Starting phenix.real_space_refine
on Tue Dec 31 06:05:06 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m67_30115/12_2024/6m67_30115.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m67_30115/12_2024/6m67_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m67_30115/12_2024/6m67_30115.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m67_30115/12_2024/6m67_30115.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m67_30115/12_2024/6m67_30115.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m67_30115/12_2024/6m67_30115.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.10s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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:
    C, B, E, D, G, F
  Time building chain proxies: 5.42, per 1000 atoms: 0.36
  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=2, 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

  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: 3.66
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 1.70
  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: 4.25

  Time building geometry restraints manager: 4.21 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: 6855
       10.17 -    20.35: 1290
       20.35 -    30.52: 560
       30.52 -    40.70: 315
       40.70 -    50.87: 58
  Dihedral angle restraints: 9078
    sinusoidal: 3527
      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 9075 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:
        2.03 -     2.60: 123
        2.60 -     3.18: 12282
        3.18 -     3.75: 24100
        3.75 -     4.33: 30743
        4.33 -     4.90: 47656
  Nonbonded interactions: 114904
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C  84 "
            pdb=" SG  CYS C 246 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS G  84 "
            pdb=" SG  CYS G 246 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS B  84 "
            pdb=" SG  CYS B 246 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS F  84 "
            pdb=" SG  CYS F 246 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS E  84 "
            pdb=" SG  CYS E 246 "
     model   vdw
     2.029 3.760
  ... (remaining 114899 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.660
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     30.250
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.380
-------------------------------------------------------------------------------
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  15309  Z= 0.350
  Angle     :  1.137   9.158  20825  Z= 0.599
  Chirality :  0.059   0.257   2471
  Planarity :  0.010   0.075   2520
  Dihedral  : 14.949  50.872   5460
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 6.79
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.007   0.001   TRP B 104 
 HIS   0.008   0.003   HIS A 106 
 PHE   0.028   0.002   PHE A 109 
 TYR   0.015   0.002   TYR E 234 
 ARG   0.008   0.001   ARG E 254 

*********************** 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  : 1.674 
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: 0.7104 (mt0) cc_final: 0.6873 (mt0)
REVERT: A   75 ARG cc_start: 0.7158 (tpp-160) cc_final: 0.6899 (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: 0.8170 (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: 0.2679
  time to fit residues: 153.8096
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  : 1.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 153 optimal weight:    2.9990
   chunk 137 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 142 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 86 optimal weight:    0.1980
   chunk 106 optimal weight:    8.9990
   chunk 165 optimal weight:    0.0060
   overall best weight:    0.6396

-------------------------------------------------------------------------------
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
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  76 GLN
G  90 GLN
G 280 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6336
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15309  Z= 0.192
  Angle     :  0.775   9.160  20825  Z= 0.393
  Chirality :  0.045   0.187   2471
  Planarity :  0.007   0.057   2520
  Dihedral  :  6.318  22.688   1981
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.55 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.18), residues: 1827
  helix: -1.55 (0.14), residues: 1113
  sheet: -2.50 (0.45), residues: 84
  loop : -3.47 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 127 
 HIS   0.003   0.001   HIS F 106 
 PHE   0.031   0.002   PHE D 299 
 TYR   0.027   0.002   TYR E 121 
 ARG   0.003   0.000   ARG A 254 

