Starting phenix.real_space_refine
on Sat Jul  4 01:21:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ud4_42146/07_2026/8ud4_42146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ud4_42146/07_2026/8ud4_42146.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ud4_42146/07_2026/8ud4_42146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ud4_42146/07_2026/8ud4_42146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ud4_42146/07_2026/8ud4_42146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ud4_42146/07_2026/8ud4_42146.cif"
  }
  resolution = 3.25
  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=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      46      5.49       5
     S      60      5.16       5
     C   11057      2.51       5
     N    2851      2.21       5
     O    3484      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 17498
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "F"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "D"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "E"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "B"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "A"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "C"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "G"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 463
          Classifications: {'RNA': 23}
          Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 22}
          Link IDs: {'rna3p': 22}
    Chain: "H"
      Number of atoms: 505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 505
          Classifications: {'RNA': 23}
          Modifications used: {'rna3p_pur': 22, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 22}
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N  AILE F  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE F  27 " occ=0.48
    residue:
      pdb=" N  AASN F  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN F  28 " occ=0.48
    residue:
      pdb=" N  AASN F  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN F  29 " occ=0.48
    residue:
      pdb=" N  AILE D  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE D  27 " occ=0.48
    residue:
      pdb=" N  AASN D  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  28 " occ=0.48
    residue:
      pdb=" N  AASN D  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  29 " occ=0.48
    residue:
      pdb=" N  AILE E  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE E  27 " occ=0.48
    residue:
      pdb=" N  AASN E  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN E  28 " occ=0.48
    residue:
      pdb=" N  AASN E  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN E  29 " occ=0.48
    residue:
      pdb=" N  AILE B  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE B  27 " occ=0.48
    residue:
      pdb=" N  AASN B  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  28 " occ=0.48
    residue:
      pdb=" N  AASN B  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  29 " occ=0.48
    ... (remaining 6 not shown)
  Time building chain proxies: 6.27, per 1000 atoms: 0.36
  Number of scatterers: 17498
  At special positions: 0
  Unit cell: (115.92, 123.28, 135.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P      46     15.00
     O    3484      8.00
     N    2851      7.00
     C   11057      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: 1.15
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3924

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 44 sheets defined
      26.2% alpha, 23.0% beta
      21 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 2.16
  Creating SS restraints...
    Processing helix  chain 'F' and resid 1 through 13
    Processing helix  chain 'F' and resid 50 through 60
    Processing helix  chain 'F' and resid 68 through 75
    Processing helix  chain 'F' and resid 113 through 117
    Processing helix  chain 'F' and resid 129 through 137
    Processing helix  chain 'F' and resid 207 through 216
    Processing helix  chain 'F' and resid 217 through 225
    Processing helix  chain 'F' and resid 231 through 236
    Processing helix  chain 'F' and resid 250 through 261
      removed outlier: 3.651A  pdb=" N   GLU F 260 " --> pdb=" O   LYS F 256 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 298 through 308
    Processing helix  chain 'D' and resid 2 through 13
    Processing helix  chain 'D' and resid 50 through 60
    Processing helix  chain 'D' and resid 68 through 75
    Processing helix  chain 'D' and resid 129 through 137
    Processing helix  chain 'D' and resid 207 through 216
    Processing helix  chain 'D' and resid 217 through 225
    Processing helix  chain 'D' and resid 231 through 236
    Processing helix  chain 'D' and resid 250 through 261
      removed outlier: 3.585A  pdb=" N   GLU D 260 " --> pdb=" O   LYS D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 308
    Processing helix  chain 'E' and resid 2 through 13
    Processing helix  chain 'E' and resid 50 through 60
    Processing helix  chain 'E' and resid 68 through 75
    Processing helix  chain 'E' and resid 113 through 117
    Processing helix  chain 'E' and resid 129 through 136
    Processing helix  chain 'E' and resid 207 through 216
    Processing helix  chain 'E' and resid 217 through 226
      removed outlier: 3.566A  pdb=" N   PHE E 221 " --> pdb=" O   ALA E 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 231 through 236
      removed outlier: 3.660A  pdb=" N   VAL E 236 " --> pdb=" O   PHE E 232 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 261
      removed outlier: 3.535A  pdb=" N   GLU E 260 " --> pdb=" O   LYS E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 308
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 50 through 60
    Processing helix  chain 'B' and resid 68 through 75
    Processing helix  chain 'B' and resid 129 through 137
      removed outlier: 3.596A  pdb=" N   LEU B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 216
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 3.584A  pdb=" N   VAL B 236 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 261
      removed outlier: 3.584A  pdb=" N   GLU B 260 " --> pdb=" O   LYS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 308
    Processing helix  chain 'A' and resid 2 through 13
    Processing helix  chain 'A' and resid 50 through 60
    Processing helix  chain 'A' and resid 68 through 75
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 129 through 137
    Processing helix  chain 'A' and resid 207 through 216
    Processing helix  chain 'A' and resid 217 through 225
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.681A  pdb=" N   VAL A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.665A  pdb=" N   GLU A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
    Processing helix  chain 'C' and resid 2 through 13
    Processing helix  chain 'C' and resid 50 through 60
    Processing helix  chain 'C' and resid 68 through 75
    Processing helix  chain 'C' and resid 129 through 137
    Processing helix  chain 'C' and resid 207 through 216
    Processing helix  chain 'C' and resid 217 through 225
    Processing helix  chain 'C' and resid 231 through 236
      removed outlier: 3.587A  pdb=" N   VAL C 236 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.599A  pdb=" N   GLU C 260 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 308
    Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27
      removed outlier: 6.685A  pdb=" N   VAL F  31 " --> pdb=" O   LEU F  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 106 through 108
      removed outlier: 8.281A  pdb=" N   THR F  98 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE F  99 " --> pdb=" O   ALA F  80 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   ASP F 124 " --> pdb=" O   ALA F  81 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   LYS F 180 " --> pdb=" O   GLN F 187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87
    Processing sheet with id=AA4, first strand: chain 'F' and resid 160 through 162
    Processing sheet with id=AA5, first strand: chain 'F' and resid 263 through 266
      removed outlier: 3.525A  pdb=" N   GLU F 266 " --> pdb=" O   PHE F 279 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ILE F 280 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   CYS F 290 " --> pdb=" O   ILE F 280 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASP F 282 " --> pdb=" O   SER F 288 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   SER F 288 " --> pdb=" O   ASP F 282 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 315 through 322
      removed outlier: 7.388A  pdb=" N   SER F 328 " --> pdb=" O   PRO F 343 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   MET F 330 " --> pdb=" O   PHE F 341 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE F 341 " --> pdb=" O   MET F 330 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP F 332 " --> pdb=" O   GLU F 339 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27
      removed outlier: 6.669A  pdb=" N   VAL D  31 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.121A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.121A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87
    Processing sheet with id=AB2, first strand: chain 'D' and resid 160 through 162
    Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 266
      removed outlier: 3.579A  pdb=" N   GLU D 266 " --> pdb=" O   PHE D 279 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   ILE D 280 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   CYS D 290 " --> pdb=" O   ILE D 280 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASP D 282 " --> pdb=" O   SER D 288 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   SER D 288 " --> pdb=" O   ASP D 282 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 315 through 322
      removed outlier: 7.483A  pdb=" N   SER D 328 " --> pdb=" O   PRO D 343 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   MET D 330 " --> pdb=" O   PHE D 341 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   PHE D 341 " --> pdb=" O   MET D 330 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   TRP D 332 " --> pdb=" O   GLU D 339 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 27
      removed outlier: 6.668A  pdb=" N   VAL E  31 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.397A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 9.114A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LYS E 180 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 87
    Processing sheet with id=AB8, first strand: chain 'E' and resid 98 through 99
      removed outlier: 8.157A  pdb=" N   THR E  98 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 162
    Processing sheet with id=AC1, first strand: chain 'E' and resid 264 through 266
      removed outlier: 4.873A  pdb=" N   ILE E 280 " --> pdb=" O   CYS E 290 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   CYS E 290 " --> pdb=" O   ILE E 280 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 315 through 322
      removed outlier: 7.345A  pdb=" N   SER E 328 " --> pdb=" O   PRO E 343 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   MET E 330 " --> pdb=" O   PHE E 341 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE E 341 " --> pdb=" O   MET E 330 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   TRP E 332 " --> pdb=" O   GLU E 339 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 24 through 27
      removed outlier: 6.732A  pdb=" N   VAL B  31 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.268A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.788A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   LYS B 180 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AC6, first strand: chain 'B' and resid 98 through 99
      removed outlier: 8.227A  pdb=" N   THR B  98 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'B' and resid 160 through 162
    Processing sheet with id=AC8, first strand: chain 'B' and resid 264 through 266
      removed outlier: 3.583A  pdb=" N   GLU B 266 " --> pdb=" O   PHE B 279 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 275 through 277
    Processing sheet with id=AD1, first strand: chain 'B' and resid 315 through 322
      removed outlier: 7.221A  pdb=" N   SER B 328 " --> pdb=" O   PRO B 343 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   MET B 330 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE B 341 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TRP B 332 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'A' and resid 24 through 27
      removed outlier: 6.717A  pdb=" N   VAL A  31 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.022A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.022A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   LYS A 180 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AD6, first strand: chain 'A' and resid 98 through 99
      removed outlier: 8.372A  pdb=" N   THR A  98 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AD8, first strand: chain 'A' and resid 264 through 266
      removed outlier: 4.997A  pdb=" N   ILE A 280 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   CYS A 290 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'A' and resid 316 through 322
      removed outlier: 3.515A  pdb=" N   TYR A 342 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'C' and resid 24 through 27
      removed outlier: 6.717A  pdb=" N   VAL C  31 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.156A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.699A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.156A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.699A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LYS C 180 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AE5, first strand: chain 'C' and resid 98 through 99
      removed outlier: 8.144A  pdb=" N   THR C  98 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE5
    Processing sheet with id=AE6, first strand: chain 'C' and resid 160 through 162
    Processing sheet with id=AE7, first strand: chain 'C' and resid 264 through 266
      removed outlier: 3.529A  pdb=" N   GLU C 264 " --> pdb=" O   THR C 281 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   ILE C 280 " --> pdb=" O   CYS C 290 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   CYS C 290 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 322
      removed outlier: 3.603A  pdb=" N   THR C 340 " --> pdb=" O   TRP C 332 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   LYS C 334 " --> pdb=" O   VAL C 338 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   VAL C 338 " --> pdb=" O   LYS C 334 " (cutoff:3.500A)

    621 hydrogen bonds defined for protein.
