Starting phenix.real_space_refine
on Sat Jul  4 02:01:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ud5_42147/07_2026/8ud5_42147.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ud5_42147/07_2026/8ud5_42147.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ud5_42147/07_2026/8ud5_42147.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ud5_42147/07_2026/8ud5_42147.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ud5_42147/07_2026/8ud5_42147.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ud5_42147/07_2026/8ud5_42147.cif"
  }
  resolution = 3.13
  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=   0.042
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      53      5.49       5
     S      60      5.16       5
     C   11133      2.51       5
     N    2880      2.21       5
     O    3538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 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: 17664
  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: 542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 542
          Classifications: {'RNA': 27}
          Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 25}
          Link IDs: {'rna3p': 26}
    Chain: "H"
      Number of atoms: 592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 592
          Classifications: {'RNA': 27}
          Modifications used: {'rna3p_pur': 25, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 26}
  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: 7.46, per 1000 atoms: 0.42
  Number of scatterers: 17664
  At special positions: 0
  Unit cell: (115.92, 118.68, 129.72, 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      53     15.00
     O    3538      8.00
     N    2880      7.00
     C   11133      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: 1.40
  Conformation dependent library (CDL) restraints added in 1.6 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:
      58 helices and 46 sheets defined
      26.3% alpha, 24.0% beta
      20 base pairs and 41 stacking pairs defined.
    Time for finding SS restraints: 2.19
  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
    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: 3.744A  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 129 through 136
    Processing helix  chain 'E' and resid 207 through 216
    Processing helix  chain 'E' and resid 217 through 225
    Processing helix  chain 'E' and resid 231 through 236
      removed outlier: 3.928A  pdb=" N   VAL E 236 " --> pdb=" O   PHE E 232 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 261
      removed outlier: 3.766A  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 113 through 117
    Processing helix  chain 'B' and resid 129 through 137
    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: 3.531A  pdb=" N   VAL B 236 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 261
      removed outlier: 3.580A  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: 3.520A  pdb=" N   VAL A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.649A  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 113 through 117
    Processing helix  chain 'C' and resid 129 through 136
    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: 3.624A  pdb=" N   VAL C 236 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.631A  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: 6.632A  pdb=" N   VAL F  31 " --> pdb=" O   LEU F  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 79 through 80
      removed outlier: 7.268A  pdb=" N   ILE F  79 " --> pdb=" O   PHE F 122 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   ASP F 124 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
      removed outlier: 4.716A  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 98 through 99
      removed outlier: 8.208A  pdb=" N   THR F  98 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162
    Processing sheet with id=AA6, first strand: chain 'F' and resid 264 through 266
      removed outlier: 3.536A  pdb=" N   GLU F 266 " --> pdb=" O   PHE F 279 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ILE F 280 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   CYS F 290 " --> pdb=" O   ILE F 280 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 315 through 322
      removed outlier: 7.357A  pdb=" N   SER F 328 " --> pdb=" O   PRO F 343 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   MET F 330 " --> pdb=" O   PHE F 341 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   PHE F 341 " --> pdb=" O   MET F 330 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TRP F 332 " --> pdb=" O   GLU F 339 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27
      removed outlier: 6.684A  pdb=" N   VAL D  31 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.190A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.574A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   LYS D 180 " --> pdb=" O   GLN D 187 " (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 98 through 99
      removed outlier: 8.236A  pdb=" N   THR D  98 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'D' and resid 160 through 162
    Processing sheet with id=AB4, first strand: chain 'D' and resid 264 through 266
      removed outlier: 4.869A  pdb=" N   ILE D 280 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   CYS D 290 " --> pdb=" O   ILE D 280 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 315 through 322
      removed outlier: 5.879A  pdb=" N   LYS D 334 " --> pdb=" O   VAL D 338 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   VAL D 338 " --> pdb=" O   LYS D 334 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 27
      removed outlier: 6.658A  pdb=" N   VAL E  31 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.176A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 8.567A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.176A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 8.567A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   LYS E 180 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 87
    Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99
      removed outlier: 8.306A  pdb=" N   THR E  98 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 162
    Processing sheet with id=AC3, first strand: chain 'E' and resid 275 through 281
      removed outlier: 4.915A  pdb=" N   ILE E 280 " --> pdb=" O   CYS E 290 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   CYS E 290 " --> pdb=" O   ILE E 280 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 315 through 322
      removed outlier: 7.151A  pdb=" N   SER E 328 " --> pdb=" O   PRO E 343 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   MET E 330 " --> pdb=" O   PHE E 341 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE E 341 " --> pdb=" O   MET E 330 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP E 332 " --> pdb=" O   GLU E 339 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 24 through 27
      removed outlier: 6.698A  pdb=" N   VAL B  31 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.220A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.730A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.220A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.730A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   LYS B 180 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AC9, first strand: chain 'B' and resid 98 through 99
      removed outlier: 8.108A  pdb=" N   THR B  98 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC9
    Processing sheet with id=AD1, first strand: chain 'B' and resid 160 through 162
    Processing sheet with id=AD2, first strand: chain 'B' and resid 264 through 266
      removed outlier: 5.005A  pdb=" N   ILE B 280 " --> pdb=" O   CYS B 290 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   CYS B 290 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 315 through 322
      removed outlier: 6.677A  pdb=" N   TRP B 332 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'A' and resid 24 through 26
      removed outlier: 6.685A  pdb=" N   VAL A  31 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.190A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.190A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   LYS A 180 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AD8, first strand: chain 'A' and resid 98 through 99
      removed outlier: 8.202A  pdb=" N   THR A  98 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD8
    Processing sheet with id=AD9, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AE1, first strand: chain 'A' and resid 264 through 266
      removed outlier: 5.093A  pdb=" N   ILE A 280 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   CYS A 290 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'A' and resid 316 through 322
      removed outlier: 7.255A  pdb=" N   SER A 328 " --> pdb=" O   PRO A 343 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   MET A 330 " --> pdb=" O   PHE A 341 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   PHE A 341 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   TRP A 332 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 24 through 26
      removed outlier: 6.634A  pdb=" N   VAL C  31 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.144A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.144A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   LYS C 180 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AE7, first strand: chain 'C' and resid 98 through 99
      removed outlier: 8.168A  pdb=" N   THR C  98 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE7
    Processing sheet with id=AE8, first strand: chain 'C' and resid 160 through 162
    Processing sheet with id=AE9, first strand: chain 'C' and resid 264 through 266
      removed outlier: 4.683A  pdb=" N   ILE C 280 " --> pdb=" O   CYS C 290 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   CYS C 290 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'C' and resid 315 through 322
      removed outlier: 3.547A  pdb=" N   THR C 340 " --> pdb=" O   TRP C 332 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   LYS C 334 " --> pdb=" O   VAL C 338 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   VAL C 338 " --> pdb=" O   LYS C 334 " (cutoff:3.500A)

