Starting phenix.real_space_refine
on Thu Mar  5 15:33:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nst_12576/03_2026/7nst_12576.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nst_12576/03_2026/7nst_12576.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nst_12576/03_2026/7nst_12576.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nst_12576/03_2026/7nst_12576.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nst_12576/03_2026/7nst_12576.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nst_12576/03_2026/7nst_12576.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
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: 5
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    8117      2.51       5
     N    2210      2.21       5
     O    2597      1.98       5
     H   10582      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23528
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 5071
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 335}
    Chain: "B"
      Number of atoms: 5071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 5071
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 335}
    Chain: "C"
      Number of atoms: 5068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 5068
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 335}
    Chain: "D"
      Number of atoms: 2317
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 289, 2306
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 22, 'TRANS': 266}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 11
      Conformer: "B"
        Number of residues, atoms: 289, 2306
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 22, 'TRANS': 266}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 11
          bond proxies already assigned to first conformer: 2332
    Chain: "E"
      Number of atoms: 6001
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 394, 5857
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 26, 'TRANS': 367}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 394, 5857
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 26, 'TRANS': 367}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 5773
  Time building chain proxies: 5.10, per 1000 atoms: 0.22
  Number of scatterers: 23528
  At special positions: 0
  Unit cell: (181.131, 104.7, 93.183, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     O    2597      8.00
     N    2210      7.00
     C    8117      6.00
     H   10582      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2980

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 16 sheets defined
      10.2% alpha, 42.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 103 through 111
      removed outlier: 3.816A  pdb=" N   ASP A 107 " --> pdb=" O   GLY A 103 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA A 108 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   TYR A 111 " --> pdb=" O   ASP A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 147
    Processing helix  chain 'A' and resid 197 through 203
      removed outlier: 3.504A  pdb=" N   GLN A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 111
      removed outlier: 3.816A  pdb=" N   ASP B 107 " --> pdb=" O   GLY B 103 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA B 108 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   TYR B 111 " --> pdb=" O   ASP B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 197 through 203
      removed outlier: 3.505A  pdb=" N   GLN B 203 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 111
      removed outlier: 3.815A  pdb=" N   ASP C 107 " --> pdb=" O   GLY C 103 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA C 108 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   TYR C 111 " --> pdb=" O   ASP C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 147
    Processing helix  chain 'C' and resid 197 through 203
      removed outlier: 3.504A  pdb=" N   GLN C 203 " --> pdb=" O   LEU C 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 125
      removed outlier: 3.521A  pdb=" N   LYS D 125 " --> pdb=" O   ALA D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 149
      removed outlier: 3.908A  pdb=" N   LYS D 147 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASP D 148 " --> pdb=" O   GLU D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 166
    Processing helix  chain 'D' and resid 276 through 280
      removed outlier: 3.893A  pdb=" N   GLY D 280 " --> pdb=" O   LYS D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 314
    Processing helix  chain 'E' and resid 53 through 65
    Processing helix  chain 'E' and resid 72 through 76
    Processing helix  chain 'E' and resid 87 through 93
      removed outlier: 3.685A  pdb=" N   TRP E  91 " --> pdb=" O   GLN E  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 137 through 139
      No H-bonds generated for 'chain 'E' and resid 137 through 139'
    Processing helix  chain 'E' and resid 140 through 158
    Processing helix  chain 'E' and resid 394 through 399
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2 through 6
    current: chain 'A' and resid 55 through 66
      removed outlier: 6.560A  pdb=" N   ASN A  64 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   THR A  81 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ASN A 101 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   GLY A 134 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 292 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ALA A 280 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   ASP A 290 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   ASP A 282 " --> pdb=" O   ASP A 288 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   ASP A 288 " --> pdb=" O   ASP A 282 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   MET A 307 " --> pdb=" O   PHE A 303 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 242
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 2 through 6
    current: chain 'B' and resid 55 through 66
      removed outlier: 6.561A  pdb=" N   ASN B  64 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   THR B  81 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ASN B 101 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   GLY B 134 " --> pdb=" O   ASN B 101 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL B 292 " --> pdb=" O   SER B 278 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ALA B 280 " --> pdb=" O   ASP B 290 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   ASP B 290 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   ASP B 282 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ASP B 288 " --> pdb=" O   ASP B 282 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   MET B 307 " --> pdb=" O   PHE B 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 242
    Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 6
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 2 through 6
    current: chain 'C' and resid 55 through 66
      removed outlier: 6.560A  pdb=" N   ASN C  64 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   THR C  81 " --> pdb=" O   ASN C  64 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ASN C 101 " --> pdb=" O   GLY C 134 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   GLY C 134 " --> pdb=" O   ASN C 101 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL C 292 " --> pdb=" O   SER C 278 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ALA C 280 " --> pdb=" O   ASP C 290 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   ASP C 290 " --> pdb=" O   ALA C 280 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   ASP C 282 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   ASP C 288 " --> pdb=" O   ASP C 282 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   MET C 307 " --> pdb=" O   PHE C 303 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 239 through 242
    Processing sheet with id=AA7, first strand: chain 'D' and resid 94 through 96
      removed outlier: 19.651A  pdb=" N   THR D 268 " --> pdb=" O   GLY D 202 " (cutoff:3.500A)
      removed outlier: 14.062A  pdb=" N   ASP D 270 " --> pdb=" O   PRO D 204 " (cutoff:3.500A)
      removed outlier: 9.518A  pdb=" N   SER D 206 " --> pdb=" O   ASP D 270 " (cutoff:3.500A)
      removed outlier: 8.535A  pdb=" N   VAL D 272 " --> pdb=" O   SER D 206 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   ARG D 274 " --> pdb=" O   PRO D 208 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL D 210 " --> pdb=" O   ARG D 274 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLY D 202 " --> pdb=" O   ASN D 183 " (cutoff:3.500A)
      removed outlier: 9.856A  pdb=" N   ASN D 183 " --> pdb=" O   GLY D 202 " (cutoff:3.500A)
      removed outlier: 9.234A  pdb=" N   ASN D 181 " --> pdb=" O   PRO D 204 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   SER D 206 " --> pdb=" O   THR D 179 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   THR D 179 " --> pdb=" O   SER D 206 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96
      removed outlier: 19.651A  pdb=" N   THR D 268 " --> pdb=" O   GLY D 202 " (cutoff:3.500A)
      removed outlier: 14.062A  pdb=" N   ASP D 270 " --> pdb=" O   PRO D 204 " (cutoff:3.500A)
      removed outlier: 9.518A  pdb=" N   SER D 206 " --> pdb=" O   ASP D 270 " (cutoff:3.500A)
      removed outlier: 8.535A  pdb=" N   VAL D 272 " --> pdb=" O   SER D 206 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   ARG D 274 " --> pdb=" O   PRO D 208 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL D 210 " --> pdb=" O   ARG D 274 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   GLN D 195 " --> pdb=" O   SER D 139 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   SER D 139 " --> pdb=" O   GLN D 195 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE D 197 " --> pdb=" O   LEU D 137 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 104
      removed outlier: 6.439A  pdb=" N   LEU D 103 " --> pdb=" O   ASN D 232 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 68 through 70
      removed outlier: 9.224A  pdb=" N   VAL E 100 " --> pdb=" O   PRO E  36 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLY E  38 " --> pdb=" O   VAL E 100 " (cutoff:3.500A)
      removed outlier: 8.918A  pdb=" N   GLY E 102 " --> pdb=" O   GLY E  38 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TYR E 112 " --> pdb=" O   LYS E 135 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   LYS E 135 " --> pdb=" O   TYR E 112 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL E 114 " --> pdb=" O   SER E 133 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   SER E 133 " --> pdb=" O   VAL E 114 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TYR E 116 " --> pdb=" O   GLN E 131 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   GLN E 131 " --> pdb=" O   TYR E 116 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   LEU E 118 " --> pdb=" O   LEU E 129 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 193 through 198
      removed outlier: 6.573A  pdb=" N   LEU E 182 " --> pdb=" O   VAL E 195 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ARG E 197 " --> pdb=" O   TYR E 180 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   TYR E 180 " --> pdb=" O   ARG E 197 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   VAL E 170 " --> pdb=" O   PHE E 423 " (cutoff:3.500A)
      removed outlier: 5.203A  pdb=" N   PHE E 423 " --> pdb=" O   VAL E 170 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   GLN E 172 " --> pdb=" O   VAL E 421 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   VAL E 421 " --> pdb=" O   GLN E 172 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 202 through 207
      removed outlier: 5.640A  pdb=" N   SER E 204 " --> pdb=" O   VAL E 217 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   VAL E 217 " --> pdb=" O   SER E 204 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU E 226 " --> pdb=" O   VAL E 239 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 251
      removed outlier: 5.790A  pdb=" N   ALA E 248 " --> pdb=" O   ALA E 261 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ALA E 261 " --> pdb=" O   ALA E 248 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 291 through 295
      removed outlier: 6.490A  pdb=" N   ALA E 303 " --> pdb=" O   PRO E 293 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   TRP E 295 " --> pdb=" O   ASN E 301 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ASN E 301 " --> pdb=" O   TRP E 295 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 333 through 339
      removed outlier: 4.314A  pdb=" N   ALA E 337 " --> pdb=" O   VAL E 347 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL E 347 " --> pdb=" O   ALA E 337 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   VAL E 339 " --> pdb=" O   PHE E 345 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   PHE E 345 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 378 through 382
      removed outlier: 6.327A  pdb=" N   ILE E 390 " --> pdb=" O   PRO E 380 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   LEU E 382 " --> pdb=" O   MET E 388 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   MET E 388 " --> pdb=" O   LEU E 382 " (cutoff:3.500A)

    580 hydrogen bonds defined for protein.