    1611 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 3.19

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 3000
        1.32 -     1.44: 4734
        1.44 -     1.57: 10038
        1.57 -     1.69: 91
        1.69 -     1.81: 90
  Bond restraints: 17953
  Sorted by residual:
  bond pdb=" CA  LYS C 149 "
       pdb=" C   LYS C 149 "
    ideal  model  delta    sigma   weight residual
    1.524  1.490  0.035 1.22e-02 6.72e+03 8.08e+00
  bond pdb=" C   THR D  98 "
       pdb=" O   THR D  98 "
    ideal  model  delta    sigma   weight residual
    1.235  1.201  0.034 1.26e-02 6.30e+03 7.49e+00
  bond pdb=" C   ILE D  99 "
       pdb=" O   ILE D  99 "
    ideal  model  delta    sigma   weight residual
    1.236  1.208  0.028 1.19e-02 7.06e+03 5.43e+00
  bond pdb=" CA  ILE D  99 "
       pdb=" CB  ILE D  99 "
    ideal  model  delta    sigma   weight residual
    1.540  1.511  0.029 1.36e-02 5.41e+03 4.60e+00
  bond pdb=" CA  VAL C 148 "
       pdb=" C   VAL C 148 "
    ideal  model  delta    sigma   weight residual
    1.524  1.496  0.027 1.28e-02 6.10e+03 4.52e+00
  ... (remaining 17948 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 24228
        2.03 -     4.06: 310
        4.06 -     6.08: 24
        6.08 -     8.11: 11
        8.11 -    10.14: 4
  Bond angle restraints: 24577
  Sorted by residual:
  angle pdb=" N   LYS C 149 "
        pdb=" CA  LYS C 149 "
        pdb=" C   LYS C 149 "
      ideal   model   delta    sigma   weight residual
     108.96  116.67   -7.71 1.59e+00 3.96e-01 2.35e+01
  angle pdb=" C4'   A H   5 "
        pdb=" C3'   A H   5 "
        pdb=" O3'   A H   5 "
      ideal   model   delta    sigma   weight residual
     113.00  106.84    6.16 1.50e+00 4.44e-01 1.69e+01
  angle pdb=" N   LYS D  89 "
        pdb=" CA  LYS D  89 "
        pdb=" C   LYS D  89 "
      ideal   model   delta    sigma   weight residual
     113.20  108.24    4.96 1.21e+00 6.83e-01 1.68e+01
  angle pdb=" C   LYS D 344 "
        pdb=" N   LEU D 345 "
        pdb=" CA  LEU D 345 "
      ideal   model   delta    sigma   weight residual
     121.54  129.05   -7.51 1.91e+00 2.74e-01 1.55e+01
  angle pdb=" C   LYS C 344 "
        pdb=" N   LEU C 345 "
        pdb=" CA  LEU C 345 "
      ideal   model   delta    sigma   weight residual
     121.54  129.02   -7.48 1.91e+00 2.74e-01 1.53e+01
  ... (remaining 24572 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.33: 9344
       19.33 -    38.65: 1040
       38.65 -    57.98: 288
       57.98 -    77.30: 64
       77.30 -    96.63: 18
  Dihedral angle restraints: 10754
    sinusoidal: 4670
      harmonic: 6084
  Sorted by residual:
  dihedral pdb=" C3'   A H   6 "
           pdb=" C4'   A H   6 "
           pdb=" O4'   A H   6 "
           pdb=" C1'   A H   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      20.00   -7.86   27.86     1      8.00e+00 1.56e-02 1.74e+01
  dihedral pdb=" C4'   A H   6 "
           pdb=" O4'   A H   6 "
           pdb=" C1'   A H   6 "
           pdb=" C2'   A H   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00   29.45  -26.45     1      8.00e+00 1.56e-02 1.57e+01
  dihedral pdb=" CA  ASP D 106 "
           pdb=" C   ASP D 106 "
           pdb=" N   ILE D 107 "
           pdb=" CA  ILE D 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.31   19.69     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 10751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 2083
       0.043 -    0.087: 500
       0.087 -    0.130: 237
       0.130 -    0.173: 31
       0.173 -    0.217: 13
  Chirality restraints: 2864
  Sorted by residual:
  chirality pdb=" C3'   U G  17 "
            pdb=" C4'   U G  17 "
            pdb=" O3'   U G  17 "
            pdb=" C2'   U G  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.69    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" C3'   U G  15 "
            pdb=" C4'   U G  15 "
            pdb=" O3'   U G  15 "
            pdb=" C2'   U G  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.68    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" C3'   U G  13 "
            pdb=" C4'   U G  13 "
            pdb=" O3'   U G  13 "
            pdb=" C2'   U G  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.67    0.20 2.00e-01 2.50e+01 9.54e-01
  ... (remaining 2861 not shown)

  Planarity restraints: 2998
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 203 "   -0.014 2.00e-02 2.50e+03   2.84e-02 8.06e+00
        pdb=" C   PHE B 203 "    0.049 2.00e-02 2.50e+03
        pdb=" O   PHE B 203 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LYS B 204 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 204 "    0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO C 205 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO C 205 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 205 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 226 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.88e+00
        pdb=" C   LYS E 226 "    0.038 2.00e-02 2.50e+03
        pdb=" O   LYS E 226 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU E 227 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2995 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1408
