Starting phenix.real_space_refine
on Wed Mar  4 07:54:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oit_20081/03_2026/6oit_20081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oit_20081/03_2026/6oit_20081.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oit_20081/03_2026/6oit_20081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oit_20081/03_2026/6oit_20081.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oit_20081/03_2026/6oit_20081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oit_20081/03_2026/6oit_20081.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      71      5.16       5
     C    7643      2.51       5
     N    2101      2.21       5
     O    2270      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12085
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1010
          Classifications: {'peptide': 123}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 1034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 1034
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 9, 'TRANS': 115}
    Chain: "C"
      Number of atoms: 2619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2619
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 325}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 1722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1722
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "E"
      Number of atoms: 2634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2634
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 327}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "F"
      Number of atoms: 2678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2678
          Classifications: {'peptide': 342}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 9, 'TRANS': 332}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 388
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 2.61, per 1000 atoms: 0.22
  Number of scatterers: 12085
  At special positions: 0
  Unit cell: (98.44, 110.21, 145.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      71     16.00
     O    2270      8.00
     N    2101      7.00
     C    7643      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 606.5 milliseconds
  

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2868

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 13 sheets defined
      54.2% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 57
      removed outlier: 3.589A  pdb=" N   SER A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLN A  57 " --> pdb=" O   ASP A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 84
    Processing helix  chain 'A' and resid 89 through 104
      removed outlier: 4.078A  pdb=" N   ASP A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.667A  pdb=" N   GLU A 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLU A 110 " --> pdb=" O   ASP A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
    Processing helix  chain 'A' and resid 118 through 136
    Processing helix  chain 'A' and resid 138 through 148
      removed outlier: 4.214A  pdb=" N   MET A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 155
      removed outlier: 3.550A  pdb=" N   SER A 154 " --> pdb=" O   MET A 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 56
    Processing helix  chain 'B' and resid 72 through 84
    Processing helix  chain 'B' and resid 89 through 102
      removed outlier: 3.557A  pdb=" N   ASN B  93 " --> pdb=" O   HIS B  89 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL B  94 " --> pdb=" O   TYR B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 3.597A  pdb=" N   ILE B 116 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 136
      removed outlier: 3.921A  pdb=" N   THR B 125 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ILE B 126 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 148
      removed outlier: 3.996A  pdb=" N   SER B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 99
      removed outlier: 4.123A  pdb=" N   SER C  58 " --> pdb=" O   LYS C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 124
    Processing helix  chain 'C' and resid 128 through 139
      removed outlier: 3.877A  pdb=" N   VAL C 132 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 153
      removed outlier: 3.511A  pdb=" N   VAL C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 160
    Processing helix  chain 'C' and resid 165 through 182
      removed outlier: 3.730A  pdb=" N   GLY C 177 " --> pdb=" O   SER C 173 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   THR C 178 " --> pdb=" O   ASN C 174 " (cutoff:3.500A)
      removed outlier: 8.338A  pdb=" N   ARG C 179 " --> pdb=" O   TYR C 175 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   SER C 180 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 196
      removed outlier: 3.831A  pdb=" N   VAL C 192 " --> pdb=" O   ASN C 188 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU C 196 " --> pdb=" O   VAL C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 216
    Processing helix  chain 'C' and resid 277 through 280
      removed outlier: 3.761A  pdb=" N   LEU C 280 " --> pdb=" O   PRO C 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 277 through 280'
    Processing helix  chain 'C' and resid 293 through 299
      removed outlier: 3.630A  pdb=" N   ASN C 297 " --> pdb=" O   THR C 293 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE C 299 " --> pdb=" O   PHE C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 314
      removed outlier: 3.563A  pdb=" N   ALA C 314 " --> pdb=" O   ASP C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 315 through 318
      removed outlier: 3.629A  pdb=" N   ILE C 318 " --> pdb=" O   LEU C 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 315 through 318'
    Processing helix  chain 'C' and resid 356 through 407
      removed outlier: 3.935A  pdb=" N   TYR C 360 " --> pdb=" O   THR C 356 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ASN C 394 " --> pdb=" O   HIS C 390 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE C 395 " --> pdb=" O   ALA C 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 125
      removed outlier: 3.950A  pdb=" N   HIS D 125 " --> pdb=" O   GLN D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 139