    630 hydrogen bonds defined for protein.
    1632 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      43 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      41 stacking parallelities
  Total time for adding SS restraints: 3.41

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5443
        1.34 -     1.45: 2718
        1.45 -     1.57: 9783
        1.57 -     1.69: 105
        1.69 -     1.81: 90
  Bond restraints: 18139
  Sorted by residual:
  bond pdb=" CA  LEU B 345 "
       pdb=" C   LEU B 345 "
    ideal  model  delta    sigma   weight residual
    1.526  1.496  0.030 1.29e-02 6.01e+03 5.49e+00
  bond pdb=" O5'   U G   7 "
       pdb=" C5'   U G   7 "
    ideal  model  delta    sigma   weight residual
    1.420  1.442 -0.022 1.50e-02 4.44e+03 2.16e+00
  bond pdb=" CB  PRO A 262 "
       pdb=" CG  PRO A 262 "
    ideal  model  delta    sigma   weight residual
    1.492  1.564 -0.072 5.00e-02 4.00e+02 2.09e+00
  bond pdb=" O5'   U G   5 "
       pdb=" C5'   U G   5 "
    ideal  model  delta    sigma   weight residual
    1.420  1.442 -0.022 1.50e-02 4.44e+03 2.08e+00
  bond pdb=" O5'   A H  29 "
       pdb=" C5'   A H  29 "
    ideal  model  delta    sigma   weight residual
    1.420  1.441 -0.021 1.50e-02 4.44e+03 2.01e+00
  ... (remaining 18134 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 24598
        1.91 -     3.81: 242
        3.81 -     5.72: 22
        5.72 -     7.63: 4
        7.63 -     9.53: 1
  Bond angle restraints: 24867
  Sorted by residual:
  angle pdb=" N   LYS B 344 "
        pdb=" CA  LYS B 344 "
        pdb=" C   LYS B 344 "
      ideal   model   delta    sigma   weight residual
     110.24  116.81   -6.57 1.30e+00 5.92e-01 2.55e+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  128.71   -7.17 1.91e+00 2.74e-01 1.41e+01
  angle pdb=" C4'   U G   4 "
        pdb=" C3'   U G   4 "
        pdb=" O3'   U G   4 "
      ideal   model   delta    sigma   weight residual
     113.00  107.58    5.42 1.50e+00 4.44e-01 1.30e+01
  angle pdb=" C4'   A H  26 "
        pdb=" C3'   A H  26 "
        pdb=" O3'   A H  26 "
      ideal   model   delta    sigma   weight residual
     113.00  107.91    5.09 1.50e+00 4.44e-01 1.15e+01
  angle pdb=" CA  PRO A 262 "
        pdb=" N   PRO A 262 "
        pdb=" CD  PRO A 262 "
      ideal   model   delta    sigma   weight residual
     112.00  107.30    4.70 1.40e+00 5.10e-01 1.13e+01
  ... (remaining 24862 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.40: 9478
       19.40 -    38.80: 991
       38.80 -    58.20: 301
       58.20 -    77.60: 74
       77.60 -    96.99: 25
  Dihedral angle restraints: 10869
    sinusoidal: 4785
      harmonic: 6084
  Sorted by residual:
  dihedral pdb=" C3'   A H  27 "
           pdb=" C4'   A H  27 "
           pdb=" O4'   A H  27 "
           pdb=" C1'   A H  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
      20.00  -10.12   30.12     1      8.00e+00 1.56e-02 2.03e+01
  dihedral pdb=" C4'   A H  27 "
           pdb=" O4'   A H  27 "
           pdb=" C1'   A H  27 "
           pdb=" C2'   A H  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00   29.51  -26.51     1      8.00e+00 1.56e-02 1.58e+01
  dihedral pdb=" C5'   A H  27 "
           pdb=" C4'   A H  27 "
           pdb=" C3'   A H  27 "
           pdb=" O3'   A H  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  108.06  -26.06     1      8.00e+00 1.56e-02 1.53e+01
  ... (remaining 10866 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 2255
       0.047 -    0.095: 427
       0.095 -    0.142: 193
       0.142 -    0.190: 23
       0.190 -    0.237: 5
  Chirality restraints: 2903
