Starting phenix.real_space_refine
on Sun Jun 15 13:56:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ud4_42146/06_2025/8ud4_42146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ud4_42146/06_2025/8ud4_42146.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ud4_42146/06_2025/8ud4_42146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ud4_42146/06_2025/8ud4_42146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ud4_42146/06_2025/8ud4_42146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ud4_42146/06_2025/8ud4_42146.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      46      5.49       5
     S      60      5.16       5
     C   11057      2.51       5
     N    2851      2.21       5
     O    3484      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17498
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "F"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "D"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "E"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "B"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "A"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "C"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "G"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 463
          Classifications: {'RNA': 23}
          Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 22}
          Link IDs: {'rna3p': 22}
    Chain: "H"
      Number of atoms: 505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 505
          Classifications: {'RNA': 23}
          Modifications used: {'rna3p_pur': 22, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 22}
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N  AILE F  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE F  27 " occ=0.48
    residue:
      pdb=" N  AASN F  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN F  28 " occ=0.48
    residue:
      pdb=" N  AASN F  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN F  29 " occ=0.48
    residue:
      pdb=" N  AILE D  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE D  27 " occ=0.48
    residue:
      pdb=" N  AASN D  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  28 " occ=0.48
    residue:
      pdb=" N  AASN D  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  29 " occ=0.48
    residue:
      pdb=" N  AILE E  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE E  27 " occ=0.48
    residue:
      pdb=" N  AASN E  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN E  28 " occ=0.48
    residue:
      pdb=" N  AASN E  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN E  29 " occ=0.48
    residue:
      pdb=" N  AILE B  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE B  27 " occ=0.48
    residue:
      pdb=" N  AASN B  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  28 " occ=0.48
    residue:
      pdb=" N  AASN B  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  29 " occ=0.48
    ... (remaining 6 not shown)
  Time building chain proxies: 19.75, per 1000 atoms: 1.13
  Number of scatterers: 17498
  At special positions: 0
  Unit cell: (115.92, 123.28, 135.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P      46     15.00
     O    3484      8.00
     N    2851      7.00
     C   11057      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.48
  Conformation dependent library (CDL) restraints added in 4.0 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 44 sheets defined
      26.2% alpha, 23.0% beta
      21 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 6.87
  Creating SS restraints...
    Processing helix  chain 'F' and resid 1 through 13
    Processing helix  chain 'F' and resid 50 through 60
    Processing helix  chain 'F' and resid 68 through 75
    Processing helix  chain 'F' and resid 113 through 117
    Processing helix  chain 'F' and resid 129 through 137
    Processing helix  chain 'F' and resid 207 through 216
    Processing helix  chain 'F' and resid 217 through 225
    Processing helix  chain 'F' and resid 231 through 236
    Processing helix  chain 'F' and resid 250 through 261
      removed outlier: 3.651A  pdb=" N   GLU F 260 " --> pdb=" O   LYS F 256 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 298 through 308
    Processing helix  chain 'D' and resid 2 through 13
    Processing helix  chain 'D' and resid 50 through 60
    Processing helix  chain 'D' and resid 68 through 75
    Processing helix  chain 'D' and resid 129 through 137
    Processing helix  chain 'D' and resid 207 through 216
    Processing helix  chain 'D' and resid 217 through 225
    Processing helix  chain 'D' and resid 231 through 236
    Processing helix  chain 'D' and resid 250 through 261
      removed outlier: 3.585A  pdb=" N   GLU D 260 " --> pdb=" O   LYS D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 308
    Processing helix  chain 'E' and resid 2 through 13
    Processing helix  chain 'E' and resid 50 through 60
    Processing helix  chain 'E' and resid 68 through 75
    Processing helix  chain 'E' and resid 113 through 117
    Processing helix  chain 'E' and resid 129 through 136
    Processing helix  chain 'E' and resid 207 through 216
    Processing helix  chain 'E' and resid 217 through 226
      removed outlier: 3.566A  pdb=" N   PHE E 221 " --> pdb=" O   ALA E 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 231 through 236
      removed outlier: 3.660A  pdb=" N   VAL E 236 " --> pdb=" O   PHE E 232 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 261
      removed outlier: 3.535A  pdb=" N   GLU E 260 " --> pdb=" O   LYS E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 308
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 50 through 60
    Processing helix  chain 'B' and resid 68 through 75
    Processing helix  chain 'B' and resid 129 through 137
      removed outlier: 3.596A  pdb=" N   LEU B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 216
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 3.584A  pdb=" N   VAL B 236 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 261
      removed outlier: 3.584A  pdb=" N   GLU B 260 " --> pdb=" O   LYS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 308
    Processing helix  chain 'A' and resid 2 through 13
    Processing helix  chain 'A' and resid 50 through 60
    Processing helix  chain 'A' and resid 68 through 75
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 129 through 137
    Processing helix  chain 'A' and resid 207 through 216
    Processing helix  chain 'A' and resid 217 through 225
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.681A  pdb=" N   VAL A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.665A  pdb=" N   GLU A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
    Processing helix  chain 'C' and resid 2 through 13
    Processing helix  chain 'C' and resid 50 through 60
    Processing helix  chain 'C' and resid 68 through 75
    Processing helix  chain 'C' and resid 129 through 137
    Processing helix  chain 'C' and resid 207 through 216
    Processing helix  chain 'C' and resid 217 through 225
    Processing helix  chain 'C' and resid 231 through 236
      removed outlier: 3.587A  pdb=" N   VAL C 236 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.599A  pdb=" N   GLU C 260 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 308
    Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27
      removed outlier: 6.685A  pdb=" N   VAL F  31 " --> pdb=" O   LEU F  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 106 through 108
      removed outlier: 8.281A  pdb=" N   THR F  98 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE F  99 " --> pdb=" O   ALA F  80 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   ASP F 124 " --> pdb=" O   ALA F  81 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   LYS F 180 " --> pdb=" O   GLN F 187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87
    Processing sheet with id=AA4, first strand: chain 'F' and resid 160 through 162
    Processing sheet with id=AA5, first strand: chain 'F' and resid 263 through 266
      removed outlier: 3.525A  pdb=" N   GLU F 266 " --> pdb=" O   PHE F 279 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ILE F 280 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   CYS F 290 " --> pdb=" O   ILE F 280 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASP F 282 " --> pdb=" O   SER F 288 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   SER F 288 " --> pdb=" O   ASP F 282 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 315 through 322
      removed outlier: 7.388A  pdb=" N   SER F 328 " --> pdb=" O   PRO F 343 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   MET F 330 " --> pdb=" O   PHE F 341 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE F 341 " --> pdb=" O   MET F 330 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP F 332 " --> pdb=" O   GLU F 339 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27
      removed outlier: 6.669A  pdb=" N   VAL D  31 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.121A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.121A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87
    Processing sheet with id=AB2, first strand: chain 'D' and resid 160 through 162
    Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 266
      removed outlier: 3.579A  pdb=" N   GLU D 266 " --> pdb=" O   PHE D 279 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   ILE D 280 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   CYS D 290 " --> pdb=" O   ILE D 280 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASP D 282 " --> pdb=" O   SER D 288 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   SER D 288 " --> pdb=" O   ASP D 282 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 315 through 322
      removed outlier: 7.483A  pdb=" N   SER D 328 " --> pdb=" O   PRO D 343 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   MET D 330 " --> pdb=" O   PHE D 341 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   PHE D 341 " --> pdb=" O   MET D 330 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   TRP D 332 " --> pdb=" O   GLU D 339 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 27
      removed outlier: 6.668A  pdb=" N   VAL E  31 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.397A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 9.114A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LYS E 180 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 87
    Processing sheet with id=AB8, first strand: chain 'E' and resid 98 through 99
      removed outlier: 8.157A  pdb=" N   THR E  98 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 162
    Processing sheet with id=AC1, first strand: chain 'E' and resid 264 through 266
      removed outlier: 4.873A  pdb=" N   ILE E 280 " --> pdb=" O   CYS E 290 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   CYS E 290 " --> pdb=" O   ILE E 280 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 315 through 322
      removed outlier: 7.345A  pdb=" N   SER E 328 " --> pdb=" O   PRO E 343 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   MET E 330 " --> pdb=" O   PHE E 341 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE E 341 " --> pdb=" O   MET E 330 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   TRP E 332 " --> pdb=" O   GLU E 339 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 24 through 27
      removed outlier: 6.732A  pdb=" N   VAL B  31 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.268A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.788A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   LYS B 180 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AC6, first strand: chain 'B' and resid 98 through 99
      removed outlier: 8.227A  pdb=" N   THR B  98 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'B' and resid 160 through 162
    Processing sheet with id=AC8, first strand: chain 'B' and resid 264 through 266
      removed outlier: 3.583A  pdb=" N   GLU B 266 " --> pdb=" O   PHE B 279 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 275 through 277
    Processing sheet with id=AD1, first strand: chain 'B' and resid 315 through 322
      removed outlier: 7.221A  pdb=" N   SER B 328 " --> pdb=" O   PRO B 343 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   MET B 330 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE B 341 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TRP B 332 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'A' and resid 24 through 27
      removed outlier: 6.717A  pdb=" N   VAL A  31 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.022A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.022A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   LYS A 180 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AD6, first strand: chain 'A' and resid 98 through 99
      removed outlier: 8.372A  pdb=" N   THR A  98 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AD8, first strand: chain 'A' and resid 264 through 266
      removed outlier: 4.997A  pdb=" N   ILE A 280 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   CYS A 290 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'A' and resid 316 through 322
      removed outlier: 3.515A  pdb=" N   TYR A 342 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'C' and resid 24 through 27
      removed outlier: 6.717A  pdb=" N   VAL C  31 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.156A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.699A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.156A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.699A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LYS C 180 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AE5, first strand: chain 'C' and resid 98 through 99
      removed outlier: 8.144A  pdb=" N   THR C  98 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE5
    Processing sheet with id=AE6, first strand: chain 'C' and resid 160 through 162
    Processing sheet with id=AE7, first strand: chain 'C' and resid 264 through 266
      removed outlier: 3.529A  pdb=" N   GLU C 264 " --> pdb=" O   THR C 281 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   ILE C 280 " --> pdb=" O   CYS C 290 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   CYS C 290 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 322
      removed outlier: 3.603A  pdb=" N   THR C 340 " --> pdb=" O   TRP C 332 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   LYS C 334 " --> pdb=" O   VAL C 338 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   VAL C 338 " --> pdb=" O   LYS C 334 " (cutoff:3.500A)

