Starting phenix.real_space_refine
on Wed Mar  4 12:43:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aa4_15293/03_2026/8aa4_15293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aa4_15293/03_2026/8aa4_15293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aa4_15293/03_2026/8aa4_15293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aa4_15293/03_2026/8aa4_15293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aa4_15293/03_2026/8aa4_15293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aa4_15293/03_2026/8aa4_15293.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      54      5.16       5
     C    8580      2.51       5
     N    2330      2.21       5
     O    2652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13616
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6808
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 871, 6800
          Classifications: {'peptide': 871}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 28, 'TRANS': 842}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 871, 6800
          Classifications: {'peptide': 871}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 28, 'TRANS': 842}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 6944
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.20, per 1000 atoms: 0.53
  Number of scatterers: 13616
  At special positions: 0
  Unit cell: (144.48, 116.1, 116.1, 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      54     16.00
     O    2652      8.00
     N    2330      7.00
     C    8580      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3176

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 16 sheets defined
      11.9% alpha, 46.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 144 through 149
      removed outlier: 3.752A  pdb=" N   ALA A 148 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   MET A 149 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 144 through 149'
    Processing helix  chain 'A' and resid 195 through 199
    Processing helix  chain 'A' and resid 200 through 202
      No H-bonds generated for 'chain 'A' and resid 200 through 202'
    Processing helix  chain 'A' and resid 212 through 217
    Processing helix  chain 'A' and resid 218 through 223
      removed outlier: 6.681A  pdb=" N   SER A 221 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG A 222 " --> pdb=" O   TYR A 219 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 223 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 223'
    Processing helix  chain 'A' and resid 261 through 276
    Processing helix  chain 'A' and resid 286 through 290
    Processing helix  chain 'A' and resid 295 through 301
    Processing helix  chain 'A' and resid 376 through 383
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 411 through 419
    Processing helix  chain 'A' and resid 706 through 710
    Processing helix  chain 'A' and resid 799 through 806
    Processing helix  chain 'A' and resid 874 through 879
    Processing helix  chain 'A' and resid 888 through 892
    Processing helix  chain 'A' and resid 919 through 921
      No H-bonds generated for 'chain 'A' and resid 919 through 921'
    Processing helix  chain 'B' and resid 144 through 149
      removed outlier: 3.752A  pdb=" N   ALA B 148 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   MET B 149 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 144 through 149'
    Processing helix  chain 'B' and resid 195 through 199
    Processing helix  chain 'B' and resid 200 through 202
      No H-bonds generated for 'chain 'B' and resid 200 through 202'
    Processing helix  chain 'B' and resid 212 through 217
    Processing helix  chain 'B' and resid 218 through 223
      removed outlier: 6.681A  pdb=" N   SER B 221 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG B 222 " --> pdb=" O   TYR B 219 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY B 223 " --> pdb=" O   GLY B 220 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 218 through 223'
    Processing helix  chain 'B' and resid 261 through 276
    Processing helix  chain 'B' and resid 286 through 290
    Processing helix  chain 'B' and resid 295 through 301
    Processing helix  chain 'B' and resid 376 through 383
    Processing helix  chain 'B' and resid 402 through 407
    Processing helix  chain 'B' and resid 411 through 419
    Processing helix  chain 'B' and resid 706 through 710
    Processing helix  chain 'B' and resid 799 through 806
    Processing helix  chain 'B' and resid 874 through 879
    Processing helix  chain 'B' and resid 888 through 892
    Processing helix  chain 'B' and resid 919 through 921
      No H-bonds generated for 'chain 'B' and resid 919 through 921'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 114
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132
      removed outlier: 3.559A  pdb=" N   ARG A 206 " --> pdb=" O   THR A 231 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LEU A 184 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ILE A 230 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL A 186 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   SER A 232 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159
    Processing sheet with id=AA4, first strand: chain 'A' and resid 588 through 590
      removed outlier: 4.053A  pdb=" N   ASP A 615 " --> pdb=" O   SER A 679 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG A 734 " --> pdb=" O   SER A 686 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLY A 722 " --> pdb=" O   ASP A 698 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU A 700 " --> pdb=" O   ASN A 720 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ASN A 720 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   LYS A 702 " --> pdb=" O   PHE A 718 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   PHE A 718 " --> pdb=" O   LYS A 702 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LYS A 723 " --> pdb=" O   LEU A 758 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 758 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLU A 857 " --> pdb=" O   LEU A 936 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LEU A 936 " --> pdb=" O   GLU A 857 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   SER A 859 " --> pdb=" O   ILE A 934 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE A 934 " --> pdb=" O   SER A 859 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   PHE A 861 " --> pdb=" O   LYS A 932 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   TYR A 928 " --> pdb=" O   ILE A 965 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE A 965 " --> pdb=" O   TYR A 928 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   ARG A 930 " --> pdb=" O   ALA A 963 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ALA A 963 " --> pdb=" O   ARG A 930 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LYS A 932 " --> pdb=" O   ASN A 961 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN A 952 " --> pdb=" O   ASN A 998 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A 956 " --> pdb=" O   GLY A 994 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR A 990 " --> pdb=" O   GLU A 960 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   VAL A 962 " --> pdb=" O   SER A 988 " (cutoff:3.500A)
