A)
      Proline residue:  E 298  - end of helix
      No H-bonds generated for 'chain 'E' and resid 294 through 300'
    Processing helix  chain 'E' and resid 311 through 316
      removed outlier: 3.925A  pdb=" N   ASP E 316 " --> pdb=" O   LEU E 312 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 317 through 320
    Processing helix  chain 'E' and resid 329 through 336
      removed outlier: 4.076A  pdb=" N   GLU E 336 " --> pdb=" O   ASN E 332 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 36 through 59
      removed outlier: 4.020A  pdb=" N   ILE F  41 " --> pdb=" O   MET F  37 " (cutoff:3.500A)
      Proline residue:  F  46  - end of helix
      removed outlier: 3.738A  pdb=" N   SER F  59 " --> pdb=" O   ALA F  55 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 87
    Processing helix  chain 'F' and resid 103 through 107
      removed outlier: 4.528A  pdb=" N   HIS F 106 " --> pdb=" O   LEU F 103 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS F 107 " --> pdb=" O   TRP F 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 103 through 107'
    Processing helix  chain 'F' and resid 108 through 131
      removed outlier: 3.765A  pdb=" N   LEU F 115 " --> pdb=" O   TYR F 111 " (cutoff:3.500A)
      Proline residue:  F 123  - end of helix
    Processing helix  chain 'F' and resid 131 through 156
    Processing helix  chain 'F' and resid 195 through 197
      No H-bonds generated for 'chain 'F' and resid 195 through 197'
    Processing helix  chain 'F' and resid 198 through 203
      removed outlier: 3.682A  pdb=" N   LYS F 203 " --> pdb=" O   TYR F 199 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 207 through 209
      No H-bonds generated for 'chain 'F' and resid 207 through 209'
    Processing helix  chain 'F' and resid 210 through 238
      removed outlier: 4.788A  pdb=" N   CYS F 216 " --> pdb=" O   LYS F 212 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ARG F 217 " --> pdb=" O   TYR F 213 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU F 218 " --> pdb=" O   ILE F 214 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU F 221 " --> pdb=" O   ARG F 217 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE F 223 " --> pdb=" O   LEU F 219 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE F 235 " --> pdb=" O   LEU F 231 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   SER F 236 " --> pdb=" O   GLY F 232 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER F 238 " --> pdb=" O   TYR F 234 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 248 through 256
      removed outlier: 4.100A  pdb=" N   ASN F 255 " --> pdb=" O   GLY F 251 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 269 through 274
    Processing helix  chain 'F' and resid 275 through 277
      No H-bonds generated for 'chain 'F' and resid 275 through 277'
    Processing helix  chain 'F' and resid 278 through 286
    Processing helix  chain 'F' and resid 287 through 293
    Processing helix  chain 'F' and resid 294 through 300
      removed outlier: 5.064A  pdb=" N   VAL F 297 " --> pdb=" O   THR F 294 " (cutoff:3.500A)
      Proline residue:  F 298  - end of helix
      No H-bonds generated for 'chain 'F' and resid 294 through 300'
    Processing helix  chain 'F' and resid 311 through 316
      removed outlier: 3.925A  pdb=" N   ASP F 316 " --> pdb=" O   LEU F 312 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 317 through 320
    Processing helix  chain 'F' and resid 329 through 336
      removed outlier: 4.076A  pdb=" N   GLU F 336 " --> pdb=" O   ASN F 332 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 59
      removed outlier: 4.019A  pdb=" N   ILE G  41 " --> pdb=" O   MET G  37 " (cutoff:3.500A)
      Proline residue:  G  46  - end of helix
      removed outlier: 3.738A  pdb=" N   SER G  59 " --> pdb=" O   ALA G  55 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 74 through 87
    Processing helix  chain 'G' and resid 103 through 107
      removed outlier: 4.528A  pdb=" N   HIS G 106 " --> pdb=" O   LEU G 103 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS G 107 " --> pdb=" O   TRP G 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 103 through 107'
    Processing helix  chain 'G' and resid 108 through 131
      removed outlier: 3.765A  pdb=" N   LEU G 115 " --> pdb=" O   TYR G 111 " (cutoff:3.500A)
      Proline residue:  G 123  - end of helix
    Processing helix  chain 'G' and resid 131 through 156
    Processing helix  chain 'G' and resid 195 through 197
      No H-bonds generated for 'chain 'G' and resid 195 through 197'
    Processing helix  chain 'G' and resid 198 through 203
      removed outlier: 3.682A  pdb=" N   LYS G 203 " --> pdb=" O   TYR G 199 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 207 through 209
      No H-bonds generated for 'chain 'G' and resid 207 through 209'
    Processing helix  chain 'G' and resid 210 through 238
      removed outlier: 4.787A  pdb=" N   CYS G 216 " --> pdb=" O   LYS G 212 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ARG G 217 " --> pdb=" O   TYR G 213 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU G 218 " --> pdb=" O   ILE G 214 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU G 221 " --> pdb=" O   ARG G 217 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE G 223 " --> pdb=" O   LEU G 219 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE G 235 " --> pdb=" O   LEU G 231 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   SER G 236 " --> pdb=" O   GLY G 232 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER G 238 " --> pdb=" O   TYR G 234 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 248 through 256
      removed outlier: 4.100A  pdb=" N   ASN G 255 " --> pdb=" O   GLY G 251 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 269 through 274
    Processing helix  chain 'G' and resid 275 through 277
      No H-bonds generated for 'chain 'G' and resid 275 through 277'
    Processing helix  chain 'G' and resid 278 through 286
    Processing helix  chain 'G' and resid 287 through 293
    Processing helix  chain 'G' and resid 294 through 300
      removed outlier: 5.063A  pdb=" N   VAL G 297 " --> pdb=" O   THR G 294 " (cutoff:3.500A)
      Proline residue:  G 298  - end of helix
      No H-bonds generated for 'chain 'G' and resid 294 through 300'
    Processing helix  chain 'G' and resid 311 through 316
      removed outlier: 3.925A  pdb=" N   ASP G 316 " --> pdb=" O   LEU G 312 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 317 through 320
    Processing helix  chain 'G' and resid 329 through 336
      removed outlier: 4.076A  pdb=" N   GLU G 336 " --> pdb=" O   ASN G 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65
      removed outlier: 3.523A  pdb=" N   SER A  65 " --> pdb=" O   LYS A 266 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65
      removed outlier: 3.522A  pdb=" N   SER B  65 " --> pdb=" O   LYS B 266 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65
      removed outlier: 3.523A  pdb=" N   SER C  65 " --> pdb=" O   LYS C 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65
      removed outlier: 3.523A  pdb=" N   SER D  65 " --> pdb=" O   LYS D 266 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65
      removed outlier: 3.523A  pdb=" N   SER E  65 " --> pdb=" O   LYS E 266 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65
      removed outlier: 3.523A  pdb=" N   SER F  65 " --> pdb=" O   LYS F 266 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65
      removed outlier: 3.523A  pdb=" N   SER G  65 " --> pdb=" O   LYS G 266 " (cutoff:3.500A)

    736 hydrogen bonds defined for protein.