  Sorted by residual:
  chirality pdb=" C3'   A G  24 "
            pdb=" C4'   A G  24 "
            pdb=" O3'   A G  24 "
            pdb=" C2'   A G  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.71    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" C3'   A H  29 "
            pdb=" C4'   A H  29 "
            pdb=" O3'   A H  29 "
            pdb=" C2'   A H  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.71    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" C3'   A H  26 "
            pdb=" C4'   A H  26 "
            pdb=" O3'   A H  26 "
            pdb=" C2'   A H  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.69    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 2900 not shown)

  Planarity restraints: 3006
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 261 "   -0.074 5.00e-02 4.00e+02   1.10e-01 1.95e+01
        pdb=" N   PRO A 262 "    0.191 5.00e-02 4.00e+02
        pdb=" CA  PRO A 262 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO A 262 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 261 "    0.066 5.00e-02 4.00e+02   9.89e-02 1.57e+01
        pdb=" N   PRO D 262 "   -0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO D 262 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO D 262 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 204 "    0.034 5.00e-02 4.00e+02   5.24e-02 4.40e+00
        pdb=" N   PRO F 205 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO F 205 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO F 205 "    0.029 5.00e-02 4.00e+02
  ... (remaining 3003 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2934
        2.77 -     3.30: 16539
        3.30 -     3.84: 30684
        3.84 -     4.37: 37739
        4.37 -     4.90: 63421
  Nonbonded interactions: 151317
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 242 "
            pdb=" OG  SER A 287 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   HIS E 242 "
            pdb=" OG  SER E 287 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG1 THR B 195 "
            pdb=" OD2 ASP B 323 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OH  TYR A 193 "
            pdb=" OE2 GLU A 304 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   HIS D 242 "
            pdb=" OG  SER D 287 "
     model   vdw
     2.293 3.040
  ... (remaining 151312 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:             6.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  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:                    0.040
  Process input model:                     23.980
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
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      :  0.002   0.072  18139  Z= 0.120
  Angle     :  0.490   9.534  24867  Z= 0.297
  Chirality :  0.046   0.237   2903
  Planarity :  0.004   0.110   3006
  Dihedral  : 18.013  96.995   6945
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 22.10 %
    Favored  : 77.63 %
  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:  0.54 (0.19), residues: 2094
  helix:  0.73 (0.23), residues: 534
  sheet:  0.54 (0.30), residues: 342
  loop :  0.26 (0.18), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 135 
 TYR   0.009   0.001   TYR A 342 
 PHE   0.027   0.001   PHE D 258 
 TRP   0.014   0.001   TRP B 332 
 HIS   0.003   0.001   HIS B 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.12 (18139)
  covalent geometry    : angle       0.48958 /  0.30 (24867)
  hydrogen bonds       : bond        0.20642 / 13.83 (  637)
  hydrogen bonds       : angle       8.36966 /  5.97 ( 1718)