    621 hydrogen bonds defined for protein.
    1611 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 5.89

  Time building geometry restraints manager: 5.26 seconds

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

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

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

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

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

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.720
  Check model and map are aligned:         0.140
  Set scattering table:                    0.190
  Process input model:                     58.370
  Find NCS groups from input model:        0.920
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   69.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  17953  Z= 0.142
  Angle     :  0.562  10.139  24577  Z= 0.321
  Chirality :  0.048   0.217   2864
  Planarity :  0.004   0.057   2998
  Dihedral  : 17.652  96.628   6830
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 23.39 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.19), residues: 2094
  helix:  0.85 (0.24), residues: 528
  sheet:  0.35 (0.29), residues: 354
  loop :  0.20 (0.18), residues: 1212

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20686 (  638)
  hydrogen bonds       : angle       8.38870 ( 1699)
  covalent geometry    : bond        0.00255 (17953)
  covalent geometry    : angle       0.56213 (24577)

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

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 231
  time to evaluate  : 1.830 
Fit side-chains
   revert: symmetry clash
REVERT: F  113 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7165 (mp0)
REVERT: E  106 ASP cc_start: 0.7281 (m-30) cc_final: 0.6975 (p0)
REVERT: B  330 MET cc_start: 0.6707 (tpp) cc_final: 0.6213 (ttm)
REVERT: C  218 MET cc_start: 0.7052 (ttt) cc_final: 0.6759 (ttm)
  outliers start: 8
  outliers final: 1
  residues processed: 234
  average time/residue: 0.3214
  time to fit residues: 112.3723
Evaluate side-chains
  208 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 1.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   96 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 175 optimal weight:    0.8980
   chunk 157 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 163 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 188 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN
E 244 GLN
B  14 HIS
A  74 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.161836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.119973 restraints weight = 122610.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 7.06
r_work: 0.2843 rms_B_bonded: 6.45 restraints_weight: 2.0000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  17953  Z= 0.162
  Angle     :  0.552  10.401  24577  Z= 0.287
  Chirality :  0.046   0.225   2864
  Planarity :  0.004   0.049   2998
  Dihedral  : 11.208  80.138   2866
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 22.74 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.19), residues: 2094
  helix:  0.65 (0.24), residues: 534
  sheet:  0.35 (0.29), residues: 360
  loop :  0.23 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  86 
 HIS   0.003   0.001   HIS B  95 
 PHE   0.014   0.002   PHE E   7 
 TYR   0.013   0.001   TYR A 225 
 ARG   0.005   0.001   ARG D  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  638)
  hydrogen bonds       : angle       5.71072 ( 1699)
  covalent geometry    : bond        0.00390 (17953)
  covalent geometry    : angle       0.55205 (24577)