      removed outlier: 3.867A  pdb=" N   VAL D 132 " --> pdb=" O   SER D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 160
      No H-bonds generated for 'chain 'D' and resid 157 through 160'
    Processing helix  chain 'D' and resid 165 through 177
    Processing helix  chain 'D' and resid 177 through 182
    Processing helix  chain 'D' and resid 188 through 196
      removed outlier: 3.881A  pdb=" N   VAL D 192 " --> pdb=" O   ASN D 188 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLU D 196 " --> pdb=" O   VAL D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 216
    Processing helix  chain 'D' and resid 270 through 273
      removed outlier: 3.857A  pdb=" N   ILE D 273 " --> pdb=" O   VAL D 270 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 270 through 273'
    Processing helix  chain 'D' and resid 307 through 314
    Processing helix  chain 'E' and resid 47 through 98
      removed outlier: 3.942A  pdb=" N   LEU E  98 " --> pdb=" O   HIS E  94 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 117 through 123
      removed outlier: 3.553A  pdb=" N   GLN E 121 " --> pdb=" O   ASP E 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 128 through 138
      removed outlier: 3.858A  pdb=" N   VAL E 132 " --> pdb=" O   SER E 128 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 165 through 177
      removed outlier: 3.814A  pdb=" N   LEU E 176 " --> pdb=" O   LEU E 172 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 188 through 196
      removed outlier: 3.805A  pdb=" N   GLU E 196 " --> pdb=" O   VAL E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 218
      removed outlier: 3.912A  pdb=" N   CYS E 212 " --> pdb=" O   ALA E 208 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LEU E 213 " --> pdb=" O   GLY E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 298
    Processing helix  chain 'E' and resid 307 through 313
    Processing helix  chain 'E' and resid 314 through 318
      removed outlier: 3.575A  pdb=" N   ILE E 318 " --> pdb=" O   LEU E 315 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 354 through 405
      removed outlier: 3.723A  pdb=" N   HIS E 390 " --> pdb=" O   VAL E 386 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 44 through 92
    Processing helix  chain 'F' and resid 118 through 125
      removed outlier: 4.180A  pdb=" N   HIS F 125 " --> pdb=" O   GLN F 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 128 through 138
      removed outlier: 3.846A  pdb=" N   VAL F 132 " --> pdb=" O   SER F 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 148 through 153
      removed outlier: 3.593A  pdb=" N   VAL F 153 " --> pdb=" O   LEU F 149 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 161
      removed outlier: 4.032A  pdb=" N   GLY F 161 " --> pdb=" O   VAL F 157 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 165 through 177
      removed outlier: 3.668A  pdb=" N   GLY F 177 " --> pdb=" O   SER F 173 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 188 through 196
      removed outlier: 3.552A  pdb=" N   VAL F 192 " --> pdb=" O   ASN F 188 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLU F 196 " --> pdb=" O   VAL F 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 209 through 218
      removed outlier: 4.548A  pdb=" N   LEU F 213 " --> pdb=" O   GLY F 209 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 270 through 273
      removed outlier: 4.111A  pdb=" N   ILE F 273 " --> pdb=" O   VAL F 270 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 270 through 273'
    Processing helix  chain 'F' and resid 289 through 294
    Processing helix  chain 'F' and resid 295 through 298
      removed outlier: 3.531A  pdb=" N   LEU F 298 " --> pdb=" O   PHE F 295 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 295 through 298'
    Processing helix  chain 'F' and resid 307 through 314
    Processing helix  chain 'F' and resid 358 through 408
    Processing helix  chain 'G' and resid 47 through 57
      removed outlier: 3.587A  pdb=" N   ALA G  53 " --> pdb=" O   ASN G  49 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLY G  57 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 84
    Processing helix  chain 'G' and resid 87 through 92
    Processing sheet with id=AA1, first strand: chain 'C' and resid 161 through 162
    Processing sheet with id=AA2, first strand: chain 'C' and resid 184 through 186
      removed outlier: 4.037A  pdb=" N   PHE C 225 " --> pdb=" O   LEU D 338 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA C 227 " --> pdb=" O   PHE D 336 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE D 336 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 268
      removed outlier: 3.940A  pdb=" N   GLY C 267 " --> pdb=" O   VAL C 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 335 through 339
      removed outlier: 6.656A  pdb=" N   VAL D 184 " --> pdb=" O   ILE D 228 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   VAL D 185 " --> pdb=" O   VAL D 154 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 161 through 162
      removed outlier: 3.681A  pdb=" N   LYS D 162 " --> pdb=" O   GLN D 274 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 267 through 268
      removed outlier: 3.742A  pdb=" N   GLY D 267 " --> pdb=" O   VAL D 304 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLN D 303 " --> pdb=" O   GLY D 321 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156
      removed outlier: 7.044A  pdb=" N   VAL E 185 " --> pdb=" O   VAL E 154 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 161 through 162
    Processing sheet with id=AA9, first strand: chain 'E' and resid 225 through 228
    Processing sheet with id=AB1, first strand: chain 'E' and resid 265 through 268
      removed outlier: 6.315A  pdb=" N   VAL E 304 " --> pdb=" O   LEU E 266 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 338 through 339
      removed outlier: 3.738A  pdb=" N   PHE F 225 " --> pdb=" O   LEU E 338 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 184 through 186
      removed outlier: 3.606A  pdb=" N   ILE F 228 " --> pdb=" O   VAL F 184 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 265 through 268
      removed outlier: 6.148A  pdb=" N   VAL F 304 " --> pdb=" O   LEU F 266 " (cutoff:3.500A)

    578 hydrogen bonds defined for protein.