*********************** 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
  220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 215
  time to evaluate  : 0.828 
Fit side-chains
REVERT: F   56 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8055 (mp0)
REVERT: B  223 GLU cc_start: 0.8180 (tp30) cc_final: 0.7712 (tt0)
REVERT: A  202 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7388 (tt0)
  outliers start: 5
  outliers final: 2
  residues processed: 219
  average time/residue: 0.1387
  time to fit residues: 47.0050
Evaluate side-chains
  207 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 204
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  136 ASN
Chi-restraints excluded: chain A residue  197 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 194 optimal weight:    5.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 200 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0370
   chunk 122 optimal weight:    0.0070
   overall best weight:    0.4878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 GLN
B 277 ASN
A 199 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.165255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.121434 restraints weight = 112230.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 4.96
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3236
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3236
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.0791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18139  Z= 0.126
  Angle     :  0.504   9.875  24867  Z= 0.279
  Chirality :  0.045   0.181   2903
  Planarity :  0.005   0.088   3006
  Dihedral  : 12.241  92.655   2985
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 21.29 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.19), residues: 2094
  helix:  0.72 (0.23), residues: 540
  sheet:  0.52 (0.29), residues: 342
  loop :  0.24 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 224 
 TYR   0.011   0.001   TYR C 179 
 PHE   0.011   0.001   PHE A 268 
 TRP   0.007   0.001   TRP E 332 
 HIS   0.003   0.001   HIS B 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 (18139)
  covalent geometry    : angle       0.50448 /  0.28 (24867)
  hydrogen bonds       : bond        0.04701 /  3.10 (  637)
  hydrogen bonds       : angle       6.03749 /  4.31 ( 1718)

*********************** 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
  251 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 221
  time to evaluate  : 0.656 
Fit side-chains
REVERT: F   56 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7048 (mp0)
REVERT: F  264 GLU cc_start: 0.7347 (mp0) cc_final: 0.7093 (mt-10)
REVERT: D  104 MET cc_start: 0.8650 (mmm) cc_final: 0.8097 (tpt)
REVERT: D  109 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8253 (mmtm)
REVERT: D  152 GLN cc_start: 0.7653 (pm20) cc_final: 0.7435 (mm-40)
REVERT: D  183 ASP cc_start: 0.8033 (m-30) cc_final: 0.7733 (m-30)
REVERT: E  233 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6657 (mm-30)
  outliers start: 30
  outliers final: 18
  residues processed: 234
  average time/residue: 0.1443
  time to fit residues: 51.6639
Evaluate side-chains
  225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 206
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  144 THR
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  200 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  218 MET
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 177 optimal weight:    0.9990
   chunk 205 optimal weight:   20.0000
   chunk 32 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 144 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  18 GLN
B  74 ASN
B 175 GLN
C 187 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.161128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.117187 restraints weight = 109913.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 5.47
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  18139  Z= 0.173
  Angle     :  0.505   9.338  24867  Z= 0.274
  Chirality :  0.046   0.170   2903
  Planarity :  0.004   0.079   3006
  Dihedral  : 12.141  91.465   2983
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.70 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.19), residues: 2094
  helix:  0.54 (0.23), residues: 546
  sheet:  0.50 (0.29), residues: 342
  loop :  0.15 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 224 
 TYR   0.016   0.001   TYR A 225 
 PHE   0.013   0.002   PHE A 268 
 TRP   0.007   0.001   TRP B  86 
 HIS   0.003   0.001   HIS C  14 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.17 (18139)
  covalent geometry    : angle       0.50516 /  0.27 (24867)
  hydrogen bonds       : bond        0.04562 /  3.04 (  637)
  hydrogen bonds       : angle       5.76087 /  4.11 ( 1718)