      removed outlier: 11.187A  pdb=" N   SER A 988 " --> pdb=" O   VAL A 962 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   ALA A 239 " --> pdb=" O   GLY A 316 " (cutoff:3.500A)
      removed outlier: 5.230A  pdb=" N   GLY A 316 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL A 305 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR A 322 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN A 346 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASN A 339 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A 353 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU A 357 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR A 420 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LEU A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TRP A 514 " --> pdb=" O   TYR A 486 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 508 " --> pdb=" O   PHE A 492 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   TYR A 519 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   SER A 547 " --> pdb=" O   TYR A 519 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER A 543 " --> pdb=" O   GLN A 523 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 645
    Processing sheet with id=AA6, first strand: chain 'A' and resid 766 through 771
      removed outlier: 6.926A  pdb=" N   PHE A 767 " --> pdb=" O   MET A 778 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   MET A 778 " --> pdb=" O   PHE A 767 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   ASN A 769 " --> pdb=" O   VAL A 776 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   VAL A 776 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 787 " --> pdb=" O   MET A 778 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 793 through 796
      removed outlier: 6.511A  pdb=" N   ARG A 818 " --> pdb=" O   ASP A 794 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 923 through 925
      removed outlier: 8.591A  pdb=" N   ASP A 981 " --> pdb=" O   LYS A 869 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   TYR A 871 " --> pdb=" O   ASP A 981 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 113 through 114
    Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 132
      removed outlier: 3.560A  pdb=" N   ARG B 206 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LEU B 184 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ILE B 230 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL B 186 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   SER B 232 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 159
    Processing sheet with id=AB3, first strand: chain 'B' and resid 588 through 590
      removed outlier: 4.053A  pdb=" N   ASP B 615 " --> pdb=" O   SER B 679 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG B 734 " --> pdb=" O   SER B 686 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLY B 722 " --> pdb=" O   ASP B 698 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   LEU B 700 " --> pdb=" O   ASN B 720 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ASN B 720 " --> pdb=" O   LEU B 700 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   LYS B 702 " --> pdb=" O   PHE B 718 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   PHE B 718 " --> pdb=" O   LYS B 702 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LYS B 723 " --> pdb=" O   LEU B 758 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 758 " --> pdb=" O   LYS B 723 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLU B 857 " --> pdb=" O   LEU B 936 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   LEU B 936 " --> pdb=" O   GLU B 857 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   SER B 859 " --> pdb=" O   ILE B 934 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ILE B 934 " --> pdb=" O   SER B 859 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   PHE B 861 " --> pdb=" O   LYS B 932 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   TYR B 928 " --> pdb=" O   ILE B 965 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B 965 " --> pdb=" O   TYR B 928 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   ARG B 930 " --> pdb=" O   ALA B 963 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ALA B 963 " --> pdb=" O   ARG B 930 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   LYS B 932 " --> pdb=" O   ASN B 961 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN B 952 " --> pdb=" O   ASN B 998 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER B 956 " --> pdb=" O   GLY B 994 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR B 990 " --> pdb=" O   GLU B 960 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   VAL B 962 " --> pdb=" O   SER B 988 " (cutoff:3.500A)
      removed outlier: 11.188A  pdb=" N   SER B 988 " --> pdb=" O   VAL B 962 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   ALA B 239 " --> pdb=" O   GLY B 316 " (cutoff:3.500A)
      removed outlier: 5.230A  pdb=" N   GLY B 316 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   VAL B 305 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TYR B 322 " --> pdb=" O   GLY B 315 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLN B 346 " --> pdb=" O   SER B 325 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASN B 339 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL B 353 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   LEU B 357 " --> pdb=" O   VAL B 353 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR B 420 " --> pdb=" O   PHE B 460 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LEU B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TRP B 514 " --> pdb=" O   TYR B 486 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA B 508 " --> pdb=" O   PHE B 492 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TYR B 519 " --> pdb=" O   SER B 547 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   SER B 547 " --> pdb=" O   TYR B 519 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER B 543 " --> pdb=" O   GLN B 523 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 638 through 645
    Processing sheet with id=AB5, first strand: chain 'B' and resid 766 through 771
      removed outlier: 6.926A  pdb=" N   PHE B 767 " --> pdb=" O   MET B 778 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   MET B 778 " --> pdb=" O   PHE B 767 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   ASN B 769 " --> pdb=" O   VAL B 776 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   VAL B 776 " --> pdb=" O   TYR B 789 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL B 787 " --> pdb=" O   MET B 778 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 793 through 796
      removed outlier: 6.511A  pdb=" N   ARG B 818 " --> pdb=" O   ASP B 794 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 923 through 925
      removed outlier: 8.591A  pdb=" N   ASP B 981 " --> pdb=" O   LYS B 869 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   TYR B 871 " --> pdb=" O   ASP B 981 " (cutoff:3.500A)