    1698 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2892
        1.33 -     1.45: 2311
        1.45 -     1.57: 6970
        1.57 -     1.69: 0
        1.69 -     1.81: 115
  Bond restraints: 12288
  Sorted by residual:
  bond pdb=" N   VAL F 283 "
       pdb=" CA  VAL F 283 "
    ideal  model  delta    sigma   weight residual
    1.460  1.498 -0.038 1.21e-02 6.83e+03 1.01e+01
  bond pdb=" N   ILE C 241 "
       pdb=" CA  ILE C 241 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.25e-02 6.40e+03 8.26e+00
  bond pdb=" N   GLY F 289 "
       pdb=" CA  GLY F 289 "
    ideal  model  delta    sigma   weight residual
    1.445  1.473 -0.028 1.01e-02 9.80e+03 7.88e+00
  bond pdb=" N   VAL D 237 "
       pdb=" CA  VAL D 237 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.52e+00
  bond pdb=" N   CYS F 282 "
       pdb=" CA  CYS F 282 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.35e-02 5.49e+03 7.01e+00
  ... (remaining 12283 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 15800
        2.12 -     4.23: 643
        4.23 -     6.35: 77
        6.35 -     8.47: 37
        8.47 -    10.58: 13
  Bond angle restraints: 16570
  Sorted by residual:
  angle pdb=" C   LEU F 252 "
        pdb=" N   LYS F 253 "
        pdb=" CA  LYS F 253 "
      ideal   model   delta    sigma   weight residual
     120.94  130.86   -9.92 1.90e+00 2.77e-01 2.73e+01
  angle pdb=" N   THR A 136 "
        pdb=" CA  THR A 136 "
        pdb=" C   THR A 136 "
      ideal   model   delta    sigma   weight residual
     109.81  120.39  -10.58 2.21e+00 2.05e-01 2.29e+01
  angle pdb=" N   THR B 136 "
        pdb=" CA  THR B 136 "
        pdb=" C   THR B 136 "
      ideal   model   delta    sigma   weight residual
     109.81  119.89  -10.08 2.21e+00 2.05e-01 2.08e+01
  angle pdb=" N   GLU E 220 "
        pdb=" CA  GLU E 220 "
        pdb=" C   GLU E 220 "
      ideal   model   delta    sigma   weight residual
     110.91  116.01   -5.10 1.17e+00 7.31e-01 1.90e+01
  angle pdb=" CA  GLY C 238 "
        pdb=" C   GLY C 238 "
        pdb=" O   GLY C 238 "
      ideal   model   delta    sigma   weight residual
     121.47  117.63    3.84 9.00e-01 1.23e+00 1.82e+01
  ... (remaining 16565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.41: 6948
       15.41 -    30.83: 399
       30.83 -    46.24: 120
       46.24 -    61.66: 13
       61.66 -    77.07: 9
  Dihedral angle restraints: 7489
    sinusoidal: 3050
      harmonic: 4439
  Sorted by residual:
  dihedral pdb=" CA  ILE D 318 "
           pdb=" C   ILE D 318 "
           pdb=" N   SER D 319 "
           pdb=" CA  SER D 319 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.80   23.20     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  PRO D 262 "
           pdb=" C   PRO D 262 "
           pdb=" N   PRO D 263 "
           pdb=" CA  PRO D 263 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.07  -22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  LEU E 256 "
           pdb=" C   LEU E 256 "
           pdb=" N   PRO E 257 "
           pdb=" CA  PRO E 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.26   22.74     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 7486 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1576
       0.075 -    0.151: 249
       0.151 -    0.226: 29
       0.226 -    0.302: 10
       0.302 -    0.377: 2
  Chirality restraints: 1866
  Sorted by residual:
  chirality pdb=" CB  ILE D 330 "
            pdb=" CA  ILE D 330 "
            pdb=" CG1 ILE D 330 "
            pdb=" CG2 ILE D 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.56e+00
  chirality pdb=" CB  ILE F 228 "
            pdb=" CA  ILE F 228 "
            pdb=" CG1 ILE F 228 "
            pdb=" CG2 ILE F 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.29e+00
  chirality pdb=" CG  LEU B 128 "
            pdb=" CB  LEU B 128 "
            pdb=" CD1 LEU B 128 "
            pdb=" CD2 LEU B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.16e+00
  ... (remaining 1863 not shown)

  Planarity restraints: 2139
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 234 "    0.019 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   ARG D 234 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   ARG D 234 "    0.024 2.00e-02 2.50e+03
        pdb=" N   PRO D 235 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG F 234 "   -0.018 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   ARG F 234 "    0.063 2.00e-02 2.50e+03
        pdb=" O   ARG F 234 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PRO F 235 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 386 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   VAL C 386 "    0.057 2.00e-02 2.50e+03
        pdb=" O   VAL C 386 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU C 387 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 2136 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1991
        2.77 -     3.30: 11162
        3.30 -     3.83: 18808
        3.83 -     4.37: 21700
        4.37 -     4.90: 37580
  Nonbonded interactions: 91241
  Sorted by model distance:
  nonbonded pdb=" O   ILE F 273 "
            pdb=" NH2 ARG F 291 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" O   GLN C 239 "
            pdb=" CB  ASP C 250 "
     model   vdw
     2.247 3.440
  nonbonded pdb=" O   GLU E 166 "
            pdb=" OG  SER E 169 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   ILE A 132 "
            pdb=" OG1 THR A 136 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   ARG E 301 "
            pdb=" OG  SER E 319 "
     model   vdw
     2.327 3.040
  ... (remaining 91236 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 39 through 45 or (resid 46 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 47 through 161))
}
ncs_group {
  reference = (chain 'C' and (resid 52 through 93 or (resid 94 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 95 through 96 or (resid 97 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 98 or resid 117 through 219 or ( \ 
resid 220 and (name N or name CA or name C or name O or name CB )) or resid 221  \ 
through 352 or resid 357 through 405))