*********************** 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
  240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 208
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: D  104 MET cc_start: 0.8751 (mmm) cc_final: 0.8263 (tpt)
REVERT: D  138 ARG cc_start: 0.8310 (mtp180) cc_final: 0.8058 (ttp-170)
REVERT: D  264 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7236 (tt0)
REVERT: B  104 MET cc_start: 0.8667 (mmm) cc_final: 0.8366 (tpt)
REVERT: A  163 ASN cc_start: 0.8154 (t0) cc_final: 0.7919 (t0)
REVERT: A  170 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7742 (mt-10)
REVERT: A  345 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6437 (tp)
  outliers start: 32
  outliers final: 21
  residues processed: 220
  average time/residue: 0.1432
  time to fit residues: 47.8692
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  103 SER
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain D residue  264 GLU
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  218 MET
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 63 optimal weight:    0.0570
   chunk 56 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 136 optimal weight:    0.6980
   chunk 150 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 147 optimal weight:    0.0000
   chunk 127 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   overall best weight:    0.4702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 187 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.164354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.123665 restraints weight = 109627.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 4.47
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18139  Z= 0.112
  Angle     :  0.475   8.782  24867  Z= 0.257
  Chirality :  0.044   0.158   2903
  Planarity :  0.004   0.072   3006
  Dihedral  : 11.965  91.945   2983
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.08 %
    Favored  : 77.15 %
  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:  0.43 (0.19), residues: 2094
  helix:  0.63 (0.23), residues: 546
  sheet:  0.54 (0.29), residues: 342
  loop :  0.16 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 224 
 TYR   0.009   0.001   TYR A 225 
 PHE   0.010   0.001   PHE A 268 
 TRP   0.006   0.001   TRP E  86 
 HIS   0.003   0.001   HIS B 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.11 (18139)
  covalent geometry    : angle       0.47484 /  0.26 (24867)
  hydrogen bonds       : bond        0.03807 /  2.53 (  637)
  hydrogen bonds       : angle       5.41560 /  3.87 ( 1718)

*********************** 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
  246 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 217
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: D  152 GLN cc_start: 0.7645 (pm20) cc_final: 0.7419 (mm-40)
REVERT: D  264 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7242 (tt0)
REVERT: B  104 MET cc_start: 0.8677 (mmm) cc_final: 0.8355 (tpt)
REVERT: A  163 ASN cc_start: 0.8185 (t0) cc_final: 0.7881 (t0)
REVERT: A  243 SER cc_start: 0.8902 (m) cc_final: 0.8697 (p)
REVERT: C  321 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8158 (m)
REVERT: C  345 LEU cc_start: 0.3998 (OUTLIER) cc_final: 0.3791 (mt)
  outliers start: 29
  outliers final: 18
  residues processed: 227
  average time/residue: 0.1451
  time to fit residues: 50.3037
Evaluate side-chains
  226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 205
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  103 SER
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain D residue  264 GLU
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  345 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 193 optimal weight:    3.9990
   chunk 120 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0370
   chunk 54 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 189 optimal weight:    0.7980
   chunk 165 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 129 optimal weight:    0.5980
   overall best weight:    0.6058

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.164049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.122979 restraints weight = 104616.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 4.44
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18139  Z= 0.125
  Angle     :  0.477   8.813  24867  Z= 0.257
  Chirality :  0.044   0.149   2903
  Planarity :  0.004   0.069   3006
  Dihedral  : 11.850  92.249   2982
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.59 %
    Favored  : 77.47 %
  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:  0.41 (0.19), residues: 2094
  helix:  0.66 (0.23), residues: 546
  sheet:  0.56 (0.29), residues: 342
  loop :  0.11 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 224 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.027   0.001   PHE D 221 
 TRP   0.006   0.001   TRP B  86 
 HIS   0.003   0.001   HIS B 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 (18139)
  covalent geometry    : angle       0.47692 /  0.26 (24867)
  hydrogen bonds       : bond        0.03737 /  2.49 (  637)
  hydrogen bonds       : angle       5.30399 /  3.78 ( 1718)

