Starting phenix.real_space_refine
on Sat Jun 14 20:12:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ud2_42144/06_2025/8ud2_42144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ud2_42144/06_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_42144/06_2025/8ud2_42144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ud2_42144/06_2025/8ud2_42144.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ud2_42144/06_2025/8ud2_42144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ud2_42144/06_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-5710/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: 7.75, 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: 3.85
  Conformation dependent library (CDL) restraints added in 3.5 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: 2.53
  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: 5.52

  Time building geometry restraints manager: 4.60 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: 0.14
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:                  0.010
  Normalize map: mean=0, sd=1:             3.890
  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:                     39.160
  Find NCS groups from input model:        0.380
  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:10.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.280
-------------------------------------------------------------------------------
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  : 1.821 
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: 1.0946
  time to fit residues: 333.9911
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  : 1.842 
-------------------------------------------------------------------------------
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: 0.2997 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    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 = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
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       5.85104 ( 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  : 1.871 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.6790 (tttt) cc_final: 0.6487 (mttp)
REVERT: B  149 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8013 (mppt)
REVERT: B  202 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6600 (pt0)
REVERT: C  149 LYS cc_start: 0.8382 (mmmm) cc_final: 0.7936 (ptmm)
REVERT: C  202 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6533 (tt0)
REVERT: C  215 GLU cc_start: 0.6867 (pt0) cc_final: 0.5839 (mp0)
REVERT: C  259 LYS cc_start: 0.6944 (tttt) cc_final: 0.6610 (mttp)
REVERT: C  330 MET cc_start: 0.7978 (mmt) cc_final: 0.7267 (mmm)
REVERT: D  149 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7931 (ptmm)
REVERT: D  202 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6566 (tt0)
REVERT: D  215 GLU cc_start: 0.6871 (pt0) cc_final: 0.5841 (mp0)
REVERT: D  259 LYS cc_start: 0.6898 (tttt) cc_final: 0.6574 (mttp)
REVERT: D  330 MET cc_start: 0.7949 (mmt) cc_final: 0.7273 (mmm)
REVERT: E  149 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8014 (mppt)
REVERT: E  259 LYS cc_start: 0.6838 (tttt) cc_final: 0.6542 (mttp)
REVERT: F  259 LYS cc_start: 0.6834 (tttt) cc_final: 0.6519 (tppt)
  outliers start: 28
  outliers final: 10
  residues processed: 259
  average time/residue: 1.4009
  time to fit residues: 407.6599
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  : 2.027 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 2 optimal weight:    0.0870
   chunk 189 optimal weight:    0.9990
   chunk 180 optimal weight:    0.0270
   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:    0.6980
   chunk 117 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.4816

-------------------------------------------------------------------------------
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 = 0.3874 r_free = 0.3874 target = 0.172774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.132113 restraints weight = 95823.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 5.69
r_work: 0.2936 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1226

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= 0.111
  Angle     :  0.493  10.838  22902  Z= 0.260
  Chirality :  0.046   0.134   2634
  Planarity :  0.003   0.032   2952
  Dihedral  :  4.568  30.949   2220
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 18.98 %
    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:  0.55 (0.19), residues: 2094
  helix:  0.85 (0.23), residues: 540
  sheet:  0.47 (0.27), residues: 342