    2187 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.08

  Time building geometry restraints manager: 1.46 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: 4336
        1.34 -     1.46: 3078
        1.46 -     1.57: 7811
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 15309
  Sorted by residual:
  bond pdb=" C   PRO A 123 "
       pdb=" N   PRO A 124 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.36e-02 5.41e+03 2.74e+00
  bond pdb=" C   PRO C 123 "
       pdb=" N   PRO C 124 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.022 1.36e-02 5.41e+03 2.74e+00
  bond pdb=" C   PRO B 123 "
       pdb=" N   PRO B 124 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.022 1.36e-02 5.41e+03 2.65e+00
  bond pdb=" C   PRO G 123 "
       pdb=" N   PRO G 124 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.36e-02 5.41e+03 2.64e+00
  bond pdb=" C   PRO F 123 "
       pdb=" N   PRO F 124 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.36e-02 5.41e+03 2.61e+00
  ... (remaining 15304 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 19294
        1.83 -     3.66: 1088
        3.66 -     5.50: 287
        5.50 -     7.33: 100
        7.33 -     9.16: 56
  Bond angle restraints: 20825
  Sorted by residual:
  angle pdb=" N   THR D 314 "
        pdb=" CA  THR D 314 "
        pdb=" C   THR D 314 "
      ideal   model   delta    sigma   weight residual
     114.56  108.03    6.53 1.27e+00 6.20e-01 2.65e+01
  angle pdb=" N   THR B 314 "
        pdb=" CA  THR B 314 "
        pdb=" C   THR B 314 "
      ideal   model   delta    sigma   weight residual
     114.56  108.04    6.52 1.27e+00 6.20e-01 2.64e+01
  angle pdb=" N   THR C 314 "
        pdb=" CA  THR C 314 "
        pdb=" C   THR C 314 "
      ideal   model   delta    sigma   weight residual
     114.56  108.04    6.52 1.27e+00 6.20e-01 2.63e+01
  angle pdb=" N   THR F 314 "
        pdb=" CA  THR F 314 "
        pdb=" C   THR F 314 "
      ideal   model   delta    sigma   weight residual
     114.56  108.05    6.51 1.27e+00 6.20e-01 2.63e+01
  angle pdb=" N   THR A 314 "
        pdb=" CA  THR A 314 "
        pdb=" C   THR A 314 "
      ideal   model   delta    sigma   weight residual
     114.56  108.05    6.51 1.27e+00 6.20e-01 2.63e+01
  ... (remaining 20820 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.17: 6873
       10.17 -    20.35: 1296
       20.35 -    30.52: 560
       30.52 -    40.70: 315
       40.70 -    50.87: 70
  Dihedral angle restraints: 9114
    sinusoidal: 3563
      harmonic: 5551
  Sorted by residual:
  dihedral pdb=" CA  LYS D 107 "
           pdb=" C   LYS D 107 "
           pdb=" N   PHE D 108 "
           pdb=" CA  PHE D 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.71  -28.29     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  LYS F 107 "
           pdb=" C   LYS F 107 "
           pdb=" N   PHE F 108 "
           pdb=" CA  PHE F 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.72  -28.28     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  LYS B 107 "
           pdb=" C   LYS B 107 "
           pdb=" N   PHE B 108 "
           pdb=" CA  PHE B 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.72  -28.28     0      5.00e+00 4.00e-02 3.20e+01
  ... (remaining 9111 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1619
       0.051 -    0.103: 649
       0.103 -    0.154: 159
       0.154 -    0.206: 37
       0.206 -    0.257: 7
  Chirality restraints: 2471
  Sorted by residual:
  chirality pdb=" CA  PHE B 109 "
            pdb=" N   PHE B 109 "
            pdb=" C   PHE B 109 "
            pdb=" CB  PHE B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  PHE F 109 "
            pdb=" N   PHE F 109 "
            pdb=" C   PHE F 109 "
            pdb=" CB  PHE F 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  PHE E 109 "
            pdb=" N   PHE E 109 "
            pdb=" C   PHE E 109 "
            pdb=" CB  PHE E 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 2468 not shown)

  Planarity restraints: 2520
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 312 "    0.050 5.00e-02 4.00e+02   7.47e-02 8.92e+00
        pdb=" N   PRO B 313 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO B 313 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 313 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 312 "    0.050 5.00e-02 4.00e+02   7.45e-02 8.87e+00
        pdb=" N   PRO C 313 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO C 313 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 313 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU G 312 "    0.050 5.00e-02 4.00e+02   7.44e-02 8.86e+00
        pdb=" N   PRO G 313 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO G 313 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO G 313 "    0.041 5.00e-02 4.00e+02
  ... (remaining 2517 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 3522
        2.78 -     3.31: 13875
        3.31 -     3.84: 25008
        3.84 -     4.37: 27524
        4.37 -     4.90: 44939
  Nonbonded interactions: 114868
  Sorted by model distance:
  nonbonded pdb=" O   PHE A  72 "
            pdb=" OG  SER B  71 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   PHE F  72 "
            pdb=" OG  SER G  71 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OG  SER A  71 "
            pdb=" O   PHE G  72 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   SER B 241 "
            pdb=" OG  SER B 241 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   SER C 241 "
            pdb=" OG  SER C 241 "
     model   vdw
     2.300 3.040
  ... (remaining 114863 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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:             1.130
  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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     12.450
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6356
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  15323  Z= 0.258
  Angle     :  1.137   9.158  20853  Z= 0.599
  Chirality :  0.059   0.257   2471
  Planarity :  0.010   0.075   2520
  Dihedral  : 14.949  50.872   5460
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  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: -4.86 (0.16), residues: 1827
  helix: -3.29 (0.10), residues: 1141
  sheet:  None (None), residues: 0
  loop : -2.81 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 254 
 TYR   0.015   0.002   TYR E 234 
 PHE   0.028   0.002   PHE A 109 
 TRP   0.007   0.001   TRP B 104 
 HIS   0.008   0.003   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 (15309)
  covalent geometry    : angle       1.13674 (20825)
  SS BOND              : bond        0.00443 (   14)
  SS BOND              : angle       1.24504 (   28)
  hydrogen bonds       : bond        0.21612 (  736)
  hydrogen bonds       : angle       8.51881 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 385
  time to evaluate  : 0.528 
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: A   56 GLN cc_start: 0.7103 (mt0) cc_final: 0.6873 (mt0)
REVERT: A   75 ARG cc_start: 0.7158 (tpp-160) cc_final: 0.6898 (ttt90)
REVERT: A  214 ILE cc_start: 0.6695 (tp) cc_final: 0.6422 (mp)
REVERT: B  242 ASP cc_start: 0.7776 (t70) cc_final: 0.7389 (m-30)
REVERT: C   83 TYR cc_start: 0.7734 (t80) cc_final: 0.7192 (t80)
REVERT: C  214 ILE cc_start: 0.6891 (tp) cc_final: 0.6659 (pt)
REVERT: C  242 ASP cc_start: 0.7566 (t70) cc_final: 0.7241 (m-30)
REVERT: D   83 TYR cc_start: 0.7572 (t80) cc_final: 0.6937 (t80)
REVERT: D  214 ILE cc_start: 0.7314 (tp) cc_final: 0.7037 (mt)
REVERT: D  242 ASP cc_start: 0.7656 (t70) cc_final: 0.7298 (m-30)
