Starting phenix.real_space_refine
on Sun Jun 15 18:02:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ud5_42147/06_2025/8ud5_42147.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ud5_42147/06_2025/8ud5_42147.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ud5_42147/06_2025/8ud5_42147.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ud5_42147/06_2025/8ud5_42147.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ud5_42147/06_2025/8ud5_42147.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ud5_42147/06_2025/8ud5_42147.cif"
  }
  resolution = 3.13
  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=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      53      5.49       5
     S      60      5.16       5
     C   11133      2.51       5
     N    2880      2.21       5
     O    3538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17664
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "F"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "D"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "E"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "B"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "A"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "C"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "G"
      Number of atoms: 542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 542
          Classifications: {'RNA': 27}
          Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 25}
          Link IDs: {'rna3p': 26}
    Chain: "H"
      Number of atoms: 592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 592
          Classifications: {'RNA': 27}
          Modifications used: {'rna3p_pur': 25, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 26}
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N  AILE F  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE F  27 " occ=0.48
    residue:
      pdb=" N  AASN F  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN F  28 " occ=0.48
    residue:
      pdb=" N  AASN F  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN F  29 " occ=0.48
    residue:
      pdb=" N  AILE D  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE D  27 " occ=0.48
    residue:
      pdb=" N  AASN D  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  28 " occ=0.48
    residue:
      pdb=" N  AASN D  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  29 " occ=0.48
    residue:
      pdb=" N  AILE E  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE E  27 " occ=0.48
    residue:
      pdb=" N  AASN E  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN E  28 " occ=0.48
    residue:
      pdb=" N  AASN E  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN E  29 " occ=0.48
    residue:
      pdb=" N  AILE B  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE B  27 " occ=0.48
    residue:
      pdb=" N  AASN B  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  28 " occ=0.48
    residue:
      pdb=" N  AASN B  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  29 " occ=0.48
    ... (remaining 6 not shown)
  Time building chain proxies: 18.77, per 1000 atoms: 1.06
  Number of scatterers: 17664
  At special positions: 0
  Unit cell: (115.92, 118.68, 129.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P      53     15.00
     O    3538      8.00
     N    2880      7.00
     C   11133      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.79
  Conformation dependent library (CDL) restraints added in 4.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 46 sheets defined
      26.3% alpha, 24.0% beta
      20 base pairs and 41 stacking pairs defined.
    Time for finding SS restraints: 5.86
  Creating SS restraints...
    Processing helix  chain 'F' and resid 1 through 13
    Processing helix  chain 'F' and resid 50 through 60
    Processing helix  chain 'F' and resid 68 through 75
    Processing helix  chain 'F' and resid 113 through 117
    Processing helix  chain 'F' and resid 129 through 137
    Processing helix  chain 'F' and resid 207 through 216
    Processing helix  chain 'F' and resid 217 through 225
    Processing helix  chain 'F' and resid 231 through 236
    Processing helix  chain 'F' and resid 250 through 261
    Processing helix  chain 'F' and resid 298 through 308
    Processing helix  chain 'D' and resid 2 through 13
    Processing helix  chain 'D' and resid 50 through 60
    Processing helix  chain 'D' and resid 68 through 75
    Processing helix  chain 'D' and resid 129 through 137
    Processing helix  chain 'D' and resid 207 through 216
    Processing helix  chain 'D' and resid 217 through 225
    Processing helix  chain 'D' and resid 231 through 236
    Processing helix  chain 'D' and resid 250 through 261
      removed outlier: 3.744A  pdb=" N   GLU D 260 " --> pdb=" O   LYS D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 308
    Processing helix  chain 'E' and resid 2 through 13
    Processing helix  chain 'E' and resid 50 through 60
    Processing helix  chain 'E' and resid 68 through 75
    Processing helix  chain 'E' and resid 129 through 136
    Processing helix  chain 'E' and resid 207 through 216
    Processing helix  chain 'E' and resid 217 through 225
    Processing helix  chain 'E' and resid 231 through 236
      removed outlier: 3.928A  pdb=" N   VAL E 236 " --> pdb=" O   PHE E 232 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 261
      removed outlier: 3.766A  pdb=" N   GLU E 260 " --> pdb=" O   LYS E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 308
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 50 through 60
    Processing helix  chain 'B' and resid 68 through 75
    Processing helix  chain 'B' and resid 113 through 117
    Processing helix  chain 'B' and resid 129 through 137
    Processing helix  chain 'B' and resid 207 through 216
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 3.531A  pdb=" N   VAL B 236 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 261
      removed outlier: 3.580A  pdb=" N   GLU B 260 " --> pdb=" O   LYS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 308
    Processing helix  chain 'A' and resid 2 through 13
    Processing helix  chain 'A' and resid 50 through 60
    Processing helix  chain 'A' and resid 68 through 75
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 129 through 137
    Processing helix  chain 'A' and resid 207 through 216
    Processing helix  chain 'A' and resid 217 through 225
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.520A  pdb=" N   VAL A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.649A  pdb=" N   GLU A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
    Processing helix  chain 'C' and resid 2 through 13
    Processing helix  chain 'C' and resid 50 through 60
    Processing helix  chain 'C' and resid 68 through 75
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'C' and resid 129 through 136
    Processing helix  chain 'C' and resid 207 through 216
    Processing helix  chain 'C' and resid 217 through 225
    Processing helix  chain 'C' and resid 231 through 236
      removed outlier: 3.624A  pdb=" N   VAL C 236 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.631A  pdb=" N   GLU C 260 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 308
    Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27
      removed outlier: 6.632A  pdb=" N   VAL F  31 " --> pdb=" O   LEU F  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 79 through 80
      removed outlier: 7.268A  pdb=" N   ILE F  79 " --> pdb=" O   PHE F 122 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   ASP F 124 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LYS F 180 " --> pdb=" O   GLN F 187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87
    Processing sheet with id=AA4, first strand: chain 'F' and resid 98 through 99
      removed outlier: 8.208A  pdb=" N   THR F  98 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162
    Processing sheet with id=AA6, first strand: chain 'F' and resid 264 through 266
      removed outlier: 3.536A  pdb=" N   GLU F 266 " --> pdb=" O   PHE F 279 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ILE F 280 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   CYS F 290 " --> pdb=" O   ILE F 280 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 315 through 322
      removed outlier: 7.357A  pdb=" N   SER F 328 " --> pdb=" O   PRO F 343 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   MET F 330 " --> pdb=" O   PHE F 341 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   PHE F 341 " --> pdb=" O   MET F 330 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TRP F 332 " --> pdb=" O   GLU F 339 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27
      removed outlier: 6.684A  pdb=" N   VAL D  31 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.190A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.574A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   LYS D 180 " --> pdb=" O   GLN D 187 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87
    Processing sheet with id=AB2, first strand: chain 'D' and resid 98 through 99
      removed outlier: 8.236A  pdb=" N   THR D  98 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'D' and resid 160 through 162
    Processing sheet with id=AB4, first strand: chain 'D' and resid 264 through 266
      removed outlier: 4.869A  pdb=" N   ILE D 280 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   CYS D 290 " --> pdb=" O   ILE D 280 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 315 through 322
      removed outlier: 5.879A  pdb=" N   LYS D 334 " --> pdb=" O   VAL D 338 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   VAL D 338 " --> pdb=" O   LYS D 334 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 27
      removed outlier: 6.658A  pdb=" N   VAL E  31 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.176A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 8.567A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.176A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 8.567A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   LYS E 180 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 87
    Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99
      removed outlier: 8.306A  pdb=" N   THR E  98 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 162
    Processing sheet with id=AC3, first strand: chain 'E' and resid 275 through 281
      removed outlier: 4.915A  pdb=" N   ILE E 280 " --> pdb=" O   CYS E 290 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   CYS E 290 " --> pdb=" O   ILE E 280 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 315 through 322
      removed outlier: 7.151A  pdb=" N   SER E 328 " --> pdb=" O   PRO E 343 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   MET E 330 " --> pdb=" O   PHE E 341 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE E 341 " --> pdb=" O   MET E 330 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP E 332 " --> pdb=" O   GLU E 339 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 24 through 27
      removed outlier: 6.698A  pdb=" N   VAL B  31 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.220A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.730A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.220A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.730A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   LYS B 180 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AC9, first strand: chain 'B' and resid 98 through 99
      removed outlier: 8.108A  pdb=" N   THR B  98 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC9
    Processing sheet with id=AD1, first strand: chain 'B' and resid 160 through 162
    Processing sheet with id=AD2, first strand: chain 'B' and resid 264 through 266
      removed outlier: 5.005A  pdb=" N   ILE B 280 " --> pdb=" O   CYS B 290 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   CYS B 290 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 315 through 322
      removed outlier: 6.677A  pdb=" N   TRP B 332 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'A' and resid 24 through 26
      removed outlier: 6.685A  pdb=" N   VAL A  31 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.190A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.190A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   LYS A 180 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AD8, first strand: chain 'A' and resid 98 through 99
      removed outlier: 8.202A  pdb=" N   THR A  98 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD8
    Processing sheet with id=AD9, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AE1, first strand: chain 'A' and resid 264 through 266
      removed outlier: 5.093A  pdb=" N   ILE A 280 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   CYS A 290 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'A' and resid 316 through 322
      removed outlier: 7.255A  pdb=" N   SER A 328 " --> pdb=" O   PRO A 343 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   MET A 330 " --> pdb=" O   PHE A 341 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   PHE A 341 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   TRP A 332 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 24 through 26
      removed outlier: 6.634A  pdb=" N   VAL C  31 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.144A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.144A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   LYS C 180 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AE7, first strand: chain 'C' and resid 98 through 99
      removed outlier: 8.168A  pdb=" N   THR C  98 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE7
    Processing sheet with id=AE8, first strand: chain 'C' and resid 160 through 162
    Processing sheet with id=AE9, first strand: chain 'C' and resid 264 through 266
      removed outlier: 4.683A  pdb=" N   ILE C 280 " --> pdb=" O   CYS C 290 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   CYS C 290 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'C' and resid 315 through 322
      removed outlier: 3.547A  pdb=" N   THR C 340 " --> pdb=" O   TRP C 332 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   LYS C 334 " --> pdb=" O   VAL C 338 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   VAL C 338 " --> pdb=" O   LYS C 334 " (cutoff:3.500A)

