Starting phenix.real_space_refine
on Wed Jun 25 23:59:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wro_37784/06_2025/8wro_37784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wro_37784/06_2025/8wro_37784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wro_37784/06_2025/8wro_37784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wro_37784/06_2025/8wro_37784.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wro_37784/06_2025/8wro_37784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wro_37784/06_2025/8wro_37784.cif"
  }
  resolution = 3.9
  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=   0.045
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     146      5.16       5
     C   19060      2.51       5
     N    4969      2.21       5
     O    5632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 29807
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1067, 8364
          Classifications: {'peptide': 1067}
          Link IDs: {'PTRANS': 57, 'TRANS': 1009}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 8295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1059, 8295
          Classifications: {'peptide': 1059}
          Link IDs: {'PTRANS': 57, 'TRANS': 1001}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 8303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1060, 8303
          Classifications: {'peptide': 1060}
          Link IDs: {'PTRANS': 57, 'TRANS': 1002}
          Chain breaks: 5
    Chain: "D"
      Number of atoms: 4845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 4845
          Classifications: {'peptide': 594}
          Link IDs: {'PTRANS': 27, 'TRANS': 566}
  Time building chain proxies: 15.96, per 1000 atoms: 0.54
  Number of scatterers: 29807
  At special positions: 0
  Unit cell: (151.84, 164.32, 236.08, 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     146     16.00
     O    5632      8.00
     N    4969      7.00
     C   19060      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=40, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 133 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 535 " - pdb=" SG  CYS A 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 614 " - pdb=" SG  CYS A 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 659 " - pdb=" SG  CYS A 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 735 " - pdb=" SG  CYS A 757 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 740 " - pdb=" SG  CYS A 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1029 " - pdb=" SG  CYS A1040 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1079 " - pdb=" SG  CYS A1123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  15 " - pdb=" SG  CYS B 133 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 288 " - pdb=" SG  CYS B 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 388 " - pdb=" SG  CYS B 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 477 " - pdb=" SG  CYS B 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 535 " - pdb=" SG  CYS B 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 614 " - pdb=" SG  CYS B 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 659 " - pdb=" SG  CYS B 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 735 " - pdb=" SG  CYS B 757 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 740 " - pdb=" SG  CYS B 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1029 " - pdb=" SG  CYS B1040 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1079 " - pdb=" SG  CYS B1123 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  15 " - pdb=" SG  CYS C 133 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 163 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 288 " - pdb=" SG  CYS C 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 333 " - pdb=" SG  CYS C 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 388 " - pdb=" SG  CYS C 522 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 535 " - pdb=" SG  CYS C 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 614 " - pdb=" SG  CYS C 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 659 " - pdb=" SG  CYS C 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 735 " - pdb=" SG  CYS C 757 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 740 " - pdb=" SG  CYS C 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1029 " - pdb=" SG  CYS C1040 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1079 " - pdb=" SG  CYS C1123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03

  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: 6.29
  Conformation dependent library (CDL) restraints added in 3.3 seconds
  

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  7100

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 48 sheets defined
      28.1% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 291 through 300
    Processing helix  chain 'A' and resid 334 through 340
    Processing helix  chain 'A' and resid 361 through 368
      removed outlier: 3.785A  pdb=" N   ASN A 367 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   PHE A 368 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
    Processing helix  chain 'A' and resid 734 through 740
    Processing helix  chain 'A' and resid 743 through 751
      removed outlier: 3.541A  pdb=" N   SER A 747 " --> pdb=" O   SER A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 754
      No H-bonds generated for 'chain 'A' and resid 752 through 754'
    Processing helix  chain 'A' and resid 756 through 775
      removed outlier: 4.312A  pdb=" N   THR A 775 " --> pdb=" O   GLN A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 778
      No H-bonds generated for 'chain 'A' and resid 776 through 778'
    Processing helix  chain 'A' and resid 813 through 823
    Processing helix  chain 'A' and resid 847 through 852
    Processing helix  chain 'A' and resid 863 through 881
    Processing helix  chain 'A' and resid 883 through 887
    Processing helix  chain 'A' and resid 894 through 905
    Processing helix  chain 'A' and resid 912 through 915
    Processing helix  chain 'A' and resid 916 through 938
      removed outlier: 4.075A  pdb=" N   GLN A 932 " --> pdb=" O   ILE A 928 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ASP A 933 " --> pdb=" O   GLY A 929 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   THR A 938 " --> pdb=" O   SER A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 964