  loop :  0.22 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  58 
 HIS   0.003   0.001   HIS F  95 
 PHE   0.023   0.002   PHE C 221 
 TYR   0.008   0.001   TYR E 225 
 ARG   0.006   0.000   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  609)
  hydrogen bonds       : angle       5.40051 ( 1683)
  covalent geometry    : bond        0.00241 (16872)
  covalent geometry    : angle       0.49339 (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
  257 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 235
  time to evaluate  : 1.837 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.6895 (tttt) cc_final: 0.6575 (mttp)
REVERT: B  149 LYS cc_start: 0.8371 (mmmm) cc_final: 0.7980 (mppt)
REVERT: B  259 LYS cc_start: 0.6798 (tttt) cc_final: 0.6508 (mttp)
REVERT: B  340 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.7121 (p)
REVERT: C  202 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6548 (tt0)
REVERT: C  259 LYS cc_start: 0.7059 (tttt) cc_final: 0.6697 (mttp)
REVERT: C  330 MET cc_start: 0.8137 (mmt) cc_final: 0.7589 (mmm)
REVERT: C  340 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7075 (p)
REVERT: D  202 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6550 (tt0)
REVERT: D  259 LYS cc_start: 0.7046 (tttt) cc_final: 0.6688 (mttp)
REVERT: D  330 MET cc_start: 0.8123 (mmt) cc_final: 0.7577 (mmm)
REVERT: D  340 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7051 (p)
REVERT: E  149 LYS cc_start: 0.8395 (mmmm) cc_final: 0.7990 (mppt)
REVERT: E  259 LYS cc_start: 0.6871 (tttt) cc_final: 0.6564 (mttp)
REVERT: E  340 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7156 (p)
REVERT: F  259 LYS cc_start: 0.6908 (tttt) cc_final: 0.6594 (mttp)
  outliers start: 22
  outliers final: 3
  residues processed: 248
  average time/residue: 1.1191
  time to fit residues: 312.6240
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  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   51 VAL
Chi-restraints excluded: chain D residue  147 SER
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 197 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 133 optimal weight:    6.9990
   chunk 159 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 117 optimal weight:    0.0060
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0270
   overall best weight:    0.7456

-------------------------------------------------------------------------------
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 = 0.3858 r_free = 0.3858 target = 0.171075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.128201 restraints weight = 84757.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 4.90
r_work: 0.2983 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
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 = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  16872  Z= 0.138
  Angle     :  0.524  11.378  22902  Z= 0.274
  Chirality :  0.046   0.135   2634
  Planarity :  0.003   0.041   2952
  Dihedral  :  4.641  16.493   2218
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 18.55 %
    Favored  : 80.11 %
  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:  0.64 (0.23), residues: 552
  sheet:  0.51 (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 C  58 
 HIS   0.003   0.001   HIS F  95 
 PHE   0.025   0.002   PHE D 221 
 TYR   0.009   0.001   TYR F 225 
 ARG   0.005   0.000   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03675 (  609)
  hydrogen bonds       : angle       5.41554 ( 1683)
  covalent geometry    : bond        0.00306 (16872)
  covalent geometry    : angle       0.52406 (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
  268 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 243
  time to evaluate  : 1.834 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7367 (tpt170)
REVERT: A  259 LYS cc_start: 0.6945 (tttt) cc_final: 0.6623 (mttp)
REVERT: B  149 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8027 (mppt)
REVERT: B  202 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6578 (tt0)
REVERT: B  259 LYS cc_start: 0.6891 (tttt) cc_final: 0.6499 (mttp)
REVERT: C  149 LYS cc_start: 0.8401 (mmmm) cc_final: 0.8043 (mppt)
REVERT: C  202 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6624 (tt0)
REVERT: C  259 LYS cc_start: 0.7100 (tttt) cc_final: 0.6626 (mttp)
REVERT: C  330 MET cc_start: 0.7998 (mmt) cc_final: 0.7405 (mmm)
REVERT: D  149 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8040 (mppt)
REVERT: D  202 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6633 (tt0)
REVERT: D  259 LYS cc_start: 0.7111 (tttt) cc_final: 0.6662 (mttp)
