Starting phenix.real_space_refine
on Sun May 18 04:02:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ud2_42144/05_2025/8ud2_42144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ud2_42144/05_2025/8ud2_42144.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ud2_42144/05_2025/8ud2_42144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ud2_42144/05_2025/8ud2_42144.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ud2_42144/05_2025/8ud2_42144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ud2_42144/05_2025/8ud2_42144.cif"
  }
  resolution = 2.33
  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=   0.062
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C   10620      2.51       5
     N    2688      2.21       5
     O    3162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16530
  Number of models: 1
  Model: ""
    Number of chains: 1
    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
  Restraints were copied for chains:
    C, B, E, D, F
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N  AILE A  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE A  27 " occ=0.48
    residue:
      pdb=" N  AASN A  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN A  28 " occ=0.48
    residue:
      pdb=" N  AASN A  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN A  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
    residue:
      pdb=" N  AILE C  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE C  27 " occ=0.48
    residue:
      pdb=" N  AASN C  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN C  28 " occ=0.48
    residue:
      pdb=" N  AASN C  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN C  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
    ... (remaining 6 not shown)
  Time building chain proxies: 7.82, per 1000 atoms: 0.47
  Number of scatterers: 16530
  At special positions: 0
  Unit cell: (115, 107.64, 122.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    3162      8.00
     N    2688      7.00
     C   10620      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: 3.70
  Conformation dependent library (CDL) restraints added in 3.7 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:
      60 helices and 48 sheets defined
      26.6% alpha, 25.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 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 136
    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
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.594A  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 '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 136
    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
    Processing helix  chain 'B' and resid 250 through 261
      removed outlier: 3.594A  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 '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
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.594A  pdb=" N   GLU C 260 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' 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 113 through 117
    Processing helix  chain 'D' and resid 129 through 136
    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: 3.593A  pdb=" N   GLU D 260 " --> pdb=" O   LYS D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 308
    Processing helix  chain 'E' and resid 2 through 13
    Processing helix  chain 'E' and resid 50 through 60
    Processing helix  chain 'E' and resid 68 through 75
    Processing helix  chain 'E' and resid 113 through 117
    Processing helix  chain 'E' and resid 129 through 136
    Processing helix  chain 'E' and resid 207 through 216
    Processing helix  chain 'E' and resid 217 through 225
    Processing helix  chain 'E' and resid 231 through 236
    Processing helix  chain 'E' and resid 250 through 261
      removed outlier: 3.593A  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 'F' and resid 2 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 136
    Processing helix  chain 'F' and resid 207 through 216
    Processing helix  chain 'F' and resid 217 through 225
    Processing helix  chain 'F' and resid 231 through 236
    Processing helix  chain 'F' and resid 250 through 261
      removed outlier: 3.594A  pdb=" N   GLU F 260 " --> pdb=" O   LYS F 256 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 298 through 308
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL A  31 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 99
      removed outlier: 7.949A  pdb=" N   THR A  98 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 266
      removed outlier: 4.908A  pdb=" N   ILE A 280 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   CYS A 290 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 322
      removed outlier: 7.446A  pdb=" N   SER A 328 " --> pdb=" O   PRO A 343 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   MET A 330 " --> pdb=" O   PHE A 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE A 341 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TRP A 332 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL B  31 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 99
      removed outlier: 7.949A  pdb=" N   THR B  98 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 162
    Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 266
      removed outlier: 4.909A  pdb=" N   ILE B 280 " --> pdb=" O   CYS B 290 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   CYS B 290 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 315 through 322
      removed outlier: 7.447A  pdb=" N   SER B 328 " --> pdb=" O   PRO B 343 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET B 330 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE B 341 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TRP B 332 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL C  31 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   LYS C 180 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AC3, first strand: chain 'C' and resid 98 through 99
      removed outlier: 7.950A  pdb=" N   THR C  98 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 162
    Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 266
      removed outlier: 4.909A  pdb=" N   ILE C 280 " --> pdb=" O   CYS C 290 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   CYS C 290 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 315 through 322
      removed outlier: 7.447A  pdb=" N   SER C 328 " --> pdb=" O   PRO C 343 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET C 330 " --> pdb=" O   PHE C 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE C 341 " --> pdb=" O   MET C 330 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TRP C 332 " --> pdb=" O   GLU C 339 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL D  31 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.726A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.726A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 86 through 87
    Processing sheet with id=AD2, first strand: chain 'D' and resid 98 through 99
      removed outlier: 7.949A  pdb=" N   THR D  98 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2
    Processing sheet with id=AD3, first strand: chain 'D' and resid 160 through 162
    Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 266
      removed outlier: 4.908A  pdb=" N   ILE D 280 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   CYS D 290 " --> pdb=" O   ILE D 280 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'D' and resid 315 through 322
      removed outlier: 7.446A  pdb=" N   SER D 328 " --> pdb=" O   PRO D 343 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET D 330 " --> pdb=" O   PHE D 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE D 341 " --> pdb=" O   MET D 330 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TRP D 332 " --> pdb=" O   GLU D 339 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL E  31 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 8.726A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 8.726A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'E' and resid 86 through 87
    Processing sheet with id=AE1, first strand: chain 'E' and resid 98 through 99
      removed outlier: 7.950A  pdb=" N   THR E  98 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE1
    Processing sheet with id=AE2, first strand: chain 'E' and resid 160 through 162
    Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 266
      removed outlier: 4.909A  pdb=" N   ILE E 280 " --> pdb=" O   CYS E 290 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   CYS E 290 " --> pdb=" O   ILE E 280 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'E' and resid 315 through 322
      removed outlier: 7.446A  pdb=" N   SER E 328 " --> pdb=" O   PRO E 343 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   MET E 330 " --> pdb=" O   PHE E 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE E 341 " --> pdb=" O   MET E 330 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TRP E 332 " --> pdb=" O   GLU E 339 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'F' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL F  31 " --> pdb=" O   LEU F  42 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'F' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE F  79 " --> pdb=" O   PHE F 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP F 124 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'F' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE F  79 " --> pdb=" O   PHE F 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP F 124 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   LYS F 180 " --> pdb=" O   GLN F 187 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'F' and resid 86 through 87
    Processing sheet with id=AE9, first strand: chain 'F' and resid 98 through 99
      removed outlier: 7.950A  pdb=" N   THR F  98 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE9
    Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 162
    Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 266
      removed outlier: 4.909A  pdb=" N   ILE F 280 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   CYS F 290 " --> pdb=" O   ILE F 280 " (cutoff:3.500A)
    Processing sheet with id=AF3, first strand: chain 'F' and resid 315 through 322
      removed outlier: 7.446A  pdb=" N   SER F 328 " --> pdb=" O   PRO F 343 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET F 330 " --> pdb=" O   PHE F 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE F 341 " --> pdb=" O   MET F 330 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TRP F 332 " --> pdb=" O   GLU F 339 " (cutoff:3.500A)