      removed outlier: 3.548A  pdb=" N   GLN A 946 " --> pdb=" O   LEU A 942 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN A 952 " --> pdb=" O   VAL A 948 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   SER A 964 " --> pdb=" O   VAL A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 981
      removed outlier: 3.934A  pdb=" N   ILE A 977 " --> pdb=" O   VAL A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 987
      removed outlier: 3.650A  pdb=" N   GLU A 987 " --> pdb=" O   PRO A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 1030
      removed outlier: 3.601A  pdb=" N   GLU A1014 " --> pdb=" O   ILE A1010 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 301
    Processing helix  chain 'B' and resid 334 through 340
      removed outlier: 3.521A  pdb=" N   VAL B 338 " --> pdb=" O   PRO B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 384
    Processing helix  chain 'B' and resid 403 through 407
      removed outlier: 3.952A  pdb=" N   ILE B 407 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 419
    Processing helix  chain 'B' and resid 735 through 740
    Processing helix  chain 'B' and resid 743 through 751
      removed outlier: 3.536A  pdb=" N   SER B 747 " --> pdb=" O   SER B 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 756 through 774
      removed outlier: 3.694A  pdb=" N   LEU B 760 " --> pdb=" O   PHE B 756 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 780
    Processing helix  chain 'B' and resid 813 through 823
    Processing helix  chain 'B' and resid 849 through 853
      removed outlier: 3.781A  pdb=" N   ASN B 853 " --> pdb=" O   GLN B 850 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 863 through 881
    Processing helix  chain 'B' and resid 883 through 887
      removed outlier: 3.564A  pdb=" N   GLY B 886 " --> pdb=" O   TRP B 883 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 905
      removed outlier: 3.598A  pdb=" N   GLY B 905 " --> pdb=" O   TYR B 901 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 910 through 916
      removed outlier: 3.907A  pdb=" N   TYR B 914 " --> pdb=" O   GLN B 910 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 916 through 938
      removed outlier: 3.685A  pdb=" N   ILE B 931 " --> pdb=" O   ALA B 927 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   GLN B 932 " --> pdb=" O   ILE B 928 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ASP B 933 " --> pdb=" O   GLY B 929 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   THR B 938 " --> pdb=" O   SER B 934 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 961
      removed outlier: 5.074A  pdb=" N   VAL B 948 " --> pdb=" O   LYS B 944 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL B 949 " --> pdb=" O   LEU B 945 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ASN B 952 " --> pdb=" O   VAL B 948 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 973 through 980
      removed outlier: 3.958A  pdb=" N   ILE B 977 " --> pdb=" O   VAL B 973 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 978 " --> pdb=" O   LEU B 974 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   SER B 979 " --> pdb=" O   ASN B 975 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 982 through 1030
      removed outlier: 4.061A  pdb=" N   GLU B 987 " --> pdb=" O   PRO B 983 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   VAL B 988 " --> pdb=" O   PRO B 984 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   GLN B 989 " --> pdb=" O   GLU B 985 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ASP B 991 " --> pdb=" O   GLU B 987 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   ARG B 992 " --> pdb=" O   VAL B 988 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU B 993 " --> pdb=" O   GLN B 989 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLU B1014 " --> pdb=" O   ILE B1010 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 301
    Processing helix  chain 'C' and resid 404 through 408
      removed outlier: 3.738A  pdb=" N   ILE C 407 " --> pdb=" O   VAL C 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 499 through 502
    Processing helix  chain 'C' and resid 734 through 739
    Processing helix  chain 'C' and resid 743 through 751
      removed outlier: 3.666A  pdb=" N   SER C 747 " --> pdb=" O   SER C 743 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 757 through 780
      removed outlier: 3.508A  pdb=" N   LYS C 761 " --> pdb=" O   CYS C 757 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   THR C 775 " --> pdb=" O   GLN C 771 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   GLN C 776 " --> pdb=" O   ASP C 772 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU C 777 " --> pdb=" O   LYS C 773 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 813 through 823
      removed outlier: 3.638A  pdb=" N   VAL C 823 " --> pdb=" O   LEU C 819 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 865 through 881
    Processing helix  chain 'C' and resid 883 through 888
      removed outlier: 3.704A  pdb=" N   ALA C 887 " --> pdb=" O   TRP C 883 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 894 through 905
    Processing helix  chain 'C' and resid 910 through 916
      removed outlier: 3.939A  pdb=" N   TYR C 914 " --> pdb=" O   GLN C 910 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 916 through 938
      removed outlier: 3.734A  pdb=" N   ILE C 931 " --> pdb=" O   ALA C 927 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   GLN C 932 " --> pdb=" O   ILE C 928 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ASP C 933 " --> pdb=" O   GLY C 929 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   THR C 938 " --> pdb=" O   SER C 934 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 939 through 941
      No H-bonds generated for 'chain 'C' and resid 939 through 941'
    Processing helix  chain 'C' and resid 942 through 961
      removed outlier: 4.621A  pdb=" N   VAL C 948 " --> pdb=" O   LYS C 944 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL C 949 " --> pdb=" O   LEU C 945 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   HIS C 951 " --> pdb=" O   ASP C 947 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 962 through 965
    Processing helix  chain 'C' and resid 973 through 980
      removed outlier: 3.809A  pdb=" N   ILE C 977 " --> pdb=" O   VAL C 973 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 982 through 985