REVERT: D  330 MET cc_start: 0.7948 (mmt) cc_final: 0.7368 (mmm)
REVERT: E  149 LYS cc_start: 0.8397 (mmmm) cc_final: 0.8036 (mppt)
REVERT: E  202 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6641 (tt0)
REVERT: E  259 LYS cc_start: 0.6926 (tttt) cc_final: 0.6563 (mttp)
REVERT: F  257 ARG cc_start: 0.7762 (tpt170) cc_final: 0.7357 (tpt170)
REVERT: F  259 LYS cc_start: 0.6965 (tttt) cc_final: 0.6639 (mttp)
  outliers start: 25
  outliers final: 14
  residues processed: 257
  average time/residue: 1.3007
  time to fit residues: 373.6354
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  : 1.870 
-------------------------------------------------------------------------------
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  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  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  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:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 186 optimal weight:    1.9990
   chunk 142 optimal weight:    0.5980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.169901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.126607 restraints weight = 87743.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 5.07
r_work: 0.2971 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  16872  Z= 0.168
  Angle     :  0.550  10.674  22902  Z= 0.290
  Chirality :  0.047   0.136   2634
  Planarity :  0.003   0.045   2952
  Dihedral  :  4.821  17.161   2214
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 18.87 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.18), residues: 2094
  helix:  0.51 (0.23), residues: 552
  sheet:  0.50 (0.26), residues: 342
  loop :  0.19 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  58 
 HIS   0.004   0.001   HIS A  95 
 PHE   0.027   0.002   PHE D 221 
 TYR   0.010   0.001   TYR F 225 
 ARG   0.006   0.001   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  609)
  hydrogen bonds       : angle       5.53028 ( 1683)
  covalent geometry    : bond        0.00377 (16872)
  covalent geometry    : angle       0.54988 (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
  268 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 246
  time to evaluate  : 1.846 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.7715 (tpt170) cc_final: 0.7254 (tpt170)
REVERT: A  259 LYS cc_start: 0.6974 (tttt) cc_final: 0.6572 (mttp)
REVERT: B  149 LYS cc_start: 0.8413 (mmmm) cc_final: 0.8041 (mppt)
REVERT: B  259 LYS cc_start: 0.7049 (tttt) cc_final: 0.6692 (ttpp)
REVERT: C  149 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8030 (mppt)
REVERT: C  202 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6663 (tt0)
REVERT: C  220 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6509 (pt0)
REVERT: C  259 LYS cc_start: 0.7154 (tttt) cc_final: 0.6639 (mttp)
REVERT: C  330 MET cc_start: 0.7908 (mmt) cc_final: 0.7306 (mmm)
REVERT: D  149 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8019 (mppt)
REVERT: D  202 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6670 (tt0)
REVERT: D  220 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6489 (pt0)
REVERT: D  259 LYS cc_start: 0.7164 (tttt) cc_final: 0.6651 (mttp)
REVERT: D  330 MET cc_start: 0.7908 (mmt) cc_final: 0.7316 (mmm)
REVERT: E  149 LYS cc_start: 0.8414 (mmmm) cc_final: 0.8043 (mppt)
REVERT: E  259 LYS cc_start: 0.7081 (tttt) cc_final: 0.6720 (ttpp)
REVERT: F  257 ARG cc_start: 0.7730 (tpt170) cc_final: 0.7355 (tpt170)
REVERT: F  259 LYS cc_start: 0.7046 (tttt) cc_final: 0.6652 (mttp)
  outliers start: 22
  outliers final: 13
  residues processed: 256
  average time/residue: 1.2178
  time to fit residues: 348.7933
Evaluate side-chains
  251 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 236
  time to evaluate  : 1.710 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 148 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9980
   chunk 164 optimal weight:    6.9990
   chunk 137 optimal weight:    0.9990
   chunk 194 optimal weight:    5.9990
   chunk 154 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.170498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.127401 restraints weight = 89754.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 4.85
r_work: 0.2980 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    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 = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  16872  Z= 0.146
  Angle     :  0.530  10.813  22902  Z= 0.279
  Chirality :  0.046   0.134   2634
  Planarity :  0.003   0.044   2952
  Dihedral  :  4.722  16.583   2214