*********************** 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
  328 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 297
  time to evaluate  : 1.710 
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: A  119 LEU cc_start: 0.8968 (mt) cc_final: 0.8304 (tt)
REVERT: A  128 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7712 (ttm170)
REVERT: A  147 ASP cc_start: 0.6363 (p0) cc_final: 0.6079 (p0)
REVERT: A  150 TYR cc_start: 0.6754 (m-10) cc_final: 0.5159 (m-80)
REVERT: B   81 ASP cc_start: 0.7809 (t70) cc_final: 0.7536 (t0)
REVERT: B   84 CYS cc_start: 0.7100 (m) cc_final: 0.6331 (p)
REVERT: C   57 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8169 (mm-30)
REVERT: C   81 ASP cc_start: 0.7784 (t70) cc_final: 0.7073 (t0)
REVERT: C   84 CYS cc_start: 0.7241 (m) cc_final: 0.6705 (p)
REVERT: C  128 ARG cc_start: 0.8410 (ttm170) cc_final: 0.8173 (ttm170)
REVERT: D  119 LEU cc_start: 0.8894 (mt) cc_final: 0.8120 (tt)
REVERT: D  127 TRP cc_start: 0.7689 (t60) cc_final: 0.7334 (t60)
REVERT: D  262 GLN cc_start: 0.7758 (pm20) cc_final: 0.7508 (pp30)
REVERT: D  279 ILE cc_start: 0.8072 (mt) cc_final: 0.7791 (mt)
REVERT: D  299 PHE cc_start: 0.6569 (t80) cc_final: 0.6336 (t80)
REVERT: E   85 TRP cc_start: 0.8287 (t60) cc_final: 0.8039 (t-100)
REVERT: E  119 LEU cc_start: 0.8696 (mp) cc_final: 0.7995 (tt)
REVERT: E  214 ILE cc_start: 0.6891 (tp) cc_final: 0.6649 (pt)
REVERT: F   81 ASP cc_start: 0.7735 (t70) cc_final: 0.7518 (t0)
REVERT: F   84 CYS cc_start: 0.7112 (m) cc_final: 0.6323 (p)
REVERT: F   85 TRP cc_start: 0.8079 (t60) cc_final: 0.7160 (t60)
REVERT: F  199 TYR cc_start: 0.7014 (m-10) cc_final: 0.6619 (m-10)
REVERT: F  279 ILE cc_start: 0.8158 (mt) cc_final: 0.7862 (mt)
REVERT: F  307 LYS cc_start: 0.7820 (mptt) cc_final: 0.7570 (mptt)
REVERT: G   81 ASP cc_start: 0.7749 (t70) cc_final: 0.7503 (t0)
REVERT: G   84 CYS cc_start: 0.6600 (m) cc_final: 0.6130 (p)
REVERT: G  124 PRO cc_start: 0.9042 (Cg_exo) cc_final: 0.8710 (Cg_endo)
REVERT: G  128 ARG cc_start: 0.8416 (ttm110) cc_final: 0.7852 (mtp-110)
  outliers start: 31
  outliers final: 7
  residues processed: 323
  average time/residue: 0.2507
  time to fit residues: 122.0835
Evaluate side-chains
  252 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 245
  time to evaluate  : 1.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain F residue   76 GLN
Chi-restraints excluded: chain F residue   88 VAL
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain G residue   76 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 137 optimal weight:    0.4980
   chunk 112 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 165 optimal weight:    2.9990
   chunk 178 optimal weight:    1.9990
   chunk 147 optimal weight:    5.9990
   chunk 164 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 132 optimal weight:    3.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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
A  90 GLN
B  76 GLN
C  76 GLN
C  90 GLN
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 GLN
E  76 GLN
F  76 GLN
F  90 GLN
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  90 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6390
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15309  Z= 0.222
  Angle     :  0.768  10.266  20825  Z= 0.384
  Chirality :  0.045   0.187   2471
  Planarity :  0.006   0.047   2520
  Dihedral  :  6.016  21.956   1981
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.81 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.19), residues: 1827
  helix: -0.77 (0.15), residues: 1155
  sheet: -2.18 (0.47), residues: 84
  loop : -3.25 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  85 
 HIS   0.004   0.001   HIS G 106 
 PHE   0.024   0.002   PHE F 299 
 TYR   0.022   0.002   TYR E 121 
 ARG   0.003   0.000   ARG A 254 