    Processing helix  chain 'C' and resid 986 through 1030
      removed outlier: 4.078A  pdb=" N   ARG C 992 " --> pdb=" O   VAL C 988 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU C 993 " --> pdb=" O   GLN C 989 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.670A  pdb=" N   GLN D  24 " --> pdb=" O   THR D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 109 through 129
      removed outlier: 3.615A  pdb=" N   TYR D 127 " --> pdb=" O   MET D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 154
      removed outlier: 3.607A  pdb=" N   ILE D 151 " --> pdb=" O   GLY D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 194
      removed outlier: 3.779A  pdb=" N   GLU D 171 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL D 172 " --> pdb=" O   TRP D 168 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LYS D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   GLN D 175 " --> pdb=" O   GLU D 171 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
    Processing helix  chain 'D' and resid 198 through 204
    Processing helix  chain 'D' and resid 218 through 252
      removed outlier: 3.597A  pdb=" N   LEU D 222 " --> pdb=" O   SER D 218 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
      removed outlier: 3.781A  pdb=" N   ASN D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 268
      removed outlier: 3.988A  pdb=" N   GLY D 268 " --> pdb=" O   HIS D 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 265 through 268'
    Processing helix  chain 'D' and resid 293 through 301
    Processing helix  chain 'D' and resid 303 through 319
    Processing helix  chain 'D' and resid 325 through 331
      removed outlier: 4.517A  pdb=" N   GLU D 329 " --> pdb=" O   GLN D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.513A  pdb=" N   PHE D 369 " --> pdb=" O   THR D 365 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 397 through 412
      removed outlier: 4.252A  pdb=" N   HIS D 401 " --> pdb=" O   ASN D 397 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLU D 402 " --> pdb=" O   GLU D 398 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA D 412 " --> pdb=" O   MET D 408 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 446
    Processing helix  chain 'D' and resid 448 through 465
      removed outlier: 4.487A  pdb=" N   PHE D 452 " --> pdb=" O   GLY D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 475 through 484
    Processing helix  chain 'D' and resid 498 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 512 through 533
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 3.933A  pdb=" N   GLY D 551 " --> pdb=" O   SER D 547 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
      removed outlier: 3.564A  pdb=" N   VAL D 573 " --> pdb=" O   ALA D 569 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 581 through 597
      Proline residue:  D 590  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 52
      removed outlier: 3.887A  pdb=" N   ASP A  50 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A 270 " --> pdb=" O   ASP A  50 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASP A 284 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62
      removed outlier: 3.988A  pdb=" N   THR A  60 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 264 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   TYR A 262 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 200 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   VAL A 224 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   SER A 202 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 128
      removed outlier: 3.938A  pdb=" N   TRP A 101 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311
      removed outlier: 3.745A  pdb=" N   GLY A 308 " --> pdb=" O   THR A 596 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   THR A 596 " --> pdb=" O   GLY A 308 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 325
      removed outlier: 3.717A  pdb=" N   VAL A 536 " --> pdb=" O   GLY A 547 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LEU A 543 " --> pdb=" O   PHE A 540 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   ASP A 571 " --> pdb=" O   ILE A 584 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA A 572 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 356
      removed outlier: 3.864A  pdb=" N   SER A 511 " --> pdb=" O   TYR A 393 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   THR A 427 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356
      removed outlier: 3.864A  pdb=" N   SER A 511 " --> pdb=" O   TYR A 393 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   THR A 427 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE A 431 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   TRP A 433 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AA9, first strand: chain 'A' and resid 661 through 664
      removed outlier: 6.238A  pdb=" N   ALA A 669 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 699 through 700
    Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725
      removed outlier: 6.851A  pdb=" N   SER A 708 " --> pdb=" O   THR A1073 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   THR A1073 " --> pdb=" O   SER A 708 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ALA A 710 " --> pdb=" O   ASN A1071 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ASN A1071 " --> pdb=" O   ALA A 710 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   GLU A1069 " --> pdb=" O   PRO A 712 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ASN A 714 " --> pdb=" O   ALA A1067 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   SER A 718 " --> pdb=" O   THR A1063 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   TYR A1064 " --> pdb=" O   HIS A1045 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   HIS A1045 " --> pdb=" O   TYR A1064 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 725
      removed outlier: 6.851A  pdb=" N   SER A 708 " --> pdb=" O   THR A1073 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   THR A1073 " --> pdb=" O   SER A 708 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ALA A 710 " --> pdb=" O   ASN A1071 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ASN A1071 " --> pdb=" O   ALA A 710 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   GLU A1069 " --> pdb=" O   PRO A 712 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ASN A 714 " --> pdb=" O   ALA A1067 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   SER A 718 " --> pdb=" O   THR A1063 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR A1073 " --> pdb=" O   SER A1094 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 730 through 732