    630 hydrogen bonds defined for protein.
    1632 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      43 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      41 stacking parallelities
  Total time for adding SS restraints: 6.42

  Time building geometry restraints manager: 5.44 seconds

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

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

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 24598
        1.91 -     3.81: 242
        3.81 -     5.72: 22
        5.72 -     7.63: 4
        7.63 -     9.53: 1
  Bond angle restraints: 24867
  Sorted by residual:
  angle pdb=" N   LYS B 344 "
        pdb=" CA  LYS B 344 "
        pdb=" C   LYS B 344 "
      ideal   model   delta    sigma   weight residual
     110.24  116.81   -6.57 1.30e+00 5.92e-01 2.55e+01
  angle pdb=" C   LYS C 344 "
        pdb=" N   LEU C 345 "
        pdb=" CA  LEU C 345 "
      ideal   model   delta    sigma   weight residual
     121.54  128.71   -7.17 1.91e+00 2.74e-01 1.41e+01
  angle pdb=" C4'   U G   4 "
        pdb=" C3'   U G   4 "
        pdb=" O3'   U G   4 "
      ideal   model   delta    sigma   weight residual
     113.00  107.58    5.42 1.50e+00 4.44e-01 1.30e+01
  angle pdb=" C4'   A H  26 "
        pdb=" C3'   A H  26 "
        pdb=" O3'   A H  26 "
      ideal   model   delta    sigma   weight residual
     113.00  107.91    5.09 1.50e+00 4.44e-01 1.15e+01
  angle pdb=" CA  PRO A 262 "
        pdb=" N   PRO A 262 "
        pdb=" CD  PRO A 262 "
      ideal   model   delta    sigma   weight residual
     112.00  107.30    4.70 1.40e+00 5.10e-01 1.13e+01
  ... (remaining 24862 not shown)

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

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

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

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2934
        2.77 -     3.30: 16539
        3.30 -     3.84: 30684
        3.84 -     4.37: 37739
        4.37 -     4.90: 63421
  Nonbonded interactions: 151317
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 242 "
            pdb=" OG  SER A 287 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   HIS E 242 "
            pdb=" OG  SER E 287 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG1 THR B 195 "
            pdb=" OD2 ASP B 323 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OH  TYR A 193 "
            pdb=" OE2 GLU A 304 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   HIS D 242 "
            pdb=" OG  SER D 287 "
     model   vdw
     2.293 3.040
  ... (remaining 151312 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.460
  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:          0.690
  Check model and map are aligned:         0.120
  Set scattering table:                    0.180
  Process input model:                     56.120
  Find NCS groups from input model:        0.710
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   65.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.072  18139  Z= 0.116
  Angle     :  0.490   9.534  24867  Z= 0.283
  Chirality :  0.046   0.237   2903
  Planarity :  0.004   0.110   3006
  Dihedral  : 18.013  96.995   6945
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 22.10 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.54 (0.19), residues: 2094
  helix:  0.73 (0.23), residues: 534
  sheet:  0.54 (0.30), residues: 342
  loop :  0.26 (0.18), residues: 1218