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 18.92 %
    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:  0.43 (0.18), residues: 2094
  helix:  0.55 (0.23), residues: 552
  sheet:  0.53 (0.27), residues: 342
  loop :  0.20 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  58 
 HIS   0.004   0.001   HIS A  95 
 PHE   0.030   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        0.03673 (  609)
  hydrogen bonds       : angle       5.42086 ( 1683)
  covalent geometry    : bond        0.00326 (16872)
  covalent geometry    : angle       0.52967 (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
  264 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 240
  time to evaluate  : 1.698 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.7769 (tpt170) cc_final: 0.7298 (tpt170)
REVERT: A  259 LYS cc_start: 0.7037 (tttt) cc_final: 0.6619 (mttp)
REVERT: B   68 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7269 (mp0)
REVERT: B  149 LYS cc_start: 0.8392 (mmmm) cc_final: 0.8030 (mppt)
REVERT: B  259 LYS cc_start: 0.7003 (tttt) cc_final: 0.6641 (ttpp)
REVERT: C  149 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8041 (mppt)
REVERT: C  202 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6642 (tt0)
REVERT: C  220 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6489 (pt0)
REVERT: C  259 LYS cc_start: 0.7141 (tttt) cc_final: 0.6628 (mttp)
REVERT: C  330 MET cc_start: 0.7978 (mmt) cc_final: 0.7405 (mmm)
REVERT: D  149 LYS cc_start: 0.8378 (mmmm) cc_final: 0.7892 (tptt)
REVERT: D  202 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6672 (tt0)
REVERT: D  220 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6445 (pt0)
REVERT: D  304 GLU cc_start: 0.7446 (tt0) cc_final: 0.7044 (tt0)
REVERT: D  330 MET cc_start: 0.7977 (mmt) cc_final: 0.7409 (mmm)
REVERT: E   68 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: E  149 LYS cc_start: 0.8397 (mmmm) cc_final: 0.8034 (mppt)
REVERT: F  257 ARG cc_start: 0.7780 (tpt170) cc_final: 0.7330 (tpt170)
REVERT: F  259 LYS cc_start: 0.7094 (tttt) cc_final: 0.6639 (mttp)
REVERT: F  284 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7602 (tm-30)
  outliers start: 24
  outliers final: 16
  residues processed: 252
  average time/residue: 1.1848
  time to fit residues: 334.5448
Evaluate side-chains
  247 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 227
  time to evaluate  : 1.964 
-------------------------------------------------------------------------------
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   68 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain D residue   12 LYS
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 D residue  306 ILE
Chi-restraints excluded: chain E residue   68 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 60 optimal weight:    0.3980
   chunk 66 optimal weight:    6.9990
   chunk 88 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 147 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 129 optimal weight:    0.0980
   chunk 180 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 277 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.172049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.129017 restraints weight = 85242.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 4.88
r_work: 0.2985 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2993
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    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 = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  16872  Z= 0.113
  Angle     :  0.499  11.019  22902  Z= 0.262
  Chirality :  0.045   0.134   2634
  Planarity :  0.003   0.042   2952
  Dihedral  :  4.489  15.203   2214
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 19.25 %
    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:  0.57 (0.18), residues: 2094
  helix:  0.79 (0.23), residues: 546
  sheet:  0.59 (0.27), residues: 342
  loop :  0.24 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  58 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.030   0.002   PHE D 221 
 TYR   0.007   0.001   TYR F 225 
 ARG   0.007   0.000   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03270 (  609)
  hydrogen bonds       : angle       5.21620 ( 1683)
  covalent geometry    : bond        0.00248 (16872)
  covalent geometry    : angle       0.49936 (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
  266 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 245
  time to evaluate  : 1.956 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 ARG cc_start: 0.7724 (tpt170) cc_final: 0.7455 (tpt170)