      removed outlier: 4.794A  pdb=" N   LYS A 730 " --> pdb=" O   LEU A 858 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1117 through 1120
    Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 27
    Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 52
    Processing sheet with id=AB8, first strand: chain 'B' and resid 81 through 82
      removed outlier: 4.207A  pdb=" N   LEU B  81 " --> pdb=" O   PHE B 235 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ARG B 234 " --> pdb=" O   PHE B 103 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   PHE B 103 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLN B 236 " --> pdb=" O   TRP B 101 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   TRP B 101 " --> pdb=" O   GLN B 236 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   LEU B 238 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL B 123 " --> pdb=" O   SER B 169 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   SER B 169 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE B 125 " --> pdb=" O   TYR B 167 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 221 through 227
      removed outlier: 6.455A  pdb=" N   SER B 202 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 274 through 276
      removed outlier: 6.966A  pdb=" N   LYS B 275 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 324
      removed outlier: 7.012A  pdb=" N   ILE B 323 " --> pdb=" O   ASN B 539 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL B 536 " --> pdb=" O   GLY B 547 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   ASP B 571 " --> pdb=" O   ILE B 584 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   GLY B 563 " --> pdb=" O   ASP B 571 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 353 through 355
      removed outlier: 3.609A  pdb=" N   GLY B 428 " --> pdb=" O   TYR B 377 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 358 through 359
      removed outlier: 6.652A  pdb=" N   CYS B 358 " --> pdb=" O   CYS B 522 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC4
    Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451
    Processing sheet with id=AC6, first strand: chain 'B' and resid 592 through 595
    Processing sheet with id=AC7, first strand: chain 'B' and resid 651 through 652
      removed outlier: 5.706A  pdb=" N   GLU B 651 " --> pdb=" O   ALA B 691 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   THR B 693 " --> pdb=" O   GLU B 651 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA B 669 " --> pdb=" O   PRO B 662 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712
      removed outlier: 3.773A  pdb=" N   THR B1073 " --> pdb=" O   SER B1094 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   GLN B1103 " --> pdb=" O   GLU B1108 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   GLU B1108 " --> pdb=" O   GLN B1103 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 716
      removed outlier: 3.647A  pdb=" N   GLU B 722 " --> pdb=" O   PHE B1059 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 716
      removed outlier: 3.703A  pdb=" N   ALA B1053 " --> pdb=" O   GLY B1056 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   TYR B1064 " --> pdb=" O   HIS B1045 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   HIS B1045 " --> pdb=" O   TYR B1064 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 733
    Processing sheet with id=AD3, first strand: chain 'B' and resid 1117 through 1122
      removed outlier: 4.437A  pdb=" N   ALA B1084 " --> pdb=" O   SER B1120 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 26 through 27
      removed outlier: 4.019A  pdb=" N   THR C  26 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL C  59 " --> pdb=" O   THR C  26 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD4
    Processing sheet with id=AD5, first strand: chain 'C' and resid 46 through 52
      removed outlier: 3.803A  pdb=" N   HIS C  46 " --> pdb=" O   LEU C 274 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU C 274 " --> pdb=" O   HIS C  46 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR C  48 " --> pdb=" O   PHE C 272 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ASP C 284 " --> pdb=" O   LYS C 275 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82
      removed outlier: 3.960A  pdb=" N   LEU C  81 " --> pdb=" O   PHE C 235 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   GLN C 236 " --> pdb=" O   TRP C 101 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   TRP C 101 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU C 238 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'C' and resid 221 through 227
      removed outlier: 6.998A  pdb=" N   SER C 202 " --> pdb=" O   PRO C 222 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL C 224 " --> pdb=" O   ILE C 200 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 309
      removed outlier: 3.515A  pdb=" N   GLY C 308 " --> pdb=" O   THR C 596 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   THR C 596 " --> pdb=" O   GLY C 308 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY C 591 " --> pdb=" O   GLN C 610 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU C 647 " --> pdb=" O   PHE C 640 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'C' and resid 322 through 323
    Processing sheet with id=AE1, first strand: chain 'C' and resid 395 through 400
      removed outlier: 4.122A  pdb=" N   ILE C 399 " --> pdb=" O   TYR C 505 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'C' and resid 449 through 451
    Processing sheet with id=AE3, first strand: chain 'C' and resid 548 through 551
    Processing sheet with id=AE4, first strand: chain 'C' and resid 661 through 662
      removed outlier: 3.760A  pdb=" N   ILE C 661 " --> pdb=" O   ALA C 669 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'C' and resid 708 through 712
    Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 716
      removed outlier: 3.500A  pdb=" N   THR C 720 " --> pdb=" O   HIS C1061 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 716