    1575 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: 5.04

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        0.79 -     1.01: 10580
        1.01 -     1.22: 3
        1.22 -     1.43: 5948
        1.43 -     1.65: 7244
        1.65 -     1.86: 42
  Bond restraints: 23817
  Sorted by residual:
  bond pdb=" ND2 ASN E 290 "
       pdb="HD22 ASN E 290 "
    ideal  model  delta    sigma   weight residual
    0.860  0.794  0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" N   ILE D  54 "
       pdb=" H   ILE D  54 "
    ideal  model  delta    sigma   weight residual
    0.860  0.916 -0.056 2.00e-02 2.50e+03 7.83e+00
  bond pdb=" N   GLY D  58 "
       pdb=" H   GLY D  58 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.76e+00
  bond pdb=" N   GLY D  57 "
       pdb=" H   GLY D  57 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.49e+00
  bond pdb=" N   HIS D  55 "
       pdb=" H   HIS D  55 "
    ideal  model  delta    sigma   weight residual
    0.860  0.909 -0.049 2.00e-02 2.50e+03 5.94e+00
  ... (remaining 23812 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.50: 41843
        6.50 -    13.00: 6
       13.00 -    19.50: 2
       19.50 -    26.00: 3
       26.00 -    32.50: 8
  Bond angle restraints: 41862
  Sorted by residual:
  angle pdb="HD22 LEU A  88 "
        pdb=" CD2 LEU A  88 "
        pdb="HD23 LEU A  88 "
      ideal   model   delta    sigma   weight residual
     110.00   77.50   32.50 3.00e+00 1.11e-01 1.17e+02
  angle pdb="HD21 LEU A  88 "
        pdb=" CD2 LEU A  88 "
        pdb="HD22 LEU A  88 "
      ideal   model   delta    sigma   weight residual
     110.00   77.70   32.30 3.00e+00 1.11e-01 1.16e+02
  angle pdb="HD11 LEU A  88 "
        pdb=" CD1 LEU A  88 "
        pdb="HD12 LEU A  88 "
      ideal   model   delta    sigma   weight residual
     110.00   78.93   31.07 3.00e+00 1.11e-01 1.07e+02
  angle pdb="HD12 LEU A  88 "
        pdb=" CD1 LEU A  88 "
        pdb="HD13 LEU A  88 "
      ideal   model   delta    sigma   weight residual
     110.00   81.00   29.00 3.00e+00 1.11e-01 9.35e+01
  angle pdb=" CG  LEU A  88 "
        pdb=" CD1 LEU A  88 "
        pdb="HD11 LEU A  88 "
      ideal   model   delta    sigma   weight residual
     109.00   80.48   28.52 3.00e+00 1.11e-01 9.04e+01
  ... (remaining 41857 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 10501
       17.81 -    35.62: 819
       35.62 -    53.43: 222
       53.43 -    71.24: 81
       71.24 -    89.04: 9
  Dihedral angle restraints: 11632
    sinusoidal: 5942
      harmonic: 5690
  Sorted by residual:
  dihedral pdb=" CA  MET E 203 "
           pdb=" C   MET E 203 "
           pdb=" N   SER E 204 "
           pdb=" CA  SER E 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.17   25.83     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  LEU E 302 "
           pdb=" C   LEU E 302 "
           pdb=" N   ALA E 303 "
           pdb=" CA  ALA E 303 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.74   23.26     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  ASP A 127 "
           pdb=" C   ASP A 127 "
           pdb=" N   PHE A 128 "
           pdb=" CA  PHE A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.15  -19.85     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 11629 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1411
       0.043 -    0.085: 322
       0.085 -    0.128: 137
       0.128 -    0.171: 13
       0.171 -    0.214: 2
  Chirality restraints: 1885
  Sorted by residual:
  chirality pdb=" CA  CYS D  33 "
            pdb=" N   CYS D  33 "
            pdb=" C   CYS D  33 "
            pdb=" CB  CYS D  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  ILE D  54 "
            pdb=" N   ILE D  54 "
            pdb=" C   ILE D  54 "
            pdb=" CB  ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.61e-01
  chirality pdb=" CA  ILE C 336 "
            pdb=" N   ILE C 336 "
            pdb=" C   ILE C 336 "
            pdb=" CB  ILE C 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.99e-01
  ... (remaining 1882 not shown)

  Planarity restraints: 3871
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO E 243 "    0.020 2.00e-02 2.50e+03   4.03e-02 1.62e+01
        pdb=" C   PRO E 243 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PRO E 243 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ARG E 244 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 244 "   -0.018 2.00e-02 2.50e+03   2.32e-02 1.61e+01
        pdb=" CG  PHE C 244 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 244 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 244 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 244 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 244 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 244 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE C 244 "    0.062 2.00e-02 2.50e+03
        pdb=" HD2 PHE C 244 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE C 244 "   -0.013 2.00e-02 2.50e+03
        pdb=" HE2 PHE C 244 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE C 244 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN E 352 "   -0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   ASN E 352 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ASN E 352 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLY E 353 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 3868 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     1.99: 297
        1.99 -     2.64: 29698
        2.64 -     3.29: 67588
        3.29 -     3.95: 89152
        3.95 -     4.60: 139687
  Nonbonded interactions: 326422
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D  35 "
            pdb=" H   HIS E 245 "
     model   vdw
     1.334 2.450
  nonbonded pdb=" HZ2 TRP D  39 "
            pdb=" H   LEU E 268 "
     model   vdw
     1.478 2.100
  nonbonded pdb=" O   ASN E 289 "
            pdb=" HG  SER E 306 "
     model   vdw
     1.506 2.450
  nonbonded pdb="HD22 ASN E 290 "
            pdb=" HE2 PHE E 304 "
     model   vdw
     1.527 2.100
  nonbonded pdb="HD22 ASN A 198 "
            pdb=" OE2 GLU D 216 "
     model   vdw
     1.569 2.450
  ... (remaining 326417 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 243 or (resid 244 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ 
E2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ 
 HE1 or name HE2 or name HZ )) or (resid 245 and (name N or name CA or name C or \ 
 name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or  \ 
name HG21 or name HG22 or name HG23)) or (resid 246 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name  \ 
HB2 or name HB3 or name HD21 or name HD22)) or resid 247 through 340))
  selection = (chain 'B' and (resid 1 through 243 or (resid 244 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ 
E2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ 
 HE1 or name HE2 or name HZ )) or (resid 245 and (name N or name CA or name C or \ 
 name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or  \ 
name HG21 or name HG22 or name HG23)) or (resid 246 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name  \ 
HB2 or name HB3 or name HD21 or name HD22)) or resid 247 through 340))
  selection = chain 'C'
}

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=0.20 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  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:             0.090
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     21.940
  Find NCS groups from input model:        0.220
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
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      :  0.003   0.070  13235  Z= 0.175
  Angle     :  0.646  10.092  17973  Z= 0.373
  Chirality :  0.044   0.214   1885
  Planarity :  0.005   0.060   2429
  Dihedral  : 13.581  89.045   4690
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.32 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  3.23 %
    Favored  : 95.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.19), residues: 1699
  helix: -1.50 (0.44), residues: 96
  sheet: -0.66 (0.18), residues: 743
  loop : -1.49 (0.19), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 287 
 TYR   0.011   0.001   TYR E 116 
 PHE   0.021   0.002   PHE E 219 
 TRP   0.028   0.003   TRP D  56 
 HIS   0.007   0.002   HIS A  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (13235)
  covalent geometry    : angle       0.64625 (17973)
  hydrogen bonds       : bond        0.15191 (  564)
  hydrogen bonds       : angle       7.07064 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  415 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 404
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7817 (ttpp) cc_final: 0.7512 (ttmm)
REVERT: A   16 LYS cc_start: 0.8712 (pttt) cc_final: 0.8461 (pttt)
REVERT: A   46 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8135 (ttmm)
REVERT: A   62 GLU cc_start: 0.7117 (tt0) cc_final: 0.6735 (tt0)
REVERT: A   74 ASP cc_start: 0.8077 (p0) cc_final: 0.7394 (p0)
REVERT: A   79 ASN cc_start: 0.7482 (m-40) cc_final: 0.7194 (m110)
REVERT: A  104 VAL cc_start: 0.7626 (m) cc_final: 0.7048 (m)
REVERT: A  144 PHE cc_start: 0.8299 (t80) cc_final: 0.8034 (t80)