REVERT: D  262 GLN cc_start: 0.7828 (pm20) cc_final: 0.7572 (pp30)
REVERT: D  279 ILE cc_start: 0.8169 (mt) cc_final: 0.7906 (mt)
REVERT: E   83 TYR cc_start: 0.7590 (t80) cc_final: 0.7356 (t80)
REVERT: E  214 ILE cc_start: 0.6888 (tp) cc_final: 0.6578 (pt)
REVERT: E  242 ASP cc_start: 0.7434 (t70) cc_final: 0.7195 (m-30)
REVERT: F  279 ILE cc_start: 0.8288 (mt) cc_final: 0.8033 (mt)
REVERT: G  124 PRO cc_start: 0.9038 (Cg_exo) cc_final: 0.8753 (Cg_endo)
REVERT: G  199 TYR cc_start: 0.7883 (m-80) cc_final: 0.7659 (m-10)
REVERT: G  214 ILE cc_start: 0.7012 (tp) cc_final: 0.6704 (mt)
REVERT: G  299 PHE cc_start: 0.7160 (t80) cc_final: 0.6938 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 385
  average time/residue: 0.1148
  time to fit residues: 66.9882
Evaluate side-chains
  243 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  90 GLN
A 280 ASN
B  56 GLN
B  76 GLN
B  90 GLN
B 280 ASN
C  56 GLN
C  76 GLN
** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 GLN
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  90 GLN
E 280 ASN
F  56 GLN
F  76 GLN
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  76 GLN
G  90 GLN
** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 280 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.193406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.159289 restraints weight = 29769.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.163818 restraints weight = 17260.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.166669 restraints weight = 11953.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.168501 restraints weight = 9348.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.169526 restraints weight = 7945.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6386
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15323  Z= 0.165
  Angle     :  0.801  10.055  20853  Z= 0.406
  Chirality :  0.046   0.199   2471
  Planarity :  0.007   0.056   2520
  Dihedral  :  6.501  23.327   1981
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.19 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.48 (0.18), residues: 1827
  helix: -1.56 (0.14), residues: 1113
  sheet: -2.43 (0.47), residues: 84
  loop : -3.52 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 254 
 TYR   0.027   0.002   TYR E 121 
 PHE   0.029   0.002   PHE D 299 
 TRP   0.014   0.002   TRP D  85 
 HIS   0.004   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (15309)
  covalent geometry    : angle       0.80092 (20825)
  SS BOND              : bond        0.00233 (   14)
  SS BOND              : angle       0.92255 (   28)
  hydrogen bonds       : bond        0.04297 (  736)
  hydrogen bonds       : angle       5.78696 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 285
  time to evaluate  : 0.600 
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: A  119 LEU cc_start: 0.9020 (mt) cc_final: 0.8338 (tt)
REVERT: A  307 LYS cc_start: 0.7935 (mptt) cc_final: 0.7733 (mptt)
REVERT: B  279 ILE cc_start: 0.7994 (mt) cc_final: 0.7776 (mt)
REVERT: C   57 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8204 (mm-30)
REVERT: D  119 LEU cc_start: 0.8941 (mt) cc_final: 0.8171 (tt)
REVERT: D  127 TRP cc_start: 0.7744 (t60) cc_final: 0.7405 (t60)
REVERT: D  279 ILE cc_start: 0.8115 (mt) cc_final: 0.7829 (mt)
REVERT: D  299 PHE cc_start: 0.6574 (t80) cc_final: 0.6334 (t80)
REVERT: E  119 LEU cc_start: 0.8724 (mp) cc_final: 0.8007 (tt)
REVERT: E  214 ILE cc_start: 0.6873 (tp) cc_final: 0.6665 (pt)
REVERT: F  199 TYR cc_start: 0.7040 (m-10) cc_final: 0.6612 (m-10)
REVERT: F  279 ILE cc_start: 0.8238 (mt) cc_final: 0.7930 (mt)
REVERT: F  307 LYS cc_start: 0.7856 (mptt) cc_final: 0.7522 (mptt)
REVERT: G  124 PRO cc_start: 0.9068 (Cg_exo) cc_final: 0.8741 (Cg_endo)
REVERT: G  128 ARG cc_start: 0.8430 (ttm110) cc_final: 0.7859 (mtp-110)
REVERT: G  307 LYS cc_start: 0.7799 (mptt) cc_final: 0.7595 (mptt)
  outliers start: 36
  outliers final: 13
  residues processed: 313
  average time/residue: 0.1044
  time to fit residues: 50.5737
Evaluate side-chains
  248 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 235
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain F residue   76 GLN
Chi-restraints excluded: chain F residue   88 VAL
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   88 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 135 optimal weight:    0.6980
   chunk 11 optimal weight:    8.9990
   chunk 67 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 156 optimal weight:   10.0000
   chunk 108 optimal weight:    0.6980
   chunk 158 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 137 optimal weight:    3.9990
   chunk 139 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 GLN
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.193409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.159607 restraints weight = 29874.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.164161 restraints weight = 17334.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.167003 restraints weight = 11947.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.168853 restraints weight = 9310.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.169931 restraints weight = 7904.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15323  Z= 0.151
  Angle     :  0.769  10.001  20853  Z= 0.384
  Chirality :  0.045   0.197   2471
  Planarity :  0.006   0.048   2520
  Dihedral  :  6.087  21.913   1981
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 22.05 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.19), residues: 1827
  helix: -0.72 (0.15), residues: 1113
  sheet: -1.73 (0.50), residues: 84
  loop : -3.43 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 254 
 TYR   0.022   0.002   TYR E 121 
 PHE   0.023   0.002   PHE F 299 
 TRP   0.014   0.001   TRP E 127 
 HIS   0.004   0.001   HIS G 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (15309)
  covalent geometry    : angle       0.76940 (20825)
  SS BOND              : bond        0.00236 (   14)
  SS BOND              : angle       0.70596 (   28)
  hydrogen bonds       : bond        0.03780 (  736)
  hydrogen bonds       : angle       5.47314 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 247
  time to evaluate  : 0.526 
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: A  103 LEU cc_start: 0.3964 (OUTLIER) cc_final: 0.1169 (mt)
REVERT: A  119 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8286 (tt)
REVERT: B  103 LEU cc_start: 0.4292 (OUTLIER) cc_final: 0.1539 (mt)
REVERT: B  279 ILE cc_start: 0.7999 (mt) cc_final: 0.7743 (mt)
REVERT: C   57 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8053 (mm-30)
REVERT: D  119 LEU cc_start: 0.8926 (mt) cc_final: 0.8275 (tt)
REVERT: D  279 ILE cc_start: 0.8179 (mt) cc_final: 0.7862 (mt)
REVERT: D  299 PHE cc_start: 0.6649 (t80) cc_final: 0.6386 (t80)
REVERT: E   83 TYR cc_start: 0.7677 (t80) cc_final: 0.7405 (t80)
REVERT: E  103 LEU cc_start: 0.5022 (OUTLIER) cc_final: 0.2304 (mt)
REVERT: E  119 LEU cc_start: 0.8734 (mp) cc_final: 0.8051 (tt)
REVERT: F   57 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8111 (mm-30)
REVERT: F  103 LEU cc_start: 0.4673 (OUTLIER) cc_final: 0.1982 (mt)
REVERT: F  199 TYR cc_start: 0.6870 (m-10) cc_final: 0.6623 (m-10)
REVERT: G  103 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.1434 (mt)
REVERT: G  128 ARG cc_start: 0.8400 (ttm110) cc_final: 0.7873 (mtp-110)
  outliers start: 49
  outliers final: 29
  residues processed: 279
  average time/residue: 0.1102
  time to fit residues: 46.9780
Evaluate side-chains
  249 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 214
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  282 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  109 PHE