      removed outlier: 6.058A  pdb=" N   TYR C1064 " --> pdb=" O   HIS C1045 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   HIS C1045 " --> pdb=" O   TYR C1064 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'C' and resid 1117 through 1122
      removed outlier: 4.481A  pdb=" N   ALA C1084 " --> pdb=" O   SER C1120 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE C1078 " --> pdb=" O   HIS C1085 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'C' and resid 1091 through 1094
    Processing sheet with id=AF1, first strand: chain 'D' and resid 131 through 132
      removed outlier: 3.647A  pdb=" N   VAL D 132 " --> pdb=" O   LEU D 142 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU D 142 " --> pdb=" O   VAL D 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF1
    Processing sheet with id=AF2, first strand: chain 'D' and resid 262 through 263
      removed outlier: 5.452A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF2
    Processing sheet with id=AF3, first strand: chain 'D' and resid 347 through 352
      removed outlier: 6.494A  pdb=" N   ASP D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)

    1041 hydrogen bonds defined for protein.
    2931 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: 11.22

  Time building geometry restraints manager: 7.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 8551
        1.33 -     1.46: 8066
        1.46 -     1.59: 13729
        1.59 -     1.71: 1
        1.71 -     1.84: 197
  Bond restraints: 30544
  Sorted by residual:
  bond pdb=" C   PRO C 983 "
       pdb=" O   PRO C 983 "
    ideal  model  delta    sigma   weight residual
    1.240  1.208  0.032 1.12e-02 7.97e+03 8.17e+00
  bond pdb=" N   GLU C 985 "
       pdb=" CA  GLU C 985 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.43e+00
  bond pdb=" CB  PRO C 334 "
       pdb=" CG  PRO C 334 "
    ideal  model  delta    sigma   weight residual
    1.492  1.602 -0.110 5.00e-02 4.00e+02 4.88e+00
  bond pdb=" N   ARG C 980 "
       pdb=" CA  ARG C 980 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.70e+00
  bond pdb=" N   ASP C 982 "
       pdb=" CA  ASP C 982 "
    ideal  model  delta    sigma   weight residual
    1.451  1.487 -0.037 1.78e-02 3.16e+03 4.23e+00
  ... (remaining 30539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.13: 41156
        3.13 -     6.25: 322
        6.25 -     9.38: 70
        9.38 -    12.51: 10
       12.51 -    15.63: 2
  Bond angle restraints: 41560
  Sorted by residual:
  angle pdb=" CG1 ILE B  19 "
        pdb=" CB  ILE B  19 "
        pdb=" CG2 ILE B  19 "
      ideal   model   delta    sigma   weight residual
     110.70   95.07   15.63 3.00e+00 1.11e-01 2.72e+01
  angle pdb=" C   GLU D 479 "
        pdb=" N   MET D 480 "
        pdb=" CA  MET D 480 "
      ideal   model   delta    sigma   weight residual
     122.06  112.47    9.59 1.86e+00 2.89e-01 2.66e+01
  angle pdb=" CB  MET B 694 "
        pdb=" CG  MET B 694 "
        pdb=" SD  MET B 694 "
      ideal   model   delta    sigma   weight residual
     112.70  127.22  -14.52 3.00e+00 1.11e-01 2.34e+01
  angle pdb=" CA  MET A 150 "
        pdb=" CB  MET A 150 "
        pdb=" CG  MET A 150 "
      ideal   model   delta    sigma   weight residual
     114.10  123.65   -9.55 2.00e+00 2.50e-01 2.28e+01
  angle pdb=" CA  PRO C 334 "
        pdb=" N   PRO C 334 "
        pdb=" CD  PRO C 334 "
      ideal   model   delta    sigma   weight residual
     112.00  105.41    6.59 1.40e+00 5.10e-01 2.21e+01
  ... (remaining 41555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 15311
       18.00 -    36.00: 2114
       36.00 -    53.99: 592
       53.99 -    71.99: 123
       71.99 -    89.99: 59
  Dihedral angle restraints: 18199
    sinusoidal: 7166
      harmonic: 11033
  Sorted by residual:
  dihedral pdb=" CB  CYS C 735 "
           pdb=" SG  CYS C 735 "
           pdb=" SG  CYS C 757 "
           pdb=" CB  CYS C 757 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.25  -86.25     1      1.00e+01 1.00e-02 8.97e+01
  dihedral pdb=" CB  CYS C  15 "
           pdb=" SG  CYS C  15 "
           pdb=" SG  CYS C 133 "
           pdb=" CB  CYS C 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.74  -78.74     1      1.00e+01 1.00e-02 7.73e+01
  dihedral pdb=" CB  CYS C 288 "
           pdb=" SG  CYS C 288 "
           pdb=" SG  CYS C 298 "
           pdb=" CB  CYS C 298 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.86   76.86     1      1.00e+01 1.00e-02 7.42e+01
  ... (remaining 18196 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 4139
       0.081 -    0.163: 475
       0.163 -    0.244: 16
       0.244 -    0.325: 2
       0.325 -    0.407: 1
  Chirality restraints: 4633
  Sorted by residual:
  chirality pdb=" CB  ILE B  19 "
            pdb=" CA  ILE B  19 "
            pdb=" CG1 ILE B  19 "
            pdb=" CG2 ILE B  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.05   -0.41 2.00e-01 2.50e+01 4.13e+00
  chirality pdb=" CB  ILE A  98 "
            pdb=" CA  ILE A  98 "
            pdb=" CG1 ILE A  98 "
            pdb=" CG2 ILE A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CG  LEU C  81 "
            pdb=" CB  LEU C  81 "
            pdb=" CD1 LEU C  81 "
            pdb=" CD2 LEU C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.04e+00
  ... (remaining 4630 not shown)

  Planarity restraints: 5380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 980 "    0.415 9.50e-02 1.11e+02   1.86e-01 2.12e+01
        pdb=" NE  ARG C 980 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 980 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 980 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 980 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 461 "    0.024 2.00e-02 2.50e+03   1.95e-02 9.47e+00
        pdb=" CG  TRP D 461 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 461 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 461 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 461 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 461 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 461 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 461 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 461 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 461 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 982 "   -0.049 5.00e-02 4.00e+02   7.41e-02 8.79e+00