*********************** 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
  306 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 253
  time to evaluate  : 1.706 
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: A  103 LEU cc_start: 0.4100 (OUTLIER) cc_final: 0.1322 (mt)
REVERT: A  128 ARG cc_start: 0.8130 (ttt-90) cc_final: 0.7697 (ttm170)
REVERT: B   81 ASP cc_start: 0.7786 (t70) cc_final: 0.7415 (t0)
REVERT: B   84 CYS cc_start: 0.7263 (m) cc_final: 0.6611 (p)
REVERT: B  103 LEU cc_start: 0.4443 (OUTLIER) cc_final: 0.1733 (mt)
REVERT: C   57 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8111 (mm-30)
REVERT: C   81 ASP cc_start: 0.7791 (t70) cc_final: 0.7156 (t0)
REVERT: C   84 CYS cc_start: 0.7599 (m) cc_final: 0.6988 (p)
REVERT: D  119 LEU cc_start: 0.8930 (mt) cc_final: 0.8281 (tt)
REVERT: D  262 GLN cc_start: 0.7772 (pm20) cc_final: 0.7489 (pp30)
REVERT: D  279 ILE cc_start: 0.8185 (mt) cc_final: 0.7859 (mt)
REVERT: D  299 PHE cc_start: 0.6699 (t80) cc_final: 0.6387 (t80)
REVERT: E   84 CYS cc_start: 0.7619 (m) cc_final: 0.7307 (t)
REVERT: E  119 LEU cc_start: 0.8723 (mp) cc_final: 0.8030 (tt)
REVERT: E  127 TRP cc_start: 0.7486 (t60) cc_final: 0.6844 (t60)
REVERT: F   81 ASP cc_start: 0.7649 (t70) cc_final: 0.7411 (t0)
REVERT: F   84 CYS cc_start: 0.7525 (m) cc_final: 0.6759 (p)
REVERT: F  103 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.2147 (mt)
REVERT: F  199 TYR cc_start: 0.6860 (m-10) cc_final: 0.6593 (m-10)
REVERT: F  279 ILE cc_start: 0.8179 (mt) cc_final: 0.7906 (mt)
REVERT: G   81 ASP cc_start: 0.7864 (t70) cc_final: 0.7375 (t0)
REVERT: G   84 CYS cc_start: 0.6851 (m) cc_final: 0.6489 (p)
REVERT: G  103 LEU cc_start: 0.4296 (OUTLIER) cc_final: 0.1721 (mt)
REVERT: G  128 ARG cc_start: 0.8417 (ttm110) cc_final: 0.7908 (mtp-110)
  outliers start: 53
  outliers final: 38
  residues processed: 290
  average time/residue: 0.2442
  time to fit residues: 108.1806
Evaluate side-chains
  254 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 212
  time to evaluate  : 1.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  270 VAL
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  109 PHE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  135 ILE
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  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  224 ILE
Chi-restraints excluded: chain E residue  242 ASP
Chi-restraints excluded: chain F residue   76 GLN
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  237 LEU
Chi-restraints excluded: chain F residue  242 ASP
Chi-restraints excluded: chain F residue  292 VAL
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  235 PHE
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 163 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 111 optimal weight:    4.9990
   chunk 166 optimal weight:    2.9990
   chunk 175 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 274 GLN
** 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  76 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.3373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15309  Z= 0.199
  Angle     :  0.749  10.500  20825  Z= 0.372
  Chirality :  0.045   0.191   2471
  Planarity :  0.006   0.045   2520
  Dihedral  :  5.788  21.863   1981
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.59 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.20), residues: 1827
  helix: -0.43 (0.15), residues: 1155
  sheet: -2.48 (0.45), residues: 91
  loop : -3.16 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  85 
 HIS   0.004   0.001   HIS F 106 
 PHE   0.019   0.001   PHE E 108 
 TYR   0.024   0.002   TYR C 121 
 ARG   0.003   0.000   ARG A 254 

*********************** 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
  302 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 236
  time to evaluate  : 1.889 
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: 0.8343 (mm-30) cc_final: 0.8124 (mm-30)
REVERT: A  103 LEU cc_start: 0.4126 (OUTLIER) cc_final: 0.1379 (mt)
REVERT: A  128 ARG cc_start: 0.8100 (ttt-90) cc_final: 0.7685 (ttm170)
REVERT: B   81 ASP cc_start: 0.7641 (t0) cc_final: 0.7308 (t0)
REVERT: B   84 CYS cc_start: 0.7147 (m) cc_final: 0.6672 (p)
REVERT: B  103 LEU cc_start: 0.4416 (OUTLIER) cc_final: 0.1704 (mt)
REVERT: C   57 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8114 (mm-30)
REVERT: C   81 ASP cc_start: 0.7769 (t70) cc_final: 0.7292 (t0)
REVERT: C   83 TYR cc_start: 0.7669 (t80) cc_final: 0.7189 (t80)
REVERT: C   84 CYS cc_start: 0.7488 (m) cc_final: 0.7015 (p)
REVERT: C  310 GLU cc_start: 0.6303 (mt-10) cc_final: 0.5802 (pm20)
REVERT: D  119 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8299 (tt)
REVERT: D  262 GLN cc_start: 0.7733 (pm20) cc_final: 0.7517 (pp30)
REVERT: D  299 PHE cc_start: 0.6729 (t80) cc_final: 0.6437 (t80)
REVERT: E  103 LEU cc_start: 0.5076 (OUTLIER) cc_final: 0.2494 (mt)
REVERT: E  119 LEU cc_start: 0.8755 (mp) cc_final: 0.8103 (tt)
REVERT: E  127 TRP cc_start: 0.7459 (t60) cc_final: 0.6996 (t60)
REVERT: E  243 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6458 (mm-30)
REVERT: F   84 CYS cc_start: 0.7276 (m) cc_final: 0.6690 (p)
REVERT: F   90 GLN cc_start: 0.7209 (mt0) cc_final: 0.6905 (mt0)
REVERT: F  103 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.2098 (mt)
REVERT: F  274 GLN cc_start: 0.7832 (tt0) cc_final: 0.7627 (tt0)
REVERT: G   81 ASP cc_start: 0.7681 (t70) cc_final: 0.7088 (t0)
REVERT: G   84 CYS cc_start: 0.6694 (m) cc_final: 0.6474 (p)
REVERT: G  103 LEU cc_start: 0.4198 (OUTLIER) cc_final: 0.1504 (mt)
REVERT: G  128 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7889 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8565 (mm) cc_final: 0.8108 (tt)
REVERT: G  299 PHE cc_start: 0.7015 (t80) cc_final: 0.6724 (t80)
  outliers start: 66
  outliers final: 35
  residues processed: 284
  average time/residue: 0.2447
  time to fit residues: 105.8170
Evaluate side-chains
  257 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 215
  time to evaluate  : 1.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
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   88 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  265 CYS
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  265 CYS
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  265 CYS
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  243 GLU
Chi-restraints excluded: chain E residue  265 CYS
Chi-restraints excluded: chain F residue   88 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  237 LEU
Chi-restraints excluded: chain F residue  265 CYS
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   56 GLN
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue  103 LEU
Chi-restraints excluded: chain G residue  235 PHE
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 146 optimal weight:    0.3980
   chunk 99 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 150 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 157 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0020
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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  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 106 HIS ** 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 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6334
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15309  Z= 0.172
  Angle     :  0.718  11.114  20825  Z= 0.355
  Chirality :  0.044   0.202   2471
  Planarity :  0.006   0.045   2520
  Dihedral  :  5.417  21.786   1981
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 25.31 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.20), residues: 1827
  helix: -0.16 (0.16), residues: 1155
  sheet: -2.35 (0.45), residues: 91
  loop : -3.26 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  85 
 HIS   0.004   0.001   HIS F 106 
 PHE   0.028   0.001   PHE F 299 
 TYR   0.025   0.001   TYR C 121 
 ARG   0.002   0.000   ARG A 128 