REVERT: A  178 ILE cc_start: 0.8349 (mp) cc_final: 0.8149 (mt)
REVERT: A  258 LEU cc_start: 0.8744 (mm) cc_final: 0.8521 (mt)
REVERT: A  262 GLN cc_start: 0.7424 (mt0) cc_final: 0.7222 (mt0)
REVERT: A  267 PHE cc_start: 0.8113 (p90) cc_final: 0.7902 (p90)
REVERT: A  272 SER cc_start: 0.8009 (p) cc_final: 0.7440 (t)
REVERT: A  330 ASP cc_start: 0.6361 (m-30) cc_final: 0.6153 (m-30)
REVERT: B    2 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6390 (tm-30)
REVERT: B    6 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7456 (ttmm)
REVERT: B   12 ASP cc_start: 0.6566 (t0) cc_final: 0.6348 (t0)
REVERT: B   16 LYS cc_start: 0.7667 (pttt) cc_final: 0.7405 (ptmm)
REVERT: B   66 GLN cc_start: 0.8090 (mm110) cc_final: 0.7839 (mm-40)
REVERT: B   71 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6703 (mt-10)
REVERT: B  104 VAL cc_start: 0.7931 (m) cc_final: 0.7201 (m)
REVERT: B  107 ASP cc_start: 0.6506 (m-30) cc_final: 0.6220 (m-30)
REVERT: B  113 ASP cc_start: 0.6876 (t0) cc_final: 0.6643 (t0)
REVERT: B  125 SER cc_start: 0.8069 (p) cc_final: 0.7810 (p)
REVERT: B  178 ILE cc_start: 0.8588 (mp) cc_final: 0.8365 (tt)
REVERT: B  181 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6767 (tm-30)
REVERT: B  196 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.7174 (mtp85)
REVERT: B  210 LYS cc_start: 0.7603 (mmmt) cc_final: 0.7393 (mmmm)
REVERT: B  294 TYR cc_start: 0.7621 (p90) cc_final: 0.7385 (p90)
REVERT: B  320 SER cc_start: 0.8431 (p) cc_final: 0.8141 (p)
REVERT: B  321 ASP cc_start: 0.7769 (p0) cc_final: 0.6609 (p0)
REVERT: C   10 LYS cc_start: 0.8232 (ttmt) cc_final: 0.8013 (ttmt)
REVERT: C   14 TYR cc_start: 0.7630 (p90) cc_final: 0.7389 (p90)
REVERT: C   40 TYR cc_start: 0.8450 (p90) cc_final: 0.8027 (p90)
REVERT: C   58 TYR cc_start: 0.8205 (p90) cc_final: 0.7970 (p90)
REVERT: C   61 TRP cc_start: 0.7742 (t60) cc_final: 0.7517 (t60)
REVERT: C  104 VAL cc_start: 0.7869 (m) cc_final: 0.7363 (m)
REVERT: C  107 ASP cc_start: 0.6617 (m-30) cc_final: 0.6408 (m-30)
REVERT: C  158 LEU cc_start: 0.8178 (tp) cc_final: 0.7802 (tt)
REVERT: C  178 ILE cc_start: 0.8294 (mp) cc_final: 0.7892 (pt)
REVERT: C  185 PHE cc_start: 0.7887 (m-80) cc_final: 0.7245 (m-80)
REVERT: C  253 LYS cc_start: 0.7659 (ttpt) cc_final: 0.7210 (ttmm)
REVERT: C  256 ASP cc_start: 0.6755 (m-30) cc_final: 0.6341 (m-30)
REVERT: C  258 LEU cc_start: 0.7993 (mm) cc_final: 0.7712 (mp)
REVERT: C  282 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6430 (m-30)
REVERT: C  293 ASN cc_start: 0.7383 (t0) cc_final: 0.7128 (t0)
REVERT: C  323 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7771 (mmmm)
REVERT: C  337 VAL cc_start: 0.8527 (t) cc_final: 0.8124 (m)
REVERT: D   37 SER cc_start: 0.5661 (OUTLIER) cc_final: 0.5461 (t)
REVERT: D  205 MET cc_start: -0.1603 (mtm) cc_final: -0.4261 (tpt)
REVERT: E  203 MET cc_start: 0.5080 (mtt) cc_final: 0.4873 (mtt)
  outliers start: 11
  outliers final: 4
  residues processed: 414
  average time/residue: 0.2602
  time to fit residues: 150.6771
Evaluate side-chains
  371 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 365
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 ASP
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  242 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:   40.0000
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:   30.0000
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 317 GLN
B 264 GLN
** C  21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  78 GLN
E  87 GLN
E 282 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.201347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.137973 restraints weight = 102279.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.142621 restraints weight = 28154.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.144661 restraints weight = 12500.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.145969 restraints weight = 7561.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.145587 restraints weight = 5827.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3663 r_free = 0.3663    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3663 r_free = 0.3663    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.3663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  13235  Z= 0.306
  Angle     :  0.661   7.131  17973  Z= 0.364
  Chirality :  0.047   0.160   1885
  Planarity :  0.005   0.058   2429
  Dihedral  :  5.295  53.486   1892
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.31 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  9.77 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.19), residues: 1699
  helix:  0.83 (0.49), residues: 91
  sheet: -0.54 (0.18), residues: 730
  loop : -0.89 (0.20), residues: 878

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 244 
 TYR   0.022   0.002   TYR E 134 
 PHE   0.017   0.002   PHE B 267 
 TRP   0.014   0.002   TRP B 214 
 HIS   0.010   0.002   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 (13235)
  covalent geometry    : angle       0.66066 (17973)
  hydrogen bonds       : bond        0.04438 (  564)
  hydrogen bonds       : angle       5.76320 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  424 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 395
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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    6 LYS cc_start: 0.8269 (ttpp) cc_final: 0.7722 (ttpp)
REVERT: A   16 LYS cc_start: 0.8644 (pttt) cc_final: 0.8254 (ptpp)
REVERT: A   42 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8236 (mtt180)
REVERT: A   46 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8189 (ttmm)
REVERT: A   62 GLU cc_start: 0.7336 (tt0) cc_final: 0.7119 (tt0)
REVERT: A   74 ASP cc_start: 0.8448 (p0) cc_final: 0.7974 (p0)
REVERT: A   79 ASN cc_start: 0.8055 (m-40) cc_final: 0.7613 (m110)
REVERT: A  122 THR cc_start: 0.8344 (t) cc_final: 0.7941 (m)
REVERT: A  126 ASP cc_start: 0.7981 (m-30) cc_final: 0.7679 (m-30)
REVERT: A  153 PHE cc_start: 0.7513 (p90) cc_final: 0.7156 (p90)
REVERT: A  210 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8209 (mmmt)
REVERT: A  221 ASP cc_start: 0.7626 (t0) cc_final: 0.7350 (p0)
REVERT: A  273 ILE cc_start: 0.8425 (mt) cc_final: 0.7897 (tp)
REVERT: A  293 ASN cc_start: 0.7902 (t0) cc_final: 0.7363 (p0)
REVERT: A  296 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7072 (tm-30)
REVERT: A  330 ASP cc_start: 0.6796 (m-30) cc_final: 0.6298 (m-30)
REVERT: B    6 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7983 (ttmm)
REVERT: B   71 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6667 (mt-10)
REVERT: B  113 ASP cc_start: 0.7366 (t0) cc_final: 0.7038 (t0)
REVERT: B  207 ASN cc_start: 0.7674 (m-40) cc_final: 0.7040 (m-40)
REVERT: B  210 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7828 (mmmm)
REVERT: B  233 GLU cc_start: 0.7071 (tt0) cc_final: 0.6798 (tt0)
REVERT: B  264 GLN cc_start: 0.8605 (tp40) cc_final: 0.8386 (tp-100)
REVERT: B  286 ILE cc_start: 0.8158 (mm) cc_final: 0.7850 (mt)
REVERT: B  296 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7373 (tm-30)
REVERT: B  306 ASN cc_start: 0.7778 (m110) cc_final: 0.7573 (m110)
REVERT: B  321 ASP cc_start: 0.8026 (p0) cc_final: 0.7594 (p0)
REVERT: C    6 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7756 (mtpp)
REVERT: C   14 TYR cc_start: 0.7919 (p90) cc_final: 0.7341 (p90)
REVERT: C   20 LEU cc_start: 0.8387 (tp) cc_final: 0.8141 (tp)
REVERT: C   25 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7516 (mmtt)
REVERT: C   62 GLU cc_start: 0.7349 (tt0) cc_final: 0.6617 (tt0)
REVERT: C  115 LEU cc_start: 0.7945 (mm) cc_final: 0.7687 (mt)
REVERT: C  126 ASP cc_start: 0.8214 (m-30) cc_final: 0.7889 (m-30)
REVERT: C  227 LEU cc_start: 0.8644 (mm) cc_final: 0.8378 (mt)
REVERT: C  253 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7320 (ttmm)
REVERT: C  296 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6533 (tm-30)
REVERT: C  323 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8064 (mmmm)
REVERT: C  337 VAL cc_start: 0.8141 (t) cc_final: 0.7623 (m)
REVERT: D  205 MET cc_start: -0.1384 (mtm) cc_final: -0.4144 (tpt)
  outliers start: 29
  outliers final: 23
  residues processed: 404
  average time/residue: 0.2574
  time to fit residues: 145.3793
Evaluate side-chains
  387 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 364
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   58 TYR
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  317 GLN
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  252 ASN
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain C residue  152 ASN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  330 ASP
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain D residue  152 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain E residue  134 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 58 optimal weight:    0.2980
   chunk 117 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0570
   chunk 153 optimal weight:   30.0000
   chunk 72 optimal weight:    0.9990
   chunk 145 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN
B 101 ASN
C  66 GLN