        2.74 -     3.28: 17142
        3.28 -     3.82: 30180
        3.82 -     4.36: 37190
        4.36 -     4.90: 62588
  Nonbonded interactions: 148508
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  45 "
            pdb=" OG1 THR A  47 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OD2 ASP D 212 "
            pdb=" OH  TYR D 225 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD2 ASP C 212 "
            pdb=" OH  TYR C 225 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   HIS A 242 "
            pdb=" OG  SER A 287 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   SER F 197 "
            pdb=" OG  SER F 197 "
     model   vdw
     2.267 3.040
  ... (remaining 148503 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             5.360
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.270
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  17953  Z= 0.145
  Angle     :  0.562  10.139  24577  Z= 0.327
  Chirality :  0.048   0.217   2864
  Planarity :  0.004   0.057   2998
  Dihedral  : 17.652  96.628   6830
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 23.39 %
    Favored  : 76.18 %
  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:  0.49 (0.19), residues: 2094
  helix:  0.85 (0.24), residues: 528
  sheet:  0.35 (0.29), residues: 354
  loop :  0.20 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  61 
 TYR   0.012   0.001   TYR D 342 
 PHE   0.022   0.001   PHE B 203 
 TRP   0.004   0.000   TRP E 332 
 HIS   0.003   0.001   HIS E  95 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.14 (17953)
  covalent geometry    : angle       0.56213 /  0.33 (24577)
  hydrogen bonds       : bond        0.20686 / 13.39 (  638)
  hydrogen bonds       : angle       8.38870 /  5.93 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 231
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
REVERT: F  113 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7165 (mp0)
REVERT: E  106 ASP cc_start: 0.7281 (m-30) cc_final: 0.6975 (p0)
REVERT: B  330 MET cc_start: 0.6707 (tpp) cc_final: 0.6213 (ttm)
REVERT: C  218 MET cc_start: 0.7052 (ttt) cc_final: 0.6759 (ttm)
  outliers start: 8
  outliers final: 1
  residues processed: 234
  average time/residue: 0.1300
  time to fit residues: 45.6890
Evaluate side-chains
  208 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   96 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 194 optimal weight:    5.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 200 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.5980
   overall best weight:    1.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 163 ASN
E 244 GLN
A  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.159372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.118590 restraints weight = 127377.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 6.86
r_work: 0.2811 rms_B_bonded: 6.39 restraints_weight: 2.0000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  17953  Z= 0.262
  Angle     :  0.620  10.200  24577  Z= 0.330
  Chirality :  0.049   0.181   2864
  Planarity :  0.005   0.047   2998
  Dihedral  : 11.474  77.967   2866
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 22.53 %
    Favored  : 75.00 %
  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:  0.17 (0.19), residues: 2094
  helix:  0.39 (0.23), residues: 534
  sheet:  0.18 (0.29), residues: 360
  loop :  0.08 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 257 
 TYR   0.018   0.002   TYR A 225 
 PHE   0.016   0.002   PHE A 203 
 TRP   0.013   0.002   TRP A  86 
 HIS   0.004   0.001   HIS C  14 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00632 /  0.26 (17953)
  covalent geometry    : angle       0.61979 /  0.33 (24577)
  hydrogen bonds       : bond        0.04675 /  3.09 (  638)
  hydrogen bonds       : angle       6.07714 /  4.27 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 213
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
REVERT: E  106 ASP cc_start: 0.7850 (m-30) cc_final: 0.6903 (p0)
REVERT: B  284 GLN cc_start: 0.8227 (tp40) cc_final: 0.7717 (tt0)
REVERT: B  296 ASP cc_start: 0.8833 (t0) cc_final: 0.8367 (t0)
REVERT: A  252 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8557 (mp)
REVERT: A  333 CYS cc_start: 0.9142 (m) cc_final: 0.8627 (m)
REVERT: C  167 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8223 (pp)
REVERT: C  226 LYS cc_start: 0.8596 (mmtm) cc_final: 0.7833 (ptmm)
REVERT: C  330 MET cc_start: 0.7285 (mmt) cc_final: 0.7040 (mmm)
  outliers start: 46
  outliers final: 26
  residues processed: 246
  average time/residue: 0.1140
  time to fit residues: 43.2430
Evaluate side-chains
  231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  132 ASP
Chi-restraints excluded: chain F residue  263 PHE
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   36 ASP
Chi-restraints excluded: chain E residue  222 ILE
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  273 SER
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  211 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 174 optimal weight:    0.9980
   chunk 207 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 154 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0870