    663 hydrogen bonds defined for protein.
    1683 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.80

  Time building geometry restraints manager: 4.37 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: 5346
        1.34 -     1.46: 2447
        1.46 -     1.57: 8989
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 16872
  Sorted by residual:
  bond pdb=" N   LEU F 345 "
       pdb=" CA  LEU F 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.21e+00
  bond pdb=" N   LEU C 345 "
       pdb=" CA  LEU C 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.20e+00
  bond pdb=" N   LEU B 345 "
       pdb=" CA  LEU B 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.16e+00
  bond pdb=" N   LEU D 345 "
       pdb=" CA  LEU D 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.15e+00
  bond pdb=" N   LEU A 345 "
       pdb=" CA  LEU A 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.13e+00
  ... (remaining 16867 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 21753
        1.06 -     2.12: 941
        2.12 -     3.18: 159
        3.18 -     4.25: 31
        4.25 -     5.31: 18
  Bond angle restraints: 22902
  Sorted by residual:
  angle pdb=" C   GLN E 188 "
        pdb=" N   LEU E 189 "
        pdb=" CA  LEU E 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.80    3.87 1.34e+00 5.57e-01 8.33e+00
  angle pdb=" C   GLN D 188 "
        pdb=" N   LEU D 189 "
        pdb=" CA  LEU D 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.81    3.86 1.34e+00 5.57e-01 8.30e+00
  angle pdb=" C   GLN B 188 "
        pdb=" N   LEU B 189 "
        pdb=" CA  LEU B 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.81    3.86 1.34e+00 5.57e-01 8.28e+00
  angle pdb=" C   GLN C 188 "
        pdb=" N   LEU C 189 "
        pdb=" CA  LEU C 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.85    3.82 1.34e+00 5.57e-01 8.13e+00
  angle pdb=" C   GLN A 188 "
        pdb=" N   LEU A 189 "
        pdb=" CA  LEU A 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.87    3.80 1.34e+00 5.57e-01 8.05e+00
  ... (remaining 22897 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 8918
       17.82 -    35.64: 868
       35.64 -    53.46: 198
       53.46 -    71.28: 84
       71.28 -    89.11: 36
  Dihedral angle restraints: 10104
    sinusoidal: 4020
      harmonic: 6084
  Sorted by residual:
  dihedral pdb=" CA  THR B 192 "
           pdb=" C   THR B 192 "
           pdb=" N   TYR B 193 "
           pdb=" CA  TYR B 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  THR D 192 "
           pdb=" C   THR D 192 "
           pdb=" N   TYR D 193 "
           pdb=" CA  TYR D 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  THR C 192 "
           pdb=" C   THR C 192 "
           pdb=" N   TYR C 193 "
           pdb=" CA  TYR C 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.56   18.44     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 10101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1359
       0.027 -    0.053: 729
       0.053 -    0.079: 268
       0.079 -    0.106: 195
       0.106 -    0.132: 83
  Chirality restraints: 2634
  Sorted by residual:
  chirality pdb=" CA  ILE B 168 "
            pdb=" N   ILE B 168 "
            pdb=" C   ILE B 168 "
            pdb=" CB  ILE B 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE E 168 "
            pdb=" N   ILE E 168 "
            pdb=" C   ILE E 168 "
            pdb=" CB  ILE E 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  VAL B 313 "
            pdb=" N   VAL B 313 "
            pdb=" C   VAL B 313 "
            pdb=" CB  VAL B 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 2631 not shown)