C 143 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.203892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.140178 restraints weight = 104036.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145108 restraints weight = 27499.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.146936 restraints weight = 12044.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.148355 restraints weight = 7195.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.147965 restraints weight = 5485.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13235  Z= 0.141
  Angle     :  0.553   8.147  17973  Z= 0.303
  Chirality :  0.044   0.157   1885
  Planarity :  0.004   0.052   2429
  Dihedral  :  4.739  42.671   1886
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.46 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.20), residues: 1699
  helix:  1.90 (0.51), residues: 93
  sheet: -0.38 (0.17), residues: 752
  loop : -0.77 (0.21), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 235 
 TYR   0.016   0.001   TYR E 134 
 PHE   0.011   0.001   PHE C 267 
 TRP   0.021   0.001   TRP D  39 
 HIS   0.006   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (13235)
  covalent geometry    : angle       0.55325 (17973)
  hydrogen bonds       : bond        0.03747 (  564)
  hydrogen bonds       : angle       5.44183 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  405 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 379
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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    7 ASP cc_start: 0.7460 (t70) cc_final: 0.7023 (t70)
REVERT: A   16 LYS cc_start: 0.8596 (pttt) cc_final: 0.8346 (ptpt)
REVERT: A   42 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8302 (mtt180)
REVERT: A   46 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8199 (ttmm)
REVERT: A   79 ASN cc_start: 0.8054 (m-40) cc_final: 0.7602 (m110)
REVERT: A   83 LEU cc_start: 0.8050 (mt) cc_final: 0.7834 (mp)
REVERT: A  126 ASP cc_start: 0.7958 (m-30) cc_final: 0.7691 (m-30)
REVERT: A  153 PHE cc_start: 0.7445 (p90) cc_final: 0.7045 (p90)
REVERT: A  210 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8216 (mmmt)
REVERT: A  221 ASP cc_start: 0.7562 (t0) cc_final: 0.7271 (p0)
REVERT: A  273 ILE cc_start: 0.8420 (mt) cc_final: 0.8088 (mt)
REVERT: A  293 ASN cc_start: 0.7916 (t0) cc_final: 0.7213 (p0)
REVERT: A  294 TYR cc_start: 0.8117 (p90) cc_final: 0.7801 (p90)
REVERT: A  318 ILE cc_start: 0.8850 (mm) cc_final: 0.8589 (mm)
REVERT: B    6 LYS cc_start: 0.8269 (ttpp) cc_final: 0.8037 (ttpp)
REVERT: B   54 ASP cc_start: 0.7279 (m-30) cc_final: 0.7020 (p0)
REVERT: B   98 TYR cc_start: 0.7521 (t80) cc_final: 0.7200 (t80)
REVERT: B  113 ASP cc_start: 0.7268 (t0) cc_final: 0.6935 (t0)
REVERT: B  140 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7297 (mtt-85)
REVERT: B  156 GLN cc_start: 0.7968 (tt0) cc_final: 0.7704 (tt0)
REVERT: B  207 ASN cc_start: 0.7689 (m-40) cc_final: 0.6988 (m-40)
REVERT: B  210 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7771 (mmmm)
REVERT: B  286 ILE cc_start: 0.8215 (mm) cc_final: 0.7901 (mt)
REVERT: B  296 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7184 (tm-30)
REVERT: B  306 ASN cc_start: 0.7727 (m110) cc_final: 0.7494 (m110)
REVERT: B  321 ASP cc_start: 0.8054 (p0) cc_final: 0.7594 (p0)
REVERT: C    6 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7772 (mtpp)
REVERT: C   14 TYR cc_start: 0.7945 (p90) cc_final: 0.7521 (p90)
REVERT: C   20 LEU cc_start: 0.8227 (tp) cc_final: 0.7999 (tp)
REVERT: C   25 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7507 (mmtt)
REVERT: C  113 ASP cc_start: 0.7705 (t0) cc_final: 0.7395 (t0)
REVERT: C  115 LEU cc_start: 0.7966 (mm) cc_final: 0.7753 (mt)
REVERT: C  126 ASP cc_start: 0.8153 (m-30) cc_final: 0.7853 (m-30)
REVERT: C  227 LEU cc_start: 0.8586 (mm) cc_final: 0.8323 (mt)
REVERT: C  246 ASN cc_start: 0.8256 (t0) cc_final: 0.8006 (t0)
REVERT: C  253 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7321 (ttmm)
REVERT: C  296 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6495 (tm-30)
REVERT: C  323 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8054 (mmmm)
REVERT: C  337 VAL cc_start: 0.8386 (t) cc_final: 0.8033 (p)
REVERT: D  205 MET cc_start: -0.1293 (mtm) cc_final: -0.4151 (tpt)
  outliers start: 26
  outliers final: 21
  residues processed: 387
  average time/residue: 0.2581
  time to fit residues: 138.5451
Evaluate side-chains
  379 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 358
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  317 GLN
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  252 ASN
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  256 ASP
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain D residue   56 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 138 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 151 optimal weight:   20.0000
   chunk 25 optimal weight:    2.9990
   chunk 149 optimal weight:   20.0000
   chunk 81 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9980
   chunk 159 optimal weight:   20.0000
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 GLN
B 200 GLN
C  66 GLN
** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.200134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.136347 restraints weight = 95099.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.141883 restraints weight = 27315.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.143878 restraints weight = 9542.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144231 restraints weight = 6691.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.143916 restraints weight = 5698.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13235  Z= 0.227
  Angle     :  0.565   4.877  17973  Z= 0.312
  Chirality :  0.045   0.167   1885
  Planarity :  0.004   0.050   2429
  Dihedral  :  4.639  41.607   1885
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.38 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.20), residues: 1699
  helix:  2.15 (0.52), residues: 93
  sheet: -0.35 (0.17), residues: 736
  loop : -0.84 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 196 
 TYR   0.016   0.002   TYR E 134 
 PHE   0.017   0.002   PHE B 267 
 TRP   0.012   0.002   TRP B 214 
 HIS   0.008   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (13235)
  covalent geometry    : angle       0.56453 (17973)
  hydrogen bonds       : bond        0.03867 (  564)
  hydrogen bonds       : angle       5.36170 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  404 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 371
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8121 (ttmm)
REVERT: A   76 GLN cc_start: 0.8628 (mp10) cc_final: 0.8142 (mp10)
REVERT: A   79 ASN cc_start: 0.8241 (m-40) cc_final: 0.7882 (m110)
REVERT: A   83 LEU cc_start: 0.8128 (mt) cc_final: 0.7844 (mp)
REVERT: A  126 ASP cc_start: 0.7985 (m-30) cc_final: 0.7618 (m-30)
REVERT: A  181 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6728 (tm-30)
REVERT: A  210 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8330 (mmmt)
REVERT: A  221 ASP cc_start: 0.7517 (t0) cc_final: 0.7290 (p0)
REVERT: A  255 GLN cc_start: 0.7263 (mt0) cc_final: 0.6938 (mt0)
REVERT: A  260 VAL cc_start: 0.8292 (t) cc_final: 0.7780 (m)
REVERT: A  273 ILE cc_start: 0.8282 (mt) cc_final: 0.7986 (mt)
REVERT: A  293 ASN cc_start: 0.8095 (t0) cc_final: 0.7509 (p0)
REVERT: A  328 SER cc_start: 0.7974 (p) cc_final: 0.7640 (m)
REVERT: B    6 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8112 (ttpt)
REVERT: B   54 ASP cc_start: 0.7292 (m-30) cc_final: 0.7028 (p0)
REVERT: B   98 TYR cc_start: 0.7589 (t80) cc_final: 0.7370 (t80)
REVERT: B  104 VAL cc_start: 0.7843 (m) cc_final: 0.7105 (m)
REVERT: B  107 ASP cc_start: 0.7060 (m-30) cc_final: 0.6823 (m-30)
REVERT: B  113 ASP cc_start: 0.7360 (t0) cc_final: 0.7010 (t0)
REVERT: B  156 GLN cc_start: 0.7991 (tt0) cc_final: 0.7594 (tt0)
REVERT: B  264 GLN cc_start: 0.8585 (tp40) cc_final: 0.8299 (tp-100)
REVERT: B  286 ILE cc_start: 0.8293 (mm) cc_final: 0.7986 (mt)
REVERT: B  296 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: B  306 ASN cc_start: 0.7800 (m110) cc_final: 0.7551 (m110)
REVERT: B  321 ASP cc_start: 0.8209 (p0) cc_final: 0.7574 (p0)
REVERT: C    6 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7819 (mtpp)
REVERT: C   14 TYR cc_start: 0.7983 (p90) cc_final: 0.7396 (p90)
REVERT: C   20 LEU cc_start: 0.8344 (tp) cc_final: 0.8122 (tp)
REVERT: C   62 GLU cc_start: 0.7378 (tt0) cc_final: 0.6641 (tt0)
REVERT: C  115 LEU cc_start: 0.8073 (mm) cc_final: 0.7773 (mt)
REVERT: C  138 THR cc_start: 0.8391 (m) cc_final: 0.7644 (p)
REVERT: C  227 LEU cc_start: 0.8583 (mm) cc_final: 0.8326 (mt)
REVERT: C  246 ASN cc_start: 0.8384 (t0) cc_final: 0.8113 (t0)
REVERT: C  253 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7313 (ttmm)
REVERT: C  296 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6496 (tm-30)
REVERT: C  323 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8157 (mmmm)
REVERT: D  205 MET cc_start: -0.1170 (mtm) cc_final: -0.4105 (tpt)
  outliers start: 33
  outliers final: 31
  residues processed: 386
  average time/residue: 0.2636
  time to fit residues: 141.3612
Evaluate side-chains
  395 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 364