        pdb=" N   PRO A 983 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 983 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 983 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 5377 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 5778
        2.77 -     3.30: 28495
        3.30 -     3.83: 51396
        3.83 -     4.37: 54580
        4.37 -     4.90: 93629
  Nonbonded interactions: 233878
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 933 "
            pdb=" OG  SER A 937 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   TYR C 310 "
            pdb=" OG  SER C 593 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN A 436 "
            pdb=" OG  SER A 440 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   SER A 964 "
            pdb=" OG  SER A 964 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   SER A  24 "
            pdb=" OG1 THR A  60 "
     model   vdw
     2.277 3.040
  ... (remaining 233873 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 14 through 140 or resid 149 through 824 or resid 847 throu \ 
gh 1137))
  selection = chain 'B'
  selection = (chain 'C' and (resid 14 through 824 or resid 847 through 1137))
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             3.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          1.090
  Check model and map are aligned:         0.190
  Set scattering table:                    0.250
  Process input model:                     61.070
  Find NCS groups from input model:        1.200
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   70.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
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      :  0.004   0.110  30584  Z= 0.192
  Angle     :  0.792  15.632  41640  Z= 0.413
  Chirality :  0.049   0.407   4633
  Planarity :  0.006   0.186   5380
  Dihedral  : 18.348  89.988  10979
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.44 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 34.33 %
    Favored  : 65.34 %
  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: -2.06 (0.13), residues: 3742
  helix:  0.45 (0.16), residues: 956
  sheet: -1.36 (0.20), residues: 616
  loop : -2.33 (0.12), residues: 2170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP D 461 
 HIS   0.009   0.001   HIS C 336 
 PHE   0.036   0.002   PHE C 397 
 TYR   0.024   0.001   TYR C 362 
 ARG   0.006   0.000   ARG C1104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14112 ( 1019)
  hydrogen bonds       : angle       6.25269 ( 2931)
  SS BOND              : bond        0.00303 (   40)
  SS BOND              : angle       1.35246 (   80)
  covalent geometry    : bond        0.00407 (30544)
  covalent geometry    : angle       0.79090 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  475 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 464
  time to evaluate  : 3.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7816 (ttpt)
REVERT: A   89 PHE cc_start: 0.8432 (t80) cc_final: 0.8001 (t80)
REVERT: A  492 TYR cc_start: 0.1387 (OUTLIER) cc_final: 0.0988 (m-80)
REVERT: A  694 MET cc_start: 0.7386 (mmt) cc_final: 0.7085 (tpt)
REVERT: A  752 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8525 (mp10)
REVERT: A  897 MET cc_start: 0.7268 (tpp) cc_final: 0.6933 (tpp)
REVERT: A  987 GLU cc_start: 0.8359 (mp0) cc_final: 0.7899 (mp0)
REVERT: B  272 PHE cc_start: 0.7340 (m-80) cc_final: 0.6543 (t80)
REVERT: B  694 MET cc_start: 0.7498 (mmm) cc_final: 0.7104 (mmm)
REVERT: B  737 MET cc_start: 0.7160 (tpp) cc_final: 0.6934 (mmm)
REVERT: B  744 THR cc_start: 0.8649 (t) cc_final: 0.8116 (t)
REVERT: B  748 ASN cc_start: 0.8940 (m110) cc_final: 0.8042 (m-40)
REVERT: B  756 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7250 (t80)
REVERT: B 1046 LEU cc_start: 0.8415 (mt) cc_final: 0.7902 (tt)
REVERT: B 1122 ASN cc_start: 0.6135 (p0) cc_final: 0.5789 (p0)
REVERT: C   81 LEU cc_start: 0.8063 (tt) cc_final: 0.7105 (mm)
REVERT: C   89 PHE cc_start: 0.7108 (t80) cc_final: 0.6513 (t80)
REVERT: C  122 ASN cc_start: 0.8001 (m-40) cc_final: 0.7213 (p0)
REVERT: C  392 VAL cc_start: 0.7276 (p) cc_final: 0.6971 (m)
REVERT: C  420 TYR cc_start: 0.6532 (t80) cc_final: 0.6321 (t80)
REVERT: C  539 ASN cc_start: 0.7935 (t0) cc_final: 0.7305 (p0)
REVERT: C  870 TYR cc_start: 0.6829 (m-80) cc_final: 0.6502 (m-80)
REVERT: C  884 THR cc_start: 0.7886 (p) cc_final: 0.7674 (t)
REVERT: D  107 VAL cc_start: 0.7224 (t) cc_final: 0.6834 (t)
REVERT: D  295 ASP cc_start: 0.8685 (t0) cc_final: 0.8344 (p0)
REVERT: D  577 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8228 (tptt)
  outliers start: 11
  outliers final: 3
  residues processed: 472
  average time/residue: 0.3783
  time to fit residues: 292.1487
Evaluate side-chains
  261 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 256
  time to evaluate  : 3.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue 1074 THR
Chi-restraints excluded: chain B residue  756 PHE
Chi-restraints excluded: chain C residue  648 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 317 optimal weight:    5.9990
   chunk 284 optimal weight:    1.9990
   chunk 158 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 192 optimal weight:    0.8980
   chunk 152 optimal weight:    0.7980
   chunk 294 optimal weight:    3.9990
   chunk 114 optimal weight:    0.8980
   chunk 179 optimal weight:    0.8980
   chunk 219 optimal weight:    6.9990
   chunk 341 optimal weight:   50.0000
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 402 ASN
B 474 ASN
** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 853 ASN
B 910 GLN
C 131 GLN
** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 ASN
** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1103 GLN
D  61 ASN
D 188 ASN
D 250 ASN
D 429 GLN
D 586 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.117714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.097738 restraints weight = 168310.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.096451 restraints weight = 122635.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.096670 restraints weight = 96888.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  30584  Z= 0.133
  Angle     :  0.630   9.601  41640  Z= 0.323
  Chirality :  0.044   0.211   4633
  Planarity :  0.005   0.072   5380
  Dihedral  :  4.848  46.926   4067
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.57 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 32.25 %
    Favored  : 63.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.13), residues: 3742