    692 hydrogen bonds defined for protein.
    1918 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: 2.77

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4488
        1.34 -     1.46: 3205
        1.46 -     1.58: 6131
        1.58 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 13928
  Sorted by residual:
  bond pdb=" N   MET B 528 "
       pdb=" CA  MET B 528 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.46e+00
  bond pdb=" N   MET A 528 "
       pdb=" CA  MET A 528 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.015 1.29e-02 6.01e+03 1.41e+00
  bond pdb=" C   VAL A 256 "
       pdb=" O   VAL A 256 "
    ideal  model  delta    sigma   weight residual
    1.232  1.239 -0.007 8.90e-03 1.26e+04 6.28e-01
  bond pdb=" C   VAL B 256 "
       pdb=" O   VAL B 256 "
    ideal  model  delta    sigma   weight residual
    1.232  1.239 -0.007 8.90e-03 1.26e+04 5.89e-01
  bond pdb=" N   GLY B 449 "
       pdb=" CA  GLY B 449 "
    ideal  model  delta    sigma   weight residual
    1.454  1.448  0.007 9.90e-03 1.02e+04 4.67e-01
  ... (remaining 13923 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.09: 18500
        1.09 -     2.17: 296
        2.17 -     3.26: 94
        3.26 -     4.35: 14
        4.35 -     5.43: 4
  Bond angle restraints: 18908
  Sorted by residual:
  angle pdb=" C   MET B 528 "
        pdb=" CA  MET B 528 "
        pdb=" CB  MET B 528 "
      ideal   model   delta    sigma   weight residual
     110.42  115.85   -5.43 1.99e+00 2.53e-01 7.45e+00
  angle pdb=" C   MET A 528 "
        pdb=" CA  MET A 528 "
        pdb=" CB  MET A 528 "
      ideal   model   delta    sigma   weight residual
     110.42  115.81   -5.39 1.99e+00 2.53e-01 7.34e+00
  angle pdb=" C   ASN A 525 "
        pdb=" N   ILE A 526 "
        pdb=" CA  ILE A 526 "
      ideal   model   delta    sigma   weight residual
     121.97  125.88   -3.91 1.80e+00 3.09e-01 4.71e+00
  angle pdb=" C   ASN B 525 "
        pdb=" N   ILE B 526 "
        pdb=" CA  ILE B 526 "
      ideal   model   delta    sigma   weight residual
     121.97  125.87   -3.90 1.80e+00 3.09e-01 4.69e+00
  angle pdb=" C   ILE A 526 "
        pdb=" N   PHE A 527 "
        pdb=" CA  PHE A 527 "
      ideal   model   delta    sigma   weight residual
     121.54  125.58   -4.04 1.91e+00 2.74e-01 4.47e+00
  ... (remaining 18903 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.47: 7838
       14.47 -    28.95: 258
       28.95 -    43.42: 44
       43.42 -    57.90: 2
       57.90 -    72.37: 2
  Dihedral angle restraints: 8144
    sinusoidal: 3146
      harmonic: 4998
  Sorted by residual:
  dihedral pdb=" CA  LEU A 329 "
           pdb=" CB  LEU A 329 "
           pdb=" CG  LEU A 329 "
           pdb=" CD1 LEU A 329 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.30   45.70     3      1.50e+01 4.44e-03 8.21e+00
  dihedral pdb=" CA  LEU B 329 "
           pdb=" CB  LEU B 329 "
           pdb=" CG  LEU B 329 "
           pdb=" CD1 LEU B 329 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.32   45.68     3      1.50e+01 4.44e-03 8.21e+00
  dihedral pdb=" CA  VAL B 335 "
           pdb=" C   VAL B 335 "
           pdb=" N   LYS B 336 "
           pdb=" CA  LYS B 336 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -166.15  -13.85     0      5.00e+00 4.00e-02 7.68e+00
  ... (remaining 8141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1253
       0.028 -    0.056: 509
       0.056 -    0.084: 110
       0.084 -    0.112: 116
       0.112 -    0.140: 44
  Chirality restraints: 2032
  Sorted by residual:
  chirality pdb=" CA  ILE B 736 "
            pdb=" N   ILE B 736 "
            pdb=" C   ILE B 736 "
            pdb=" CB  ILE B 736 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  ILE A 736 "
            pdb=" N   ILE A 736 "
            pdb=" C   ILE A 736 "
            pdb=" CB  ILE A 736 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.88e-01
  chirality pdb=" CA  ILE B 955 "
            pdb=" N   ILE B 955 "
            pdb=" C   ILE B 955 "
            pdb=" CB  ILE B 955 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 2029 not shown)