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  109 PHE
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  242 ASP
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue  103 LEU
Chi-restraints excluded: chain G residue  237 LEU
Chi-restraints excluded: chain G residue  319 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 137 optimal weight:    0.6980
   chunk 133 optimal weight:    2.9990
   chunk 112 optimal weight:    0.6980
   chunk 169 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 129 optimal weight:    0.0970
   chunk 115 optimal weight:    5.9990
   chunk 101 optimal weight:    0.0470
   chunk 166 optimal weight:    0.9990
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 GLN
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 274 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.196556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.162564 restraints weight = 29667.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.167233 restraints weight = 17364.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.170200 restraints weight = 11927.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.172175 restraints weight = 9250.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.173283 restraints weight = 7803.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15323  Z= 0.127
  Angle     :  0.726  10.158  20853  Z= 0.361
  Chirality :  0.044   0.181   2471
  Planarity :  0.006   0.046   2520
  Dihedral  :  5.587  21.547   1981
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.89 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.20), residues: 1827
  helix: -0.37 (0.16), residues: 1148
  sheet: -1.85 (0.49), residues: 91
  loop : -3.15 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  75 
 TYR   0.025   0.002   TYR C 121 
 PHE   0.019   0.001   PHE E 108 
 TRP   0.007   0.001   TRP D  85 
 HIS   0.003   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (15309)
  covalent geometry    : angle       0.72669 (20825)
  SS BOND              : bond        0.00081 (   14)
  SS BOND              : angle       0.50888 (   28)
  hydrogen bonds       : bond        0.03137 (  736)
  hydrogen bonds       : angle       5.21463 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 254
  time to evaluate  : 0.481 
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: A   57 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: A  128 ARG cc_start: 0.8053 (ttt-90) cc_final: 0.7534 (ttm170)
REVERT: B  103 LEU cc_start: 0.4180 (OUTLIER) cc_final: 0.1537 (mt)
REVERT: B  237 LEU cc_start: 0.7229 (tt) cc_final: 0.6889 (tp)
REVERT: B  272 ILE cc_start: 0.7893 (pt) cc_final: 0.7684 (tp)
REVERT: B  279 ILE cc_start: 0.7885 (mt) cc_final: 0.7649 (mt)
REVERT: C   57 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8030 (mm-30)
REVERT: C  274 GLN cc_start: 0.7922 (tt0) cc_final: 0.7684 (tt0)
REVERT: C  310 GLU cc_start: 0.6188 (mt-10) cc_final: 0.5759 (pm20)
REVERT: D  103 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.2636 (mt)
REVERT: D  237 LEU cc_start: 0.7808 (tt) cc_final: 0.7563 (tp)
REVERT: D  262 GLN cc_start: 0.6166 (pp30) cc_final: 0.5949 (pp30)
REVERT: D  299 PHE cc_start: 0.6591 (t80) cc_final: 0.6314 (t80)
REVERT: E  119 LEU cc_start: 0.8709 (mp) cc_final: 0.8073 (tt)
REVERT: F   57 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8150 (mm-30)
REVERT: F  226 LEU cc_start: 0.8426 (mm) cc_final: 0.8113 (tt)
REVERT: F  274 GLN cc_start: 0.7784 (tt0) cc_final: 0.7529 (tt0)
REVERT: F  279 ILE cc_start: 0.8031 (mm) cc_final: 0.7831 (mt)
REVERT: G  128 ARG cc_start: 0.8384 (ttm110) cc_final: 0.7847 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8556 (mm) cc_final: 0.8094 (tt)
  outliers start: 55
  outliers final: 23
  residues processed: 288
  average time/residue: 0.1086
  time to fit residues: 47.7234
Evaluate side-chains
  241 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 216
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  109 PHE
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain F residue   88 VAL
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  237 LEU
Chi-restraints excluded: chain G residue  319 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 168 optimal weight:    1.9990
   chunk 72 optimal weight:    0.1980
   chunk 42 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 174 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 166 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 274 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 GLN
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 GLN
D 274 GLN
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  56 GLN
** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.196556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.162727 restraints weight = 29525.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.167361 restraints weight = 17261.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.170298 restraints weight = 11885.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.172245 restraints weight = 9231.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.173536 restraints weight = 7790.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6333
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15323  Z= 0.135
  Angle     :  0.739  10.489  20853  Z= 0.365
  Chirality :  0.044   0.268   2471
  Planarity :  0.006   0.044   2520
  Dihedral  :  5.481  21.952   1981
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 25.07 %
    Favored  : 71.43 %
  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: -1.86 (0.20), residues: 1827
  helix: -0.18 (0.16), residues: 1155
  sheet: -1.78 (0.51), residues: 91
  loop : -3.26 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 254 
 TYR   0.028   0.001   TYR C 121 
 PHE   0.031   0.001   PHE F 299 
 TRP   0.018   0.001   TRP D  85 
 HIS   0.005   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (15309)
  covalent geometry    : angle       0.73793 (20825)
  SS BOND              : bond        0.00227 (   14)
  SS BOND              : angle       1.30445 (   28)
  hydrogen bonds       : bond        0.03207 (  736)
  hydrogen bonds       : angle       5.16036 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 231
  time to evaluate  : 0.544 
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: A   57 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8102 (mm-30)
REVERT: A  103 LEU cc_start: 0.3976 (OUTLIER) cc_final: 0.1217 (mt)
REVERT: A  128 ARG cc_start: 0.7942 (ttt-90) cc_final: 0.7489 (ttm170)
REVERT: B  103 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.1666 (mt)
REVERT: B  237 LEU cc_start: 0.7286 (tt) cc_final: 0.6948 (tp)
REVERT: B  279 ILE cc_start: 0.7924 (mt) cc_final: 0.7681 (mt)
REVERT: C   57 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8077 (mm-30)
REVERT: C  109 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6925 (t80)
REVERT: C  274 GLN cc_start: 0.7914 (tt0) cc_final: 0.7683 (tt0)
REVERT: C  310 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5706 (pm20)
REVERT: D  262 GLN cc_start: 0.6001 (pp30) cc_final: 0.5774 (pp30)
REVERT: D  299 PHE cc_start: 0.6635 (t80) cc_final: 0.6342 (t80)
REVERT: E  103 LEU cc_start: 0.4799 (OUTLIER) cc_final: 0.2194 (mt)
REVERT: F   57 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8167 (mm-30)
REVERT: F  103 LEU cc_start: 0.4429 (OUTLIER) cc_final: 0.1788 (mt)
REVERT: F  226 LEU cc_start: 0.8548 (mm) cc_final: 0.8228 (tt)
REVERT: G  103 LEU cc_start: 0.3975 (OUTLIER) cc_final: 0.1521 (mt)
REVERT: G  128 ARG cc_start: 0.8363 (ttm110) cc_final: 0.7848 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8635 (mm) cc_final: 0.8175 (tt)