   chunk 38 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   chunk 127 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0050
   overall best weight:    0.4372

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 136 ASN
E 163 ASN
C 136 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.162313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.120518 restraints weight = 126865.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 6.96
r_work: 0.2848 rms_B_bonded: 6.45 restraints_weight: 2.0000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  17953  Z= 0.115
  Angle     :  0.517  11.563  24577  Z= 0.271
  Chirality :  0.045   0.217   2864
  Planarity :  0.004   0.043   2998
  Dihedral  : 11.245  75.538   2864
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 24.14 %
    Favored  : 74.73 %
  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:  0.31 (0.19), residues: 2094
  helix:  0.62 (0.24), residues: 534
  sheet:  0.21 (0.29), residues: 360
  loop :  0.13 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 135 
 TYR   0.013   0.001   TYR D 342 
 PHE   0.013   0.001   PHE C   7 
 TRP   0.011   0.001   TRP D  86 
 HIS   0.003   0.001   HIS D 249 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 (17953)
  covalent geometry    : angle       0.51706 /  0.27 (24577)
  hydrogen bonds       : bond        0.04026 /  2.66 (  638)
  hydrogen bonds       : angle       5.60188 /  3.94 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: F  340 THR cc_start: 0.5649 (OUTLIER) cc_final: 0.4865 (p)
REVERT: E  106 ASP cc_start: 0.7629 (m-30) cc_final: 0.6777 (p0)
REVERT: E  227 LEU cc_start: 0.8708 (mm) cc_final: 0.8399 (mm)
REVERT: B  257 ARG cc_start: 0.7208 (tpp-160) cc_final: 0.6964 (tpp-160)
REVERT: B  282 ASP cc_start: 0.8631 (t0) cc_final: 0.8228 (t0)
REVERT: A  326 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8357 (mt-10)
REVERT: A  333 CYS cc_start: 0.9063 (m) cc_final: 0.8859 (m)
REVERT: C  226 LYS cc_start: 0.8572 (mmtm) cc_final: 0.7873 (ptmm)
REVERT: C  330 MET cc_start: 0.7352 (mmt) cc_final: 0.7111 (mmm)
  outliers start: 21
  outliers final: 9
  residues processed: 231
  average time/residue: 0.1281
  time to fit residues: 45.2616
Evaluate side-chains
  211 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 200
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  340 THR
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   36 ASP
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  326 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 179 optimal weight:    0.7980
   chunk 166 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 109 optimal weight:    0.0570
   chunk 89 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 207 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   overall best weight:    0.7098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 139 ASN
** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.159245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.117306 restraints weight = 122657.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 6.59
r_work: 0.2844 rms_B_bonded: 6.35 restraints_weight: 2.0000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17953  Z= 0.139
  Angle     :  0.513  10.753  24577  Z= 0.269
  Chirality :  0.045   0.259   2864
  Planarity :  0.004   0.040   2998
  Dihedral  : 11.050  73.889   2864
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 23.49 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.19), residues: 2094
  helix:  0.64 (0.24), residues: 534
  sheet:  0.17 (0.28), residues: 360
  loop :  0.12 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  90 
 TYR   0.012   0.001   TYR D 278 
 PHE   0.013   0.001   PHE E   7 
 TRP   0.010   0.001   TRP E 332 
 HIS   0.003   0.001   HIS E 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 (17953)
  covalent geometry    : angle       0.51326 /  0.27 (24577)
  hydrogen bonds       : bond        0.03637 /  2.40 (  638)
  hydrogen bonds       : angle       5.38658 /  3.78 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 209
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: F  340 THR cc_start: 0.5677 (OUTLIER) cc_final: 0.4927 (p)
REVERT: D  167 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8568 (pp)
REVERT: D  264 GLU cc_start: 0.7653 (mp0) cc_final: 0.7379 (mp0)
REVERT: E  106 ASP cc_start: 0.7726 (m-30) cc_final: 0.6840 (p0)
REVERT: E  135 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7791 (mtt90)
REVERT: E  227 LEU cc_start: 0.8674 (mm) cc_final: 0.8348 (mm)
REVERT: B  296 ASP cc_start: 0.8768 (t0) cc_final: 0.8337 (t0)
REVERT: A  333 CYS cc_start: 0.9065 (m) cc_final: 0.8583 (m)
REVERT: C  167 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8295 (pp)
REVERT: C  226 LYS cc_start: 0.8603 (mmtm) cc_final: 0.7945 (ptmm)
  outliers start: 34
  outliers final: 24
  residues processed: 236
  average time/residue: 0.1201
  time to fit residues: 43.9585
Evaluate side-chains
  223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  166 THR
Chi-restraints excluded: chain F residue  245 LEU
Chi-restraints excluded: chain F residue  263 PHE
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  300 ASP