*********************** 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
  250 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 220
  time to evaluate  : 1.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  340 THR cc_start: 0.5733 (OUTLIER) cc_final: 0.4956 (p)
REVERT: E  106 ASP cc_start: 0.7597 (m-30) cc_final: 0.6946 (p0)
REVERT: E  216 LEU cc_start: 0.7870 (mp) cc_final: 0.7609 (mp)
REVERT: E  224 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7711 (ttp-170)
REVERT: E  227 LEU cc_start: 0.8596 (mm) cc_final: 0.8301 (mm)
REVERT: B  296 ASP cc_start: 0.8774 (t0) cc_final: 0.8338 (t0)
REVERT: A  252 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8518 (mp)
REVERT: C  226 LYS cc_start: 0.8613 (mmtm) cc_final: 0.7893 (ptmm)
REVERT: C  330 MET cc_start: 0.7299 (mmt) cc_final: 0.7056 (mmm)
  outliers start: 30
  outliers final: 15
  residues processed: 241
  average time/residue: 0.2879
  time to fit residues: 105.3049
Evaluate side-chains
  218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 201
  time to evaluate  : 1.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  263 PHE
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  340 THR
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   36 ASP
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 156 optimal weight:    0.0370
   chunk 198 optimal weight:    8.9990
   chunk 195 optimal weight:    0.9980
   chunk 44 optimal weight:    0.3980
   chunk 190 optimal weight:    0.8980
   chunk 67 optimal weight:    8.9990
   chunk 167 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 132 optimal weight:    5.9990
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.162965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.121014 restraints weight = 123105.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 7.00
r_work: 0.2853 rms_B_bonded: 6.43 restraints_weight: 2.0000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17953  Z= 0.131
  Angle     :  0.518  11.832  24577  Z= 0.267
  Chirality :  0.045   0.214   2864
  Planarity :  0.003   0.043   2998
  Dihedral  : 10.689  74.931   2864
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.01 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.19), residues: 2094
  helix:  0.69 (0.24), residues: 534
  sheet:  0.30 (0.29), residues: 342
  loop :  0.23 (0.18), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  86 
 HIS   0.003   0.001   HIS B 337 
 PHE   0.013   0.001   PHE E   7 
 TYR   0.018   0.001   TYR D 278 
 ARG   0.005   0.000   ARG D  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  638)
  hydrogen bonds       : angle       5.30820 ( 1699)
  covalent geometry    : bond        0.00313 (17953)
  covalent geometry    : angle       0.51847 (24577)

*********************** 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
  254 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 221
  time to evaluate  : 1.825 
Fit side-chains
   revert: symmetry clash
REVERT: E  106 ASP cc_start: 0.7609 (m-30) cc_final: 0.7011 (p0)
REVERT: E  135 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7757 (mtt90)
REVERT: E  224 ARG cc_start: 0.8095 (ttp-170) cc_final: 0.7721 (ttp-170)
REVERT: E  227 LEU cc_start: 0.8664 (mm) cc_final: 0.8340 (mm)
REVERT: B  277 ASN cc_start: 0.8805 (m-40) cc_final: 0.8453 (m-40)
REVERT: B  296 ASP cc_start: 0.8695 (t0) cc_final: 0.8260 (t0)
REVERT: C  126 ARG cc_start: 0.8938 (mpp80) cc_final: 0.8718 (mpp80)
REVERT: C  226 LYS cc_start: 0.8591 (mmtm) cc_final: 0.7908 (ptmm)
REVERT: C  330 MET cc_start: 0.7340 (mmt) cc_final: 0.7096 (mmm)
  outliers start: 33
  outliers final: 17
  residues processed: 246
  average time/residue: 0.2779
  time to fit residues: 104.6838
Evaluate side-chains
  223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 206
  time to evaluate  : 1.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
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 54 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0040
   chunk 173 optimal weight:    1.9990
   chunk 198 optimal weight:    9.9990
   chunk 104 optimal weight:    0.1980
   chunk 141 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 128 optimal weight:    0.8980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.163367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.121434 restraints weight = 125660.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 6.82
r_work: 0.2878 rms_B_bonded: 6.27 restraints_weight: 2.0000
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  17953  Z= 0.111
  Angle     :  0.497  10.895  24577  Z= 0.256
  Chirality :  0.044   0.419   2864
  Planarity :  0.003   0.040   2998
  Dihedral  : 10.311  75.831   2864
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 23.23 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.19), residues: 2094
  helix:  0.65 (0.24), residues: 540
  sheet:  0.34 (0.29), residues: 342
  loop :  0.28 (0.19), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 
 PHE   0.013   0.001   PHE C   7 
 TYR   0.014   0.001   TYR D 278 
 ARG   0.008   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03144 (  638)
  hydrogen bonds       : angle       4.99033 ( 1699)
  covalent geometry    : bond        0.00262 (17953)
  covalent geometry    : angle       0.49728 (24577)