  outliers start: 59
  outliers final: 33
  residues processed: 274
  average time/residue: 0.1119
  time to fit residues: 46.4027
Evaluate side-chains
  248 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 208
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   54 PHE
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  319 HIS
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  109 PHE
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  109 PHE
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  103 LEU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  237 LEU
Chi-restraints excluded: chain G residue  319 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 58 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 140 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
F 274 GLN
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.192843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.158908 restraints weight = 29730.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.163341 restraints weight = 17380.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.166221 restraints weight = 12086.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.168099 restraints weight = 9460.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.169362 restraints weight = 8024.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  15323  Z= 0.182
  Angle     :  0.779  10.709  20853  Z= 0.387
  Chirality :  0.046   0.186   2471
  Planarity :  0.005   0.041   2520
  Dihedral  :  5.670  25.612   1981
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.24 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 25.49 %
    Favored  : 69.83 %
  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: -1.85 (0.20), residues: 1827
  helix: -0.20 (0.16), residues: 1162
  sheet: -1.60 (0.53), residues: 91
  loop : -3.25 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 254 
 TYR   0.028   0.002   TYR C 121 
 PHE   0.019   0.002   PHE B 109 
 TRP   0.008   0.001   TRP D  85 
 HIS   0.004   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (15309)
  covalent geometry    : angle       0.77836 (20825)
  SS BOND              : bond        0.00345 (   14)
  SS BOND              : angle       1.22204 (   28)
  hydrogen bonds       : bond        0.03559 (  736)
  hydrogen bonds       : angle       5.21201 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 226
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8138 (mm-30)
REVERT: A  103 LEU cc_start: 0.4341 (OUTLIER) cc_final: 0.1549 (mt)
REVERT: A  128 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7465 (ttm170)
REVERT: B  103 LEU cc_start: 0.4609 (OUTLIER) cc_final: 0.1813 (mt)
REVERT: B  299 PHE cc_start: 0.6499 (t80) cc_final: 0.6268 (t80)
REVERT: C   57 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8166 (mm-30)
REVERT: C  109 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7183 (t80)
REVERT: C  274 GLN cc_start: 0.7945 (tt0) cc_final: 0.7672 (tt0)
REVERT: C  310 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5746 (pm20)
REVERT: D  299 PHE cc_start: 0.6726 (t80) cc_final: 0.6501 (t80)
REVERT: E   63 GLN cc_start: 0.6018 (tp40) cc_final: 0.5631 (mp10)
REVERT: E  103 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.2435 (mt)
REVERT: E  310 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5719 (pm20)
REVERT: F  103 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.1860 (mt)
REVERT: F  109 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7316 (t80)
REVERT: F  226 LEU cc_start: 0.8637 (mm) cc_final: 0.8325 (tt)
REVERT: G  103 LEU cc_start: 0.4472 (OUTLIER) cc_final: 0.1836 (mt)
REVERT: G  128 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7845 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8713 (mm) cc_final: 0.8291 (tt)
  outliers start: 79
  outliers final: 43
  residues processed: 287
  average time/residue: 0.1054
  time to fit residues: 46.3100
Evaluate side-chains
  259 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 207
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain B residue   54 PHE
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  319 HIS
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 PHE
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  282 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  109 PHE
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  310 GLU
Chi-restraints excluded: chain E residue  319 HIS
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  109 PHE
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue  103 LEU
Chi-restraints excluded: chain G residue  223 ILE
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  237 LEU
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  319 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 149 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 110 optimal weight:   10.0000
   chunk 164 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 176 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
G  56 GLN
** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.194506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.160712 restraints weight = 29039.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.165265 restraints weight = 16797.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.168164 restraints weight = 11581.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.170053 restraints weight = 8989.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.171306 restraints weight = 7600.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6374
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15323  Z= 0.147
  Angle     :  0.747  10.628  20853  Z= 0.369
  Chirality :  0.045   0.216   2471
  Planarity :  0.005   0.043   2520
  Dihedral  :  5.538  27.656   1981
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 25.79 %
    Favored  : 68.52 %
  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: -1.68 (0.20), residues: 1827
  helix: -0.10 (0.16), residues: 1162
  sheet: -1.50 (0.52), residues: 91
  loop : -3.14 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 254 
 TYR   0.028   0.002   TYR C 121 
 PHE   0.021   0.001   PHE F 273 
 TRP   0.011   0.001   TRP E  85 
 HIS   0.004   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (15309)
  covalent geometry    : angle       0.74626 (20825)
  SS BOND              : bond        0.00191 (   14)
  SS BOND              : angle       0.98146 (   28)
  hydrogen bonds       : bond        0.03192 (  736)
  hydrogen bonds       : angle       5.10670 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 222
  time to evaluate  : 0.567 
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: A   57 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8156 (mm-30)
REVERT: A  101 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5253 (pp)
REVERT: A  103 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.1984 (mt)
REVERT: A  128 ARG cc_start: 0.7924 (ttt-90) cc_final: 0.7427 (ttm170)
REVERT: A  129 PHE cc_start: 0.8340 (m-10) cc_final: 0.8135 (m-10)
REVERT: B  103 LEU cc_start: 0.4551 (OUTLIER) cc_final: 0.1757 (mt)
REVERT: B  237 LEU cc_start: 0.7397 (tt) cc_final: 0.7047 (tp)
REVERT: B  275 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6126 (tt)
REVERT: C   36 LYS cc_start: 0.7993 (mttm) cc_final: 0.7501 (pttm)
REVERT: C   57 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8232 (mm-30)
REVERT: C  101 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5149 (pp)
REVERT: C  103 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.3169 (mt)
REVERT: C  109 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7144 (t80)