  helix:  1.04 (0.17), residues: 971
  sheet: -1.27 (0.21), residues: 619
  loop : -2.15 (0.13), residues: 2152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 461 
 HIS   0.014   0.001   HIS A1080 
 PHE   0.029   0.001   PHE B 189 
 TYR   0.022   0.002   TYR C 914 
 ARG   0.011   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 ( 1019)
  hydrogen bonds       : angle       5.09822 ( 2931)
  SS BOND              : bond        0.00221 (   40)
  SS BOND              : angle       1.28158 (   80)
  covalent geometry    : bond        0.00294 (30544)
  covalent geometry    : angle       0.62767 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 132
    poor density    : 271
  time to evaluate  : 3.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LEU cc_start: 0.7865 (mm) cc_final: 0.7173 (tp)
REVERT: A  321 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8385 (pm20)
REVERT: A  402 ASN cc_start: 0.4206 (OUTLIER) cc_final: 0.3406 (p0)
REVERT: A  752 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8159 (mp10)
REVERT: A 1027 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.8117 (t)
REVERT: B   98 ILE cc_start: 0.5975 (OUTLIER) cc_final: 0.5654 (tt)
REVERT: B  187 ARG cc_start: 0.6682 (mtt180) cc_final: 0.6244 (mtt180)
REVERT: B  272 PHE cc_start: 0.7082 (m-80) cc_final: 0.6465 (t80)
REVERT: B  293 LEU cc_start: 0.8227 (tp) cc_final: 0.7951 (tt)
REVERT: B  744 THR cc_start: 0.8690 (t) cc_final: 0.8071 (t)
REVERT: B  748 ASN cc_start: 0.8856 (m110) cc_final: 0.8180 (m-40)
REVERT: B 1046 LEU cc_start: 0.8371 (mt) cc_final: 0.8024 (tt)
REVERT: C   81 LEU cc_start: 0.7503 (tt) cc_final: 0.6977 (mm)
REVERT: C  122 ASN cc_start: 0.7915 (m-40) cc_final: 0.7137 (p0)
REVERT: C  539 ASN cc_start: 0.7748 (t0) cc_final: 0.7092 (p0)
REVERT: C  728 MET cc_start: 0.8785 (ppp) cc_final: 0.7321 (ppp)
REVERT: C  982 ASP cc_start: 0.8032 (p0) cc_final: 0.7699 (p0)
REVERT: D   74 LYS cc_start: 0.5704 (tptt) cc_final: 0.4785 (tptt)
REVERT: D  192 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7671 (tpm170)
REVERT: D  295 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8105 (p0)
REVERT: D  332 MET cc_start: -0.1058 (tmm) cc_final: -0.2566 (ptp)
REVERT: D  427 ASP cc_start: 0.5496 (OUTLIER) cc_final: 0.5253 (m-30)
REVERT: D  480 MET cc_start: 0.1003 (OUTLIER) cc_final: 0.0800 (ttp)
REVERT: D  506 VAL cc_start: 0.3731 (OUTLIER) cc_final: 0.3338 (p)
  outliers start: 132
  outliers final: 49
  residues processed: 386
  average time/residue: 0.3854
  time to fit residues: 246.8273
Evaluate side-chains
  279 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 222
  time to evaluate  : 3.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   75 ARG
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  718 SER
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue 1027 SER
Chi-restraints excluded: chain A residue 1065 VAL
Chi-restraints excluded: chain A residue 1072 PHE
Chi-restraints excluded: chain A residue 1135 TYR
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  441 LYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  729 THR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  853 ASN
Chi-restraints excluded: chain B residue  952 ASN
Chi-restraints excluded: chain B residue  981 LEU
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  302 SER
Chi-restraints excluded: chain C residue  554 LYS
Chi-restraints excluded: chain C residue  614 CYS
Chi-restraints excluded: chain C residue  756 PHE
Chi-restraints excluded: chain C residue  778 VAL
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  803 LEU
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  919 LEU
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue  988 VAL
Chi-restraints excluded: chain C residue 1037 VAL
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain C residue 1101 VAL
Chi-restraints excluded: chain C residue 1135 TYR
Chi-restraints excluded: chain D residue   40 PHE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  295 ASP
Chi-restraints excluded: chain D residue  427 ASP
Chi-restraints excluded: chain D residue  480 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  555 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 211 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 162 optimal weight:    6.9990
   chunk 242 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 226 optimal weight:    0.2980
   chunk 153 optimal weight:    0.9990
   chunk 328 optimal weight:    0.4980
   chunk 238 optimal weight:    0.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 182 ASN
A 314 ASN
B 131 GLN
B 474 ASN
** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 610 GLN
B 748 ASN
B 853 ASN
B 946 GLN
B1007 GLN
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  46 HIS
C  66 HIS
** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 748 ASN
C 898 GLN
C1055 HIS
D 340 GLN
D 580 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.116472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.096015 restraints weight = 167323.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.094366 restraints weight = 125428.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.094444 restraints weight = 107679.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  30584  Z= 0.120
  Angle     :  0.596   9.669  41640  Z= 0.300
  Chirality :  0.043   0.185   4633
  Planarity :  0.004   0.061   5380
  Dihedral  :  4.520  24.420   4060
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.76 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 32.10 %
    Favored  : 63.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.50 (0.13), residues: 3742
  helix:  1.27 (0.17), residues: 964
  sheet: -1.23 (0.21), residues: 580
  loop : -2.09 (0.12), residues: 2198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 477 
 HIS   0.014   0.001   HIS C  46 
 PHE   0.022   0.001   PHE B 397 
 TYR   0.024   0.001   TYR B 348 
 ARG   0.008   0.000   ARG C 902 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 ( 1019)
  hydrogen bonds       : angle       4.87691 ( 2931)
  SS BOND              : bond        0.00347 (   40)
  SS BOND              : angle       1.05979 (   80)
  covalent geometry    : bond        0.00260 (30544)
  covalent geometry    : angle       0.59441 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 132
    poor density    : 243
