Starting phenix.real_space_refine
on Thu Jul 31 18:00:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aa4_15293/07_2025/8aa4_15293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aa4_15293/07_2025/8aa4_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_15293/07_2025/8aa4_15293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aa4_15293/07_2025/8aa4_15293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aa4_15293/07_2025/8aa4_15293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aa4_15293/07_2025/8aa4_15293.cif"
  }
  resolution = 3.1
  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=   0.002
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 18.67, per 1000 atoms: 1.37
  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: 3.03
  Conformation dependent library (CDL) restraints added in 2.9 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: 1.62
  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: 5.48

  Time building geometry restraints manager: 3.81 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: 0.07
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:             2.640
  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:          0.630
  Check model and map are aligned:         0.100
  Set scattering table:                    0.150
  Process input model:                     46.040
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.740
-------------------------------------------------------------------------------
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 (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:  0.39 (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
 TRP   0.011   0.001   TRP A 455 
 HIS   0.001   0.000   HIS B 665 
 PHE   0.008   0.001   PHE B 527 
 TYR   0.006   0.001   TYR A 265 
 ARG   0.001   0.000   ARG B 302 

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

*********************** 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  : 1.419 
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: 0.2125
  time to fit residues: 22.5097
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  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:   20.0000
   chunk 131 optimal weight:    8.9990
   chunk 73 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0170
   chunk 88 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 136 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0010
   chunk 82 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9980
   chunk 158 optimal weight:    6.9990
   overall best weight:    3.0028

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
A 490 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 481 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: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.065638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.051922 restraints weight = 69581.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 3.09
r_work: 0.3117 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3134
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    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 = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13928  Z= 0.182
  Angle     :  0.581   6.265  18908  Z= 0.324
  Chirality :  0.045   0.148   2032
  Planarity :  0.004   0.037   2470
  Dihedral  :  4.006  19.251   1890
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.41 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.90 %
    Favored  : 97.82 %
  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:  0.13 (0.21), residues: 1732
  helix: -1.07 (0.43), residues: 132
  sheet:  1.23 (0.18), residues: 774
  loop : -0.85 (0.22), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.005   0.001   HIS B 806 
 PHE   0.017   0.002   PHE B 527 
 TYR   0.017   0.002   TYR B 265 
 ARG   0.003   0.001   ARG A 302 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05469 (  692)
  hydrogen bonds       : angle       5.62623 ( 1918)
  covalent geometry    : bond        0.00418 (13928)
  covalent geometry    : angle       0.58107 (18908)

*********************** 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
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 1.580 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7586 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 59
  average time/residue: 0.2285
  time to fit residues: 22.0155
Evaluate side-chains
  57 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
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 55 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 155 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 143 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 111 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 105 optimal weight:    9.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 GLN
** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 401 GLN
B 417 HIS
** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 769 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.065833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.052232 restraints weight = 65359.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 3.00
r_work: 0.3130 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    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 = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.1940

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= 0.140
  Angle     :  0.529   6.253  18908  Z= 0.294
  Chirality :  0.044   0.147   2032
  Planarity :  0.003   0.031   2470
  Dihedral  :  3.927  18.353   1890
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.24 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  2.11 %
    Favored  : 97.55 %
  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:  0.19 (0.20), residues: 1732
  helix: -0.82 (0.44), residues: 120
  sheet:  1.22 (0.18), residues: 782
  loop : -0.83 (0.22), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 455 
 HIS   0.005   0.001   HIS B 806 
 PHE   0.012   0.001   PHE B 527 
 TYR   0.013   0.001   TYR B 265 
 ARG   0.002   0.000   ARG B 906 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04778 (  692)
  hydrogen bonds       : angle       5.16028 ( 1918)
  covalent geometry    : bond        0.00310 (13928)
  covalent geometry    : angle       0.52924 (18908)

*********************** 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
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 1.453 
Fit side-chains
REVERT: A  955 ILE cc_start: 0.9046 (mt) cc_final: 0.8835 (tt)
REVERT: B  742 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7753 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 58
  average time/residue: 0.2138
  time to fit residues: 21.3166
Evaluate side-chains
  59 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
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 43 optimal weight:    6.9990
   chunk 143 optimal weight:    0.9980
   chunk 107 optimal weight:   10.0000
   chunk 61 optimal weight:    8.9990
   chunk 151 optimal weight:   20.0000
   chunk 170 optimal weight:    8.9990
   chunk 165 optimal weight:    7.9990
   chunk 142 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3485 r_free = 0.3485 target = 0.064245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.051022 restraints weight = 52958.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.70
r_work: 0.3098 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13928  Z= 0.215
  Angle     :  0.603   7.139  18908  Z= 0.338
  Chirality :  0.046   0.150   2032
  Planarity :  0.004   0.048   2470
  Dihedral  :  4.367  21.076   1890
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.22 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  2.59 %
    Favored  : 96.94 %
  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: -0.21 (0.20), residues: 1732
  helix: -1.59 (0.40), residues: 132
  sheet:  1.05 (0.17), residues: 800
  loop : -1.15 (0.22), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 455 
 HIS   0.006   0.002   HIS B 806 
 PHE   0.014   0.002   PHE A 527 
 TYR   0.019   0.002   TYR B 265 
 ARG   0.004   0.000   ARG B 906 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05418 (  692)
  hydrogen bonds       : angle       5.18487 ( 1918)
  covalent geometry    : bond        0.00507 (13928)
  covalent geometry    : angle       0.60294 (18908)