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain F residue  340 THR
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   36 ASP
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  222 ILE
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  328 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 141 optimal weight:    0.7980
   chunk 124 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0270
   chunk 133 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 174 optimal weight:    0.9980
   chunk 185 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0870
   overall best weight:    0.4816

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 139 ASN
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.180779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.142196 restraints weight = 126397.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 6.10
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  17953  Z= 0.109
  Angle     :  0.503  10.406  24577  Z= 0.261
  Chirality :  0.044   0.245   2864
  Planarity :  0.004   0.038   2998
  Dihedral  : 10.862  73.748   2864
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 23.28 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.19), residues: 2094
  helix:  0.72 (0.24), residues: 534
  sheet:  0.19 (0.29), residues: 342
  loop :  0.15 (0.18), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 135 
 TYR   0.014   0.001   TYR D 342 
 PHE   0.013   0.001   PHE C   7 
 TRP   0.008   0.001   TRP D  86 
 HIS   0.003   0.001   HIS D 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.11 (17953)
  covalent geometry    : angle       0.50272 /  0.26 (24577)
  hydrogen bonds       : bond        0.03347 /  2.22 (  638)
  hydrogen bonds       : angle       5.16377 /  3.63 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 209
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8762 (t) cc_final: 0.8438 (m)
REVERT: E  106 ASP cc_start: 0.7231 (m-30) cc_final: 0.6738 (p0)
REVERT: E  135 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7857 (mtt90)
REVERT: E  227 LEU cc_start: 0.8375 (mm) cc_final: 0.8171 (mm)
REVERT: B  218 MET cc_start: 0.7097 (ttt) cc_final: 0.6812 (ttt)
REVERT: B  284 GLN cc_start: 0.8177 (tp40) cc_final: 0.7686 (tt0)
REVERT: A  333 CYS cc_start: 0.7788 (m) cc_final: 0.7573 (m)
REVERT: C  226 LYS cc_start: 0.8527 (mmtm) cc_final: 0.8203 (ptmm)
  outliers start: 38
  outliers final: 23
  residues processed: 239
  average time/residue: 0.1126
  time to fit residues: 41.8745
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 205
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  245 LEU
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 183 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0170
   chunk 192 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 109 optimal weight:    0.1980
   chunk 104 optimal weight:    0.8980
   chunk 155 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   overall best weight:    0.5420

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 139 ASN
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.180579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.142260 restraints weight = 127890.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 6.13
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  17953  Z= 0.115
  Angle     :  0.502  10.625  24577  Z= 0.260
  Chirality :  0.044   0.217   2864
  Planarity :  0.003   0.036   2998
  Dihedral  : 10.676  73.603   2864
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 23.23 %
    Favored  : 74.95 %
  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:  0.36 (0.19), residues: 2094
  helix:  0.64 (0.24), residues: 540
  sheet:  0.21 (0.29), residues: 342
  loop :  0.19 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 126 
 TYR   0.015   0.001   TYR D 278 
 PHE   0.014   0.001   PHE E 240 
 TRP   0.013   0.001   TRP F 332 
 HIS   0.003   0.001   HIS D 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 (17953)
  covalent geometry    : angle       0.50180 /  0.26 (24577)
  hydrogen bonds       : bond        0.03300 /  2.19 (  638)
  hydrogen bonds       : angle       5.07735 /  3.57 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 212
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8629 (t) cc_final: 0.8350 (m)
REVERT: D  264 GLU cc_start: 0.7513 (mp0) cc_final: 0.7065 (tt0)
REVERT: E  106 ASP cc_start: 0.7302 (m-30) cc_final: 0.6830 (p0)
REVERT: E  135 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7860 (mtt90)
REVERT: B  218 MET cc_start: 0.7072 (ttt) cc_final: 0.6812 (ttt)
REVERT: B  277 ASN cc_start: 0.8186 (m-40) cc_final: 0.7965 (m-40)
REVERT: B  284 GLN cc_start: 0.8173 (tp40) cc_final: 0.7674 (tt0)
REVERT: A  333 CYS cc_start: 0.7809 (m) cc_final: 0.7551 (m)
REVERT: C  226 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8175 (ptmm)
  outliers start: 34
  outliers final: 28
  residues processed: 239
  average time/residue: 0.1269
  time to fit residues: 46.4559
Evaluate side-chains
  231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  245 LEU
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 188 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 146 optimal weight:    0.2980