  Planarity restraints: 2952
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 110 "   -0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO E 111 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO E 111 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E 111 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 110 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO C 111 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C 111 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 111 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 110 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.89e+00
        pdb=" N   PRO F 111 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO F 111 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO F 111 "    0.019 5.00e-02 4.00e+02
  ... (remaining 2949 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 4744
        2.81 -     3.34: 14847
        3.34 -     3.86: 30023
        3.86 -     4.38: 35609
        4.38 -     4.90: 58582
  Nonbonded interactions: 143805
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 117 "
            pdb=" ND2 ASN C 139 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ALA F 117 "
            pdb=" ND2 ASN F 139 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ALA A 117 "
            pdb=" ND2 ASN A 139 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ALA E 117 "
            pdb=" ND2 ASN E 139 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ALA D 117 "
            pdb=" ND2 ASN D 139 "
     model   vdw
     2.293 3.120
  ... (remaining 143800 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: 0.13
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             3.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     38.230
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  16872  Z= 0.138
  Angle     :  0.532   5.308  22902  Z= 0.324
  Chirality :  0.045   0.132   2634
  Planarity :  0.003   0.034   2952
  Dihedral  : 16.449  89.106   6180
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.74 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.19), residues: 2094
  helix:  0.69 (0.23), residues: 528
  sheet:  0.50 (0.29), residues: 312
  loop :  0.21 (0.18), residues: 1254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F  58 
 HIS   0.004   0.001   HIS C  95 
 PHE   0.009   0.001   PHE C 221 
 TYR   0.006   0.001   TYR C 324 
 ARG   0.001   0.000   ARG B 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15356 (  609)
  hydrogen bonds       : angle       7.84473 ( 1683)
  covalent geometry    : bond        0.00264 (16872)
  covalent geometry    : angle       0.53202 (22902)

*********************** 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
  270 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 250
  time to evaluate  : 1.816 
Fit side-chains
REVERT: B  149 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7706 (mppt)
REVERT: B  239 ASP cc_start: 0.7288 (t0) cc_final: 0.7026 (t0)
REVERT: B  284 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6658 (tm130)
REVERT: C   19 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7991 (mp10)
REVERT: C  149 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7546 (ptmm)
REVERT: C  330 MET cc_start: 0.7205 (mmt) cc_final: 0.7000 (mmt)
REVERT: D   19 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7994 (mp10)
REVERT: D  149 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7517 (ptmm)
REVERT: D  330 MET cc_start: 0.7184 (mmt) cc_final: 0.6981 (mmt)
REVERT: E  149 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7713 (mppt)
  outliers start: 20
  outliers final: 9
  residues processed: 268
  average time/residue: 1.0639
  time to fit residues: 323.2425
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 219
  time to evaluate  : 1.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain C residue  300 ASP
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain E residue  340 THR
Chi-restraints excluded: chain F residue  300 ASP
Chi-restraints excluded: chain F residue  340 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:    1.9990
   chunk 154 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 104 optimal weight:    0.0370
   chunk 82 optimal weight:    1.9990
   chunk 159 optimal weight:    2.9990
   chunk 61 optimal weight:    0.2980
   chunk 97 optimal weight:    5.9990
   chunk 119 optimal weight:    4.9990
   chunk 185 optimal weight:    0.3980
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
B  19 GLN
C 152 GLN
D 152 GLN
E  19 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.173057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.130094 restraints weight = 86674.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 4.87
r_work: 0.2998 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  16872  Z= 0.109
  Angle     :  0.501   9.373  22902  Z= 0.266
  Chirality :  0.046   0.131   2634
  Planarity :  0.003   0.024   2952
  Dihedral  :  5.023  52.267   2226
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.66 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.19), residues: 2094
  helix:  0.74 (0.23), residues: 540
  sheet:  0.55 (0.26), residues: 354
  loop :  0.20 (0.19), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  58 
 HIS   0.003   0.001   HIS C  95 
 PHE   0.021   0.001   PHE D 221 
 TYR   0.008   0.001   TYR A 225 
 ARG   0.006   0.001   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03812 (  609)
  hydrogen bonds       : angle       5.85105 ( 1683)
  covalent geometry    : bond        0.00231 (16872)
  covalent geometry    : angle       0.50093 (22902)