*********************** 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
  64 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 1.450 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7750 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 60
  average time/residue: 0.2099
  time to fit residues: 21.3184
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  : 1.439 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 172 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 130 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 124 optimal weight:    1.9990
   chunk 161 optimal weight:    7.9990
   chunk 101 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 166 optimal weight:    0.8980
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 806 HIS
** B 537 ASN ** 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 = 0.3503 r_free = 0.3503 target = 0.065033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.051483 restraints weight = 65478.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 3.00
r_work: 0.3104 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  13928  Z= 0.156
  Angle     :  0.543   6.794  18908  Z= 0.304
  Chirality :  0.044   0.150   2032
  Planarity :  0.004   0.035   2470
  Dihedral  :  4.193  19.367   1890
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.99 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  3.13 %
    Favored  : 96.53 %
  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: -0.09 (0.20), residues: 1732
  helix: -1.10 (0.43), residues: 120
  sheet:  1.00 (0.17), residues: 806
  loop : -1.02 (0.22), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 455 
 HIS   0.005   0.001   HIS B 806 
 PHE   0.013   0.001   PHE A 527 
 TYR   0.016   0.001   TYR B 265 
 ARG   0.002   0.000   ARG B 906 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04656 (  692)
  hydrogen bonds       : angle       5.04197 ( 1918)
  covalent geometry    : bond        0.00353 (13928)
  covalent geometry    : angle       0.54322 (18908)

*********************** 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
  60 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 1.466 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7703 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 0.2159
  time to fit residues: 20.9328
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  : 1.565 
-------------------------------------------------------------------------------
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 131 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 104 optimal weight:    0.7980
   chunk 143 optimal weight:    2.9990
   chunk 169 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 166 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 515 ASN
A 537 ASN
A 809 GLN
A 913 ASN
B 496 HIS
B 537 ASN
B 769 ASN
B 806 HIS
B 809 GLN
B 913 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.066782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.053103 restraints weight = 69919.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 3.13
r_work: 0.3144 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3155
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  13928  Z= 0.098
  Angle     :  0.480   6.015  18908  Z= 0.266
  Chirality :  0.043   0.148   2032
  Planarity :  0.003   0.034   2470
  Dihedral  :  3.849  16.119   1890
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.53 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  3.40 %
    Favored  : 96.26 %
  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:  0.09 (0.20), residues: 1732
  helix: -0.70 (0.44), residues: 120
  sheet:  1.07 (0.17), residues: 798
  loop : -0.86 (0.22), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 455 
 HIS   0.004   0.001   HIS B 806 
 PHE   0.014   0.001   PHE A 527 
 TYR   0.011   0.001   TYR B 265 
 ARG   0.002   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  692)
  hydrogen bonds       : angle       4.78510 ( 1918)
  covalent geometry    : bond        0.00196 (13928)
  covalent geometry    : angle       0.47965 (18908)

*********************** 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
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 1.612 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7691 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 58
  average time/residue: 0.2369
  time to fit residues: 22.6009
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  : 1.574 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 116 optimal weight:   10.0000
   chunk 160 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 126 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 156 optimal weight:    7.9990
   overall best weight:    2.0988

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.065781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.052533 restraints weight = 52508.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.71
r_work: 0.3136 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  13928  Z= 0.133
  Angle     :  0.509   6.469  18908  Z= 0.285
  Chirality :  0.044   0.148   2032
  Planarity :  0.003   0.036   2470
  Dihedral  :  3.950  17.217   1890
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.93 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.95 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.20), residues: 1732
  helix: -0.78 (0.44), residues: 120
  sheet:  1.07 (0.17), residues: 798
  loop : -0.90 (0.22), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 455 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.013   0.001   PHE A 527 
 TYR   0.015   0.001   TYR B 265 
 ARG   0.003   0.000   ARG A 805 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04167 (  692)
  hydrogen bonds       : angle       4.79435 ( 1918)
  covalent geometry    : bond        0.00297 (13928)
  covalent geometry    : angle       0.50934 (18908)

*********************** 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
  61 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 1.426 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7775 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 57
  average time/residue: 0.2099
  time to fit residues: 20.2472
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  : 1.425 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 119 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0000
   chunk 163 optimal weight:    0.5980
   chunk 9 optimal weight:    8.9990
   chunk 126 optimal weight:    9.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    1.4988