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 TYR
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  201 GLU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  252 ASN
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain C residue   90 TYR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain E residue  134 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 146 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 160 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0980
   chunk 141 optimal weight:    8.9990
   chunk 103 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 116 optimal weight:    0.0870
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 ASN
A 262 GLN
A 293 ASN
E 131 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.202198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137151 restraints weight = 101900.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.142499 restraints weight = 25676.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.144985 restraints weight = 10236.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.146361 restraints weight = 6054.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 64)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.146780 restraints weight = 4670.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13235  Z= 0.148
  Angle     :  0.527   5.154  17973  Z= 0.291
  Chirality :  0.044   0.166   1885
  Planarity :  0.003   0.046   2429
  Dihedral  :  4.516  40.835   1885
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.56 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.20), residues: 1699
  helix:  2.73 (0.51), residues: 93
  sheet: -0.26 (0.17), residues: 742
  loop : -0.82 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 167 
 TYR   0.017   0.001   TYR C 106 
 PHE   0.012   0.001   PHE C 267 
 TRP   0.009   0.001   TRP B 214 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (13235)
  covalent geometry    : angle       0.52741 (17973)
  hydrogen bonds       : bond        0.03488 (  564)
  hydrogen bonds       : angle       5.23394 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  393 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 361
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8124 (ttmm)
REVERT: A   76 GLN cc_start: 0.8632 (mp10) cc_final: 0.8175 (mp10)
REVERT: A   79 ASN cc_start: 0.8164 (m-40) cc_final: 0.7836 (m110)
REVERT: A   83 LEU cc_start: 0.8086 (mt) cc_final: 0.7839 (mp)
REVERT: A  126 ASP cc_start: 0.7970 (m-30) cc_final: 0.7601 (m-30)
REVERT: A  181 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6694 (tm-30)
REVERT: A  273 ILE cc_start: 0.8275 (mt) cc_final: 0.8032 (mt)
REVERT: A  293 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7474 (p0)
REVERT: A  306 ASN cc_start: 0.7799 (m-40) cc_final: 0.7573 (m110)
REVERT: B    6 LYS cc_start: 0.8361 (ttpp) cc_final: 0.7927 (ttmm)
REVERT: B   98 TYR cc_start: 0.7572 (t80) cc_final: 0.6882 (t80)
REVERT: B  104 VAL cc_start: 0.7831 (m) cc_final: 0.7400 (m)
REVERT: B  113 ASP cc_start: 0.7334 (t0) cc_final: 0.6994 (t0)
REVERT: B  125 SER cc_start: 0.8387 (m) cc_final: 0.7846 (t)
REVERT: B  156 GLN cc_start: 0.7954 (tt0) cc_final: 0.7599 (tt0)
REVERT: B  254 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7972 (p)
REVERT: B  264 GLN cc_start: 0.8447 (tp40) cc_final: 0.8197 (tp-100)
REVERT: B  286 ILE cc_start: 0.8313 (mm) cc_final: 0.7997 (mt)
REVERT: B  296 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7089 (tm-30)
REVERT: B  306 ASN cc_start: 0.7772 (m110) cc_final: 0.7553 (m110)
REVERT: C    6 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7806 (mtpp)
REVERT: C   14 TYR cc_start: 0.8029 (p90) cc_final: 0.7594 (p90)
REVERT: C   20 LEU cc_start: 0.8315 (tp) cc_final: 0.8086 (tp)
REVERT: C   71 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7859 (mt-10)
REVERT: C   81 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8255 (p)
REVERT: C  115 LEU cc_start: 0.8118 (mm) cc_final: 0.7772 (mt)
REVERT: C  138 THR cc_start: 0.8351 (m) cc_final: 0.7621 (p)
REVERT: C  227 LEU cc_start: 0.8531 (mm) cc_final: 0.8276 (mt)
REVERT: C  246 ASN cc_start: 0.8354 (t0) cc_final: 0.8038 (t0)
REVERT: C  253 LYS cc_start: 0.7899 (ttpt) cc_final: 0.7314 (ttmm)
REVERT: C  296 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6526 (tm-30)
REVERT: C  323 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8149 (mmmm)
REVERT: D  205 MET cc_start: -0.1253 (mtm) cc_final: -0.4099 (tpt)
  outliers start: 32
  outliers final: 25
  residues processed: 376
  average time/residue: 0.2581
  time to fit residues: 135.7330
Evaluate side-chains
  387 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 359
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 TYR
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  252 ASN
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   90 TYR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  256 ASP
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain E residue  134 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 148 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0270
   chunk 81 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 155 optimal weight:   20.0000
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.1042

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.201139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.136063 restraints weight = 101907.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.141430 restraints weight = 25652.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.143889 restraints weight = 10143.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.145272 restraints weight = 5950.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.145662 restraints weight = 4564.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  13235  Z= 0.195
  Angle     :  0.543   5.187  17973  Z= 0.301
  Chirality :  0.044   0.170   1885
  Planarity :  0.003   0.047   2429
  Dihedral  :  4.497  40.393   1885
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.02 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.20), residues: 1699
  helix:  2.70 (0.51), residues: 95
  sheet: -0.33 (0.17), residues: 766
  loop : -0.90 (0.22), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 244 
 TYR   0.014   0.001   TYR A  58 
 PHE   0.020   0.001   PHE B 267 
 TRP   0.010   0.001   TRP B 214 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (13235)
  covalent geometry    : angle       0.54322 (17973)
  hydrogen bonds       : bond        0.03603 (  564)
  hydrogen bonds       : angle       5.22328 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  404 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 366
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8577 (mtt180) cc_final: 0.8376 (mtt180)
REVERT: A   46 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8122 (ttmm)
REVERT: A   74 ASP cc_start: 0.8473 (p0) cc_final: 0.8209 (p0)
REVERT: A   79 ASN cc_start: 0.8241 (m-40) cc_final: 0.7982 (m110)
REVERT: A  126 ASP cc_start: 0.7971 (m-30) cc_final: 0.7601 (m-30)
REVERT: A  181 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6709 (tm-30)
REVERT: A  273 ILE cc_start: 0.8275 (mt) cc_final: 0.8052 (mt)
REVERT: A  293 ASN cc_start: 0.8043 (t0) cc_final: 0.7836 (p0)
REVERT: B    6 LYS cc_start: 0.8395 (ttpp) cc_final: 0.8176 (ttpt)
REVERT: B   98 TYR cc_start: 0.7610 (t80) cc_final: 0.6949 (t80)
REVERT: B  104 VAL cc_start: 0.7875 (m) cc_final: 0.7436 (m)
REVERT: B  113 ASP cc_start: 0.7390 (t0) cc_final: 0.7029 (t0)
REVERT: B  125 SER cc_start: 0.8370 (m) cc_final: 0.7838 (t)
REVERT: B  156 GLN cc_start: 0.7959 (tt0) cc_final: 0.7589 (tt0)
REVERT: B  254 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7943 (p)
REVERT: B  264 GLN cc_start: 0.8557 (tp40) cc_final: 0.8270 (tp-100)
REVERT: B  286 ILE cc_start: 0.8302 (mm) cc_final: 0.8019 (mt)
REVERT: B  306 ASN cc_start: 0.7790 (m110) cc_final: 0.7569 (m110)
REVERT: C    6 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7775 (mtpp)
REVERT: C   14 TYR cc_start: 0.8117 (p90) cc_final: 0.7657 (p90)
REVERT: C   20 LEU cc_start: 0.8355 (tp) cc_final: 0.8131 (tp)
REVERT: C  115 LEU cc_start: 0.8183 (mm) cc_final: 0.7843 (mt)
REVERT: C  227 LEU cc_start: 0.8536 (mm) cc_final: 0.8297 (mt)
REVERT: C  238 THR cc_start: 0.9101 (m) cc_final: 0.8672 (p)
REVERT: C  246 ASN cc_start: 0.8318 (t0) cc_final: 0.8001 (t0)
REVERT: C  296 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6585 (tm-30)
REVERT: C  323 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8155 (mmmm)
REVERT: D  205 MET cc_start: -0.1191 (mtm) cc_final: -0.4052 (tpt)
  outliers start: 38
  outliers final: 33
  residues processed: 382
  average time/residue: 0.2590
  time to fit residues: 137.7553
Evaluate side-chains
  399 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 365
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 TYR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  201 GLU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  329 ASP
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   90 TYR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  256 ASP
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  339 GLN