  Planarity restraints: 2470
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 783 "   -0.015 5.00e-02 4.00e+02   2.32e-02 8.62e-01
        pdb=" N   PRO A 784 "    0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 784 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 784 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 783 "    0.015 5.00e-02 4.00e+02   2.31e-02 8.52e-01
        pdb=" N   PRO B 784 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO B 784 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 784 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 190 "    0.014 5.00e-02 4.00e+02   2.14e-02 7.35e-01
        pdb=" N   PRO A 191 "   -0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO A 191 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 191 "    0.012 5.00e-02 4.00e+02
  ... (remaining 2467 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2151
        2.77 -     3.30: 11727
        3.30 -     3.84: 20743
        3.84 -     4.37: 23542
        4.37 -     4.90: 45403
  Nonbonded interactions: 103566
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 283 "
            pdb=" OH  TYR A 406 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OH  TYR B 283 "
            pdb=" OH  TYR B 406 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG1 THR B 571 "
            pdb=" OG  SER B 595 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR A 571 "
            pdb=" OG  SER A 595 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD1 ASP B 550 "
            pdb=" OH  TYR B 633 "
     model   vdw
     2.276 3.040
  ... (remaining 103561 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.930
  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:             0.030
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     18.950
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
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      :  0.001   0.017  13928  Z= 0.075
  Angle     :  0.407   5.433  18908  Z= 0.225
  Chirality :  0.041   0.140   2032
  Planarity :  0.002   0.023   2470
  Dihedral  :  7.457  72.370   4968
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.66 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.21), residues: 1732
  helix: -0.61 (0.47), residues: 142
  sheet:  1.37 (0.20), residues: 780
  loop : -0.71 (0.23), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 302 
 TYR   0.006   0.001   TYR A 265 
 PHE   0.008   0.001   PHE B 527 
 TRP   0.011   0.001   TRP A 455 
 HIS   0.001   0.000   HIS B 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00130 (13928)
  covalent geometry    : angle       0.40732 (18908)
  hydrogen bonds       : bond        0.27746 (  692)
  hydrogen bonds       : angle       8.83139 ( 1918)

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

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.506 
Fit side-chains
REVERT: B  699 MET cc_start: 0.8600 (ttm) cc_final: 0.8330 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0957
  time to fit residues: 10.0243
Evaluate side-chains
  55 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0050
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    2.4002