*********************** 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
  270 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 236
  time to evaluate  : 2.078 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.9041 (t) cc_final: 0.8759 (m)
REVERT: E  106 ASP cc_start: 0.7484 (m-30) cc_final: 0.7058 (p0)
REVERT: E  135 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7830 (mtt90)
REVERT: E  163 ASN cc_start: 0.8581 (t0) cc_final: 0.8214 (t0)
REVERT: E  224 ARG cc_start: 0.8100 (ttp-170) cc_final: 0.7836 (ttp-170)
REVERT: B  218 MET cc_start: 0.7187 (ttt) cc_final: 0.6953 (ttt)
REVERT: B  277 ASN cc_start: 0.8755 (m-40) cc_final: 0.8453 (m-40)
REVERT: B  284 GLN cc_start: 0.8342 (tp40) cc_final: 0.7744 (tt0)
REVERT: B  296 ASP cc_start: 0.8653 (t0) cc_final: 0.8259 (t0)
REVERT: A  223 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8642 (pt0)
REVERT: C  226 LYS cc_start: 0.8539 (mmtm) cc_final: 0.7900 (ptmm)
REVERT: C  330 MET cc_start: 0.7326 (mmt) cc_final: 0.7122 (mmm)
  outliers start: 34
  outliers final: 20
  residues processed: 263
  average time/residue: 0.3126
  time to fit residues: 125.5498
Evaluate side-chains
  236 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 216
  time to evaluate  : 1.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  245 LEU
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 146 optimal weight:    0.9990
   chunk 207 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 143 optimal weight:    1.9990
   chunk 198 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 72 optimal weight:    0.4980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
D 139 ASN
A  14 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.161336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.119825 restraints weight = 134889.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 7.22
r_work: 0.2825 rms_B_bonded: 6.56 restraints_weight: 2.0000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  17953  Z= 0.145
  Angle     :  0.523  10.204  24577  Z= 0.269
  Chirality :  0.045   0.391   2864
  Planarity :  0.003   0.039   2998
  Dihedral  : 10.205  76.561   2864
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 23.60 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.19), residues: 2094
  helix:  0.63 (0.24), residues: 540
  sheet:  0.30 (0.29), residues: 342
  loop :  0.22 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  86 
 HIS   0.003   0.001   HIS B 337 
 PHE   0.013   0.001   PHE E   7 
 TYR   0.015   0.001   TYR D 278 
 ARG   0.006   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  638)
  hydrogen bonds       : angle       5.03160 ( 1699)
  covalent geometry    : bond        0.00352 (17953)
  covalent geometry    : angle       0.52309 (24577)