  selection = (chain 'E' and (resid 52 through 93 or (resid 94 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 95 through 96 or (resid 97 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 98 or resid 117 through 352 or r \ 
esid 357 through 405))
  selection = (chain 'F' and (resid 52 through 98 or resid 117 through 218 or (resid 219 throu \ 
gh 220 and (name N or name CA or name C or name O or name CB )) or resid 221 thr \ 
ough 405))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.760
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  12288  Z= 0.303
  Angle     :  1.020  10.583  16570  Z= 0.557
  Chirality :  0.059   0.377   1866
  Planarity :  0.008   0.071   2139
  Dihedral  : 11.442  77.069   4621
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  7.18 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.18), residues: 1506
  helix: -1.22 (0.16), residues: 732
  sheet: -3.06 (0.83), residues: 30
  loop : -1.78 (0.20), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F 308 
 TYR   0.022   0.002   TYR E 198 
 PHE   0.042   0.003   PHE A 104 
 TRP   0.015   0.003   TRP B 127 
 HIS   0.018   0.003   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 (12288)
  covalent geometry    : angle       1.02020 (16570)
  hydrogen bonds       : bond        0.14935 (  578)
  hydrogen bonds       : angle       6.03550 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 301
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.8769 (tp30) cc_final: 0.8557 (tp30)
REVERT: C  245 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8258 (mt)
REVERT: C  357 MET cc_start: 0.7360 (ptp) cc_final: 0.7100 (ptm)
REVERT: C  367 MET cc_start: 0.7778 (tpp) cc_final: 0.7271 (tpp)
REVERT: G   74 MET cc_start: 0.7038 (tpt) cc_final: 0.6695 (tpp)
  outliers start: 6
  outliers final: 2
  residues processed: 307
  average time/residue: 0.1144
  time to fit residues: 48.9521
Evaluate side-chains
  180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 177
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain E residue  237 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    0.0030
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0570
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    6.9990
   overall best weight:    0.4708

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

Flipped N/Q/H residues before XYZ refinement:
A 118 HIS
B  63 ASN
B 111 GLN
B 118 HIS
C  92 GLN
C 174 ASN
C 297 ASN
D 201 HIS
D 246 GLN
D 297 ASN
E  65 ASN
E 297 ASN
E 303 GLN
F 167 ASN
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 297 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.189106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.157728 restraints weight = 13954.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.155424 restraints weight = 21592.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.157189 restraints weight = 19294.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.156923 restraints weight = 12848.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.157398 restraints weight = 12272.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12288  Z= 0.134
  Angle     :  0.586   7.923  16570  Z= 0.301
  Chirality :  0.041   0.175   1866
  Planarity :  0.005   0.056   2139
  Dihedral  :  5.134  55.664   1656
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 11.18 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.42 (0.20), residues: 1506
  helix:  0.82 (0.19), residues: 754
  sheet: -2.78 (0.88), residues: 30
  loop : -1.37 (0.21), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 347 
 TYR   0.018   0.001   TYR D 286 
 PHE   0.022   0.002   PHE F  76 
 TRP   0.009   0.001   TRP G  82 
 HIS   0.006   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (12288)
  covalent geometry    : angle       0.58622 (16570)
  hydrogen bonds       : bond        0.05323 (  578)
  hydrogen bonds       : angle       4.12349 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 199
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 MET cc_start: 0.8946 (mmt) cc_final: 0.8703 (tpp)
REVERT: A  123 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7549 (tp30)
REVERT: C  245 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8096 (mt)
REVERT: C  357 MET cc_start: 0.7579 (ptp) cc_final: 0.7040 (ptm)
REVERT: E   63 MET cc_start: 0.7972 (mtt) cc_final: 0.7736 (mtm)
  outliers start: 37
  outliers final: 12
  residues processed: 225
  average time/residue: 0.1117
  time to fit residues: 36.3621
Evaluate side-chains
  179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain F residue   85 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
B  97 GLN
C 211 HIS
D 246 GLN
E 240 HIS
F  80 GLN
F 337 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.184856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.154094 restraints weight = 14246.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.152126 restraints weight = 22668.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.153161 restraints weight = 22493.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.153519 restraints weight = 15080.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.153955 restraints weight = 13860.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12288  Z= 0.160
  Angle     :  0.584   7.467  16570  Z= 0.297
  Chirality :  0.043   0.169   1866
  Planarity :  0.004   0.055   2139
  Dihedral  :  4.763  52.625   1653
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.31 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.21), residues: 1506
  helix:  1.57 (0.19), residues: 756
  sheet: -2.59 (0.89), residues: 30
  loop : -1.15 (0.21), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 404 
 TYR   0.013   0.001   TYR C 296 
 PHE   0.016   0.002   PHE E 393 
 TRP   0.007   0.001   TRP B 127 
 HIS   0.006   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12288)
  covalent geometry    : angle       0.58446 (16570)
  hydrogen bonds       : bond        0.05204 (  578)
  hydrogen bonds       : angle       3.93910 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 173
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7619 (tp30)
REVERT: C   74 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8304 (mt)
REVERT: C  170 GLN cc_start: 0.8098 (tp40) cc_final: 0.7690 (tp40)