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 159 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 173 optimal weight:    0.5980
   chunk 189 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 136 ASN
A  14 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.180244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.142004 restraints weight = 127529.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 6.01
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3574
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  17953  Z= 0.121
  Angle     :  0.507  10.302  24577  Z= 0.262
  Chirality :  0.045   0.308   2864
  Planarity :  0.003   0.036   2998
  Dihedral  : 10.521  73.496   2864
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 23.44 %
    Favored  : 74.84 %
  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:  0.36 (0.19), residues: 2094
  helix:  0.64 (0.24), residues: 540
  sheet:  0.21 (0.29), residues: 342
  loop :  0.18 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 126 
 TYR   0.014   0.001   TYR D 278 
 PHE   0.017   0.001   PHE E 203 
 TRP   0.008   0.001   TRP D  86 
 HIS   0.003   0.001   HIS D 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.12 (17953)
  covalent geometry    : angle       0.50689 /  0.26 (24577)
  hydrogen bonds       : bond        0.03275 /  2.17 (  638)
  hydrogen bonds       : angle       5.02729 /  3.53 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 212
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8643 (t) cc_final: 0.8317 (m)
REVERT: E  106 ASP cc_start: 0.7314 (m-30) cc_final: 0.6841 (p0)
REVERT: B  218 MET cc_start: 0.7150 (ttt) cc_final: 0.6897 (ttt)
REVERT: B  284 GLN cc_start: 0.8155 (tp40) cc_final: 0.7669 (tt0)
REVERT: B  296 ASP cc_start: 0.7986 (t0) cc_final: 0.7696 (t0)
REVERT: A  333 CYS cc_start: 0.7809 (m) cc_final: 0.7589 (m)
REVERT: C  226 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8213 (ptmm)
  outliers start: 32
  outliers final: 28
  residues processed: 236
  average time/residue: 0.1183
  time to fit residues: 42.9679
Evaluate side-chains
  231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  245 LEU
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 135 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   chunk 189 optimal weight:    0.5980
   chunk 114 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 174 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 188 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 136 ASN
E 163 ASN
B 277 ASN
C 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.179211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.140295 restraints weight = 128081.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 6.19
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  17953  Z= 0.144
  Angle     :  0.517  10.061  24577  Z= 0.267
  Chirality :  0.045   0.204   2864
  Planarity :  0.004   0.035   2998
  Dihedral  : 10.417  73.463   2864
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 23.49 %
    Favored  : 74.78 %
  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:  0.30 (0.19), residues: 2094
  helix:  0.58 (0.24), residues: 540
  sheet:  0.07 (0.29), residues: 348
  loop :  0.19 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 126 
 TYR   0.016   0.001   TYR D 278 
 PHE   0.013   0.001   PHE E   7 
 TRP   0.010   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.14 (17953)
  covalent geometry    : angle       0.51745 /  0.27 (24577)
  hydrogen bonds       : bond        0.03400 /  2.26 (  638)
  hydrogen bonds       : angle       5.05245 /  3.54 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 208
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8806 (t) cc_final: 0.8364 (m)
REVERT: D  264 GLU cc_start: 0.7557 (mp0) cc_final: 0.7159 (tt0)
REVERT: B  218 MET cc_start: 0.7220 (ttt) cc_final: 0.6980 (ttt)
REVERT: B  284 GLN cc_start: 0.8193 (tp40) cc_final: 0.7692 (tt0)
REVERT: A  333 CYS cc_start: 0.7798 (m) cc_final: 0.7562 (m)
REVERT: C  226 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8196 (ptmm)
  outliers start: 32
  outliers final: 23
  residues processed: 233
  average time/residue: 0.1128
  time to fit residues: 40.8675
Evaluate side-chains
  226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 140 optimal weight:    0.0570
   chunk 84 optimal weight:    0.0980
   chunk 156 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 183 optimal weight:    1.9990
   chunk 184 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 168 optimal weight:    0.7980
   chunk 203 optimal weight:    4.9990
   overall best weight:    0.5098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 136 ASN
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.180481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.141465 restraints weight = 124573.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 6.09
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17953  Z= 0.111
  Angle     :  0.506  10.166  24577  Z= 0.261
  Chirality :  0.044   0.204   2864
  Planarity :  0.003   0.035   2998
  Dihedral  : 10.328  73.511   2864
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 24.09 %
    Favored  : 74.52 %