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain E residue  134 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 73 optimal weight:    0.7980
   chunk 113 optimal weight:    8.9990
   chunk 110 optimal weight:   50.0000
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 167 optimal weight:   10.0000
   chunk 163 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 GLN
B  60 GLN
** C  21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.197482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.133596 restraints weight = 89455.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.138643 restraints weight = 24021.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.141062 restraints weight = 9743.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142284 restraints weight = 5810.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.142762 restraints weight = 4532.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3637
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  13235  Z= 0.328
  Angle     :  0.621   6.053  17973  Z= 0.345
  Chirality :  0.046   0.158   1885
  Planarity :  0.004   0.045   2429
  Dihedral  :  4.753  40.172   1885
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 16.54 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.20), residues: 1699
  helix:  1.29 (0.51), residues: 116
  sheet: -0.44 (0.17), residues: 762
  loop : -0.90 (0.22), residues: 821

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 167 
 TYR   0.026   0.002   TYR B  58 
 PHE   0.025   0.002   PHE B 129 
 TRP   0.015   0.002   TRP B 214 
 HIS   0.010   0.002   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00658 (13235)
  covalent geometry    : angle       0.62065 (17973)
  hydrogen bonds       : bond        0.04272 (  564)
  hydrogen bonds       : angle       5.46490 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  422 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 377
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.8396 (ttpp) cc_final: 0.7891 (ttpp)
REVERT: A   16 LYS cc_start: 0.8741 (ptpt) cc_final: 0.8485 (ptpp)
REVERT: A   46 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8132 (ttmm)
REVERT: A  122 THR cc_start: 0.8471 (t) cc_final: 0.8179 (m)
REVERT: A  126 ASP cc_start: 0.7962 (m-30) cc_final: 0.7581 (m-30)
REVERT: A  181 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6674 (tm-30)
REVERT: A  210 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8427 (mmmt)
REVERT: A  260 VAL cc_start: 0.8349 (t) cc_final: 0.7958 (m)
REVERT: A  273 ILE cc_start: 0.8322 (mt) cc_final: 0.8088 (mt)
REVERT: A  293 ASN cc_start: 0.8284 (t0) cc_final: 0.7864 (p0)
REVERT: A  305 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7903 (ptpt)
REVERT: B    6 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8266 (ttpt)
REVERT: B   98 TYR cc_start: 0.7701 (t80) cc_final: 0.7263 (t80)
REVERT: B  104 VAL cc_start: 0.8041 (m) cc_final: 0.7234 (m)
REVERT: B  107 ASP cc_start: 0.7118 (m-30) cc_final: 0.6845 (m-30)
REVERT: B  113 ASP cc_start: 0.7414 (t0) cc_final: 0.7004 (t0)
REVERT: B  115 LEU cc_start: 0.8739 (mm) cc_final: 0.8499 (mt)
REVERT: B  118 PHE cc_start: 0.8097 (m-80) cc_final: 0.7892 (m-80)
REVERT: B  156 GLN cc_start: 0.7818 (tt0) cc_final: 0.7410 (tt0)
REVERT: B  254 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7920 (p)
REVERT: B  264 GLN cc_start: 0.8640 (tp40) cc_final: 0.8302 (tp-100)
REVERT: B  286 ILE cc_start: 0.8321 (mm) cc_final: 0.8019 (mt)
REVERT: C    6 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7701 (mtpp)
REVERT: C   14 TYR cc_start: 0.8188 (p90) cc_final: 0.7736 (p90)
REVERT: C   16 LYS cc_start: 0.8615 (pttt) cc_final: 0.8257 (ptpp)
REVERT: C   20 LEU cc_start: 0.8385 (tp) cc_final: 0.8159 (tp)
REVERT: C   97 ASP cc_start: 0.6715 (p0) cc_final: 0.6411 (p0)
REVERT: C  107 ASP cc_start: 0.7479 (m-30) cc_final: 0.7188 (m-30)
REVERT: C  115 LEU cc_start: 0.8346 (mm) cc_final: 0.8111 (mt)
REVERT: C  125 SER cc_start: 0.8665 (p) cc_final: 0.8458 (t)
REVERT: C  126 ASP cc_start: 0.8045 (m-30) cc_final: 0.7727 (m-30)
REVERT: C  138 THR cc_start: 0.8257 (m) cc_final: 0.7853 (p)
REVERT: C  181 GLU cc_start: 0.6513 (tm-30) cc_final: 0.6292 (tm-30)
REVERT: C  227 LEU cc_start: 0.8567 (mm) cc_final: 0.8348 (mt)
REVERT: C  246 ASN cc_start: 0.8353 (t0) cc_final: 0.8006 (t0)
REVERT: C  253 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7613 (mtpp)
REVERT: C  296 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6736 (tm-30)
REVERT: C  323 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8176 (mmmm)
REVERT: D  205 MET cc_start: -0.1076 (mtm) cc_final: -0.3996 (tpt)
  outliers start: 45
  outliers final: 38
  residues processed: 395
  average time/residue: 0.2612
  time to fit residues: 143.3730
Evaluate side-chains
  404 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 365
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  201 GLU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain C residue    7 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   90 TYR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  256 ASP
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain C residue  305 LYS
Chi-restraints excluded: chain C residue  319 ASP
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  339 GLN
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain E residue  134 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 167 optimal weight:    9.9990
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 109 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9980
   chunk 168 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 GLN
** B   9 ASN ** 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 = 0.4349 r_free = 0.4349 target = 0.199737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.137679 restraints weight = 111552.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.142380 restraints weight = 30064.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.144526 restraints weight = 11187.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.144873 restraints weight = 7069.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.144346 restraints weight = 5607.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.4711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  13235  Z= 0.170
  Angle     :  0.554   5.314  17973  Z= 0.306
  Chirality :  0.044   0.193   1885
  Planarity :  0.004   0.068   2429
  Dihedral  :  4.542  39.411   1885
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 18.35 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.20), residues: 1699
  helix:  2.89 (0.52), residues: 95
  sheet: -0.30 (0.17), residues: 765
  loop : -0.95 (0.21), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 140 
 TYR   0.017   0.002   TYR C   4 
 PHE   0.013   0.001   PHE B 129 
 TRP   0.010   0.001   TRP B 214 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (13235)
  covalent geometry    : angle       0.55352 (17973)
  hydrogen bonds       : bond        0.03561 (  564)
  hydrogen bonds       : angle       5.21944 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  404 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 368
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LYS cc_start: 0.8664 (ptpt) cc_final: 0.8195 (ptpp)
REVERT: A   46 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8067 (ttmm)
REVERT: A   74 ASP cc_start: 0.8501 (p0) cc_final: 0.8205 (p0)
REVERT: A  126 ASP cc_start: 0.7963 (m-30) cc_final: 0.7591 (m-30)
REVERT: A  181 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6703 (tm-30)
REVERT: A  218 LEU cc_start: 0.8367 (tp) cc_final: 0.7956 (mm)
REVERT: A  260 VAL cc_start: 0.8396 (t) cc_final: 0.7945 (m)
REVERT: A  273 ILE cc_start: 0.8307 (mt) cc_final: 0.8103 (mt)
REVERT: A  293 ASN cc_start: 0.8350 (t0) cc_final: 0.7793 (p0)
REVERT: A  305 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7837 (ptpt)
REVERT: B    6 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8245 (ttpt)
REVERT: B   16 LYS cc_start: 0.8066 (ptmt) cc_final: 0.7771 (ptmt)
REVERT: B   62 GLU cc_start: 0.7010 (tt0) cc_final: 0.6290 (tt0)
REVERT: B   98 TYR cc_start: 0.7573 (t80) cc_final: 0.7026 (t80)
REVERT: B  104 VAL cc_start: 0.7986 (m) cc_final: 0.7330 (m)
REVERT: B  107 ASP cc_start: 0.7102 (m-30) cc_final: 0.6849 (m-30)
REVERT: B  113 ASP cc_start: 0.7438 (t0) cc_final: 0.7061 (t0)
REVERT: B  118 PHE cc_start: 0.8123 (m-80) cc_final: 0.7902 (m-80)
REVERT: B  125 SER cc_start: 0.8345 (m) cc_final: 0.7828 (t)
REVERT: B  156 GLN cc_start: 0.7864 (tt0) cc_final: 0.7573 (tt0)
REVERT: B  254 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7838 (p)
REVERT: B  264 GLN cc_start: 0.8531 (tp40) cc_final: 0.8200 (tp-100)
REVERT: B  265 PHE cc_start: 0.7952 (m-80) cc_final: 0.7605 (m-10)
REVERT: B  273 ILE cc_start: 0.8062 (mt) cc_final: 0.7724 (tt)
REVERT: B  286 ILE cc_start: 0.8300 (mm) cc_final: 0.8027 (mt)
REVERT: C    6 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7642 (mtpp)
REVERT: C   14 TYR cc_start: 0.8247 (p90) cc_final: 0.7770 (p90)
REVERT: C   16 LYS cc_start: 0.8565 (pttt) cc_final: 0.8212 (ptpp)
REVERT: C   46 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8260 (mtmm)