REVERT: C  245 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8125 (mt)
REVERT: D  133 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5762 (tp)
REVERT: E   63 MET cc_start: 0.7932 (mtt) cc_final: 0.7693 (mtm)
REVERT: E  385 GLN cc_start: 0.7073 (mt0) cc_final: 0.6835 (mt0)
REVERT: F  319 SER cc_start: 0.8199 (p) cc_final: 0.7990 (p)
  outliers start: 42
  outliers final: 19
  residues processed: 207
  average time/residue: 0.1048
  time to fit residues: 32.2589
Evaluate side-chains
  179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue  168 LEU
Chi-restraints excluded: chain E residue  346 VAL
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain F residue  164 ASN
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  352 THR
Chi-restraints excluded: chain F residue  402 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 120 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 134 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0570
   chunk 81 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.4104

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

Flipped N/Q/H residues before XYZ refinement:
C  92 GLN
D 246 GLN
F  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.183778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.152722 restraints weight = 14254.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.150281 restraints weight = 23865.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.151782 restraints weight = 22263.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.152050 restraints weight = 15175.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.152453 restraints weight = 14197.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12288  Z= 0.159
  Angle     :  0.576   8.802  16570  Z= 0.291
  Chirality :  0.043   0.183   1866
  Planarity :  0.004   0.052   2139
  Dihedral  :  4.656  49.543   1653
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 12.54 %
    Favored  : 83.76 %
  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:  0.68 (0.22), residues: 1506
  helix:  1.92 (0.19), residues: 757
  sheet: -2.54 (0.89), residues: 30
  loop : -1.08 (0.21), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 147 
 TYR   0.014   0.001   TYR C 296 
 PHE   0.018   0.002   PHE E 299 
 TRP   0.006   0.001   TRP B 127 
 HIS   0.006   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (12288)
  covalent geometry    : angle       0.57551 (16570)
  hydrogen bonds       : bond        0.04988 (  578)
  hydrogen bonds       : angle       3.81722 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 166
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   74 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8346 (mt)
REVERT: C  245 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8004 (mt)
REVERT: C  348 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7364 (t80)
REVERT: C  381 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8067 (mt)
REVERT: D  133 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5707 (tp)
REVERT: E   63 MET cc_start: 0.7974 (mtt) cc_final: 0.7732 (mtm)
REVERT: E  385 GLN cc_start: 0.7123 (mt0) cc_final: 0.6909 (mt0)
REVERT: F  319 SER cc_start: 0.8080 (p) cc_final: 0.7858 (p)
  outliers start: 49
  outliers final: 37
  residues processed: 203
  average time/residue: 0.1067
  time to fit residues: 32.1016
Evaluate side-chains
  198 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 156
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   84 MET
Chi-restraints excluded: chain C residue   92 GLN
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  348 PHE
Chi-restraints excluded: chain C residue  381 ILE
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  299 PHE
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue   71 GLU
Chi-restraints excluded: chain E residue   85 ASP
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  168 LEU
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  292 GLU
Chi-restraints excluded: chain E residue  346 VAL
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  164 ASN
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  352 THR
Chi-restraints excluded: chain F residue  402 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 122 optimal weight:    0.8980
   chunk 103 optimal weight:    0.0970
   chunk 21 optimal weight:    0.8980
   chunk 90 optimal weight:    0.1980
   chunk 47 optimal weight:    4.9990
   chunk 141 optimal weight:    0.9980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
C 174 ASN
D 246 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.186871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.158500 restraints weight = 14080.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.156997 restraints weight = 19207.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.157128 restraints weight = 17937.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.155284 restraints weight = 15641.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.155714 restraints weight = 12931.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12288  Z= 0.111
  Angle     :  0.521   7.690  16570  Z= 0.262
  Chirality :  0.040   0.196   1866
  Planarity :  0.004   0.048   2139
  Dihedral  :  4.367  45.501   1653
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.90 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.22), residues: 1506
  helix:  2.26 (0.19), residues: 762
  sheet: -2.44 (0.92), residues: 30
  loop : -0.93 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 147 
 TYR   0.011   0.001   TYR C 296 
 PHE   0.014   0.001   PHE F  76 
 TRP   0.006   0.001   TRP A 127 
 HIS   0.008   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (12288)
  covalent geometry    : angle       0.52087 (16570)
  hydrogen bonds       : bond        0.04472 (  578)
  hydrogen bonds       : angle       3.62007 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 172
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7407 (ttm170)
REVERT: C   74 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8312 (mt)
REVERT: C  245 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7951 (mt)
REVERT: C  348 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7218 (t80)
REVERT: D  133 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5614 (tp)