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20642 (  637)
  hydrogen bonds       : angle       8.36966 ( 1718)
  covalent geometry    : bond        0.00220 (18139)
  covalent geometry    : angle       0.48957 (24867)

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

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 215
  time to evaluate  : 1.979 
Fit side-chains
REVERT: F   56 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8055 (mp0)
REVERT: B  223 GLU cc_start: 0.8180 (tp30) cc_final: 0.7712 (tt0)
REVERT: A  202 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7388 (tt0)
  outliers start: 5
  outliers final: 2
  residues processed: 219
  average time/residue: 0.2958
  time to fit residues: 99.5648
Evaluate side-chains
  207 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 204
  time to evaluate  : 1.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  136 ASN
Chi-restraints excluded: chain A residue  197 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 175 optimal weight:    0.9990
   chunk 157 optimal weight:    4.9990
   chunk 87 optimal weight:    0.2980
   chunk 53 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 163 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0770
   chunk 121 optimal weight:    0.6980
   chunk 188 optimal weight:    0.1980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
** B  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
B 187 GLN
A 199 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.165754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.124938 restraints weight = 108279.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 4.46
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  18139  Z= 0.110
  Angle     :  0.494  10.183  24867  Z= 0.264
  Chirality :  0.044   0.175   2903
  Planarity :  0.004   0.085   3006
  Dihedral  : 12.035  88.787   2985
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.40 %
    Favored  : 76.99 %
  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:  0.66 (0.19), residues: 2094
  helix:  0.76 (0.23), residues: 546
  sheet:  0.73 (0.30), residues: 342
  loop :  0.33 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 332 
 HIS   0.003   0.001   HIS B 337 
 PHE   0.010   0.001   PHE B   7 
 TYR   0.011   0.001   TYR A 225 
 ARG   0.006   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  637)
  hydrogen bonds       : angle       5.69241 ( 1718)
  covalent geometry    : bond        0.00245 (18139)
  covalent geometry    : angle       0.49358 (24867)

*********************** 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
  260 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 231
  time to evaluate  : 1.733 
Fit side-chains
   revert: symmetry clash
REVERT: F  264 GLU cc_start: 0.7496 (mp0) cc_final: 0.7206 (mt-10)
REVERT: D  152 GLN cc_start: 0.7616 (pm20) cc_final: 0.7353 (tp40)
REVERT: D  183 ASP cc_start: 0.8032 (m-30) cc_final: 0.7728 (m-30)
REVERT: B  104 MET cc_start: 0.8687 (mmm) cc_final: 0.8364 (tpt)
REVERT: A  163 ASN cc_start: 0.8080 (t0) cc_final: 0.7788 (t0)
REVERT: C  321 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8099 (m)
  outliers start: 29
  outliers final: 15
  residues processed: 241
  average time/residue: 0.2856
  time to fit residues: 104.6928
Evaluate side-chains
  227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 211
  time to evaluate  : 1.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 144 optimal weight:    0.0270
   chunk 154 optimal weight:    1.9990
   chunk 180 optimal weight:    1.9990
   chunk 135 optimal weight:    9.9990
   chunk 131 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 39 optimal weight:    0.3980
   chunk 81 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.8040

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

Flipped N/Q/H residues before XYZ refinement:
F 163 ASN
** B  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 GLN
C 187 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.163890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.122640 restraints weight = 114794.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 4.51
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  18139  Z= 0.154
  Angle     :  0.509   9.160  24867  Z= 0.267
  Chirality :  0.045   0.159   2903
  Planarity :  0.004   0.078   3006
  Dihedral  : 11.799  92.494   2982
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.51 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.56 (0.19), residues: 2094
  helix:  0.66 (0.23), residues: 546
  sheet:  0.73 (0.29), residues: 342
  loop :  0.24 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 332 
 HIS   0.003   0.001   HIS B 337 
 PHE   0.011   0.001   PHE F 134 
 TYR   0.014   0.001   TYR A 225 
 ARG   0.005   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03907 (  637)
  hydrogen bonds       : angle       5.48099 ( 1718)
  covalent geometry    : bond        0.00371 (18139)
  covalent geometry    : angle       0.50855 (24867)