REVERT: C  274 GLN cc_start: 0.7933 (tt0) cc_final: 0.7699 (tt0)
REVERT: C  310 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5796 (pm20)
REVERT: D  299 PHE cc_start: 0.6757 (t80) cc_final: 0.6543 (t80)
REVERT: E   63 GLN cc_start: 0.6018 (tp40) cc_final: 0.5747 (mp10)
REVERT: E   83 TYR cc_start: 0.7633 (t80) cc_final: 0.7350 (t80)
REVERT: E  101 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5537 (pp)
REVERT: E  103 LEU cc_start: 0.4988 (OUTLIER) cc_final: 0.2376 (mt)
REVERT: E  310 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5724 (pm20)
REVERT: F   85 TRP cc_start: 0.8060 (t60) cc_final: 0.7840 (t60)
REVERT: F  101 LEU cc_start: 0.5487 (OUTLIER) cc_final: 0.5242 (pp)
REVERT: F  103 LEU cc_start: 0.4621 (OUTLIER) cc_final: 0.1899 (mt)
REVERT: F  109 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7280 (t80)
REVERT: F  226 LEU cc_start: 0.8683 (mm) cc_final: 0.8353 (tt)
REVERT: F  279 ILE cc_start: 0.8262 (mm) cc_final: 0.8061 (mt)
REVERT: G  103 LEU cc_start: 0.4215 (OUTLIER) cc_final: 0.1601 (mt)
REVERT: G  109 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.6900 (t80)
REVERT: G  128 ARG cc_start: 0.8421 (ttm110) cc_final: 0.7873 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8721 (mm) cc_final: 0.8266 (tt)
  outliers start: 96
  outliers final: 62
  residues processed: 297
  average time/residue: 0.1100
  time to fit residues: 49.7134
Evaluate side-chains
  284 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 206
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   54 PHE
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  319 HIS
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 PHE
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  282 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  109 PHE
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  242 ASP
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  310 GLU
Chi-restraints excluded: chain E residue  319 HIS
Chi-restraints excluded: chain F residue   54 PHE
Chi-restraints excluded: chain F residue   81 ASP
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  109 PHE
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  103 LEU
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  237 LEU
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  319 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 175 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0050
   chunk 36 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 160 optimal weight:    0.6980
   chunk 134 optimal weight:    0.8980
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 106 HIS
F  90 GLN
G  56 GLN
G 106 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.195921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.161729 restraints weight = 29377.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.166315 restraints weight = 17055.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.169269 restraints weight = 11743.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.171202 restraints weight = 9122.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.172466 restraints weight = 7696.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6340
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15323  Z= 0.130
  Angle     :  0.736  10.903  20853  Z= 0.362
  Chirality :  0.044   0.219   2471
  Planarity :  0.005   0.043   2520
  Dihedral  :  5.331  20.845   1981
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 27.50 %
    Favored  : 67.93 %
  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: -1.53 (0.20), residues: 1827
  helix:  0.06 (0.16), residues: 1162
  sheet: -1.00 (0.55), residues: 84
  loop : -3.24 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 254 
 TYR   0.026   0.001   TYR C 121 
 PHE   0.034   0.001   PHE F 299 
 TRP   0.006   0.001   TRP B  74 
 HIS   0.003   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (15309)
  covalent geometry    : angle       0.73483 (20825)
  SS BOND              : bond        0.00178 (   14)
  SS BOND              : angle       1.35016 (   28)
  hydrogen bonds       : bond        0.02946 (  736)
  hydrogen bonds       : angle       5.03567 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 226
  time to evaluate  : 0.462 
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: A   57 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8156 (mm-30)
REVERT: A  103 LEU cc_start: 0.4658 (OUTLIER) cc_final: 0.1950 (mt)
REVERT: A  109 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7059 (t80)
REVERT: A  128 ARG cc_start: 0.7918 (ttt-90) cc_final: 0.7424 (ttm170)
REVERT: A  129 PHE cc_start: 0.8315 (m-10) cc_final: 0.8087 (m-10)
REVERT: B  119 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8581 (tp)
REVERT: B  237 LEU cc_start: 0.7436 (tt) cc_final: 0.7155 (tp)
REVERT: B  275 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6149 (tt)
REVERT: C   36 LYS cc_start: 0.8009 (mttm) cc_final: 0.7501 (pttm)
REVERT: C   57 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: C  101 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5184 (pp)
REVERT: C  103 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.2876 (mt)
REVERT: C  109 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7067 (t80)
REVERT: C  310 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5802 (pm20)
REVERT: D  262 GLN cc_start: 0.6114 (pp30) cc_final: 0.5821 (pp30)
REVERT: D  279 ILE cc_start: 0.8059 (mm) cc_final: 0.7682 (mt)
REVERT: E   63 GLN cc_start: 0.5954 (tp40) cc_final: 0.5685 (mp10)
REVERT: E   83 TYR cc_start: 0.7467 (t80) cc_final: 0.7145 (t80)
REVERT: E  101 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5604 (pp)
REVERT: E  103 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.2276 (mt)
REVERT: E  310 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5682 (pm20)
REVERT: F   85 TRP cc_start: 0.8077 (t60) cc_final: 0.7802 (t-100)
REVERT: F  103 LEU cc_start: 0.4519 (OUTLIER) cc_final: 0.1823 (mt)
REVERT: F  109 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7203 (t80)
REVERT: F  226 LEU cc_start: 0.8661 (mm) cc_final: 0.8322 (tt)
REVERT: F  279 ILE cc_start: 0.8042 (mm) cc_final: 0.7767 (mt)
REVERT: G  109 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.6881 (t80)
REVERT: G  128 ARG cc_start: 0.8421 (ttm110) cc_final: 0.7848 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8717 (mm) cc_final: 0.8252 (tt)
  outliers start: 77
  outliers final: 53
  residues processed: 287
  average time/residue: 0.1114
  time to fit residues: 48.3024
Evaluate side-chains
  281 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 214
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  319 HIS
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   54 PHE
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 PHE
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  109 PHE
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  242 ASP
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  310 GLU
Chi-restraints excluded: chain E residue  319 HIS
Chi-restraints excluded: chain F residue   54 PHE
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  109 PHE
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue  103 LEU
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  319 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 146 optimal weight:    0.0870
   chunk 131 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 158 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 154 optimal weight:    0.0370
   chunk 28 optimal weight:    5.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    1.0040

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 274 GLN
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