REVERT: E   63 MET cc_start: 0.7974 (mtt) cc_final: 0.7706 (mtm)
REVERT: E  315 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8330 (mm)
REVERT: E  385 GLN cc_start: 0.6977 (mt0) cc_final: 0.6750 (mt0)
  outliers start: 42
  outliers final: 25
  residues processed: 207
  average time/residue: 0.1051
  time to fit residues: 32.2743
Evaluate side-chains
  187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  348 PHE
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  299 PHE
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   85 ASP
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  402 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 140 optimal weight:    0.0030
   chunk 86 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 114 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 126 optimal weight:    0.9980
   overall best weight:    1.1394

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

Flipped N/Q/H residues before XYZ refinement:
C  92 GLN
C 340 ASN
D 246 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.184765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.156118 restraints weight = 14027.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.154891 restraints weight = 19591.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.155104 restraints weight = 19607.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.154076 restraints weight = 16848.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.154282 restraints weight = 15561.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12288  Z= 0.138
  Angle     :  0.554   9.453  16570  Z= 0.276
  Chirality :  0.042   0.235   1866
  Planarity :  0.004   0.050   2139
  Dihedral  :  4.314  41.839   1653
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 13.60 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.22), residues: 1506
  helix:  2.42 (0.19), residues: 762
  sheet: -2.47 (0.92), residues: 30
  loop : -0.87 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 147 
 TYR   0.015   0.001   TYR C 296 
 PHE   0.036   0.002   PHE F  76 
 TRP   0.006   0.001   TRP B 127 
 HIS   0.010   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12288)
  covalent geometry    : angle       0.55402 (16570)
  hydrogen bonds       : bond        0.04504 (  578)
  hydrogen bonds       : angle       3.59519 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 163
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7575 (ttm170)
REVERT: A  139 HIS cc_start: 0.7204 (OUTLIER) cc_final: 0.6901 (m-70)
REVERT: C   74 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8266 (mt)
REVERT: C  245 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7973 (mt)
REVERT: C  348 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7216 (t80)
REVERT: D  133 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5798 (tp)
REVERT: D  272 MET cc_start: 0.6871 (mpt) cc_final: 0.6664 (mpt)
REVERT: E   63 MET cc_start: 0.7955 (mtt) cc_final: 0.7704 (mtm)
REVERT: E  385 GLN cc_start: 0.7052 (mt0) cc_final: 0.6834 (mt0)
REVERT: F  178 THR cc_start: 0.8774 (t) cc_final: 0.8497 (m)
REVERT: G   74 MET cc_start: 0.6849 (tpp) cc_final: 0.6344 (tpp)
  outliers start: 53
  outliers final: 36
  residues processed: 206
  average time/residue: 0.1050
  time to fit residues: 31.9715
Evaluate side-chains
  194 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 153
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  139 HIS
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   92 GLN
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  348 PHE
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  299 PHE
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  292 GLU
Chi-restraints excluded: chain E residue  346 VAL
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  258 ASN
Chi-restraints excluded: chain F residue  275 ILE
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  352 THR
Chi-restraints excluded: chain F residue  402 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 47 optimal weight:    0.1980
   chunk 12 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 120 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 119 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
C  92 GLN
D 246 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.183683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.154731 restraints weight = 14162.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.153860 restraints weight = 21360.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.154527 restraints weight = 18979.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.153858 restraints weight = 13641.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.154418 restraints weight = 13656.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12288  Z= 0.156
  Angle     :  0.577  11.325  16570  Z= 0.285
  Chirality :  0.043   0.310   1866
  Planarity :  0.004   0.048   2139
  Dihedral  :  4.322  40.353   1653
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 14.43 %
    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:  1.26 (0.22), residues: 1506
  helix:  2.42 (0.19), residues: 762
  sheet: -2.45 (0.92), residues: 30
  loop : -0.83 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 147 
 TYR   0.016   0.001   TYR C 296 
 PHE   0.039   0.002   PHE F  76 
 TRP   0.005   0.001   TRP A 127 
 HIS   0.010   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12288)
  covalent geometry    : angle       0.57684 (16570)
  hydrogen bonds       : bond        0.04596 (  578)
  hydrogen bonds       : angle       3.62449 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 158
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 ARG cc_start: 0.7965 (ttp-110) cc_final: 0.7607 (ttm170)
REVERT: A  139 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6819 (m-70)
REVERT: C   74 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8323 (mt)
REVERT: C  245 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8003 (mt)
REVERT: C  348 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7099 (t80)
REVERT: D  133 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5742 (tp)
REVERT: D  272 MET cc_start: 0.6918 (mpt) cc_final: 0.6696 (mpt)