*********************** 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
  248 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 217
  time to evaluate  : 1.920 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.9097 (t) cc_final: 0.8742 (m)
REVERT: D  264 GLU cc_start: 0.7672 (mp0) cc_final: 0.6907 (tt0)
REVERT: E  106 ASP cc_start: 0.7580 (m-30) cc_final: 0.7039 (p0)
REVERT: E  135 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7929 (mtt90)
REVERT: E  163 ASN cc_start: 0.8671 (t0) cc_final: 0.8304 (t0)
REVERT: B  202 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7115 (tp30)
REVERT: B  257 ARG cc_start: 0.7088 (tpp80) cc_final: 0.6796 (tpp-160)
REVERT: B  277 ASN cc_start: 0.8838 (m-40) cc_final: 0.8484 (m-40)
REVERT: B  284 GLN cc_start: 0.8350 (tp40) cc_final: 0.7737 (tt0)
REVERT: B  296 ASP cc_start: 0.8770 (t0) cc_final: 0.8352 (t0)
REVERT: A  223 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8618 (pt0)
REVERT: C  226 LYS cc_start: 0.8538 (mmtm) cc_final: 0.7966 (ptmm)
REVERT: C  330 MET cc_start: 0.7468 (mmt) cc_final: 0.7238 (mmm)
  outliers start: 31
  outliers final: 22
  residues processed: 241
  average time/residue: 0.2970
  time to fit residues: 108.8737
Evaluate side-chains
  221 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 1.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 189 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 127 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 182 optimal weight:    0.9980
   chunk 125 optimal weight:    0.9980
   chunk 174 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
D 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.160572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.118507 restraints weight = 127481.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 7.09
r_work: 0.2821 rms_B_bonded: 6.37 restraints_weight: 2.0000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  17953  Z= 0.158
  Angle     :  0.536  11.372  24577  Z= 0.273
  Chirality :  0.046   0.411   2864
  Planarity :  0.004   0.038   2998
  Dihedral  : 10.150  74.966   2864
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 23.49 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.19), residues: 2094
  helix:  0.54 (0.24), residues: 540
  sheet:  0.14 (0.29), residues: 348
  loop :  0.21 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  86 
 HIS   0.003   0.001   HIS B 337 
 PHE   0.014   0.001   PHE E   7 
 TYR   0.014   0.001   TYR D 278 
 ARG   0.006   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 (  638)
  hydrogen bonds       : angle       5.04081 ( 1699)
  covalent geometry    : bond        0.00384 (17953)
  covalent geometry    : angle       0.53573 (24577)

*********************** 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
  248 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 212
  time to evaluate  : 2.053 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.9088 (t) cc_final: 0.8718 (m)
REVERT: D   96 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6396 (tt)
REVERT: D  264 GLU cc_start: 0.7704 (mp0) cc_final: 0.6942 (tt0)
REVERT: E   36 ASP cc_start: 0.7898 (m-30) cc_final: 0.7502 (t70)
REVERT: E   97 SER cc_start: 0.9070 (m) cc_final: 0.8823 (p)
REVERT: E  135 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7906 (mtt90)
REVERT: E  163 ASN cc_start: 0.8660 (t0) cc_final: 0.8320 (t0)
REVERT: B  202 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7192 (tp30)
REVERT: B  257 ARG cc_start: 0.6993 (tpp80) cc_final: 0.6717 (tpp-160)
REVERT: B  277 ASN cc_start: 0.8870 (m-40) cc_final: 0.8487 (m-40)
REVERT: B  284 GLN cc_start: 0.8359 (tp40) cc_final: 0.7722 (tt0)
REVERT: B  296 ASP cc_start: 0.8790 (t0) cc_final: 0.8352 (t0)
REVERT: A  223 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8656 (pt0)
REVERT: C  226 LYS cc_start: 0.8549 (mmtm) cc_final: 0.7887 (ptmm)
REVERT: C  330 MET cc_start: 0.7404 (mmt) cc_final: 0.7135 (mmm)
  outliers start: 36
  outliers final: 27
  residues processed: 239
  average time/residue: 0.2999
  time to fit residues: 109.4745
Evaluate side-chains
  229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 200
  time to evaluate  : 2.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 159 optimal weight:    0.7980
   chunk 155 optimal weight:    1.9990
   chunk 171 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 190 optimal weight:    0.0970
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    0.3980
   chunk 194 optimal weight:    5.9990
   chunk 157 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D 139 ASN
D 187 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.180548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.141949 restraints weight = 130040.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 6.13
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  17953  Z= 0.122
  Angle     :  0.514  10.310  24577  Z= 0.262
  Chirality :  0.045   0.449   2864
  Planarity :  0.003   0.036   2998
  Dihedral  : 10.043  73.760   2864
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.28 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.19), residues: 2094
  helix:  0.62 (0.24), residues: 540
  sheet:  0.26 (0.29), residues: 342
  loop :  0.20 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 
 PHE   0.013   0.001   PHE E   7 
 TYR   0.014   0.001   TYR D 278 
 ARG   0.005   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  638)
  hydrogen bonds       : angle       4.88141 ( 1699)
  covalent geometry    : bond        0.00293 (17953)
  covalent geometry    : angle       0.51423 (24577)