*********************** 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
  243 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 1.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  104 MET cc_start: 0.8717 (mmm) cc_final: 0.8174 (tpt)
REVERT: D  138 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7995 (ttp-170)
REVERT: B  104 MET cc_start: 0.8700 (mmm) cc_final: 0.8373 (tpt)
REVERT: A  163 ASN cc_start: 0.8165 (t0) cc_final: 0.7863 (t0)
REVERT: A  345 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6516 (tp)
REVERT: C  321 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8244 (m)
  outliers start: 29
  outliers final: 17
  residues processed: 222
  average time/residue: 0.3299
  time to fit residues: 111.9525
Evaluate side-chains
  224 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 205
  time to evaluate  : 1.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  285 THR
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain D residue  344 LYS
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 198 optimal weight:    4.9990
   chunk 194 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   chunk 183 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 185 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 161 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
F 163 ASN
B  18 GLN
C 163 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.165028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.124011 restraints weight = 96694.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 4.39
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18139  Z= 0.124
  Angle     :  0.488   8.907  24867  Z= 0.255
  Chirality :  0.044   0.168   2903
  Planarity :  0.004   0.071   3006
  Dihedral  : 11.632  92.472   2982
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 21.56 %
    Favored  : 76.77 %
  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:  0.53 (0.19), residues: 2094
  helix:  0.68 (0.23), residues: 546
  sheet:  0.70 (0.29), residues: 342
  loop :  0.20 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 332 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.011   0.001   PHE A 268 
 TYR   0.011   0.001   TYR A 225 
 ARG   0.006   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  637)
  hydrogen bonds       : angle       5.21090 ( 1718)
  covalent geometry    : bond        0.00294 (18139)
  covalent geometry    : angle       0.48777 (24867)

*********************** 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
  237 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 210
  time to evaluate  : 1.768 
Fit side-chains
REVERT: F   56 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6955 (mp0)
REVERT: D  138 ARG cc_start: 0.8276 (mtp180) cc_final: 0.7978 (ttp-170)
REVERT: D  152 GLN cc_start: 0.7576 (pm20) cc_final: 0.7309 (tp40)
REVERT: D  296 ASP cc_start: 0.8192 (t0) cc_final: 0.7928 (t0)
REVERT: B   16 ASP cc_start: 0.7541 (t0) cc_final: 0.7280 (t0)
REVERT: B  104 MET cc_start: 0.8688 (mmm) cc_final: 0.8362 (tpt)
REVERT: A  248 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8601 (mp)
REVERT: A  345 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6496 (tp)
  outliers start: 27
  outliers final: 17
  residues processed: 222
  average time/residue: 0.2902
  time to fit residues: 98.8887
Evaluate side-chains
  221 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 201
  time to evaluate  : 1.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 161 optimal weight:    1.9990
   chunk 155 optimal weight:    2.9990
   chunk 113 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0030
   chunk 205 optimal weight:   10.0000
   chunk 128 optimal weight:    1.9990
   chunk 160 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 202 optimal weight:    0.0870
   chunk 133 optimal weight:    2.9990
   chunk 197 optimal weight:    0.9980
   overall best weight:    0.4768

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.167361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.126906 restraints weight = 123330.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 4.59
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  18139  Z= 0.109
  Angle     :  0.478   8.527  24867  Z= 0.249
  Chirality :  0.044   0.173   2903
  Planarity :  0.004   0.068   3006
  Dihedral  : 11.522  92.346   2982
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 21.18 %
    Favored  : 76.83 %
  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:  0.55 (0.19), residues: 2094
  helix:  0.75 (0.23), residues: 546
  sheet:  0.72 (0.29), residues: 342
  loop :  0.19 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  86 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.025   0.001   PHE D 221 
 TYR   0.010   0.001   TYR A 225 
 ARG   0.006   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03221 (  637)
  hydrogen bonds       : angle       5.01357 ( 1718)
  covalent geometry    : bond        0.00254 (18139)
  covalent geometry    : angle       0.47798 (24867)