REVERT: E   63 MET cc_start: 0.7948 (mtt) cc_final: 0.7719 (mtm)
REVERT: E  385 GLN cc_start: 0.7091 (mt0) cc_final: 0.6875 (mt0)
REVERT: F  178 THR cc_start: 0.8783 (t) cc_final: 0.8517 (m)
  outliers start: 50
  outliers final: 40
  residues processed: 198
  average time/residue: 0.0989
  time to fit residues: 29.0757
Evaluate side-chains
  199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 154
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  139 HIS
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   92 GLN
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  348 PHE
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  299 PHE
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  168 LEU
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  292 GLU
Chi-restraints excluded: chain E residue  346 VAL
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  164 ASN
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  258 ASN
Chi-restraints excluded: chain F residue  275 ILE
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  352 THR
Chi-restraints excluded: chain F residue  402 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 111 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 68 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 137 optimal weight:    5.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
C  92 GLN
D 246 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.184436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.154063 restraints weight = 14041.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.151922 restraints weight = 21211.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.153564 restraints weight = 20132.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.153488 restraints weight = 13353.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.153482 restraints weight = 14579.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12288  Z= 0.160
  Angle     :  0.582  11.496  16570  Z= 0.289
  Chirality :  0.043   0.328   1866
  Planarity :  0.004   0.049   2139
  Dihedral  :  4.327  38.525   1653
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 14.73 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.22), residues: 1506
  helix:  2.41 (0.19), residues: 762
  sheet: -1.37 (1.14), residues: 25
  loop : -0.79 (0.22), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 147 
 TYR   0.017   0.001   TYR C 296 
 PHE   0.019   0.002   PHE E 299 
 TRP   0.005   0.001   TRP A 127 
 HIS   0.009   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (12288)
  covalent geometry    : angle       0.58218 (16570)
  hydrogen bonds       : bond        0.04653 (  578)
  hydrogen bonds       : angle       3.65491 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 153
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 ARG cc_start: 0.7957 (ttp-110) cc_final: 0.7601 (ttm170)
REVERT: A  139 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6920 (m-70)
REVERT: C   74 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8165 (mt)
REVERT: C  245 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8025 (mt)
REVERT: C  348 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7037 (t80)
REVERT: D  133 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5746 (tp)
REVERT: D  272 MET cc_start: 0.6954 (mpt) cc_final: 0.6710 (mpt)
REVERT: E   63 MET cc_start: 0.7946 (mtt) cc_final: 0.7706 (mtm)
REVERT: E  385 GLN cc_start: 0.7106 (mt0) cc_final: 0.6866 (mt0)
REVERT: F  178 THR cc_start: 0.8798 (t) cc_final: 0.8522 (m)
REVERT: F  367 MET cc_start: 0.8238 (tpp) cc_final: 0.8035 (tpp)
  outliers start: 54
  outliers final: 39
  residues processed: 197
  average time/residue: 0.1131
  time to fit residues: 32.4697
Evaluate side-chains
  196 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 152
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  139 HIS
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   92 GLN
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  348 PHE
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  299 PHE
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  168 LEU
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  292 GLU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  346 VAL
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  164 ASN
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  275 ILE
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  352 THR
Chi-restraints excluded: chain F residue  402 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 65 optimal weight:    0.0060
   chunk 63 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0970
   chunk 135 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 130 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 148 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
D 246 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.186052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.157414 restraints weight = 13966.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.156308 restraints weight = 21758.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.157377 restraints weight = 21407.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.157932 restraints weight = 14544.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.158304 restraints weight = 13497.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12288  Z= 0.128
  Angle     :  0.561  11.406  16570  Z= 0.277
  Chirality :  0.042   0.312   1866
  Planarity :  0.004   0.048   2139
  Dihedral  :  4.202  36.181   1653
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.41 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.22), residues: 1506
  helix:  2.53 (0.19), residues: 762
  sheet: -1.40 (1.10), residues: 25
  loop : -0.71 (0.22), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  55 
 TYR   0.014   0.001   TYR C 296 
 PHE   0.041   0.002   PHE F  76 
 TRP   0.005   0.001   TRP A 127 
 HIS   0.008   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12288)
  covalent geometry    : angle       0.56056 (16570)
  hydrogen bonds       : bond        0.04391 (  578)
  hydrogen bonds       : angle       3.57178 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 162