*********************** 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
  272 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 244
  time to evaluate  : 2.072 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.6796 (tttt) cc_final: 0.6491 (mttp)
REVERT: B  149 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8013 (mppt)
REVERT: B  202 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6602 (pt0)
REVERT: C  149 LYS cc_start: 0.8382 (mmmm) cc_final: 0.7938 (ptmm)
REVERT: C  202 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6536 (tt0)
REVERT: C  215 GLU cc_start: 0.6868 (pt0) cc_final: 0.5843 (mp0)
REVERT: C  259 LYS cc_start: 0.6953 (tttt) cc_final: 0.6619 (mttp)
REVERT: C  330 MET cc_start: 0.7984 (mmt) cc_final: 0.7277 (mmm)
REVERT: D  149 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7935 (ptmm)
REVERT: D  202 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6569 (tt0)
REVERT: D  215 GLU cc_start: 0.6872 (pt0) cc_final: 0.5844 (mp0)
REVERT: D  259 LYS cc_start: 0.6905 (tttt) cc_final: 0.6582 (mttp)
REVERT: D  330 MET cc_start: 0.7957 (mmt) cc_final: 0.7283 (mmm)
REVERT: E  149 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8014 (mppt)
REVERT: E  259 LYS cc_start: 0.6843 (tttt) cc_final: 0.6549 (mttp)
REVERT: F  259 LYS cc_start: 0.6837 (tttt) cc_final: 0.6522 (tppt)
  outliers start: 28
  outliers final: 10
  residues processed: 259
  average time/residue: 1.1654
  time to fit residues: 338.6830
Evaluate side-chains
  236 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 223
  time to evaluate  : 1.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain E residue  340 THR
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  261 SER
Chi-restraints excluded: chain F residue  340 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 189 optimal weight:    0.8980
   chunk 180 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 119 optimal weight:    4.9990
   chunk 187 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9990
   chunk 117 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  19 GLN
C 152 GLN
D 152 GLN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.170341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.129194 restraints weight = 95394.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 5.75
r_work: 0.2901 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16872  Z= 0.155
  Angle     :  0.538  10.410  22902  Z= 0.285
  Chirality :  0.047   0.136   2634
  Planarity :  0.003   0.031   2952
  Dihedral  :  4.961  34.773   2220
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 18.76 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.18), residues: 2094
  helix:  0.50 (0.23), residues: 552
  sheet:  0.39 (0.26), residues: 342
  loop :  0.23 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  58 
 HIS   0.004   0.001   HIS A  95 
 PHE   0.022   0.002   PHE D 221 
 TYR   0.009   0.001   TYR F 225 
 ARG   0.006   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04022 (  609)
  hydrogen bonds       : angle       5.67473 ( 1683)
  covalent geometry    : bond        0.00345 (16872)
  covalent geometry    : angle       0.53760 (22902)

*********************** 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
  276 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 249
  time to evaluate  : 2.268 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.6926 (tttt) cc_final: 0.6599 (mttp)
REVERT: B  149 LYS cc_start: 0.8407 (mmmm) cc_final: 0.8008 (mppt)
REVERT: B  340 THR cc_start: 0.7406 (OUTLIER) cc_final: 0.7036 (p)
REVERT: C  202 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6655 (tt0)
REVERT: C  259 LYS cc_start: 0.7086 (tttt) cc_final: 0.6697 (mttp)
REVERT: C  277 ASN cc_start: 0.9144 (m-40) cc_final: 0.8917 (m110)
REVERT: C  330 MET cc_start: 0.8128 (mmt) cc_final: 0.7568 (mmm)
REVERT: D  202 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6661 (tt0)
REVERT: D  259 LYS cc_start: 0.7117 (tttt) cc_final: 0.6713 (mttp)
REVERT: D  277 ASN cc_start: 0.9137 (m-40) cc_final: 0.8901 (m110)
REVERT: D  330 MET cc_start: 0.8132 (mmt) cc_final: 0.7586 (mmm)
REVERT: E  149 LYS cc_start: 0.8436 (mmmm) cc_final: 0.8026 (mppt)
REVERT: E  259 LYS cc_start: 0.6905 (tttt) cc_final: 0.6582 (mttp)
REVERT: E  340 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7069 (p)
REVERT: F  259 LYS cc_start: 0.6933 (tttt) cc_final: 0.6611 (mttp)
  outliers start: 27
  outliers final: 11
  residues processed: 263
  average time/residue: 1.2434
  time to fit residues: 365.6293
Evaluate side-chains
  257 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 242
  time to evaluate  : 1.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain E residue  340 THR
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 197 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 116 optimal weight:    0.0980
   chunk 133 optimal weight:    6.9990
   chunk 159 optimal weight:    4.9990
   chunk 112 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
B 277 ASN
C 152 GLN
D 152 GLN
E  19 GLN
E 277 ASN
F  19 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.172284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.129473 restraints weight = 85063.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 5.10
r_work: 0.3001 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  16872  Z= 0.112
  Angle     :  0.496  11.306  22902  Z= 0.261
  Chirality :  0.045   0.134   2634
  Planarity :  0.003   0.039   2952
  Dihedral  :  4.524  16.381   2218
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.92 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.18), residues: 2094
  helix:  0.70 (0.23), residues: 552
  sheet:  0.55 (0.27), residues: 342
  loop :  0.26 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  58 
 HIS   0.003   0.001   HIS F  95 
 PHE   0.025   0.002   PHE D 221 
 TYR   0.008   0.001   TYR E 225 
 ARG   0.006   0.000   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03340 (  609)
  hydrogen bonds       : angle       5.31666 ( 1683)
  covalent geometry    : bond        0.00244 (16872)
  covalent geometry    : angle       0.49599 (22902)