*********************** 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
  301 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 240
  time to evaluate  : 1.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ARG cc_start: 0.8012 (ttt-90) cc_final: 0.7602 (ttm170)
REVERT: B   81 ASP cc_start: 0.7568 (t0) cc_final: 0.7328 (t0)
REVERT: B   84 CYS cc_start: 0.7000 (m) cc_final: 0.6635 (p)
REVERT: B  237 LEU cc_start: 0.7337 (tt) cc_final: 0.6943 (tp)
REVERT: C   57 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8062 (mm-30)
REVERT: C   81 ASP cc_start: 0.7654 (t70) cc_final: 0.7089 (t0)
REVERT: C   84 CYS cc_start: 0.7218 (m) cc_final: 0.6906 (p)
REVERT: C  274 GLN cc_start: 0.7808 (tt0) cc_final: 0.7553 (tt0)
REVERT: C  310 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5811 (pm20)
REVERT: D  272 ILE cc_start: 0.7963 (pt) cc_final: 0.7694 (tp)
REVERT: D  299 PHE cc_start: 0.6714 (t80) cc_final: 0.6404 (t80)
REVERT: E  109 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7090 (t80)
REVERT: F  226 LEU cc_start: 0.8440 (mm) cc_final: 0.8127 (tt)
REVERT: F  274 GLN cc_start: 0.7805 (tt0) cc_final: 0.7585 (tt0)
REVERT: G   81 ASP cc_start: 0.7629 (t70) cc_final: 0.7354 (t0)
REVERT: G   84 CYS cc_start: 0.6492 (m) cc_final: 0.6280 (p)
REVERT: G  103 LEU cc_start: 0.4103 (OUTLIER) cc_final: 0.1494 (mt)
REVERT: G  128 ARG cc_start: 0.8360 (ttm110) cc_final: 0.7841 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8668 (mm) cc_final: 0.8224 (tt)
  outliers start: 61
  outliers final: 33
  residues processed: 278
  average time/residue: 0.2691
  time to fit residues: 111.3184
Evaluate side-chains
  244 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 208
  time to evaluate  : 1.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
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 A residue  315 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  265 CYS
Chi-restraints excluded: chain C residue  135 ILE
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   81 ASP
Chi-restraints excluded: chain D residue  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  265 CYS
Chi-restraints excluded: chain D residue  279 ILE
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   81 ASP
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  265 CYS
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  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  224 ILE
Chi-restraints excluded: chain G residue  235 PHE
Chi-restraints excluded: chain G residue  265 CYS
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 59 optimal weight:    5.9990
   chunk 158 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 176 optimal weight:    0.9980
   chunk 146 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    2.9988

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  15309  Z= 0.377
  Angle     :  0.882  10.573  20825  Z= 0.443
  Chirality :  0.051   0.223   2471
  Planarity :  0.006   0.042   2520
  Dihedral  :  6.147  22.632   1981
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 24.96 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.20), residues: 1827
  helix: -0.49 (0.15), residues: 1169
  sheet: -1.47 (0.53), residues: 84
  loop : -3.22 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  85 
 HIS   0.007   0.002   HIS F 106 
 PHE   0.029   0.002   PHE A 109 
 TYR   0.030   0.002   TYR C 121 
 ARG   0.007   0.001   ARG A 254 