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
A 496 HIS
A 515 ASN
** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 628 GLN
A 665 HIS
A 753 ASN
A 769 ASN
** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 401 GLN
B 481 ASN
B 496 HIS
B 515 ASN
** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 628 GLN
B 665 HIS
B 753 ASN
B 840 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.066272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.052570 restraints weight = 79550.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 3.81
r_work: 0.3113 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13928  Z= 0.157
  Angle     :  0.559   5.883  18908  Z= 0.311
  Chirality :  0.045   0.147   2032
  Planarity :  0.004   0.030   2470
  Dihedral  :  3.850  18.144   1890
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.41 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  1.70 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.21), residues: 1732
  helix: -0.89 (0.44), residues: 132
  sheet:  1.26 (0.18), residues: 788
  loop : -0.77 (0.23), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 302 
 TYR   0.015   0.001   TYR B 265 
 PHE   0.017   0.001   PHE B 527 
 TRP   0.015   0.001   TRP B 455 
 HIS   0.005   0.001   HIS B 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (13928)
  covalent geometry    : angle       0.55928 (18908)
  hydrogen bonds       : bond        0.04961 (  692)
  hydrogen bonds       : angle       5.61080 ( 1918)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.550 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7586 (t80)
  outliers start: 5
  outliers final: 2
  residues processed: 59
  average time/residue: 0.0950
  time to fit residues: 9.1880
Evaluate side-chains
  58 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 173 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0870
   chunk 20 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 171 optimal weight:    0.0770
   overall best weight:    1.2322

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

Flipped N/Q/H residues before XYZ refinement:
A 537 ASN
B 537 ASN
B 769 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.067298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.053338 restraints weight = 83437.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 3.40
r_work: 0.3150 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  13928  Z= 0.103
  Angle     :  0.487   5.691  18908  Z= 0.269
  Chirality :  0.043   0.147   2032
  Planarity :  0.003   0.030   2470
  Dihedral  :  3.648  16.337   1890
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.89 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.04 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.20), residues: 1732
  helix: -0.39 (0.46), residues: 120
  sheet:  1.34 (0.18), residues: 786
  loop : -0.70 (0.23), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 476 
 TYR   0.010   0.001   TYR A 519 
 PHE   0.013   0.001   PHE B 527 
 TRP   0.017   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 (13928)
  covalent geometry    : angle       0.48712 (18908)
  hydrogen bonds       : bond        0.04082 (  692)
  hydrogen bonds       : angle       5.05191 ( 1918)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.575 
Fit side-chains
REVERT: A  955 ILE cc_start: 0.8943 (mt) cc_final: 0.8742 (tt)
REVERT: B  742 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7605 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 60
  average time/residue: 0.0915
  time to fit residues: 8.8530
Evaluate side-chains
  59 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 168 optimal weight:    8.9990
   chunk 29 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 128 optimal weight:    8.9990
   chunk 10 optimal weight:    0.3980
   chunk 92 optimal weight:    7.9990
   overall best weight:    4.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 417 HIS
B 769 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.064316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.050712 restraints weight = 65854.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 3.01
r_work: 0.3083 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  13928  Z= 0.238
  Angle     :  0.610   6.959  18908  Z= 0.341
  Chirality :  0.046   0.155   2032
  Planarity :  0.004   0.049   2470
  Dihedral  :  4.317  21.461   1890
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.16 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  2.24 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.20), residues: 1732
  helix: -1.53 (0.40), residues: 132
  sheet:  1.10 (0.17), residues: 798
  loop : -1.08 (0.22), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 906 
 TYR   0.019   0.002   TYR B 265 
 PHE   0.013   0.002   PHE B 844 
 TRP   0.018   0.001   TRP A 455 
 HIS   0.006   0.002   HIS B 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 (13928)
  covalent geometry    : angle       0.60968 (18908)
  hydrogen bonds       : bond        0.05507 (  692)
  hydrogen bonds       : angle       5.18225 ( 1918)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.517 
Fit side-chains
REVERT: A  955 ILE cc_start: 0.8987 (mt) cc_final: 0.8771 (tt)
REVERT: B  742 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7697 (t80)
  outliers start: 7
  outliers final: 4
  residues processed: 58
  average time/residue: 0.0931
  time to fit residues: 9.0907
Evaluate side-chains
  60 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 108 optimal weight:    3.9990
   chunk 141 optimal weight:    7.9990
   chunk 96 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 165 optimal weight:    5.9990
   chunk 125 optimal weight:    9.9990
   chunk 172 optimal weight:    0.0000
   chunk 85 optimal weight:    4.9990
   chunk 144 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    2.5190