*********************** 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
  254 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 221
  time to evaluate  : 2.000 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8749 (t) cc_final: 0.8505 (m)
REVERT: D  187 GLN cc_start: 0.8049 (mt0) cc_final: 0.7657 (mt0)
REVERT: D  264 GLU cc_start: 0.7710 (mp0) cc_final: 0.7343 (tt0)
REVERT: E  135 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7946 (mtt90)
REVERT: B  202 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7158 (tp30)
REVERT: B  257 ARG cc_start: 0.7235 (tpp80) cc_final: 0.6945 (tpp-160)
REVERT: B  277 ASN cc_start: 0.8311 (m-40) cc_final: 0.8078 (m-40)
REVERT: B  284 GLN cc_start: 0.8290 (tp40) cc_final: 0.7737 (tt0)
REVERT: B  296 ASP cc_start: 0.8061 (t0) cc_final: 0.7770 (t0)
REVERT: C  226 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8198 (ptmm)
  outliers start: 33
  outliers final: 26
  residues processed: 246
  average time/residue: 0.2965
  time to fit residues: 111.5166
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  : 1.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  245 LEU
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9980
   chunk 193 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 151 optimal weight:    0.8980
   chunk 112 optimal weight:    0.0070
   chunk 190 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.9802

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

Flipped N/Q/H residues before XYZ refinement:
C 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.178614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.139800 restraints weight = 135905.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 6.20
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3563
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  17953  Z= 0.167
  Angle     :  0.541  10.356  24577  Z= 0.275
  Chirality :  0.046   0.456   2864
  Planarity :  0.004   0.036   2998
  Dihedral  : 10.074  74.529   2864
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 23.39 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.19), residues: 2094
  helix:  0.50 (0.24), residues: 540
  sheet:  0.11 (0.29), residues: 348
  loop :  0.17 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 
 PHE   0.016   0.002   PHE E 203 
 TYR   0.014   0.001   TYR D 278 
 ARG   0.005   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03372 (  638)
  hydrogen bonds       : angle       5.04149 ( 1699)
  covalent geometry    : bond        0.00408 (17953)
  covalent geometry    : angle       0.54084 (24577)

*********************** 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
  235 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 201
  time to evaluate  : 1.868 
Fit side-chains
   revert: symmetry clash
REVERT: D  264 GLU cc_start: 0.7708 (mp0) cc_final: 0.7358 (tt0)
REVERT: E  135 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7986 (mtt90)
REVERT: B  202 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7267 (tp30)
REVERT: B  257 ARG cc_start: 0.7221 (tpp80) cc_final: 0.6933 (tpp-160)
REVERT: B  284 GLN cc_start: 0.8263 (tp40) cc_final: 0.7692 (tt0)
REVERT: B  296 ASP cc_start: 0.8189 (t0) cc_final: 0.7890 (t0)
REVERT: C  226 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8159 (ptmm)
  outliers start: 34
  outliers final: 26
  residues processed: 224
  average time/residue: 0.2856
  time to fit residues: 98.0843
Evaluate side-chains
  220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 1.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 2 optimal weight:    0.0050
   chunk 96 optimal weight:    0.9990
   chunk 127 optimal weight:    0.9990
   chunk 161 optimal weight:    0.8980
   chunk 119 optimal weight:    1.9990
   chunk 162 optimal weight:    0.8980
   chunk 93 optimal weight:    4.9990
   chunk 138 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 141 optimal weight:    0.5980
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
D 136 ASN
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.180133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.141048 restraints weight = 120578.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 5.96
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  17953  Z= 0.128
  Angle     :  0.522  10.308  24577  Z= 0.264
  Chirality :  0.045   0.445   2864
  Planarity :  0.003   0.036   2998
  Dihedral  : 10.006  73.486   2864
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 23.87 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.19), residues: 2094
  helix:  0.57 (0.24), residues: 540
  sheet:  0.28 (0.29), residues: 342
  loop :  0.16 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 
 PHE   0.013   0.001   PHE E   7 
 TYR   0.013   0.001   TYR D 278 
 ARG   0.005   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03098 (  638)
  hydrogen bonds       : angle       4.90420 ( 1699)
  covalent geometry    : bond        0.00308 (17953)
  covalent geometry    : angle       0.52183 (24577)