G  56 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.195351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.161018 restraints weight = 29674.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.165544 restraints weight = 17443.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.168400 restraints weight = 12130.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.170278 restraints weight = 9518.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.171474 restraints weight = 8071.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6361
moved from start:          0.4489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  15323  Z= 0.146
  Angle     :  0.774  13.288  20853  Z= 0.379
  Chirality :  0.046   0.309   2471
  Planarity :  0.005   0.043   2520
  Dihedral  :  5.358  20.386   1981
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 27.45 %
    Favored  : 67.40 %
  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: -1.53 (0.20), residues: 1827
  helix:  0.06 (0.16), residues: 1162
  sheet: -1.02 (0.56), residues: 84
  loop : -3.24 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 254 
 TYR   0.027   0.002   TYR E 121 
 PHE   0.020   0.001   PHE B 108 
 TRP   0.009   0.001   TRP B 127 
 HIS   0.005   0.001   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (15309)
  covalent geometry    : angle       0.77140 (20825)
  SS BOND              : bond        0.00212 (   14)
  SS BOND              : angle       1.88928 (   28)
  hydrogen bonds       : bond        0.03092 (  736)
  hydrogen bonds       : angle       5.04656 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 218
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: A  101 LEU cc_start: 0.5558 (OUTLIER) cc_final: 0.5205 (pp)
REVERT: A  103 LEU cc_start: 0.4483 (OUTLIER) cc_final: 0.1703 (mt)
REVERT: A  109 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7107 (t80)
REVERT: A  128 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.7211 (mtp-110)
REVERT: A  129 PHE cc_start: 0.8362 (m-10) cc_final: 0.8086 (m-10)
REVERT: A  279 ILE cc_start: 0.8200 (mt) cc_final: 0.7850 (mt)
REVERT: B  119 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8540 (mm)
REVERT: B  237 LEU cc_start: 0.7472 (tt) cc_final: 0.7216 (tp)
REVERT: B  275 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6145 (tt)
REVERT: C   36 LYS cc_start: 0.8053 (mttm) cc_final: 0.7518 (pttm)
REVERT: C   57 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8101 (mm-30)
REVERT: C  101 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.5178 (pp)
REVERT: C  103 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.2754 (mt)
REVERT: C  109 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7113 (t80)
REVERT: C  279 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7617 (mt)
REVERT: C  310 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5756 (pm20)
REVERT: D  109 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7459 (t80)
REVERT: D  262 GLN cc_start: 0.6083 (pp30) cc_final: 0.5786 (pp30)
REVERT: D  279 ILE cc_start: 0.8094 (mm) cc_final: 0.7721 (mt)
REVERT: E   63 GLN cc_start: 0.5966 (tp40) cc_final: 0.5689 (mp10)
REVERT: E   83 TYR cc_start: 0.7579 (t80) cc_final: 0.7295 (t80)
REVERT: E  101 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5526 (pp)
REVERT: E  103 LEU cc_start: 0.5068 (OUTLIER) cc_final: 0.2434 (mt)
REVERT: E  310 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5710 (pm20)
REVERT: F   36 LYS cc_start: 0.7927 (mttm) cc_final: 0.7553 (pttp)
REVERT: F  101 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.5198 (pp)
REVERT: F  103 LEU cc_start: 0.4484 (OUTLIER) cc_final: 0.1784 (mt)
REVERT: F  109 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7355 (t80)
REVERT: F  140 LYS cc_start: 0.6858 (mmtt) cc_final: 0.6644 (mmmt)
REVERT: F  226 LEU cc_start: 0.8663 (mm) cc_final: 0.8336 (tt)
REVERT: F  279 ILE cc_start: 0.8079 (mm) cc_final: 0.7826 (mt)
REVERT: G  103 LEU cc_start: 0.4019 (OUTLIER) cc_final: 0.1606 (mt)
REVERT: G  109 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6891 (t80)
REVERT: G  128 ARG cc_start: 0.8388 (ttm110) cc_final: 0.7832 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8709 (mm) cc_final: 0.8243 (tt)
  outliers start: 87
  outliers final: 58
  residues processed: 290
  average time/residue: 0.1148
  time to fit residues: 50.0306
Evaluate side-chains
  288 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 211
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   54 PHE
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  279 ILE
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  319 HIS
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   54 PHE
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 PHE
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  109 PHE
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  242 ASP
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  310 GLU
Chi-restraints excluded: chain E residue  319 HIS
Chi-restraints excluded: chain F residue   54 PHE
Chi-restraints excluded: chain F residue   81 ASP
Chi-restraints excluded: chain F residue   89 GLN
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  109 PHE
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue  103 LEU
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain G residue  223 ILE
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  237 LEU
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  270 VAL
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  319 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 165 optimal weight:    0.9990
   chunk 115 optimal weight:    5.9990
   chunk 84 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 144 optimal weight:    0.0980
   chunk 178 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 274 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 274 GLN
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  56 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.197274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.163341 restraints weight = 29301.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.167922 restraints weight = 17005.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.170861 restraints weight = 11709.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.172772 restraints weight = 9108.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.174045 restraints weight = 7691.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6307
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  15323  Z= 0.133
  Angle     :  0.765  12.019  20853  Z= 0.372
  Chirality :  0.045   0.221   2471
  Planarity :  0.005   0.043   2520
  Dihedral  :  5.212  19.783   1981
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 28.04 %
    Favored  : 67.34 %
  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: -1.48 (0.20), residues: 1827
  helix:  0.14 (0.16), residues: 1162
  sheet: -1.00 (0.56), residues: 84
  loop : -3.31 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 254 
 TYR   0.026   0.001   TYR E 121 
 PHE   0.035   0.001   PHE F 299 
 TRP   0.009   0.001   TRP F  85 
 HIS   0.004   0.001   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (15309)
  covalent geometry    : angle       0.76370 (20825)
  SS BOND              : bond        0.00096 (   14)
  SS BOND              : angle       1.53072 (   28)
  hydrogen bonds       : bond        0.02896 (  736)
  hydrogen bonds       : angle       4.95487 ( 2187)

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

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

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3654 Ramachandran restraints generated.