*********************** 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
  240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 209
  time to evaluate  : 1.979 
Fit side-chains
   revert: symmetry clash
REVERT: D  109 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8311 (mmtt)
REVERT: D  152 GLN cc_start: 0.7594 (pm20) cc_final: 0.7323 (tp40)
REVERT: E  254 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7602 (mp)
REVERT: B   16 ASP cc_start: 0.7538 (t0) cc_final: 0.7270 (t0)
REVERT: B  224 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7727 (ttm-80)
REVERT: A  163 ASN cc_start: 0.8053 (t0) cc_final: 0.7778 (t0)
REVERT: A  248 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8494 (mp)
REVERT: A  296 ASP cc_start: 0.8289 (t0) cc_final: 0.8052 (t0)
REVERT: A  345 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6304 (tp)
  outliers start: 31
  outliers final: 22
  residues processed: 225
  average time/residue: 0.2890
  time to fit residues: 101.0322
Evaluate side-chains
  230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 1.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  320 VAL
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 169 optimal weight:    0.7980
   chunk 176 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0040
   chunk 190 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 171 optimal weight:    0.3980
   chunk 124 optimal weight:    3.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
F 163 ASN
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN
C 163 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.165800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.124881 restraints weight = 105627.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 4.44
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  18139  Z= 0.118
  Angle     :  0.483   6.613  24867  Z= 0.250
  Chirality :  0.044   0.174   2903
  Planarity :  0.004   0.065   3006
  Dihedral  : 11.435  91.790   2982
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.13 %
    Favored  : 76.51 %
  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:  0.52 (0.19), residues: 2094
  helix:  0.73 (0.23), residues: 546
  sheet:  0.69 (0.29), residues: 342
  loop :  0.17 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 332 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.032   0.001   PHE D 221 
 TYR   0.011   0.001   TYR A 225 
 ARG   0.005   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (  637)
  hydrogen bonds       : angle       4.99181 ( 1718)
  covalent geometry    : bond        0.00280 (18139)
  covalent geometry    : angle       0.48255 (24867)

*********************** 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
  243 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 1.760 
Fit side-chains
   revert: symmetry clash
REVERT: F  264 GLU cc_start: 0.7392 (mp0) cc_final: 0.7089 (mt-10)
REVERT: D  138 ARG cc_start: 0.8295 (mtp180) cc_final: 0.8082 (ttp-170)
REVERT: D  152 GLN cc_start: 0.7602 (pm20) cc_final: 0.7323 (tp40)
REVERT: D  296 ASP cc_start: 0.8227 (t0) cc_final: 0.7964 (t0)
REVERT: E  254 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7581 (mp)
REVERT: B   16 ASP cc_start: 0.7543 (t0) cc_final: 0.7281 (t0)
REVERT: A  163 ASN cc_start: 0.8091 (t0) cc_final: 0.7824 (t0)
REVERT: A  248 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8464 (mp)
REVERT: A  345 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6535 (tp)
  outliers start: 38
  outliers final: 27
  residues processed: 225
  average time/residue: 0.2859
  time to fit residues: 99.5039
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 198
  time to evaluate  : 1.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  320 VAL
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   36 ASP
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  218 MET
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 132 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0870
   chunk 158 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 142 optimal weight:    0.0050
   chunk 49 optimal weight:    0.9980
   chunk 139 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 108 optimal weight:    0.0270
   overall best weight:    0.3830

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

Flipped N/Q/H residues before XYZ refinement:
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN
C 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.167301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.126514 restraints weight = 114152.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 4.55
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  18139  Z= 0.098
  Angle     :  0.468   6.441  24867  Z= 0.243
  Chirality :  0.043   0.175   2903
  Planarity :  0.003   0.063   3006
  Dihedral  : 11.313  90.598   2982
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.29 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.58 (0.19), residues: 2094
  helix:  0.72 (0.23), residues: 552
  sheet:  0.75 (0.29), residues: 342
  loop :  0.23 (0.19), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  86 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.028   0.001   PHE D 221 
 TYR   0.009   0.001   TYR A 225 
 ARG   0.005   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03085 (  637)
  hydrogen bonds       : angle       4.84368 ( 1718)
  covalent geometry    : bond        0.00226 (18139)
  covalent geometry    : angle       0.46844 (24867)