*********************** 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
  262 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 236
  time to evaluate  : 1.858 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.6835 (tttt) cc_final: 0.6519 (mttp)
REVERT: B  149 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8016 (mppt)
REVERT: C  149 LYS cc_start: 0.8385 (mmmm) cc_final: 0.7903 (tptt)
REVERT: C  202 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6584 (tt0)
REVERT: C  220 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6363 (pt0)
REVERT: C  233 GLU cc_start: 0.6632 (mp0) cc_final: 0.6383 (pm20)
REVERT: C  259 LYS cc_start: 0.7080 (tttt) cc_final: 0.6597 (mttp)
REVERT: C  330 MET cc_start: 0.8011 (mmt) cc_final: 0.7456 (mmm)
REVERT: D  149 LYS cc_start: 0.8387 (mmmm) cc_final: 0.7897 (tptt)
REVERT: D  202 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6599 (tt0)
REVERT: D  220 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6346 (pt0)
REVERT: D  233 GLU cc_start: 0.6643 (mp0) cc_final: 0.6395 (pm20)
REVERT: D  259 LYS cc_start: 0.7084 (tttt) cc_final: 0.6618 (mttp)
REVERT: D  304 GLU cc_start: 0.7388 (tt0) cc_final: 0.7031 (tt0)
REVERT: D  330 MET cc_start: 0.7998 (mmt) cc_final: 0.7459 (mmm)
REVERT: E  149 LYS cc_start: 0.8393 (mmmm) cc_final: 0.8019 (mppt)
REVERT: F  259 LYS cc_start: 0.6928 (tttt) cc_final: 0.6595 (mttp)
  outliers start: 26
  outliers final: 7
  residues processed: 250
  average time/residue: 1.1696
  time to fit residues: 328.2252
Evaluate side-chains
  236 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 227
  time to evaluate  : 1.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0270
   chunk 36 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 186 optimal weight:    1.9990
   chunk 142 optimal weight:    0.5980
   overall best weight:    0.6440

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C 152 GLN
D 152 GLN
D 199 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.171505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.128543 restraints weight = 87954.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 4.93
r_work: 0.2965 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  16872  Z= 0.126
  Angle     :  0.511  11.808  22902  Z= 0.268
  Chirality :  0.046   0.135   2634
  Planarity :  0.003   0.042   2952
  Dihedral  :  4.547  16.039   2214
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 19.19 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.18), residues: 2094
  helix:  0.69 (0.23), residues: 552
  sheet:  0.56 (0.26), residues: 342
  loop :  0.24 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  58 
 HIS   0.003   0.001   HIS F  95 
 PHE   0.025   0.002   PHE C 221 
 TYR   0.008   0.001   TYR F 225 
 ARG   0.006   0.000   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  609)
  hydrogen bonds       : angle       5.30649 ( 1683)
  covalent geometry    : bond        0.00279 (16872)
  covalent geometry    : angle       0.51102 (22902)

*********************** 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
  259 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 241
  time to evaluate  : 1.819 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.7709 (tpt170) cc_final: 0.7246 (tpt170)
REVERT: A  259 LYS cc_start: 0.6939 (tttt) cc_final: 0.6613 (mttp)
REVERT: B  149 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8011 (mppt)
REVERT: B  202 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6529 (tt0)
REVERT: C  149 LYS cc_start: 0.8363 (mmmm) cc_final: 0.8024 (mppt)
REVERT: C  202 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6628 (tt0)
REVERT: C  233 GLU cc_start: 0.6646 (mp0) cc_final: 0.6405 (pm20)
REVERT: C  259 LYS cc_start: 0.7105 (tttt) cc_final: 0.6625 (mttp)
REVERT: C  330 MET cc_start: 0.7956 (mmt) cc_final: 0.7422 (mmm)
REVERT: D  149 LYS cc_start: 0.8363 (mmmm) cc_final: 0.8008 (mppt)
REVERT: D  202 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6639 (tt0)
REVERT: D  233 GLU cc_start: 0.6657 (mp0) cc_final: 0.6415 (pm20)
REVERT: D  259 LYS cc_start: 0.7122 (tttt) cc_final: 0.6649 (mttp)
REVERT: D  330 MET cc_start: 0.7967 (mmt) cc_final: 0.7444 (mmm)
REVERT: E  149 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8011 (mppt)
REVERT: E  259 LYS cc_start: 0.7110 (tttt) cc_final: 0.6744 (ttpp)
REVERT: F  257 ARG cc_start: 0.7743 (tpt170) cc_final: 0.7241 (tpt170)
REVERT: F  259 LYS cc_start: 0.6949 (tttt) cc_final: 0.6593 (mttp)
  outliers start: 18
  outliers final: 13
  residues processed: 251
  average time/residue: 1.2258
  time to fit residues: 343.4164
Evaluate side-chains
  244 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 228
  time to evaluate  : 1.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  232 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 148 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 7 optimal weight:    0.3980
   chunk 103 optimal weight:    0.8980
   chunk 164 optimal weight:    0.6980
   chunk 137 optimal weight:    0.9990
   chunk 194 optimal weight:    5.9990
   chunk 154 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0370
   chunk 93 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C 152 GLN
D 152 GLN
E  19 GLN
F  19 GLN
F 277 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.172449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.129622 restraints weight = 90240.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 5.00
r_work: 0.2985 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  16872  Z= 0.110
  Angle     :  0.497  11.438  22902  Z= 0.259
  Chirality :  0.045   0.133   2634
  Planarity :  0.003   0.043   2952
  Dihedral  :  4.428  15.193   2214
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 19.41 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.62 (0.18), residues: 2094
  helix:  0.77 (0.23), residues: 552
  sheet:  0.64 (0.26), residues: 342
  loop :  0.29 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  58 
 HIS   0.003   0.001   HIS F  95 
 PHE   0.027   0.002   PHE C 221 
 TYR   0.008   0.001   TYR F 225 
 ARG   0.006   0.000   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03229 (  609)
  hydrogen bonds       : angle       5.15252 ( 1683)
  covalent geometry    : bond        0.00240 (16872)
  covalent geometry    : angle       0.49698 (22902)