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

Flipped N/Q/H residues before XYZ refinement:
A 671 GLN
A 806 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.065165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.051185 restraints weight = 83853.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 3.40
r_work: 0.3088 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  13928  Z= 0.155
  Angle     :  0.541   6.690  18908  Z= 0.302
  Chirality :  0.044   0.149   2032
  Planarity :  0.004   0.034   2470
  Dihedral  :  4.143  19.232   1890
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.82 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  2.93 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.20), residues: 1732
  helix: -1.10 (0.43), residues: 120
  sheet:  1.05 (0.17), residues: 802
  loop : -0.98 (0.22), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 906 
 TYR   0.016   0.001   TYR B 265 
 PHE   0.012   0.001   PHE A 527 
 TRP   0.014   0.001   TRP A 455 
 HIS   0.005   0.001   HIS B 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (13928)
  covalent geometry    : angle       0.54074 (18908)
  hydrogen bonds       : bond        0.04617 (  692)
  hydrogen bonds       : angle       5.02304 ( 1918)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.583 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7689 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 58
  average time/residue: 0.0886
  time to fit residues: 8.7241
Evaluate side-chains
  59 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 83 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 131 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0470
   chunk 136 optimal weight:    8.9990
   chunk 162 optimal weight:    4.9990
   overall best weight:    3.2086

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.064552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.051393 restraints weight = 51922.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.67
r_work: 0.3110 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8767
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13928  Z= 0.185
  Angle     :  0.564   7.071  18908  Z= 0.316
  Chirality :  0.045   0.148   2032
  Planarity :  0.004   0.041   2470
  Dihedral  :  4.260  19.960   1890
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.22 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.13 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.20), residues: 1732
  helix: -1.53 (0.40), residues: 132
  sheet:  0.99 (0.17), residues: 802
  loop : -1.14 (0.22), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 906 
 TYR   0.018   0.001   TYR B 265 
 PHE   0.012   0.002   PHE A 527 
 TRP   0.016   0.001   TRP A 455 
 HIS   0.005   0.001   HIS B 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (13928)
  covalent geometry    : angle       0.56406 (18908)
  hydrogen bonds       : bond        0.04958 (  692)
  hydrogen bonds       : angle       5.01969 ( 1918)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.551 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7736 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 57
  average time/residue: 0.0914
  time to fit residues: 8.8756
Evaluate side-chains
  60 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 168 optimal weight:    9.9990
   chunk 63 optimal weight:    9.9990
   chunk 105 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 121 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 115 optimal weight:    9.9990
   chunk 118 optimal weight:    6.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    3.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.064505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.050462 restraints weight = 89365.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.50
r_work: 0.3065 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13928  Z= 0.183
  Angle     :  0.562   7.102  18908  Z= 0.316
  Chirality :  0.045   0.149   2032
  Planarity :  0.004   0.040   2470
  Dihedral  :  4.291  19.943   1890
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.14
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.16 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.67 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.20), residues: 1732
  helix: -1.51 (0.40), residues: 132
  sheet:  0.96 (0.17), residues: 790
  loop : -1.14 (0.22), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 906 
 TYR   0.018   0.001   TYR B 265 
 PHE   0.013   0.002   PHE A 527 
 TRP   0.017   0.001   TRP A 455 
 HIS   0.005   0.001   HIS B 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (13928)
  covalent geometry    : angle       0.56250 (18908)
  hydrogen bonds       : bond        0.04903 (  692)
  hydrogen bonds       : angle       4.99543 ( 1918)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.549 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7729 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 57
  average time/residue: 0.0932
  time to fit residues: 9.0867
Evaluate side-chains
  60 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 108 optimal weight:    4.9990
   chunk 121 optimal weight:    2.9990
   chunk 139 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 154 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   chunk 92 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 769 ASN
** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.065834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.052492 restraints weight = 56502.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.81
r_work: 0.3136 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  13928  Z= 0.119
  Angle     :  0.501   6.462  18908  Z= 0.280
  Chirality :  0.044   0.149   2032
  Planarity :  0.003   0.033   2470
  Dihedral  :  4.006  17.195   1890
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.64 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  3.88 %
    Favored  : 95.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.20), residues: 1732
  helix: -0.89 (0.44), residues: 120
  sheet:  1.02 (0.17), residues: 800
  loop : -0.96 (0.22), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 906 
 TYR   0.013   0.001   TYR B 265 
 PHE   0.013   0.001   PHE A 527 
 TRP   0.016   0.001   TRP A 455 
 HIS   0.005   0.001   HIS B 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (13928)
  covalent geometry    : angle       0.50135 (18908)
  hydrogen bonds       : bond        0.04001 (  692)
  hydrogen bonds       : angle       4.80232 ( 1918)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7744 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 0.0954
  time to fit residues: 9.1409
Evaluate side-chains
  59 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 139 optimal weight:    6.9990
   chunk 126 optimal weight:    9.9990
   chunk 57 optimal weight:    7.9990
   chunk 86 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 125 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 769 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.063353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.049244 restraints weight = 89673.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 3.51
r_work: 0.3026 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  13928  Z= 0.282
  Angle     :  0.650   7.854  18908  Z= 0.365
  Chirality :  0.048   0.175   2032
  Planarity :  0.005   0.062   2470
  Dihedral  :  4.611  22.324   1890
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.97 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.95 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.19), residues: 1732
  helix: -1.73 (0.40), residues: 132
  sheet:  0.91 (0.17), residues: 764
  loop : -1.28 (0.21), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 906 
 TYR   0.022   0.002   TYR B 265 
 PHE   0.013   0.002   PHE B 844 
 TRP   0.021   0.002   TRP A 455 
 HIS   0.007   0.002   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 (13928)
  covalent geometry    : angle       0.65040 (18908)
  hydrogen bonds       : bond        0.05847 (  692)
  hydrogen bonds       : angle       5.09982 ( 1918)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.529 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7766 (t80)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0918
  time to fit residues: 8.9786
Evaluate side-chains
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  455 TRP
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 129 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 119 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 154 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.063657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.049500 restraints weight = 92558.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 3.57
r_work: 0.3035 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  13928  Z= 0.243
  Angle     :  0.617   7.712  18908  Z= 0.346
  Chirality :  0.047   0.161   2032
  Planarity :  0.005   0.055   2470
  Dihedral  :  4.561  21.609   1890
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.68 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.95 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.19), residues: 1732
  helix: -1.77 (0.39), residues: 132
  sheet:  0.78 (0.17), residues: 792
  loop : -1.33 (0.22), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 906 
 TYR   0.021   0.002   TYR B 265 
 PHE   0.012   0.002   PHE B 922 
 TRP   0.021   0.002   TRP A 455 
 HIS   0.006   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (13928)
  covalent geometry    : angle       0.61701 (18908)
  hydrogen bonds       : bond        0.05493 (  692)
  hydrogen bonds       : angle       5.07986 ( 1918)