REVERT: A  259 LYS cc_start: 0.7009 (tttt) cc_final: 0.6639 (mttp)
REVERT: B  149 LYS cc_start: 0.8362 (mmmm) cc_final: 0.8010 (mppt)
REVERT: B  202 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6502 (tt0)
REVERT: C  149 LYS cc_start: 0.8343 (mmmm) cc_final: 0.8014 (mppt)
REVERT: C  202 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6599 (tt0)
REVERT: C  220 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6488 (pt0)
REVERT: C  259 LYS cc_start: 0.7109 (tttt) cc_final: 0.6599 (mttp)
REVERT: C  330 MET cc_start: 0.7896 (mmt) cc_final: 0.7604 (mmm)
REVERT: D  149 LYS cc_start: 0.8334 (mmmm) cc_final: 0.7992 (mppt)
REVERT: D  202 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6608 (tt0)
REVERT: D  220 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6464 (pt0)
REVERT: D  304 GLU cc_start: 0.7223 (tt0) cc_final: 0.6838 (tt0)
REVERT: D  330 MET cc_start: 0.7902 (mmt) cc_final: 0.7610 (mmm)
REVERT: E   68 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7138 (mp0)
REVERT: E  149 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8001 (mppt)
REVERT: E  202 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6484 (tt0)
REVERT: F  257 ARG cc_start: 0.7731 (tpt170) cc_final: 0.7486 (tpt170)
REVERT: F  259 LYS cc_start: 0.7029 (tttt) cc_final: 0.6663 (mttp)
REVERT: F  284 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7564 (tm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 255
  average time/residue: 1.5618
  time to fit residues: 445.9226
Evaluate side-chains
  252 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 235
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
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  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   68 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 112 optimal weight:    0.5980
   chunk 147 optimal weight:    0.3980
   chunk 31 optimal weight:    5.9990
   chunk 74 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0070
   chunk 184 optimal weight:    0.0570
   chunk 57 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 157 optimal weight:    0.0270
   overall best weight:    0.1574

-------------------------------------------------------------------------------
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
C 277 ASN
D 152 GLN
D 277 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 = 0.3914 r_free = 0.3914 target = 0.176902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.139266 restraints weight = 82571.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 5.25
r_work: 0.2993 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    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 = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  16872  Z= 0.079
  Angle     :  0.464  11.468  22902  Z= 0.241
  Chirality :  0.045   0.132   2634
  Planarity :  0.003   0.041   2952
  Dihedral  :  3.994  14.408   2214
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 19.35 %
    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:  0.82 (0.19), residues: 2094
  helix:  1.02 (0.24), residues: 546
  sheet:  0.82 (0.27), residues: 342
  loop :  0.36 (0.19), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 332 
 HIS   0.002   0.001   HIS C  95 
 PHE   0.030   0.001   PHE D 221 
 TYR   0.006   0.001   TYR F 225 
 ARG   0.007   0.000   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02497 (  609)
  hydrogen bonds       : angle       4.72876 ( 1683)
  covalent geometry    : bond        0.00167 (16872)
  covalent geometry    : angle       0.46414 (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
  244 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 225
  time to evaluate  : 1.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6601 (tt0)
REVERT: A  257 ARG cc_start: 0.7675 (tpt170) cc_final: 0.7399 (tpt170)
REVERT: A  259 LYS cc_start: 0.6927 (tttt) cc_final: 0.6608 (mttp)
REVERT: B  149 LYS cc_start: 0.8324 (mmmm) cc_final: 0.7940 (mppt)
REVERT: B  202 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6391 (tt0)
REVERT: B  265 LEU cc_start: 0.8335 (mt) cc_final: 0.7990 (tp)
REVERT: B  277 ASN cc_start: 0.8888 (m110) cc_final: 0.8647 (m-40)
REVERT: C  149 LYS cc_start: 0.8327 (mmmm) cc_final: 0.7824 (tptt)
REVERT: C  202 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6403 (tt0)
REVERT: C  259 LYS cc_start: 0.7024 (tttt) cc_final: 0.6555 (mttp)
REVERT: C  330 MET cc_start: 0.7996 (mmt) cc_final: 0.7708 (mmm)
REVERT: D  149 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7807 (tptt)
REVERT: D  202 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6386 (tt0)