*********************** 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
  255 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 235
  time to evaluate  : 1.903 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.7706 (tpt170) cc_final: 0.7430 (tpt170)
REVERT: A  259 LYS cc_start: 0.6915 (tttt) cc_final: 0.6596 (mttp)
REVERT: B  149 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8012 (mppt)
REVERT: B  202 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6540 (tt0)
REVERT: C  149 LYS cc_start: 0.8344 (mmmm) cc_final: 0.7872 (tptt)
REVERT: C  202 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6600 (tt0)
REVERT: C  220 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6592 (pt0)
REVERT: C  233 GLU cc_start: 0.6635 (mp0) cc_final: 0.6398 (pm20)
REVERT: C  259 LYS cc_start: 0.7070 (tttt) cc_final: 0.6580 (mttp)
REVERT: C  330 MET cc_start: 0.7943 (mmt) cc_final: 0.7364 (mmm)
REVERT: D  149 LYS cc_start: 0.8358 (mmmm) cc_final: 0.7869 (tptt)
REVERT: D  202 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6614 (tt0)
REVERT: D  220 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6560 (pt0)
REVERT: D  233 GLU cc_start: 0.6640 (mp0) cc_final: 0.6403 (pm20)
REVERT: D  259 LYS cc_start: 0.7082 (tttt) cc_final: 0.6601 (mttp)
REVERT: D  330 MET cc_start: 0.7936 (mmt) cc_final: 0.7359 (mmm)
REVERT: E  149 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8010 (mppt)
REVERT: E  259 LYS cc_start: 0.7079 (tttt) cc_final: 0.6699 (ttpp)
REVERT: F  257 ARG cc_start: 0.7728 (tpt170) cc_final: 0.7229 (tpt170)
REVERT: F  259 LYS cc_start: 0.6973 (tttt) cc_final: 0.6623 (mttp)
  outliers start: 20
  outliers final: 12
  residues processed: 247
  average time/residue: 1.1938
  time to fit residues: 329.4236
Evaluate side-chains
  243 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 228
  time to evaluate  : 2.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  232 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 147 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 180 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  19 GLN
C 152 GLN
D 152 GLN
E  19 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.170515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.127464 restraints weight = 85121.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 4.74
r_work: 0.2978 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2953
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  16872  Z= 0.149
  Angle     :  0.530  11.137  22902  Z= 0.278
  Chirality :  0.047   0.136   2634
  Planarity :  0.003   0.044   2952
  Dihedral  :  4.692  16.757   2214
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 19.19 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.18), residues: 2094
  helix:  0.61 (0.23), residues: 552
  sheet:  0.57 (0.26), residues: 342
  loop :  0.24 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  58 
 HIS   0.004   0.001   HIS F  95 
 PHE   0.026   0.002   PHE C 221 
 TYR   0.009   0.001   TYR F 225 
 ARG   0.006   0.001   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (  609)
  hydrogen bonds       : angle       5.35247 ( 1683)
  covalent geometry    : bond        0.00332 (16872)
  covalent geometry    : angle       0.52961 (22902)

*********************** 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
  263 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 241
  time to evaluate  : 1.924 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.7764 (tpt170) cc_final: 0.7318 (tpt170)
REVERT: A  259 LYS cc_start: 0.7020 (tttt) cc_final: 0.6678 (mttp)
REVERT: B  149 LYS cc_start: 0.8385 (mmmm) cc_final: 0.8031 (mppt)
REVERT: B  202 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6603 (tt0)
REVERT: B  259 LYS cc_start: 0.7006 (tttt) cc_final: 0.6669 (ttpp)
REVERT: C  149 LYS cc_start: 0.8358 (mmmm) cc_final: 0.8028 (mppt)
REVERT: C  202 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6640 (tt0)
REVERT: C  220 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6595 (pt0)
REVERT: C  233 GLU cc_start: 0.6743 (mp0) cc_final: 0.6492 (pm20)
REVERT: C  259 LYS cc_start: 0.7120 (tttt) cc_final: 0.6621 (mttp)
REVERT: C  330 MET cc_start: 0.7941 (mmt) cc_final: 0.7662 (mmm)
REVERT: D  149 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8017 (mppt)
REVERT: D  202 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6664 (tt0)
REVERT: D  220 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6573 (pt0)
REVERT: D  233 GLU cc_start: 0.6753 (mp0) cc_final: 0.6505 (pm20)
REVERT: D  259 LYS cc_start: 0.7136 (tttt) cc_final: 0.6653 (mttp)
REVERT: D  330 MET cc_start: 0.7948 (mmt) cc_final: 0.7672 (mmm)
REVERT: E  149 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8037 (mppt)
REVERT: E  259 LYS cc_start: 0.7029 (tttt) cc_final: 0.6688 (ttpp)
REVERT: F  257 ARG cc_start: 0.7799 (tpt170) cc_final: 0.7351 (tpt170)
REVERT: F  259 LYS cc_start: 0.7073 (tttt) cc_final: 0.6698 (mttp)
  outliers start: 22
  outliers final: 13
  residues processed: 251
  average time/residue: 1.1969
  time to fit residues: 336.5614
Evaluate side-chains
  247 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 231
  time to evaluate  : 1.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 147 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 184 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 157 optimal weight:    4.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C 152 GLN
C 277 ASN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.168358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.125204 restraints weight = 80705.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 4.78
r_work: 0.2958 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  16872  Z= 0.229
  Angle     :  0.603  10.909  22902  Z= 0.320
  Chirality :  0.049   0.138   2634
  Planarity :  0.004   0.048   2952
  Dihedral  :  5.095  18.651   2214
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 19.62 %
    Favored  : 79.41 %
  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:  0.24 (0.18), residues: 2094
  helix:  0.30 (0.22), residues: 552
  sheet:  0.45 (0.26), residues: 342
  loop :  0.13 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  58 
 HIS   0.005   0.001   HIS F  95 
 PHE   0.027   0.002   PHE D 221 
 TYR   0.011   0.002   TYR F 225 
 ARG   0.006   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  609)
  hydrogen bonds       : angle       5.68877 ( 1683)
  covalent geometry    : bond        0.00518 (16872)
  covalent geometry    : angle       0.60321 (22902)