  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:  0.35 (0.19), residues: 2094
  helix:  0.63 (0.24), residues: 540
  sheet:  0.19 (0.29), residues: 342
  loop :  0.18 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 126 
 TYR   0.013   0.001   TYR D 278 
 PHE   0.014   0.001   PHE D 329 
 TRP   0.008   0.001   TRP D  86 
 HIS   0.003   0.001   HIS D 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.11 (17953)
  covalent geometry    : angle       0.50646 /  0.26 (24577)
  hydrogen bonds       : bond        0.03198 /  2.12 (  638)
  hydrogen bonds       : angle       4.95282 /  3.47 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 217
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8782 (t) cc_final: 0.8285 (m)
REVERT: D  264 GLU cc_start: 0.7552 (mp0) cc_final: 0.7170 (tt0)
REVERT: E  241 SER cc_start: 0.8786 (m) cc_final: 0.8573 (p)
REVERT: B   87 ASP cc_start: 0.8184 (t0) cc_final: 0.7910 (t0)
REVERT: B  218 MET cc_start: 0.7160 (ttt) cc_final: 0.6918 (ttt)
REVERT: B  284 GLN cc_start: 0.8187 (tp40) cc_final: 0.7688 (tt0)
REVERT: C  226 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8223 (ptmm)
REVERT: C  330 MET cc_start: 0.7076 (mmm) cc_final: 0.6678 (mmt)
  outliers start: 26
  outliers final: 21
  residues processed: 237
  average time/residue: 0.1142
  time to fit residues: 42.1625
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 207
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 134 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 0 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 188 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 193 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 136 ASN
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.179719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.141071 restraints weight = 130364.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 6.20
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3574
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17953  Z= 0.132
  Angle     :  0.510  10.135  24577  Z= 0.264
  Chirality :  0.045   0.199   2864
  Planarity :  0.004   0.036   2998
  Dihedral  : 10.265  73.473   2864
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 24.30 %
    Favored  : 74.46 %
  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:  0.31 (0.19), residues: 2094
  helix:  0.61 (0.24), residues: 540
  sheet:  0.18 (0.29), residues: 342
  loop :  0.15 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 126 
 TYR   0.014   0.001   TYR D 278 
 PHE   0.013   0.001   PHE E   7 
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.13 (17953)
  covalent geometry    : angle       0.51043 /  0.26 (24577)
  hydrogen bonds       : bond        0.03295 /  2.19 (  638)
  hydrogen bonds       : angle       4.97708 /  3.49 ( 1699)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8805 (t) cc_final: 0.8360 (m)
REVERT: D  264 GLU cc_start: 0.7525 (mp0) cc_final: 0.7181 (tt0)
REVERT: E  241 SER cc_start: 0.8779 (m) cc_final: 0.8570 (p)
REVERT: B  218 MET cc_start: 0.7224 (ttt) cc_final: 0.7000 (ttt)
REVERT: B  284 GLN cc_start: 0.8188 (tp40) cc_final: 0.7690 (tt0)
REVERT: C  226 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8195 (ptmm)
  outliers start: 23
  outliers final: 22
  residues processed: 226
  average time/residue: 0.1244
  time to fit residues: 43.2951
Evaluate side-chains
  223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 154 optimal weight:    0.0370
   chunk 65 optimal weight:    2.9990
   chunk 139 optimal weight:    0.9990
   chunk 105 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0770
   chunk 33 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0670
   chunk 108 optimal weight:    0.0970
   chunk 92 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 148 optimal weight:    2.9990
   overall best weight:    0.1752

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  14 HIS
D 136 ASN
D 187 GLN
E 163 ASN
B 175 GLN
A 130 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.183151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.144983 restraints weight = 130506.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 6.16
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  17953  Z= 0.089
  Angle     :  0.496  10.144  24577  Z= 0.256
  Chirality :  0.043   0.196   2864
  Planarity :  0.003   0.037   2998
  Dihedral  : 10.173  73.533   2864
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 24.46 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.19), residues: 2094
  helix:  0.70 (0.24), residues: 540
  sheet:  0.35 (0.29), residues: 330
  loop :  0.25 (0.18), residues: 1224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 126 
 TYR   0.012   0.001   TYR D 278 
 PHE   0.012   0.001   PHE C   7 
 TRP   0.009   0.001   TRP D  86 
 HIS   0.003   0.001   HIS D 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00200 /  0.09 (17953)
  covalent geometry    : angle       0.49619 /  0.26 (24577)
  hydrogen bonds       : bond        0.02959 /  1.97 (  638)
  hydrogen bonds       : angle       4.81577 /  3.39 ( 1699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3326.40 seconds
wall clock time: 58 minutes 3.98 seconds (3483.98 seconds total)