*********************** 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
  241 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 209
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
REVERT: B  104 MET cc_start: 0.8677 (mmm) cc_final: 0.8357 (tpt)
REVERT: A  163 ASN cc_start: 0.8218 (t0) cc_final: 0.7845 (t0)
REVERT: A  170 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7595 (mt-10)
REVERT: A  248 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8519 (mp)
REVERT: A  345 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6506 (tp)
REVERT: C  321 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8189 (m)
  outliers start: 32
  outliers final: 21
  residues processed: 224
  average time/residue: 0.1444
  time to fit residues: 49.4889
Evaluate side-chains
  230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  103 SER
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain E residue  300 ASP
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 111 optimal weight:    0.8980
   chunk 162 optimal weight:    1.9990
   chunk 178 optimal weight:    1.9990
   chunk 191 optimal weight:    5.9990
   chunk 151 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 163 ASN
E 136 ASN
A  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.160715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.116276 restraints weight = 107124.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 5.25
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  18139  Z= 0.231
  Angle     :  0.546   8.430  24867  Z= 0.290
  Chirality :  0.048   0.190   2903
  Planarity :  0.004   0.069   3006
  Dihedral  : 11.914  92.764   2982
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 20.81 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.19), residues: 2094
  helix:  0.40 (0.23), residues: 546
  sheet:  0.55 (0.29), residues: 342
  loop : -0.04 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 224 
 TYR   0.018   0.002   TYR A 225 
 PHE   0.024   0.002   PHE D 221 
 TRP   0.009   0.001   TRP A 332 
 HIS   0.004   0.001   HIS C  14 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00571 /  0.23 (18139)
  covalent geometry    : angle       0.54589 /  0.29 (24867)
  hydrogen bonds       : bond        0.04193 /  2.79 (  637)
  hydrogen bonds       : angle       5.52337 /  3.92 ( 1718)

*********************** 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
  244 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 210
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
REVERT: D  104 MET cc_start: 0.8756 (mmm) cc_final: 0.8494 (tpt)
REVERT: B  104 MET cc_start: 0.8665 (mmm) cc_final: 0.8371 (tpt)
REVERT: B  147 SER cc_start: 0.8588 (p) cc_final: 0.8369 (p)
REVERT: A  170 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7753 (mt-10)
REVERT: A  248 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8603 (mp)
REVERT: A  345 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6483 (tp)
REVERT: C  264 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6683 (mt-10)
REVERT: C  321 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8336 (m)
REVERT: C  345 LEU cc_start: 0.3816 (OUTLIER) cc_final: 0.3606 (mt)
  outliers start: 34
  outliers final: 21
  residues processed: 227
  average time/residue: 0.1391
  time to fit residues: 48.7605
Evaluate side-chains
  229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  103 SER
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  211 ILE
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  345 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 133 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 199 optimal weight:    0.6980
   chunk 207 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   chunk 191 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 143 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0570
   overall best weight:    0.5898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 163 ASN
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 199 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.165843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.120460 restraints weight = 106753.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 6.15
r_work: 0.2627 rms_B_bonded: 5.61 restraints_weight: 2.0000
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2578 r_free = 0.2578    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2578 r_free = 0.2578    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  18139  Z= 0.127
  Angle     :  0.491   8.673  24867  Z= 0.261
  Chirality :  0.044   0.158   2903
  Planarity :  0.004   0.066   3006
  Dihedral  : 11.800  92.821   2982
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.29 %
    Favored  : 76.67 %
  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:  0.25 (0.19), residues: 2094
  helix:  0.53 (0.23), residues: 546
  sheet:  0.50 (0.29), residues: 342
  loop : -0.00 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 224 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.031   0.001   PHE D 221 
 TRP   0.007   0.001   TRP B  86 
 HIS   0.004   0.001   HIS B 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 (18139)
  covalent geometry    : angle       0.49124 /  0.26 (24867)
  hydrogen bonds       : bond        0.03644 /  2.41 (  637)
  hydrogen bonds       : angle       5.25649 /  3.75 ( 1718)

*********************** 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
  239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 207
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
REVERT: B  104 MET cc_start: 0.9127 (mmm) cc_final: 0.8839 (tpt)
REVERT: B  147 SER cc_start: 0.8116 (p) cc_final: 0.7881 (p)
REVERT: B  223 GLU cc_start: 0.8163 (tp30) cc_final: 0.7895 (tt0)
REVERT: A  170 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7671 (mt-10)
REVERT: A  345 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6496 (tp)
REVERT: C  264 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7329 (mt-10)
REVERT: C  321 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8320 (m)
REVERT: C  345 LEU cc_start: 0.3976 (OUTLIER) cc_final: 0.3669 (mt)
  outliers start: 32
  outliers final: 24
  residues processed: 222
  average time/residue: 0.1416
  time to fit residues: 48.2365
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  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  103 SER
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain E residue  300 ASP
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  345 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 162 optimal weight:    0.9990
   chunk 135 optimal weight:   10.0000
   chunk 170 optimal weight:    0.2980
   chunk 204 optimal weight:   30.0000
   chunk 6 optimal weight:    0.6980
   chunk 200 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0870
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.5760