REVERT: D  259 LYS cc_start: 0.7023 (tttt) cc_final: 0.6544 (mttp)
REVERT: D  330 MET cc_start: 0.8018 (mmt) cc_final: 0.7732 (mmm)
REVERT: E  149 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7939 (mppt)
REVERT: E  202 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6403 (tt0)
REVERT: F  202 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6556 (tt0)
REVERT: F  257 ARG cc_start: 0.7668 (tpt170) cc_final: 0.7391 (tpt170)
REVERT: F  259 LYS cc_start: 0.6918 (tttt) cc_final: 0.6604 (mttp)
REVERT: F  277 ASN cc_start: 0.9059 (m110) cc_final: 0.8848 (m-40)
  outliers start: 19
  outliers final: 11
  residues processed: 233
  average time/residue: 1.4168
  time to fit residues: 370.6320
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 214
  time to evaluate  : 3.342 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 78 optimal weight:    0.2980
   chunk 119 optimal weight:    3.9990
   chunk 132 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 125 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0060
   chunk 26 optimal weight:    2.9990
   chunk 181 optimal weight:    0.7980
   chunk 73 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.4596

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.172845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.130737 restraints weight = 88788.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 4.92
r_work: 0.3024 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  16872  Z= 0.105
  Angle     :  0.485  11.186  22902  Z= 0.253
  Chirality :  0.045   0.132   2634
  Planarity :  0.003   0.042   2952
  Dihedral  :  4.275  14.807   2214
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 20.00 %
    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:  0.78 (0.19), residues: 2094
  helix:  0.97 (0.23), residues: 546
  sheet:  0.83 (0.26), residues: 342
  loop :  0.33 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  58 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.030   0.002   PHE D 221 
 TYR   0.007   0.001   TYR A  32 
 ARG   0.007   0.000   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03067 (  609)
  hydrogen bonds       : angle       4.95975 ( 1683)
  covalent geometry    : bond        0.00227 (16872)
  covalent geometry    : angle       0.48504 (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
  236 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 222
  time to evaluate  : 2.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6652 (tt0)
REVERT: A  257 ARG cc_start: 0.7732 (tpt170) cc_final: 0.7443 (tpt170)
REVERT: A  259 LYS cc_start: 0.6943 (tttt) cc_final: 0.6637 (mttp)
REVERT: B  149 LYS cc_start: 0.8342 (mmmm) cc_final: 0.8019 (mppt)
REVERT: B  265 LEU cc_start: 0.8393 (mt) cc_final: 0.8065 (tp)
REVERT: C  149 LYS cc_start: 0.8381 (mmmm) cc_final: 0.7899 (tptt)
REVERT: C  202 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6499 (tt0)
REVERT: C  259 LYS cc_start: 0.7062 (tttt) cc_final: 0.6561 (mttp)
REVERT: C  330 MET cc_start: 0.7870 (mmt) cc_final: 0.7634 (mmm)
REVERT: D  149 LYS cc_start: 0.8391 (mmmm) cc_final: 0.7901 (tptt)
REVERT: D  202 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6464 (tt0)
REVERT: D  259 LYS cc_start: 0.7039 (tttt) cc_final: 0.6563 (mttp)
REVERT: D  330 MET cc_start: 0.7889 (mmt) cc_final: 0.7654 (mmm)
REVERT: E  149 LYS cc_start: 0.8344 (mmmm) cc_final: 0.8015 (mppt)
REVERT: E  202 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6512 (tt0)
REVERT: F  202 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6612 (tt0)
REVERT: F  257 ARG cc_start: 0.7733 (tpt170) cc_final: 0.7444 (tpt170)
REVERT: F  259 LYS cc_start: 0.6950 (tttt) cc_final: 0.6613 (mttp)
  outliers start: 14
  outliers final: 12
  residues processed: 230
  average time/residue: 1.2342
  time to fit residues: 318.3717
Evaluate side-chains
  233 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 219
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
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  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  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  232 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 177 optimal weight:    0.0170
   chunk 52 optimal weight:    2.9990
   chunk 198 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 166 optimal weight:    6.9990
   chunk 105 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 190 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 277 ASN
B  19 GLN
C 152 GLN
D 152 GLN