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.8848 (tp30) cc_final: 0.8637 (tp30)
REVERT: A  139 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6937 (m-70)
REVERT: C   74 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8157 (mt)
REVERT: C  245 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7996 (mt)
REVERT: C  348 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6989 (t80)
REVERT: D  133 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5895 (tp)
REVERT: D  272 MET cc_start: 0.6927 (mpt) cc_final: 0.6667 (mpt)
REVERT: E   63 MET cc_start: 0.7916 (mtt) cc_final: 0.7689 (mtm)
REVERT: E  385 GLN cc_start: 0.7082 (mt0) cc_final: 0.6880 (mt0)
REVERT: F  178 THR cc_start: 0.8785 (t) cc_final: 0.8502 (m)
  outliers start: 45
  outliers final: 36
  residues processed: 199
  average time/residue: 0.1062
  time to fit residues: 31.1146
Evaluate side-chains
  197 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 156
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  139 HIS
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  125 THR
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  348 PHE
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  299 PHE
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   85 ASP
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  168 LEU
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain E residue  292 GLU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  402 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 129 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 70 optimal weight:    0.1980
   chunk 112 optimal weight:   10.0000
   chunk 103 optimal weight:    0.0670
   chunk 67 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.6524

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

Flipped N/Q/H residues before XYZ refinement:
C  92 GLN
D 246 GLN
D 303 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.188490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.157852 restraints weight = 13957.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.155283 restraints weight = 22400.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.157478 restraints weight = 21643.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.157396 restraints weight = 14496.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.158004 restraints weight = 14508.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12288  Z= 0.111
  Angle     :  0.547  11.204  16570  Z= 0.270
  Chirality :  0.041   0.308   1866
  Planarity :  0.004   0.048   2139
  Dihedral  :  3.991  32.495   1653
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.31 %
    Favored  : 80.82 %
  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 (0.22), residues: 1506
  helix:  2.71 (0.19), residues: 757
  sheet: -1.16 (1.13), residues: 25
  loop : -0.53 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  55 
 TYR   0.014   0.001   TYR C 296 
 PHE   0.016   0.001   PHE F  76 
 TRP   0.005   0.001   TRP A 127 
 HIS   0.008   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (12288)
  covalent geometry    : angle       0.54709 (16570)
  hydrogen bonds       : bond        0.04034 (  578)
  hydrogen bonds       : angle       3.45660 ( 1698)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 167
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.8808 (tp30) cc_final: 0.8238 (tp30)
REVERT: C   74 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8228 (mt)
REVERT: C  245 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7978 (mt)
REVERT: C  348 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6848 (t80)
REVERT: D  133 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5759 (tp)
REVERT: D  272 MET cc_start: 0.6839 (mpt) cc_final: 0.6592 (mpt)
REVERT: E   63 MET cc_start: 0.7931 (mtt) cc_final: 0.7685 (mtm)
REVERT: E  385 GLN cc_start: 0.7020 (mt0) cc_final: 0.6817 (mt0)
REVERT: F  178 THR cc_start: 0.8702 (t) cc_final: 0.8438 (m)
REVERT: G   74 MET cc_start: 0.6546 (tpp) cc_final: 0.6328 (tpp)
  outliers start: 38
  outliers final: 26
  residues processed: 198
  average time/residue: 0.1068
  time to fit residues: 30.7344
Evaluate side-chains
  186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 MET
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   92 GLN
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  348 PHE
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  299 PHE
Chi-restraints excluded: chain D residue  303 GLN
Chi-restraints excluded: chain D residue  323 VAL
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  335 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain E residue  292 GLU
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 142 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.188437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.158111 restraints weight = 13914.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.155545 restraints weight = 21935.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.157512 restraints weight = 21227.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.157312 restraints weight = 13770.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.157731 restraints weight = 12844.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.284  12288  Z= 0.229
  Angle     :  0.995  59.199  16570  Z= 0.592
  Chirality :  0.045   0.636   1866
  Planarity :  0.004   0.048   2139
  Dihedral  :  4.030  32.547   1653
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.31 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.07 %
  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:  1.71 (0.22), residues: 1506
  helix:  2.70 (0.19), residues: 757
  sheet: -1.37 (1.08), residues: 25
  loop : -0.52 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  55 
 TYR   0.011   0.001   TYR C 175 
 PHE   0.016   0.001   PHE F  76 
 TRP   0.005   0.001   TRP A 127 
 HIS   0.007   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (12288)
  covalent geometry    : angle       0.99483 (16570)
  hydrogen bonds       : bond        0.04071 (  578)
  hydrogen bonds       : angle       3.45707 ( 1698)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1845.51 seconds
wall clock time: 32 minutes 43.16 seconds (1963.16 seconds total)