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 163 ASN
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 HIS
A 136 ASN
C 163 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.164965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.119999 restraints weight = 106272.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 6.28
r_work: 0.2610 rms_B_bonded: 6.20 restraints_weight: 2.0000
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18139  Z= 0.124
  Angle     :  0.483   8.509  24867  Z= 0.258
  Chirality :  0.044   0.162   2903
  Planarity :  0.004   0.065   3006
  Dihedral  : 11.737  92.936   2982
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.67 %
    Favored  : 76.56 %
  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:  0.61 (0.23), residues: 546
  sheet:  0.51 (0.29), residues: 342
  loop :  0.01 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 224 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.029   0.001   PHE D 221 
 TRP   0.007   0.001   TRP B  86 
 HIS   0.004   0.001   HIS B 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.12 (18139)
  covalent geometry    : angle       0.48327 /  0.26 (24867)
  hydrogen bonds       : bond        0.03571 /  2.34 (  637)
  hydrogen bonds       : angle       5.17358 /  3.69 ( 1718)

*********************** 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
  233 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 206
  time to evaluate  : 0.577 
Fit side-chains
REVERT: F  208 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8006 (tp-100)
REVERT: E  254 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7282 (mp)
REVERT: B  104 MET cc_start: 0.9142 (mmm) cc_final: 0.8862 (tpt)
REVERT: B  147 SER cc_start: 0.8117 (p) cc_final: 0.7874 (p)
REVERT: B  223 GLU cc_start: 0.8178 (tp30) cc_final: 0.7860 (tt0)
REVERT: A  163 ASN cc_start: 0.8845 (t0) cc_final: 0.8629 (t0)
REVERT: A  170 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7685 (mt-10)
REVERT: A  345 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6557 (tp)
REVERT: C  264 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7282 (mt-10)
REVERT: C  321 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8329 (m)
REVERT: C  345 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.3694 (mt)
  outliers start: 27
  outliers final: 20
  residues processed: 218
  average time/residue: 0.1387
  time to fit residues: 46.2660
Evaluate side-chains
  225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 200
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  103 SER
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  345 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 159 optimal weight:    4.9990
   chunk 126 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0770
   chunk 27 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 127 optimal weight:    0.6980
   overall best weight:    0.6538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 163 ASN
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN
C 163 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.165112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.119629 restraints weight = 113319.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 6.48
r_work: 0.2620 rms_B_bonded: 6.10 restraints_weight: 2.0000
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2557 r_free = 0.2557    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2557 r_free = 0.2557    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  18139  Z= 0.130
  Angle     :  0.483   8.499  24867  Z= 0.258
  Chirality :  0.045   0.165   2903
  Planarity :  0.004   0.065   3006
  Dihedral  : 11.567  92.933   2979
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.34 %
    Favored  : 76.61 %
  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:  0.61 (0.23), residues: 546
  sheet:  0.54 (0.30), residues: 342
  loop :  0.00 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 224 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.028   0.001   PHE D 221 
 TRP   0.006   0.001   TRP B  86 
 HIS   0.004   0.001   HIS B 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.13 (18139)
  covalent geometry    : angle       0.48310 /  0.26 (24867)
  hydrogen bonds       : bond        0.03532 /  2.30 (  637)
  hydrogen bonds       : angle       5.14258 /  3.66 ( 1718)

*********************** 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
  234 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 202
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
REVERT: F  208 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8026 (tp-100)
REVERT: D  296 ASP cc_start: 0.8789 (t0) cc_final: 0.8342 (t0)
REVERT: E  254 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7317 (mp)
REVERT: B  104 MET cc_start: 0.9138 (mmm) cc_final: 0.8860 (tpt)
REVERT: B  147 SER cc_start: 0.8119 (p) cc_final: 0.7873 (p)
REVERT: B  223 GLU cc_start: 0.8161 (tp30) cc_final: 0.7805 (tt0)
REVERT: A  163 ASN cc_start: 0.8854 (t0) cc_final: 0.8644 (t0)
REVERT: A  170 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7688 (mt-10)
REVERT: A  345 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6551 (tp)
REVERT: C  264 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7486 (mt-10)
REVERT: C  321 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8326 (m)
REVERT: C  345 LEU cc_start: 0.4004 (OUTLIER) cc_final: 0.3700 (mt)
  outliers start: 32
  outliers final: 23
  residues processed: 218
  average time/residue: 0.1416
  time to fit residues: 47.2294
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 200
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  103 SER
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  345 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 79 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9990
   chunk 123 optimal weight:    3.9990
   chunk 145 optimal weight:    2.9990
   chunk 204 optimal weight:   30.0000
   chunk 100 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0770
   chunk 183 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   overall best weight:    0.6140