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 = 0.3868 r_free = 0.3868 target = 0.172448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.129502 restraints weight = 85535.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 4.99
r_work: 0.3010 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    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 = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  16872  Z= 0.116
  Angle     :  0.500  11.237  22902  Z= 0.262
  Chirality :  0.045   0.133   2634
  Planarity :  0.003   0.042   2952
  Dihedral  :  4.422  15.027   2214
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 19.89 %
    Favored  : 79.14 %
  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:  0.70 (0.18), residues: 2094
  helix:  0.78 (0.23), residues: 552
  sheet:  0.79 (0.26), residues: 342
  loop :  0.34 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  58 
 HIS   0.003   0.001   HIS F  95 
 PHE   0.030   0.002   PHE C 221 
 TYR   0.007   0.001   TYR A  32 
 ARG   0.006   0.000   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03229 (  609)
  hydrogen bonds       : angle       5.05128 ( 1683)
  covalent geometry    : bond        0.00256 (16872)
  covalent geometry    : angle       0.50009 (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
  241 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 223
  time to evaluate  : 1.928 
Fit side-chains
REVERT: A  202 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6711 (tt0)
REVERT: A  257 ARG cc_start: 0.7716 (tpt170) cc_final: 0.7430 (tpt170)
REVERT: A  259 LYS cc_start: 0.6990 (tttt) cc_final: 0.6640 (mttp)
REVERT: B  149 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8020 (mppt)
REVERT: B  202 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6530 (tt0)
REVERT: B  265 LEU cc_start: 0.8416 (mt) cc_final: 0.8087 (tp)
REVERT: C  149 LYS cc_start: 0.8362 (mmmm) cc_final: 0.7888 (tptt)
REVERT: C  202 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6568 (tt0)
REVERT: C  259 LYS cc_start: 0.7033 (tttt) cc_final: 0.6527 (mttp)
REVERT: C  330 MET cc_start: 0.7868 (mmt) cc_final: 0.7607 (mmm)
REVERT: D  149 LYS cc_start: 0.8370 (mmmm) cc_final: 0.7889 (tptt)
REVERT: D  202 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6525 (tt0)
REVERT: D  259 LYS cc_start: 0.6950 (tttt) cc_final: 0.6397 (mttp)
REVERT: D  330 MET cc_start: 0.7878 (mmt) cc_final: 0.7619 (mmm)
REVERT: E  149 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8035 (mppt)
REVERT: E  202 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6528 (tt0)
REVERT: F  257 ARG cc_start: 0.7708 (tpt170) cc_final: 0.7421 (tpt170)
REVERT: F  259 LYS cc_start: 0.7003 (tttt) cc_final: 0.6622 (mttp)
  outliers start: 18
  outliers final: 11
  residues processed: 233
  average time/residue: 1.2380
  time to fit residues: 325.4753
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 214
  time to evaluate  : 1.946 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 130 optimal weight:    3.9990
   chunk 109 optimal weight:    0.0070
   chunk 156 optimal weight:    0.0270
   chunk 115 optimal weight:    1.9990
   chunk 160 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 116 optimal weight:    2.9990
   chunk 172 optimal weight:    0.0470
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.2754

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.174803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.134486 restraints weight = 92656.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 5.69
r_work: 0.3000 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    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 = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  16872  Z= 0.089
  Angle     :  0.474  11.538  22902  Z= 0.247
  Chirality :  0.045   0.132   2634
  Planarity :  0.003   0.041   2952
  Dihedral  :  4.170  14.624   2214
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 20.16 %
    Favored  : 79.14 %
  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:  0.83 (0.19), residues: 2094
  helix:  0.88 (0.23), residues: 552
  sheet:  0.89 (0.26), residues: 342
  loop :  0.42 (0.19), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  58 
 HIS   0.003   0.001   HIS C  95 
 PHE   0.031   0.001   PHE D 221 
 TYR   0.007   0.001   TYR A 225 
 ARG   0.006   0.000   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02762 (  609)
  hydrogen bonds       : angle       4.82416 ( 1683)
  covalent geometry    : bond        0.00189 (16872)
  covalent geometry    : angle       0.47404 (22902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13401.49 seconds
wall clock time: 233 minutes 0.18 seconds (13980.18 seconds total)