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

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

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3464 Ramachandran restraints generated.
    1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.427 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7710 (t80)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0924
  time to fit residues: 9.0738
Evaluate side-chains
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  455 TRP
Chi-restraints excluded: chain B residue  736 ILE
Chi-restraints excluded: chain B residue  742 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 67 optimal weight:    9.9990
   chunk 118 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   chunk 121 optimal weight:    2.9990
   chunk 151 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 136 optimal weight:   10.0000
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.064876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.051646 restraints weight = 52772.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.71
r_work: 0.3112 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13928  Z= 0.149
  Angle     :  0.535   7.059  18908  Z= 0.300
  Chirality :  0.044   0.151   2032
  Planarity :  0.004   0.036   2470
  Dihedral  :  4.250  19.445   1890
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.22 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  4.08 %
    Favored  : 95.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.20), residues: 1732
  helix: -1.53 (0.40), residues: 132
  sheet:  0.88 (0.17), residues: 798
  loop : -1.23 (0.22), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 906 
 TYR   0.016   0.001   TYR B 265 
 PHE   0.013   0.001   PHE A 527 
 TRP   0.018   0.001   TRP A 455 
 HIS   0.005   0.001   HIS B 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (13928)
  covalent geometry    : angle       0.53545 (18908)
  hydrogen bonds       : bond        0.04498 (  692)
  hydrogen bonds       : angle       4.91686 ( 1918)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3903.93 seconds
wall clock time: 67 minutes 12.86 seconds (4032.86 seconds total)