*********************** 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
  330 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 229
  time to evaluate  : 1.737 
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  107 LYS cc_start: 0.8452 (mttm) cc_final: 0.8187 (mttm)
REVERT: A  128 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7550 (ttm170)
REVERT: B  103 LEU cc_start: 0.5156 (OUTLIER) cc_final: 0.2343 (mt)
REVERT: B  119 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8658 (tp)
REVERT: B  299 PHE cc_start: 0.6726 (t80) cc_final: 0.6367 (t80)
REVERT: C   57 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8285 (mm-30)
REVERT: C  109 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7377 (t80)
REVERT: D  243 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6688 (mm-30)
REVERT: D  299 PHE cc_start: 0.6925 (t80) cc_final: 0.6697 (t80)
REVERT: E   56 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6452 (mt0)
REVERT: E   89 GLN cc_start: 0.7229 (pp30) cc_final: 0.6951 (pp30)
REVERT: E  109 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7816 (t80)
REVERT: F  103 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.2682 (mt)
REVERT: F  107 LYS cc_start: 0.8264 (mttp) cc_final: 0.7966 (mttt)
REVERT: F  109 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7514 (t80)
REVERT: F  120 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8056 (mp)
REVERT: F  226 LEU cc_start: 0.8782 (mm) cc_final: 0.8383 (tt)
REVERT: G  103 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.2353 (mt)
REVERT: G  109 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6967 (t80)
REVERT: G  128 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7901 (mtp-110)
REVERT: G  299 PHE cc_start: 0.7093 (t80) cc_final: 0.6851 (t80)
  outliers start: 101
  outliers final: 57
  residues processed: 303
  average time/residue: 0.2390
  time to fit residues: 110.4454
Evaluate side-chains
  267 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 200
  time to evaluate  : 1.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  119 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  265 CYS
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  292 VAL
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  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  265 CYS
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 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  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  265 CYS
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue   81 ASP
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  235 PHE
Chi-restraints excluded: chain E residue  242 ASP
Chi-restraints excluded: chain E residue  265 CYS
Chi-restraints excluded: chain E residue  279 ILE
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain F residue   81 ASP
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  265 CYS
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  319 HIS
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  223 ILE
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  265 CYS
Chi-restraints excluded: chain G residue  282 VAL
Chi-restraints excluded: chain G residue  291 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 169 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 100 optimal weight:    0.1980
   chunk 128 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0770
   chunk 148 optimal weight:    7.9990
   chunk 98 optimal weight:    3.9990
   chunk 175 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.5742

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6373
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15309  Z= 0.184
  Angle     :  0.756  10.701  20825  Z= 0.371
  Chirality :  0.045   0.220   2471
  Planarity :  0.005   0.045   2520
  Dihedral  :  5.617  22.641   1981
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 27.80 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.20), residues: 1827
  helix: -0.18 (0.16), residues: 1155
  sheet: -1.90 (0.49), residues: 91
  loop : -3.27 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  74 
 HIS   0.003   0.001   HIS F 106 
 PHE   0.029   0.001   PHE F 299 
 TYR   0.026   0.001   TYR C 121 
 ARG   0.002   0.000   ARG F 217 

*********************** 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
  305 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 234
  time to evaluate  : 1.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.4445 (OUTLIER) cc_final: 0.1717 (mt)
REVERT: A  109 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.6870 (t80)
REVERT: A  128 ARG cc_start: 0.7901 (ttt-90) cc_final: 0.7507 (ttm170)
REVERT: B  103 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.1981 (mt)
REVERT: B  237 LEU cc_start: 0.7403 (tt) cc_final: 0.7053 (tp)
REVERT: B  299 PHE cc_start: 0.6730 (t80) cc_final: 0.6392 (t80)
REVERT: C   36 LYS cc_start: 0.8007 (mttm) cc_final: 0.7627 (pttm)
REVERT: C   57 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: C  103 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.3029 (mt)
REVERT: C  109 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.6925 (t80)
REVERT: C  310 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5938 (pm20)
REVERT: D  274 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7227 (tt0)
REVERT: D  291 VAL cc_start: 0.8448 (t) cc_final: 0.8230 (p)
REVERT: E   56 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6534 (mt0)
REVERT: E   63 GLN cc_start: 0.6419 (tp40) cc_final: 0.5793 (mp10)
REVERT: E   84 CYS cc_start: 0.7290 (m) cc_final: 0.7052 (t)
REVERT: E  103 LEU cc_start: 0.5166 (OUTLIER) cc_final: 0.2521 (mt)
REVERT: E  109 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7461 (t80)
REVERT: E  310 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5980 (pm20)
REVERT: F  109 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7267 (t80)
REVERT: F  226 LEU cc_start: 0.8642 (mm) cc_final: 0.8336 (tt)
REVERT: G  103 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.1884 (mt)
REVERT: G  109 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.6917 (t80)
REVERT: G  128 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7840 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8731 (mm) cc_final: 0.8272 (tt)
REVERT: G  299 PHE cc_start: 0.7073 (t80) cc_final: 0.6790 (t80)
  outliers start: 71
  outliers final: 41
  residues processed: 286
  average time/residue: 0.2659
  time to fit residues: 112.9973
Evaluate side-chains
  262 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 207
  time to evaluate  : 1.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
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  270 VAL
Chi-restraints excluded: chain A residue  319 HIS
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  265 CYS
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  265 CYS
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  319 HIS
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  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  265 CYS
Chi-restraints excluded: chain D residue  274 GLN
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   81 ASP
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  265 CYS
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  109 PHE
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  265 CYS
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   54 PHE
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  265 CYS
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 108 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 104 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 111 optimal weight:    0.3980
   chunk 119 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 274 GLN
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 274 GLN
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6374
moved from start:          0.4420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15309  Z= 0.191
  Angle     :  0.753  10.396  20825  Z= 0.370
  Chirality :  0.044   0.174   2471
  Planarity :  0.005   0.043   2520
  Dihedral  :  5.470  20.185   1981
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 27.98 %
    Favored  : 67.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.20), residues: 1827
  helix: -0.09 (0.16), residues: 1162
  sheet: -1.73 (0.49), residues: 84
  loop : -3.26 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  85 
 HIS   0.003   0.001   HIS B 106 
 PHE   0.019   0.001   PHE E 108 
 TYR   0.027   0.001   TYR C 121 
 ARG   0.002   0.000   ARG A 254 