    1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 229
  time to evaluate  : 0.569 
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: A   57 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8189 (mm-30)
REVERT: A  101 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.5157 (pp)
REVERT: A  103 LEU cc_start: 0.4438 (OUTLIER) cc_final: 0.1830 (mt)
REVERT: A  109 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7056 (t80)
REVERT: A  128 ARG cc_start: 0.7900 (ttt-90) cc_final: 0.7327 (mtp-110)
REVERT: A  129 PHE cc_start: 0.8345 (m-10) cc_final: 0.8090 (m-10)
REVERT: A  279 ILE cc_start: 0.8207 (mt) cc_final: 0.7846 (mt)
REVERT: B  119 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8303 (mt)
REVERT: C   36 LYS cc_start: 0.8001 (mttm) cc_final: 0.7515 (pttt)
REVERT: C   57 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8118 (mm-30)
REVERT: C  101 LEU cc_start: 0.5427 (OUTLIER) cc_final: 0.5152 (pp)
REVERT: C  103 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.2612 (mt)
REVERT: C  109 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7056 (t80)
REVERT: C  310 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5809 (pm20)
REVERT: D  109 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7366 (t80)
REVERT: D  262 GLN cc_start: 0.5955 (pp30) cc_final: 0.5677 (pp30)
REVERT: D  279 ILE cc_start: 0.8117 (mm) cc_final: 0.7812 (mt)
REVERT: E   63 GLN cc_start: 0.5885 (tp40) cc_final: 0.5680 (mp10)
REVERT: E   83 TYR cc_start: 0.7331 (t80) cc_final: 0.7084 (t80)
REVERT: E  101 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5537 (pp)
REVERT: E  103 LEU cc_start: 0.4971 (OUTLIER) cc_final: 0.2318 (mt)
REVERT: E  310 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5829 (pm20)
REVERT: F   36 LYS cc_start: 0.7925 (mttm) cc_final: 0.7595 (pttp)
REVERT: F  101 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.5077 (pp)
REVERT: F  103 LEU cc_start: 0.4326 (OUTLIER) cc_final: 0.1762 (mt)
REVERT: F  109 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7241 (t80)
REVERT: F  140 LYS cc_start: 0.6862 (mmtt) cc_final: 0.6647 (mmmt)
REVERT: F  201 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8502 (mmtt)
REVERT: F  226 LEU cc_start: 0.8667 (mm) cc_final: 0.8351 (tt)
REVERT: F  272 ILE cc_start: 0.7999 (pt) cc_final: 0.7770 (tp)
REVERT: F  279 ILE cc_start: 0.8158 (mm) cc_final: 0.7926 (mt)
REVERT: G  103 LEU cc_start: 0.4015 (OUTLIER) cc_final: 0.1546 (mt)
REVERT: G  109 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.6921 (t80)
REVERT: G  128 ARG cc_start: 0.8379 (ttm110) cc_final: 0.7821 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8690 (mm) cc_final: 0.8225 (tt)
  outliers start: 78
  outliers final: 48
  residues processed: 290
  average time/residue: 0.1068
  time to fit residues: 46.6834
Evaluate side-chains
  275 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 210
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   54 PHE
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  319 HIS
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   54 PHE
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 PHE
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  109 PHE
Chi-restraints excluded: chain E residue  242 ASP
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  310 GLU
Chi-restraints excluded: chain E residue  319 HIS
Chi-restraints excluded: chain F residue   54 PHE
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  109 PHE
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue  103 LEU
Chi-restraints excluded: chain G residue  109 PHE
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  237 LEU
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  270 VAL
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  319 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 157 optimal weight:    0.5980
   chunk 159 optimal weight:    0.4980
   chunk 173 optimal weight:    3.9990
   chunk 151 optimal weight:    5.9990
   chunk 146 optimal weight:    0.0050
   chunk 131 optimal weight:    0.5980
   chunk 138 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 111 optimal weight:    0.5980
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 274 GLN
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  56 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.198366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.164104 restraints weight = 29320.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.168616 restraints weight = 17227.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.171552 restraints weight = 12008.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.173462 restraints weight = 9412.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.174722 restraints weight = 7995.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6293
moved from start:          0.4809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  15323  Z= 0.131
  Angle     :  0.766  12.730  20853  Z= 0.372
  Chirality :  0.044   0.259   2471
  Planarity :  0.005   0.043   2520
  Dihedral  :  5.139  24.335   1981
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 28.39 %
    Favored  : 67.40 %
  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: -1.43 (0.20), residues: 1827
  helix:  0.18 (0.16), residues: 1162
  sheet: -0.96 (0.56), residues: 84
  loop : -3.31 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 254 
 TYR   0.027   0.001   TYR C 121 
 PHE   0.018   0.001   PHE A 108 
 TRP   0.010   0.001   TRP F  85 
 HIS   0.005   0.001   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (15309)
  covalent geometry    : angle       0.76432 (20825)
  SS BOND              : bond        0.00333 (   14)
  SS BOND              : angle       1.54674 (   28)
  hydrogen bonds       : bond        0.02916 (  736)
  hydrogen bonds       : angle       4.93290 ( 2187)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2608.46 seconds
wall clock time: 46 minutes 2.28 seconds (2762.28 seconds total)