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 163 ASN
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN
C 163 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.165232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.120304 restraints weight = 107793.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 6.33
r_work: 0.2619 rms_B_bonded: 6.23 restraints_weight: 2.0000
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2553 r_free = 0.2553    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2553 r_free = 0.2553    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18139  Z= 0.125
  Angle     :  0.482   8.525  24867  Z= 0.257
  Chirality :  0.044   0.166   2903
  Planarity :  0.004   0.065   3006
  Dihedral  : 11.504  92.879   2979
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.45 %
    Favored  : 76.61 %
  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 (0.23), residues: 546
  sheet:  0.55 (0.29), residues: 342
  loop :  0.01 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 224 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.028   0.001   PHE D 221 
 TRP   0.007   0.001   TRP B  86 
 HIS   0.004   0.001   HIS C 249 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 (18139)
  covalent geometry    : angle       0.48223 /  0.26 (24867)
  hydrogen bonds       : bond        0.03472 /  2.26 (  637)
  hydrogen bonds       : angle       5.09247 /  3.63 ( 1718)

********************** 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
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 198
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: F  208 GLN cc_start: 0.8329 (tp-100) cc_final: 0.8020 (tp-100)
REVERT: F  264 GLU cc_start: 0.7482 (mp0) cc_final: 0.7014 (mt-10)
REVERT: D  296 ASP cc_start: 0.8802 (t0) cc_final: 0.8356 (t0)
REVERT: E  254 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7320 (mp)
REVERT: B  104 MET cc_start: 0.9134 (mmm) cc_final: 0.8855 (tpt)
REVERT: B  147 SER cc_start: 0.8109 (p) cc_final: 0.7858 (p)
REVERT: B  223 GLU cc_start: 0.8180 (tp30) cc_final: 0.7808 (tt0)
REVERT: A  163 ASN cc_start: 0.8874 (t0) cc_final: 0.8670 (t0)
REVERT: A  170 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7723 (mt-10)
REVERT: A  259 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7101 (mttp)
REVERT: A  345 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6556 (tp)
REVERT: C  264 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7477 (mt-10)
REVERT: C  321 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8337 (m)
REVERT: C  345 LEU cc_start: 0.4012 (OUTLIER) cc_final: 0.3704 (mt)
  outliers start: 30
  outliers final: 22
  residues processed: 212
  average time/residue: 0.1389
  time to fit residues: 45.3928
Evaluate side-chains
  225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  103 SER
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain C residue  345 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 145 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0970
   chunk 141 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 177 optimal weight:    0.2980
   chunk 92 optimal weight:    0.7980
   chunk 190 optimal weight:    0.9980
   chunk 90 optimal weight:    0.3980
   chunk 57 optimal weight:    0.0070
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.2996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.166568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.121608 restraints weight = 119295.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 6.57
r_work: 0.2667 rms_B_bonded: 5.58 restraints_weight: 2.0000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  18139  Z= 0.095
  Angle     :  0.466   8.539  24867  Z= 0.249
  Chirality :  0.044   0.167   2903
  Planarity :  0.004   0.065   3006
  Dihedral  : 11.414  92.611   2979
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 21.51 %
    Favored  : 76.61 %
  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:  0.39 (0.19), residues: 2094
  helix:  0.69 (0.23), residues: 546
  sheet:  0.58 (0.29), residues: 342
  loop :  0.06 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 224 
 TYR   0.008   0.001   TYR A 342 
 PHE   0.028   0.001   PHE D 221 
 TRP   0.007   0.001   TRP B  86 
 HIS   0.004   0.001   HIS B 337 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.09 (18139)
  covalent geometry    : angle       0.46616 /  0.25 (24867)
  hydrogen bonds       : bond        0.03269 /  2.10 (  637)
  hydrogen bonds       : angle       4.94413 /  3.52 ( 1718)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4050.49 seconds
wall clock time: 70 minutes 41.37 seconds (4241.37 seconds total)