REVERT: C   97 ASP cc_start: 0.6623 (p0) cc_final: 0.6371 (p0)
REVERT: C  107 ASP cc_start: 0.7426 (m-30) cc_final: 0.7158 (m-30)
REVERT: C  115 LEU cc_start: 0.8285 (mm) cc_final: 0.8074 (mt)
REVERT: C  138 THR cc_start: 0.8234 (m) cc_final: 0.7855 (p)
REVERT: C  181 GLU cc_start: 0.6537 (tm-30) cc_final: 0.6309 (tm-30)
REVERT: C  227 LEU cc_start: 0.8524 (mm) cc_final: 0.8291 (mt)
REVERT: C  238 THR cc_start: 0.9118 (m) cc_final: 0.8787 (p)
REVERT: C  246 ASN cc_start: 0.8357 (t0) cc_final: 0.8010 (t0)
REVERT: C  253 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7441 (mtpp)
REVERT: C  296 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6741 (tm-30)
REVERT: C  323 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8148 (mmmm)
REVERT: C  337 VAL cc_start: 0.8242 (t) cc_final: 0.7941 (p)
REVERT: D  205 MET cc_start: -0.0835 (mtm) cc_final: -0.3872 (tpt)
  outliers start: 36
  outliers final: 29
  residues processed: 384
  average time/residue: 0.2576
  time to fit residues: 138.1737
Evaluate side-chains
  394 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 364
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   90 TYR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  256 ASP
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  339 GLN
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain E residue  134 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 138 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0040
   chunk 161 optimal weight:   20.0000
   chunk 24 optimal weight:    0.3980
   chunk 132 optimal weight:   10.0000
   chunk 117 optimal weight:    7.9990
   overall best weight:    1.0796

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 GLN
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  69 ASN
D 301 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.199223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.135157 restraints weight = 106752.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.141093 restraints weight = 28999.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.143196 restraints weight = 9922.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.143849 restraints weight = 7409.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.143643 restraints weight = 5486.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.4871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  13235  Z= 0.197
  Angle     :  0.555   5.700  17973  Z= 0.306
  Chirality :  0.044   0.181   1885
  Planarity :  0.004   0.067   2429
  Dihedral  :  4.469  38.421   1885
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.57 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.20), residues: 1699
  helix:  2.93 (0.53), residues: 98
  sheet: -0.30 (0.18), residues: 764
  loop : -0.93 (0.22), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 140 
 TYR   0.018   0.002   TYR A  58 
 PHE   0.014   0.001   PHE B 129 
 TRP   0.011   0.001   TRP B 214 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (13235)
  covalent geometry    : angle       0.55468 (17973)
  hydrogen bonds       : bond        0.03569 (  564)
  hydrogen bonds       : angle       5.15774 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  407 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 373
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LYS cc_start: 0.8691 (ptpt) cc_final: 0.8386 (ptpp)
REVERT: A   46 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8061 (ttmm)
REVERT: A   74 ASP cc_start: 0.8516 (p0) cc_final: 0.8212 (p0)
REVERT: A  126 ASP cc_start: 0.8023 (m-30) cc_final: 0.7617 (m-30)
REVERT: A  181 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6689 (tm-30)
REVERT: A  218 LEU cc_start: 0.8408 (tp) cc_final: 0.7999 (mm)
REVERT: A  260 VAL cc_start: 0.8429 (t) cc_final: 0.7961 (m)
REVERT: A  273 ILE cc_start: 0.8320 (mt) cc_final: 0.7994 (mt)
REVERT: A  293 ASN cc_start: 0.8381 (t0) cc_final: 0.7659 (p0)
REVERT: A  305 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7839 (ptpt)
REVERT: B    6 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8256 (ttpt)
REVERT: B   16 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7825 (ptmt)
REVERT: B   98 TYR cc_start: 0.7608 (t80) cc_final: 0.7147 (t80)
REVERT: B  104 VAL cc_start: 0.7982 (m) cc_final: 0.7325 (m)
REVERT: B  107 ASP cc_start: 0.7112 (m-30) cc_final: 0.6837 (m-30)
REVERT: B  113 ASP cc_start: 0.7459 (t0) cc_final: 0.7044 (t0)
REVERT: B  118 PHE cc_start: 0.8110 (m-80) cc_final: 0.7882 (m-80)
REVERT: B  125 SER cc_start: 0.8366 (m) cc_final: 0.7844 (t)
REVERT: B  156 GLN cc_start: 0.7861 (tt0) cc_final: 0.7563 (tt0)
REVERT: B  254 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7862 (p)
REVERT: B  264 GLN cc_start: 0.8530 (tp40) cc_final: 0.8173 (tp-100)
REVERT: B  265 PHE cc_start: 0.7970 (m-80) cc_final: 0.7600 (m-10)
REVERT: B  273 ILE cc_start: 0.8045 (mt) cc_final: 0.7688 (tt)
REVERT: B  286 ILE cc_start: 0.8279 (mm) cc_final: 0.8015 (mt)
REVERT: B  296 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7191 (tm-30)
REVERT: C    6 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7688 (mtpp)
REVERT: C   16 LYS cc_start: 0.8585 (pttt) cc_final: 0.8221 (ptpp)
REVERT: C   25 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7374 (mmtt)
REVERT: C   46 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8292 (mtmm)
REVERT: C   97 ASP cc_start: 0.6644 (p0) cc_final: 0.6405 (p0)
REVERT: C  107 ASP cc_start: 0.7461 (m-30) cc_final: 0.7251 (m-30)
REVERT: C  115 LEU cc_start: 0.8305 (mm) cc_final: 0.8076 (mt)
REVERT: C  138 THR cc_start: 0.8238 (m) cc_final: 0.7855 (p)
REVERT: C  181 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6308 (tm-30)
REVERT: C  183 GLU cc_start: 0.6651 (tt0) cc_final: 0.6390 (mt-10)
REVERT: C  227 LEU cc_start: 0.8520 (mm) cc_final: 0.8285 (mt)
REVERT: C  238 THR cc_start: 0.9137 (m) cc_final: 0.8799 (p)
REVERT: C  246 ASN cc_start: 0.8364 (t0) cc_final: 0.8034 (t0)
REVERT: C  296 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6835 (tm-30)
REVERT: C  323 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8136 (mmmm)
REVERT: C  337 VAL cc_start: 0.8268 (t) cc_final: 0.7982 (p)
REVERT: D  205 MET cc_start: -0.0831 (mtm) cc_final: -0.3877 (tpt)
  outliers start: 34
  outliers final: 32
  residues processed: 388
  average time/residue: 0.2569
  time to fit residues: 138.8066
Evaluate side-chains
  402 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 369
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 TYR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   90 TYR
Chi-restraints excluded: chain C residue  152 ASN
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain C residue  213 GLN
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  256 ASP
Chi-restraints excluded: chain C residue  272 SER
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  339 GLN
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain E residue  134 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 139 optimal weight:    0.6980
   chunk 158 optimal weight:    0.0010
   chunk 149 optimal weight:    6.9990
   chunk 144 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 106 optimal weight:    0.4980
   chunk 73 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 GLN
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 GLN
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** 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 = 0.4353 r_free = 0.4353 target = 0.200247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.136364 restraints weight = 107905.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.142740 restraints weight = 28179.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.144005 restraints weight = 9681.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.144803 restraints weight = 7024.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.144698 restraints weight = 5643.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3646
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3646 r_free = 0.3646    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3646 r_free = 0.3646    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3646
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.4907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13235  Z= 0.127
  Angle     :  0.533   6.281  17973  Z= 0.293
  Chirality :  0.044   0.177   1885
  Planarity :  0.004   0.063   2429
  Dihedral  :  4.371  37.401   1885
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.32 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.20), residues: 1699
  helix:  3.10 (0.53), residues: 98
  sheet: -0.22 (0.18), residues: 765
  loop : -0.88 (0.22), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 140 
 TYR   0.021   0.001   TYR B 313 
 PHE   0.011   0.001   PHE B 128 
 TRP   0.009   0.001   TRP D  39 
 HIS   0.004   0.001   HIS C  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13235)
  covalent geometry    : angle       0.53334 (17973)
  hydrogen bonds       : bond        0.03271 (  564)
  hydrogen bonds       : angle       5.05715 ( 1575)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   16 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue THR   25 is missing expected H atoms. Skipping.