*********************** 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
  259 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 241
  time to evaluate  : 1.908 
Fit side-chains
REVERT: A  193 TYR cc_start: 0.8887 (m-80) cc_final: 0.8649 (m-80)
REVERT: A  257 ARG cc_start: 0.7768 (tpt170) cc_final: 0.7427 (tpt170)
REVERT: A  259 LYS cc_start: 0.7025 (tttt) cc_final: 0.6537 (mttp)
REVERT: A  284 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7634 (tm-30)
REVERT: B  149 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8060 (mppt)
REVERT: B  304 GLU cc_start: 0.7307 (tt0) cc_final: 0.7102 (tt0)
REVERT: C  149 LYS cc_start: 0.8365 (mmmm) cc_final: 0.7880 (tptt)
REVERT: C  202 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6666 (tt0)
REVERT: C  233 GLU cc_start: 0.6757 (mp0) cc_final: 0.6484 (pm20)
REVERT: C  330 MET cc_start: 0.7893 (mmt) cc_final: 0.7480 (mmm)
REVERT: D  149 LYS cc_start: 0.8358 (mmmm) cc_final: 0.7871 (tptt)
REVERT: D  202 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6650 (tt0)
REVERT: D  233 GLU cc_start: 0.6765 (mp0) cc_final: 0.6493 (pm20)
REVERT: D  330 MET cc_start: 0.7881 (mmt) cc_final: 0.7468 (mmm)
REVERT: E  149 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8057 (mppt)
REVERT: F  193 TYR cc_start: 0.8885 (m-80) cc_final: 0.8646 (m-80)
REVERT: F  257 ARG cc_start: 0.7789 (tpt170) cc_final: 0.7432 (tpt170)
REVERT: F  259 LYS cc_start: 0.7037 (tttt) cc_final: 0.6555 (mttp)
REVERT: F  284 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7644 (tm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 247
  average time/residue: 1.2259
  time to fit residues: 338.4256
Evaluate side-chains
  249 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 232
  time to evaluate  : 2.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  284 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 132 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 125 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 181 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C 152 GLN
C 277 ASN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.170360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.127510 restraints weight = 88146.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 4.74
r_work: 0.2984 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  16872  Z= 0.143
  Angle     :  0.529  11.333  22902  Z= 0.279
  Chirality :  0.046   0.134   2634
  Planarity :  0.003   0.046   2952
  Dihedral  :  4.756  16.768   2214
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 19.62 %
    Favored  : 79.25 %
  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 (0.18), residues: 2094
  helix:  0.57 (0.23), residues: 546
  sheet:  0.52 (0.26), residues: 342
  loop :  0.18 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  58 
 HIS   0.004   0.001   HIS F  95 
 PHE   0.031   0.002   PHE D 221 
 TYR   0.008   0.001   TYR F 225 
 ARG   0.006   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  609)
  hydrogen bonds       : angle       5.39215 ( 1683)
  covalent geometry    : bond        0.00317 (16872)
  covalent geometry    : angle       0.52948 (22902)