*********************** 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
  308 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 225
  time to evaluate  : 1.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5484 (pp)
REVERT: A  103 LEU cc_start: 0.4233 (OUTLIER) cc_final: 0.1479 (mt)
REVERT: A  109 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7090 (t80)
REVERT: A  128 ARG cc_start: 0.7940 (ttt-90) cc_final: 0.7498 (ttm170)
REVERT: B  103 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.2285 (mt)
REVERT: B  299 PHE cc_start: 0.6828 (t80) cc_final: 0.6477 (t80)
REVERT: C   36 LYS cc_start: 0.8024 (mttm) cc_final: 0.7650 (pttm)
REVERT: C   57 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8175 (mm-30)
REVERT: C  101 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5396 (pp)
REVERT: C  103 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.2882 (mt)
REVERT: C  109 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7035 (t80)
REVERT: C  310 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5908 (pm20)
REVERT: D  109 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7406 (t80)
REVERT: D  274 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7258 (tt0)
REVERT: D  299 PHE cc_start: 0.6618 (t80) cc_final: 0.6248 (t80)
REVERT: E   56 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6504 (mt0)
REVERT: E   63 GLN cc_start: 0.6475 (tp40) cc_final: 0.5823 (mp10)
REVERT: E  101 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5823 (pp)
REVERT: E  103 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.2589 (mt)
REVERT: E  109 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7600 (t80)
REVERT: E  310 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5935 (pm20)
REVERT: F  109 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7209 (t80)
REVERT: F  226 LEU cc_start: 0.8678 (mm) cc_final: 0.8368 (tt)
REVERT: G  103 LEU cc_start: 0.4584 (OUTLIER) cc_final: 0.1939 (mt)
REVERT: G  109 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.6871 (t80)
REVERT: G  128 ARG cc_start: 0.8415 (ttm110) cc_final: 0.7873 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8739 (mm) cc_final: 0.8259 (tt)
REVERT: G  299 PHE cc_start: 0.7091 (t80) cc_final: 0.6787 (t80)
  outliers start: 83
  outliers final: 53
  residues processed: 287
  average time/residue: 0.2562
  time to fit residues: 109.5940
Evaluate side-chains
  283 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 212
  time to evaluate  : 1.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
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  235 PHE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   54 PHE
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  118 ILE
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  265 CYS
Chi-restraints excluded: chain B residue  279 ILE
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  135 ILE
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  265 CYS
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  319 HIS
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  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  265 CYS
Chi-restraints excluded: chain D residue  274 GLN
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   81 ASP
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  265 CYS
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  109 PHE
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  235 PHE
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  265 CYS
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   54 PHE
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   81 ASP
Chi-restraints excluded: chain G residue   89 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  258 THR
Chi-restraints excluded: chain G residue  265 CYS
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 159 optimal weight:    1.9990
   chunk 168 optimal weight:    0.4980
   chunk 153 optimal weight:    7.9990
   chunk 163 optimal weight:    0.4980
   chunk 98 optimal weight:    0.0670
   chunk 71 optimal weight:    0.9990
   chunk 128 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 147 optimal weight:    0.9990
   chunk 154 optimal weight:    4.9990
   chunk 162 optimal weight:    5.9990
   overall best weight:    0.6122