Residue ILE   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue SER   50 is missing expected H atoms. Skipping.
Residue SER   52 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Evaluate side-chains
  402 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 373
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.8316 (ttpp) cc_final: 0.7846 (ttpp)
REVERT: A   16 LYS cc_start: 0.8635 (ptpt) cc_final: 0.8337 (ptpp)
REVERT: A   20 LEU cc_start: 0.8048 (tp) cc_final: 0.7617 (tp)
REVERT: A   46 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8054 (ttmm)
REVERT: A   74 ASP cc_start: 0.8463 (p0) cc_final: 0.8163 (p0)
REVERT: A  126 ASP cc_start: 0.8013 (m-30) cc_final: 0.7606 (m-30)
REVERT: A  181 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6711 (tm-30)
REVERT: A  218 LEU cc_start: 0.8354 (tp) cc_final: 0.7957 (mm)
REVERT: A  260 VAL cc_start: 0.8419 (t) cc_final: 0.7967 (m)
REVERT: A  273 ILE cc_start: 0.8191 (mt) cc_final: 0.7953 (mt)
REVERT: A  293 ASN cc_start: 0.8406 (t0) cc_final: 0.7590 (p0)
REVERT: A  305 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7831 (ptpt)
REVERT: A  339 GLN cc_start: 0.8110 (pt0) cc_final: 0.7895 (pt0)
REVERT: B    6 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8242 (ttpt)
REVERT: B   16 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7807 (ptmt)
REVERT: B   42 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7788 (mtt180)
REVERT: B   62 GLU cc_start: 0.6964 (tt0) cc_final: 0.6237 (tt0)
REVERT: B   98 TYR cc_start: 0.7550 (t80) cc_final: 0.7060 (t80)
REVERT: B  104 VAL cc_start: 0.7947 (m) cc_final: 0.7461 (m)
REVERT: B  113 ASP cc_start: 0.7440 (t0) cc_final: 0.7026 (t0)
REVERT: B  118 PHE cc_start: 0.8100 (m-80) cc_final: 0.7894 (m-80)
REVERT: B  125 SER cc_start: 0.8361 (m) cc_final: 0.7820 (t)
REVERT: B  156 GLN cc_start: 0.7885 (tt0) cc_final: 0.7469 (tt0)
REVERT: B  254 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7825 (p)
REVERT: B  264 GLN cc_start: 0.8453 (tp40) cc_final: 0.8149 (tp-100)
REVERT: B  265 PHE cc_start: 0.7936 (m-80) cc_final: 0.7570 (m-10)
REVERT: B  273 ILE cc_start: 0.8052 (mt) cc_final: 0.7682 (tt)
REVERT: B  286 ILE cc_start: 0.8280 (mm) cc_final: 0.8027 (mt)
REVERT: B  296 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7206 (tm-30)
REVERT: C    6 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7680 (mtpp)
REVERT: C   14 TYR cc_start: 0.8270 (p90) cc_final: 0.7791 (p90)
REVERT: C   16 LYS cc_start: 0.8555 (pttt) cc_final: 0.8185 (ptpp)
REVERT: C   25 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7375 (mmtt)
REVERT: C   46 LYS cc_start: 0.8578 (mtmm) cc_final: 0.8224 (mtmm)
REVERT: C   97 ASP cc_start: 0.6597 (p0) cc_final: 0.6372 (p0)
REVERT: C  107 ASP cc_start: 0.7465 (m-30) cc_final: 0.7241 (m-30)
REVERT: C  112 THR cc_start: 0.8328 (p) cc_final: 0.7997 (t)
REVERT: C  115 LEU cc_start: 0.8269 (mm) cc_final: 0.7956 (mt)
REVERT: C  138 THR cc_start: 0.8223 (m) cc_final: 0.7838 (p)
REVERT: C  181 GLU cc_start: 0.6534 (tm-30) cc_final: 0.6299 (tm-30)
REVERT: C  183 GLU cc_start: 0.6688 (tt0) cc_final: 0.6421 (mt-10)
REVERT: C  227 LEU cc_start: 0.8452 (mm) cc_final: 0.8232 (mt)
REVERT: C  238 THR cc_start: 0.9121 (m) cc_final: 0.8811 (p)
REVERT: C  246 ASN cc_start: 0.8376 (t0) cc_final: 0.8049 (t0)
REVERT: C  296 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6797 (tm-30)
REVERT: C  323 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8141 (mmmm)
REVERT: C  337 VAL cc_start: 0.8279 (t) cc_final: 0.7998 (p)
REVERT: D  205 MET cc_start: -0.0783 (mtm) cc_final: -0.3871 (tpt)
  outliers start: 29
  outliers final: 25
  residues processed: 383
  average time/residue: 0.2626
  time to fit residues: 139.9658
Evaluate side-chains
  396 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 370
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain B residue   10 LYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  236 ASN
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   90 TYR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  256 ASP
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  339 GLN
Chi-restraints excluded: chain D residue   56 TRP
Chi-restraints excluded: chain E residue  134 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 138 optimal weight:    0.9980
   chunk 159 optimal weight:   20.0000
   chunk 108 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 123 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 164 optimal weight:    6.9990
   chunk 110 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 168 optimal weight:    6.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.197083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.132392 restraints weight = 104567.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.137869 restraints weight = 27592.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.139728 restraints weight = 11846.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.141194 restraints weight = 7118.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.141039 restraints weight = 5450.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3596 r_free = 0.3596    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3596 r_free = 0.3596    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.5091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  13235  Z= 0.266
  Angle     :  0.571   5.992  17973  Z= 0.318
  Chirality :  0.045   0.170   1885
  Planarity :  0.004   0.060   2429
  Dihedral  :  4.479  37.359   1885
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.27 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.25 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.20), residues: 1699
  helix:  1.75 (0.52), residues: 116
  sheet: -0.35 (0.18), residues: 762
  loop : -0.93 (0.22), residues: 821

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 140 
 TYR   0.022   0.002   TYR A  58 
 PHE   0.017   0.002   PHE B 129 
 TRP   0.013   0.002   TRP B 214 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (13235)
  covalent geometry    : angle       0.57107 (17973)
  hydrogen bonds       : bond        0.03787 (  564)
  hydrogen bonds       : angle       5.19287 ( 1575)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5196.66 seconds
wall clock time: 88 minutes 58.06 seconds (5338.06 seconds total)