*********************** 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
  241 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 209
  time to evaluate  : 1.963 
Fit side-chains
   revert: symmetry clash
REVERT: F  264 GLU cc_start: 0.7418 (mp0) cc_final: 0.7135 (mt-10)
REVERT: D  109 LYS cc_start: 0.8442 (mmtm) cc_final: 0.8217 (mmtt)
REVERT: D  152 GLN cc_start: 0.7553 (pm20) cc_final: 0.7305 (tp40)
REVERT: B   16 ASP cc_start: 0.7512 (t0) cc_final: 0.7250 (t0)
REVERT: B  224 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7672 (ttm-80)
REVERT: A  163 ASN cc_start: 0.8076 (t0) cc_final: 0.7822 (t0)
REVERT: A  170 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7596 (mt-10)
REVERT: A  233 GLU cc_start: 0.8109 (mp0) cc_final: 0.7834 (mp0)
REVERT: A  248 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8440 (mp)
  outliers start: 32
  outliers final: 23
  residues processed: 224
  average time/residue: 0.2858
  time to fit residues: 99.2759
Evaluate side-chains
  230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 1.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   36 ASP
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  250 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 191 optimal weight:    5.9990
   chunk 177 optimal weight:    0.0010
   chunk 166 optimal weight:    0.9980
   chunk 194 optimal weight:    2.9990
   chunk 201 optimal weight:    2.9990
   chunk 186 optimal weight:    0.8980
   chunk 176 optimal weight:    0.5980
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
F 163 ASN
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.166905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.126015 restraints weight = 119665.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 4.53
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18139  Z= 0.133
  Angle     :  0.489   6.461  24867  Z= 0.254
  Chirality :  0.044   0.175   2903
  Planarity :  0.004   0.064   3006
  Dihedral  : 11.218  89.546   2979
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.24 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.62 (0.23), residues: 552
  sheet:  0.75 (0.29), residues: 342
  loop :  0.17 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 332 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.027   0.001   PHE D 221 
 TYR   0.012   0.001   TYR A 225 
 ARG   0.005   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03366 (  637)
  hydrogen bonds       : angle       5.01123 ( 1718)
  covalent geometry    : bond        0.00321 (18139)
  covalent geometry    : angle       0.48949 (24867)

*********************** 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
  237 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 203
  time to evaluate  : 1.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  109 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8331 (mmtt)
REVERT: D  296 ASP cc_start: 0.8205 (t0) cc_final: 0.7953 (t0)
REVERT: B   16 ASP cc_start: 0.7515 (t0) cc_final: 0.7237 (t0)
REVERT: B  224 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7709 (ttm-80)
REVERT: A  163 ASN cc_start: 0.8081 (t0) cc_final: 0.7821 (t0)
REVERT: A  170 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7633 (mt-10)
REVERT: A  248 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8485 (mp)
REVERT: A  345 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6347 (tp)
  outliers start: 34
  outliers final: 25
  residues processed: 222
  average time/residue: 0.2769
  time to fit residues: 95.6201
Evaluate side-chains
  229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 201
  time to evaluate  : 1.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  155 VAL
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  320 VAL
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   36 ASP
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  250 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 192 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 67 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 196 optimal weight:    0.2980
   chunk 121 optimal weight:    0.0020
   chunk 97 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 170 optimal weight:    0.6980
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
F 163 ASN
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.165061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.123880 restraints weight = 109286.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 4.50
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  18139  Z= 0.144
  Angle     :  0.500   6.516  24867  Z= 0.260
  Chirality :  0.045   0.176   2903
  Planarity :  0.004   0.063   3006
  Dihedral  : 11.228  88.588   2979
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 21.40 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.42 (0.19), residues: 2094
  helix:  0.53 (0.23), residues: 552
  sheet:  0.70 (0.30), residues: 342
  loop :  0.14 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 332 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.030   0.001   PHE D 221 
 TYR   0.012   0.001   TYR A 225 
 ARG   0.005   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  637)
  hydrogen bonds       : angle       5.06291 ( 1718)
  covalent geometry    : bond        0.00351 (18139)
  covalent geometry    : angle       0.49974 (24867)