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.066405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.052260 restraints weight = 90922.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 3.57
r_work: 0.3110 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.2360

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= 0.109
  Angle     :  0.485   6.129  18908  Z= 0.270
  Chirality :  0.043   0.148   2032
  Planarity :  0.003   0.034   2470
  Dihedral  :  3.847  16.249   1890
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.29 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.01 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.20), residues: 1732
  helix: -0.63 (0.44), residues: 120
  sheet:  1.09 (0.17), residues: 798
  loop : -0.84 (0.22), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 455 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.014   0.001   PHE A 527 
 TYR   0.012   0.001   TYR B 265 
 ARG   0.003   0.000   ARG A 805 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03727 (  692)
  hydrogen bonds       : angle       4.69190 ( 1918)
  covalent geometry    : bond        0.00231 (13928)
  covalent geometry    : angle       0.48482 (18908)

*********************** 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  : 1.570 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7716 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 0.2147
  time to fit residues: 20.5165
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  : 1.559 
-------------------------------------------------------------------------------
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 166 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 147 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 107 optimal weight:   10.0000
   chunk 117 optimal weight:    7.9990
   chunk 109 optimal weight:    6.9990
   chunk 139 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 138 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 809 GLN
A 913 ASN
B 809 GLN
B 913 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.063314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.049926 restraints weight = 57397.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.81
r_work: 0.3066 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.046  13928  Z= 0.314
  Angle     :  0.669   7.804  18908  Z= 0.375
  Chirality :  0.049   0.185   2032
  Planarity :  0.005   0.065   2470
  Dihedral  :  4.629  22.535   1890
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.14 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  3.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.19), residues: 1732
  helix: -1.74 (0.39), residues: 132
  sheet:  0.94 (0.17), residues: 764
  loop : -1.25 (0.21), residues: 836

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05976 (  692)
  hydrogen bonds       : angle       5.09398 ( 1918)
  covalent geometry    : bond        0.00753 (13928)
  covalent geometry    : angle       0.66922 (18908)

*********************** 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
  62 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 1.584 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7802 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 57
  average time/residue: 0.2160
  time to fit residues: 20.9583
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  : 1.538 
-------------------------------------------------------------------------------
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  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 12 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    6.9990
   chunk 144 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0670
   chunk 2 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 122 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
B 809 GLN
B 913 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.066414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.053145 restraints weight = 55258.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.78
r_work: 0.3154 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  13928  Z= 0.098
  Angle     :  0.488   6.334  18908  Z= 0.272
  Chirality :  0.043   0.150   2032
  Planarity :  0.003   0.034   2470
  Dihedral  :  4.001  16.932   1890
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.83 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.29 %
    Favored  : 95.44 %
  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: -0.02 (0.20), residues: 1732
  helix: -0.75 (0.44), residues: 120
  sheet:  1.01 (0.17), residues: 796
  loop : -0.96 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 455 
 HIS   0.002   0.001   HIS A 665 
 PHE   0.016   0.001   PHE A 527 
 TYR   0.011   0.001   TYR B 265 
 ARG   0.002   0.000   ARG A 805 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  692)
  hydrogen bonds       : angle       4.79592 ( 1918)
  covalent geometry    : bond        0.00192 (13928)
  covalent geometry    : angle       0.48822 (18908)

********************** 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
  58 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 1.496 
Fit side-chains
REVERT: B  742 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7754 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 56
  average time/residue: 0.2064
  time to fit residues: 19.6494
Evaluate side-chains
  58 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 123 optimal weight:    0.5980
   chunk 90 optimal weight:    0.3980
   chunk 1 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   chunk 148 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
** B 913 ASN ** 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 = 0.3498 r_free = 0.3498 target = 0.064975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.051755 restraints weight = 51777.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.68
r_work: 0.3117 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    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 = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.2504

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= 0.163
  Angle     :  0.540   6.972  18908  Z= 0.302
  Chirality :  0.044   0.148   2032
  Planarity :  0.004   0.037   2470
  Dihedral  :  4.140  18.368   1890
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.99 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.29 %
    Favored  : 95.37 %
  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: -0.20 (0.20), residues: 1732
  helix: -1.29 (0.41), residues: 132
  sheet:  1.00 (0.17), residues: 784
  loop : -1.08 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 455 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.013   0.001   PHE A 527 
 TYR   0.018   0.001   TYR B 265 
 ARG   0.003   0.000   ARG A 805 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04582 (  692)
  hydrogen bonds       : angle       4.83130 ( 1918)
  covalent geometry    : bond        0.00375 (13928)
  covalent geometry    : angle       0.53975 (18908)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8616.98 seconds
wall clock time: 147 minutes 32.87 seconds (8852.87 seconds total)