-------------------------------------------------------------------------------
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**
** D  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 GLN
D 274 GLN
** E  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  89 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6347
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  15309  Z= 0.189
  Angle     :  0.760  11.193  20825  Z= 0.371
  Chirality :  0.044   0.234   2471
  Planarity :  0.005   0.043   2520
  Dihedral  :  5.359  19.092   1981
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 28.69 %
    Favored  : 66.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.20), residues: 1827
  helix:  0.03 (0.16), residues: 1162
  sheet: -1.91 (0.49), residues: 84
  loop : -3.27 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  85 
 HIS   0.003   0.001   HIS B 106 
 PHE   0.021   0.001   PHE F 299 
 TYR   0.027   0.001   TYR C 121 
 ARG   0.002   0.000   ARG F 217 

*********************** 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
  306 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 224
  time to evaluate  : 1.693 
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  101 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5419 (pp)
REVERT: A  103 LEU cc_start: 0.4124 (OUTLIER) cc_final: 0.1312 (mt)
REVERT: A  109 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7026 (t80)
REVERT: A  128 ARG cc_start: 0.7916 (ttt-90) cc_final: 0.7556 (ttm170)
REVERT: A  198 GLN cc_start: 0.8167 (pp30) cc_final: 0.7422 (pm20)
REVERT: B  103 LEU cc_start: 0.4466 (OUTLIER) cc_final: 0.2047 (mt)
REVERT: B  237 LEU cc_start: 0.7423 (tt) cc_final: 0.7205 (tp)
REVERT: B  299 PHE cc_start: 0.6848 (t80) cc_final: 0.6468 (t80)
REVERT: C   36 LYS cc_start: 0.8041 (mttm) cc_final: 0.7648 (pttm)
REVERT: C   57 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8161 (mm-30)
REVERT: C  109 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6963 (t80)
REVERT: C  310 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5920 (pm20)
REVERT: D  109 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7456 (t80)
REVERT: D  291 VAL cc_start: 0.8560 (t) cc_final: 0.8264 (p)
REVERT: D  299 PHE cc_start: 0.6583 (t80) cc_final: 0.6364 (t80)
REVERT: E   56 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6425 (mt0)
REVERT: E   63 GLN cc_start: 0.6422 (tp40) cc_final: 0.5791 (mp10)
REVERT: E  101 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5766 (pp)
REVERT: E  103 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.2546 (mt)
REVERT: E  109 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7624 (t80)
REVERT: E  310 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5898 (pm20)
REVERT: F  103 LEU cc_start: 0.4319 (OUTLIER) cc_final: 0.1906 (mt)
REVERT: F  109 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7163 (t80)
REVERT: F  226 LEU cc_start: 0.8690 (mm) cc_final: 0.8378 (tt)
REVERT: F  279 ILE cc_start: 0.8091 (mm) cc_final: 0.7848 (mp)
REVERT: G  101 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5807 (pt)
REVERT: G  103 LEU cc_start: 0.4531 (OUTLIER) cc_final: 0.1896 (mt)
REVERT: G  109 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.6899 (t80)
REVERT: G  128 ARG cc_start: 0.8417 (ttm110) cc_final: 0.7857 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8678 (mm) cc_final: 0.8230 (tt)
REVERT: G  299 PHE cc_start: 0.7114 (t80) cc_final: 0.6818 (t80)
  outliers start: 82
  outliers final: 57
  residues processed: 289
  average time/residue: 0.2532
  time to fit residues: 110.2493
Evaluate side-chains
  282 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 208
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
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  235 PHE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   54 PHE
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain B residue   81 ASP
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  265 CYS
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  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  265 CYS
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   76 GLN
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  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  265 CYS
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   81 ASP
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  258 THR
Chi-restraints excluded: chain E residue  265 CYS
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  276 LEU
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  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  265 CYS
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   54 PHE
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   81 ASP
Chi-restraints excluded: chain G residue   89 GLN
Chi-restraints excluded: chain G residue  101 LEU
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  258 THR
Chi-restraints excluded: chain G residue  265 CYS
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 107 optimal weight:    5.9990
   chunk 172 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 120 optimal weight:    0.2980
   chunk 181 optimal weight:    0.1980
   chunk 166 optimal weight:    9.9990
   chunk 144 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 111 optimal weight:    0.6980
   chunk 88 optimal weight:    6.9990
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6336
moved from start:          0.4692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15309  Z= 0.189
  Angle     :  0.779  13.490  20825  Z= 0.374
  Chirality :  0.045   0.282   2471
  Planarity :  0.005   0.044   2520
  Dihedral  :  5.245  18.344   1981
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 29.16 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.20), residues: 1827
  helix:  0.13 (0.16), residues: 1162
  sheet: -1.87 (0.51), residues: 84
  loop : -3.30 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F  85 
 HIS   0.003   0.001   HIS F 106 
 PHE   0.035   0.001   PHE C 299 
 TYR   0.027   0.001   TYR C 121 
 ARG   0.002   0.000   ARG D  75 