*********************** 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
  232 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 201
  time to evaluate  : 2.026 
Fit side-chains
   revert: symmetry clash
REVERT: F   56 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6967 (mp0)
REVERT: D  109 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8326 (mmtt)
REVERT: D  296 ASP cc_start: 0.8223 (t0) cc_final: 0.7953 (t0)
REVERT: D  344 LYS cc_start: 0.6835 (ptmm) cc_final: 0.6230 (ptmm)
REVERT: B   16 ASP cc_start: 0.7598 (t0) cc_final: 0.7316 (t0)
REVERT: B  224 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7707 (ttm-80)
REVERT: A  163 ASN cc_start: 0.8140 (t0) cc_final: 0.7883 (t0)
REVERT: A  170 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7650 (mt-10)
REVERT: A  248 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8485 (mp)
REVERT: A  345 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6269 (tp)
  outliers start: 31
  outliers final: 23
  residues processed: 217
  average time/residue: 0.2873
  time to fit residues: 96.5459
Evaluate side-chains
  226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 1.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  320 VAL
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   36 ASP
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  254 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  250 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 178 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 140 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 186 optimal weight:    0.0040
   chunk 134 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 107 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN
C 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.166364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.125048 restraints weight = 111038.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 4.55
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3254
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3254
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  18139  Z= 0.115
  Angle     :  0.485   6.530  24867  Z= 0.253
  Chirality :  0.044   0.201   2903
  Planarity :  0.004   0.063   3006
  Dihedral  : 11.209  87.430   2979
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.34 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.46 (0.19), residues: 2094
  helix:  0.59 (0.23), residues: 552
  sheet:  0.72 (0.30), residues: 342
  loop :  0.16 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  86 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.030   0.001   PHE D 221 
 TYR   0.010   0.001   TYR A 225 
 ARG   0.005   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  637)
  hydrogen bonds       : angle       4.96881 ( 1718)
  covalent geometry    : bond        0.00275 (18139)
  covalent geometry    : angle       0.48490 (24867)

********************** 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
  236 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 206
  time to evaluate  : 1.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  296 ASP cc_start: 0.8196 (t0) cc_final: 0.7935 (t0)
REVERT: D  344 LYS cc_start: 0.6897 (ptmm) cc_final: 0.6262 (ptmm)
REVERT: B   16 ASP cc_start: 0.7564 (t0) cc_final: 0.7291 (t0)
REVERT: B  224 ARG cc_start: 0.7975 (ttm170) cc_final: 0.7682 (ttm-80)
REVERT: A  163 ASN cc_start: 0.8196 (t0) cc_final: 0.7946 (t0)
REVERT: A  170 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7635 (mt-10)
REVERT: A  248 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8450 (mp)
REVERT: A  345 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6234 (tp)
  outliers start: 30
  outliers final: 24
  residues processed: 222
  average time/residue: 0.2819
  time to fit residues: 97.3232
Evaluate side-chains
  227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 200
  time to evaluate  : 1.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   47 THR
Chi-restraints excluded: chain F residue   56 GLU
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  228 GLU
Chi-restraints excluded: chain F residue  232 PHE
Chi-restraints excluded: chain F residue  320 VAL
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   36 ASP
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  250 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0270
   chunk 31 optimal weight:    5.9990
   chunk 133 optimal weight:    4.9990
   chunk 194 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 163 optimal weight:    0.9980
   chunk 166 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 205 optimal weight:   10.0000
   chunk 199 optimal weight:    1.9990
   overall best weight:    0.7438

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

Flipped N/Q/H residues before XYZ refinement:
F 163 ASN
** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN
C 163 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.165889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.122914 restraints weight = 109587.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 5.05
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  18139  Z= 0.142
  Angle     :  0.503   8.433  24867  Z= 0.261
  Chirality :  0.045   0.206   2903
  Planarity :  0.004   0.064   3006
  Dihedral  : 11.242  86.272   2979
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 21.45 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.40 (0.19), residues: 2094
  helix:  0.53 (0.23), residues: 552
  sheet:  0.72 (0.30), residues: 342
  loop :  0.11 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 332 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.029   0.001   PHE D 221 
 TYR   0.012   0.001   TYR A 225 
 ARG   0.005   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03458 (  637)
  hydrogen bonds       : angle       5.04705 ( 1718)
  covalent geometry    : bond        0.00344 (18139)
  covalent geometry    : angle       0.50308 (24867)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9030.25 seconds
wall clock time: 160 minutes 38.67 seconds (9638.67 seconds total)