*********************** 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
  226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 198
  time to evaluate  : 1.974 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8736 (t) cc_final: 0.8431 (m)
REVERT: D  264 GLU cc_start: 0.7595 (mp0) cc_final: 0.7326 (tt0)
REVERT: E  135 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7977 (mtt90)
REVERT: B  202 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7266 (tp30)
REVERT: B  257 ARG cc_start: 0.7187 (tpp80) cc_final: 0.6973 (tpp-160)
REVERT: B  277 ASN cc_start: 0.8395 (m-40) cc_final: 0.8095 (m-40)
REVERT: B  284 GLN cc_start: 0.8222 (tp40) cc_final: 0.7697 (tt0)
REVERT: B  296 ASP cc_start: 0.8086 (t0) cc_final: 0.7791 (t0)
REVERT: C  330 MET cc_start: 0.7056 (mmm) cc_final: 0.6775 (mmt)
  outliers start: 28
  outliers final: 26
  residues processed: 217
  average time/residue: 0.3051
  time to fit residues: 100.7298
Evaluate side-chains
  220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 1.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 177 optimal weight:    0.7980
   chunk 201 optimal weight:    0.0970
   chunk 99 optimal weight:    0.9980
   chunk 118 optimal weight:    0.8980
   chunk 129 optimal weight:    2.9990
   chunk 143 optimal weight:    0.3980
   chunk 133 optimal weight:    2.9990
   chunk 117 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 137 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
D 136 ASN
E 163 ASN
B 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.180432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.141699 restraints weight = 125524.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 5.94
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17953  Z= 0.121
  Angle     :  0.517  10.334  24577  Z= 0.262
  Chirality :  0.045   0.444   2864
  Planarity :  0.003   0.035   2998
  Dihedral  :  9.955  73.500   2864
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 23.66 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.19), residues: 2094
  helix:  0.61 (0.24), residues: 540
  sheet:  0.31 (0.29), residues: 342
  loop :  0.17 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 
 PHE   0.013   0.001   PHE E   7 
 TYR   0.013   0.001   TYR D 278 
 ARG   0.005   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03035 (  638)
  hydrogen bonds       : angle       4.86534 ( 1699)
  covalent geometry    : bond        0.00290 (17953)
  covalent geometry    : angle       0.51701 (24577)

********************** 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
  230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 202
  time to evaluate  : 2.130 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8805 (t) cc_final: 0.8373 (m)
REVERT: D  264 GLU cc_start: 0.7558 (mp0) cc_final: 0.7251 (tt0)
REVERT: E  135 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7977 (mtt90)
REVERT: B   87 ASP cc_start: 0.8078 (t0) cc_final: 0.7832 (t0)
REVERT: B  202 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7280 (tp30)
REVERT: B  257 ARG cc_start: 0.7195 (tpp80) cc_final: 0.6993 (tpp-160)
REVERT: B  296 ASP cc_start: 0.8074 (t0) cc_final: 0.7781 (t0)
REVERT: C  330 MET cc_start: 0.7086 (mmm) cc_final: 0.6654 (mmt)
  outliers start: 28
  outliers final: 25
  residues processed: 220
  average time/residue: 0.3166
  time to fit residues: 106.5290
Evaluate side-chains
  219 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 193
  time to evaluate  : 1.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 138 optimal weight:    0.7980
   chunk 188 optimal weight:    0.0170
   chunk 101 optimal weight:    6.9990
   chunk 110 optimal weight:    0.1980
   chunk 80 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 140 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 193 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
D 136 ASN
** A  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.180990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.141979 restraints weight = 126211.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 6.05
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17953  Z= 0.113
  Angle     :  0.513  10.313  24577  Z= 0.260
  Chirality :  0.045   0.444   2864
  Planarity :  0.003   0.035   2998
  Dihedral  :  9.929  73.502   2864
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 23.87 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.19), residues: 2094
  helix:  0.61 (0.24), residues: 540
  sheet:  0.47 (0.30), residues: 330
  loop :  0.21 (0.18), residues: 1224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 
 PHE   0.013   0.001   PHE E   7 
 TYR   0.027   0.001   TYR D 278 
 ARG   0.005   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02974 (  638)
  hydrogen bonds       : angle       4.83969 ( 1699)
  covalent geometry    : bond        0.00269 (17953)
  covalent geometry    : angle       0.51301 (24577)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8784.05 seconds
wall clock time: 154 minutes 7.32 seconds (9247.32 seconds total)