*********************** 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
  255 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 234
  time to evaluate  : 1.917 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.7786 (tpt170) cc_final: 0.7529 (tpt170)
REVERT: A  284 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7614 (tm-30)
REVERT: B  149 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8022 (mppt)
REVERT: C  149 LYS cc_start: 0.8358 (mmmm) cc_final: 0.7885 (tptt)
REVERT: C  202 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6620 (tt0)
REVERT: C  220 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6567 (pt0)
REVERT: C  233 GLU cc_start: 0.6766 (mp0) cc_final: 0.6504 (pm20)
REVERT: C  304 GLU cc_start: 0.7438 (tt0) cc_final: 0.7085 (tt0)
REVERT: C  330 MET cc_start: 0.7962 (mmt) cc_final: 0.7643 (mmm)
REVERT: D  149 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7855 (tptt)
REVERT: D  202 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6628 (tt0)
REVERT: D  220 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6580 (pt0)
REVERT: D  233 GLU cc_start: 0.6767 (mp0) cc_final: 0.6506 (pm20)
REVERT: D  304 GLU cc_start: 0.7431 (tt0) cc_final: 0.7080 (tt0)
REVERT: D  330 MET cc_start: 0.7950 (mmt) cc_final: 0.7631 (mmm)
REVERT: E  149 LYS cc_start: 0.8391 (mmmm) cc_final: 0.8038 (mppt)
REVERT: F  257 ARG cc_start: 0.7800 (tpt170) cc_final: 0.7324 (tpt170)
REVERT: F  284 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7617 (tm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 242
  average time/residue: 1.1797
  time to fit residues: 319.4149
Evaluate side-chains
  250 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 232
  time to evaluate  : 1.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  284 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 177 optimal weight:    0.2980
   chunk 52 optimal weight:    3.9990
   chunk 198 optimal weight:    0.0370
   chunk 4 optimal weight:    2.9990
   chunk 166 optimal weight:    1.9990
   chunk 105 optimal weight:    0.4980
   chunk 67 optimal weight:   10.0000
   chunk 190 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C 152 GLN
C 277 ASN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.170556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.127643 restraints weight = 85304.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 4.79
r_work: 0.2988 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  16872  Z= 0.139
  Angle     :  0.525  11.229  22902  Z= 0.277
  Chirality :  0.046   0.134   2634
  Planarity :  0.003   0.047   2952
  Dihedral  :  4.716  16.623   2214
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 19.78 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.18), residues: 2094
  helix:  0.60 (0.23), residues: 546
  sheet:  0.56 (0.26), residues: 342
  loop :  0.18 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  58 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.033   0.002   PHE D 221 
 TYR   0.008   0.001   TYR F 225 
 ARG   0.007   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  609)
  hydrogen bonds       : angle       5.35300 ( 1683)
  covalent geometry    : bond        0.00309 (16872)
  covalent geometry    : angle       0.52468 (22902)

********************** 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
  250 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 231
  time to evaluate  : 1.840 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.7743 (tpt170) cc_final: 0.7295 (tpt170)
REVERT: A  284 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7582 (tm-30)
REVERT: B  149 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8010 (mppt)
REVERT: C  149 LYS cc_start: 0.8351 (mmmm) cc_final: 0.7866 (tptt)
REVERT: C  202 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6624 (tt0)
REVERT: C  220 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6580 (pt0)
REVERT: C  233 GLU cc_start: 0.6757 (mp0) cc_final: 0.6501 (pm20)
REVERT: C  304 GLU cc_start: 0.7330 (tt0) cc_final: 0.6969 (tt0)
REVERT: C  330 MET cc_start: 0.7933 (mmt) cc_final: 0.7614 (mmm)
REVERT: D  149 LYS cc_start: 0.8349 (mmmm) cc_final: 0.7857 (tptt)
REVERT: D  202 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6634 (tt0)
REVERT: D  220 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6581 (pt0)
REVERT: D  233 GLU cc_start: 0.6760 (mp0) cc_final: 0.6501 (pm20)
REVERT: D  304 GLU cc_start: 0.7324 (tt0) cc_final: 0.6964 (tt0)
REVERT: D  330 MET cc_start: 0.7930 (mmt) cc_final: 0.7611 (mmm)
REVERT: E  149 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8025 (mppt)
REVERT: E  202 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6640 (tt0)
REVERT: F  257 ARG cc_start: 0.7767 (tpt170) cc_final: 0.7298 (tpt170)
REVERT: F  284 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7583 (tm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 238
  average time/residue: 1.2380
  time to fit residues: 330.7493
Evaluate side-chains
  248 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 229
  time to evaluate  : 1.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  202 GLU
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  284 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0370
   chunk 156 optimal weight:    0.9990
   chunk 115 optimal weight:    0.5980
   chunk 160 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 116 optimal weight:    0.0270
   chunk 172 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.2916

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C 152 GLN
C 277 ASN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.173690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.133374 restraints weight = 92533.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 5.80
r_work: 0.2962 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  16872  Z= 0.092
  Angle     :  0.483  11.585  22902  Z= 0.252
  Chirality :  0.045   0.132   2634
  Planarity :  0.003   0.044   2952
  Dihedral  :  4.307  14.766   2214
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 19.73 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.67 (0.19), residues: 2094
  helix:  0.87 (0.23), residues: 546
  sheet:  0.72 (0.26), residues: 342
  loop :  0.28 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  58 
 HIS   0.003   0.001   HIS C  95 
 PHE   0.033   0.002   PHE D 221 
 TYR   0.006   0.001   TYR F 225 
 ARG   0.006   0.000   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02890 (  609)
  hydrogen bonds       : angle       4.99695 ( 1683)
  covalent geometry    : bond        0.00195 (16872)
  covalent geometry    : angle       0.48303 (22902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12597.20 seconds
wall clock time: 217 minutes 35.03 seconds (13055.03 seconds total)