********************** 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
  308 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 227
  time to evaluate  : 1.809 
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  101 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5414 (pp)
REVERT: A  103 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.1521 (mt)
REVERT: A  109 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7032 (t80)
REVERT: A  128 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7516 (ttm170)
REVERT: A  279 ILE cc_start: 0.8209 (mt) cc_final: 0.7955 (mt)
REVERT: B  103 LEU cc_start: 0.4302 (OUTLIER) cc_final: 0.1772 (mt)
REVERT: B  127 TRP cc_start: 0.7768 (t60) cc_final: 0.7497 (t60)
REVERT: B  237 LEU cc_start: 0.7366 (tt) cc_final: 0.7151 (tp)
REVERT: B  299 PHE cc_start: 0.6747 (t80) cc_final: 0.6448 (t80)
REVERT: C   36 LYS cc_start: 0.8047 (mttm) cc_final: 0.7629 (pttm)
REVERT: C   57 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8173 (mm-30)
REVERT: C  103 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.2268 (mt)
REVERT: C  109 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6970 (t80)
REVERT: C  310 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5956 (pm20)
REVERT: D  109 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7440 (t80)
REVERT: D  274 GLN cc_start: 0.7241 (tt0) cc_final: 0.7040 (tt0)
REVERT: D  291 VAL cc_start: 0.8534 (t) cc_final: 0.8258 (p)
REVERT: D  299 PHE cc_start: 0.6566 (t80) cc_final: 0.6209 (t80)
REVERT: E   56 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6416 (mt0)
REVERT: E   63 GLN cc_start: 0.6418 (tp40) cc_final: 0.5794 (mp10)
REVERT: E  101 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5757 (pp)
REVERT: E  103 LEU cc_start: 0.5074 (OUTLIER) cc_final: 0.2409 (mt)
REVERT: E  109 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7643 (t80)
REVERT: E  310 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5984 (pm20)
REVERT: F  103 LEU cc_start: 0.4397 (OUTLIER) cc_final: 0.1852 (mt)
REVERT: F  109 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7264 (t80)
REVERT: F  226 LEU cc_start: 0.8658 (mm) cc_final: 0.8346 (tt)
REVERT: F  279 ILE cc_start: 0.7907 (mm) cc_final: 0.7601 (mp)
REVERT: G  101 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5812 (pt)
REVERT: G  103 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.1897 (mt)
REVERT: G  109 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.6989 (t80)
REVERT: G  128 ARG cc_start: 0.8384 (ttm110) cc_final: 0.7837 (mtp-110)
REVERT: G  226 LEU cc_start: 0.8664 (mm) cc_final: 0.8211 (tt)
  outliers start: 81
  outliers final: 57
  residues processed: 292
  average time/residue: 0.2505
  time to fit residues: 109.7932
Evaluate side-chains
  289 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 214
  time to evaluate  : 1.754 
-------------------------------------------------------------------------------
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  235 PHE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   76 GLN
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  265 CYS
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  103 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  235 PHE
Chi-restraints excluded: chain C residue  265 CYS
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   76 GLN
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  235 PHE
Chi-restraints excluded: chain D residue  242 ASP
Chi-restraints excluded: chain D residue  265 CYS
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  319 HIS
Chi-restraints excluded: chain E residue   56 GLN
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   81 ASP
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  235 PHE
Chi-restraints excluded: chain E residue  245 VAL
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  265 CYS
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  276 LEU
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  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  237 LEU
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  265 CYS
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  319 HIS
Chi-restraints excluded: chain G residue   54 PHE
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   81 ASP
Chi-restraints excluded: chain G residue  101 LEU
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  258 THR
Chi-restraints excluded: chain G residue  265 CYS
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 114 optimal weight:    1.9990
   chunk 153 optimal weight:    0.0000
   chunk 44 optimal weight:    0.9990
   chunk 133 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 40 optimal weight:    4.9990
   chunk 144 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 148 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.198083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.163035 restraints weight = 29196.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.167416 restraints weight = 17144.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.170268 restraints weight = 12105.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15309  Z= 0.187
  Angle     :  0.775  13.431  20825  Z= 0.372
  Chirality :  0.044   0.241   2471
  Planarity :  0.005   0.043   2520
  Dihedral  :  5.158  18.962   1981
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 29.16 %
    Favored  : 66.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.20), residues: 1827
  helix:  0.23 (0.16), residues: 1162
  sheet: -1.77 (0.52), residues: 84
  loop : -3.32 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 127 
 HIS   0.003   0.001   HIS F 106 
 PHE   0.036   0.001   PHE F 299 
 TYR   0.027   0.001   TYR C 121 
 ARG   0.004   0.000   ARG D  75 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3018.52 seconds
wall clock time: 57 minutes 2.16 seconds (3422.16 seconds total)