  time to evaluate  : 3.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LEU cc_start: 0.7889 (mm) cc_final: 0.7221 (tp)
REVERT: A  321 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8389 (pm20)
REVERT: A  402 ASN cc_start: 0.4248 (OUTLIER) cc_final: 0.3430 (p0)
REVERT: A  982 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7756 (m-30)
REVERT: A  987 GLU cc_start: 0.8026 (mp0) cc_final: 0.7720 (mp0)
REVERT: B  150 MET cc_start: 0.6181 (mmp) cc_final: 0.5792 (mmt)
REVERT: B  187 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6511 (mtt180)
REVERT: B  272 PHE cc_start: 0.7115 (m-80) cc_final: 0.6596 (t80)
REVERT: B  293 LEU cc_start: 0.8256 (tp) cc_final: 0.8020 (tt)
REVERT: B  477 CYS cc_start: -0.0431 (OUTLIER) cc_final: -0.3591 (p)
REVERT: B  744 THR cc_start: 0.8595 (t) cc_final: 0.8035 (t)
REVERT: B  748 ASN cc_start: 0.8876 (m-40) cc_final: 0.8087 (m-40)
REVERT: C   81 LEU cc_start: 0.7500 (tt) cc_final: 0.6952 (mm)
REVERT: C   89 PHE cc_start: 0.7039 (t80) cc_final: 0.6774 (t80)
REVERT: C  122 ASN cc_start: 0.7894 (m-40) cc_final: 0.7160 (p0)
REVERT: C  189 PHE cc_start: 0.6745 (m-80) cc_final: 0.6481 (m-10)
REVERT: C  539 ASN cc_start: 0.7745 (t0) cc_final: 0.7048 (p0)
REVERT: C  728 MET cc_start: 0.8735 (ppp) cc_final: 0.7154 (ppp)
REVERT: C 1065 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7459 (m)
REVERT: D   74 LYS cc_start: 0.5658 (tptt) cc_final: 0.4879 (tptt)
REVERT: D   75 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.4695 (pt0)
REVERT: D   82 MET cc_start: 0.4457 (ppp) cc_final: 0.4169 (ppp)
REVERT: D  192 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7639 (tpm170)
REVERT: D  295 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8078 (p0)
REVERT: D  318 VAL cc_start: 0.2949 (t) cc_final: 0.2657 (t)
REVERT: D  364 VAL cc_start: -0.2105 (OUTLIER) cc_final: -0.3003 (t)
REVERT: D  480 MET cc_start: 0.1579 (OUTLIER) cc_final: 0.1243 (ppp)
REVERT: D  506 VAL cc_start: 0.3468 (OUTLIER) cc_final: 0.3115 (p)
REVERT: D  557 MET cc_start: 0.1735 (tmm) cc_final: 0.1397 (ttt)
  outliers start: 132
  outliers final: 60
  residues processed: 364
  average time/residue: 0.3594
  time to fit residues: 220.9575
Evaluate side-chains
  279 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 209
  time to evaluate  : 3.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  718 SER
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue  982 ASP
Chi-restraints excluded: chain A residue 1065 VAL
Chi-restraints excluded: chain A residue 1072 PHE
Chi-restraints excluded: chain A residue 1135 TYR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  221 GLU
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  610 GLN
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  729 THR
Chi-restraints excluded: chain B residue  757 CYS
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  981 LEU
Chi-restraints excluded: chain B residue 1034 SER
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  302 SER
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  554 LYS
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  614 CYS
Chi-restraints excluded: chain C residue  756 PHE
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  803 LEU
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  861 LEU
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  875 LEU
Chi-restraints excluded: chain C residue  898 GLN
Chi-restraints excluded: chain C residue  919 LEU
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue  988 VAL
Chi-restraints excluded: chain C residue 1037 VAL
Chi-restraints excluded: chain C residue 1065 VAL
Chi-restraints excluded: chain C residue 1072 PHE
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain D residue   75 GLU
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  295 ASP
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  480 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  580 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 168 optimal weight:    4.9990
   chunk 162 optimal weight:    5.9990
   chunk 312 optimal weight:    6.9990
   chunk 158 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 170 optimal weight:    0.9980
   chunk 243 optimal weight:   20.0000
   chunk 179 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
A 748 ASN
B 474 ASN
B 502 HIS
B 892 GLN
B 917 GLN
** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 ASN
** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 101 GLN
D 239 HIS
D 580 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.111678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.090227 restraints weight = 162712.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.087491 restraints weight = 107138.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.088253 restraints weight = 92967.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  30584  Z= 0.166
  Angle     :  0.616  10.860  41640  Z= 0.315
  Chirality :  0.043   0.248   4633
  Planarity :  0.005   0.066   5380
  Dihedral  :  4.567  27.776   4060
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.08 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 31.89 %
    Favored  : 63.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.14), residues: 3742
  helix:  1.15 (0.17), residues: 990
  sheet: -1.23 (0.21), residues: 580
  loop : -2.05 (0.13), residues: 2172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP D 461 
 HIS   0.012   0.001   HIS D 239 
 PHE   0.020   0.001   PHE B 397 
 TYR   0.046   0.002   TYR C 262 
 ARG   0.009   0.001   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 ( 1019)
  hydrogen bonds       : angle       4.89357 ( 2931)
  SS BOND              : bond        0.00773 (   40)
  SS BOND              : angle       0.99673 (   80)
  covalent geometry    : bond        0.00361 (30544)
  covalent geometry    : angle       0.61528 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 151
    poor density    : 218
  time to evaluate  : 7.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LEU cc_start: 0.7851 (mm) cc_final: 0.7144 (tp)
REVERT: A  150 MET cc_start: 0.7555 (ppp) cc_final: 0.7320 (tmm)
REVERT: A  402 ASN cc_start: 0.4309 (OUTLIER) cc_final: 0.3313 (p0)
REVERT: B  198 PHE cc_start: 0.7276 (m-80) cc_final: 0.7065 (m-80)
REVERT: B  272 PHE cc_start: 0.7160 (m-80) cc_final: 0.6808 (t80)
REVERT: B  477 CYS cc_start: -0.0194 (OUTLIER) cc_final: -0.3309 (p)
REVERT: B  744 THR cc_start: 0.8486 (t) cc_final: 0.8146 (t)
REVERT: B  748 ASN cc_start: 0.8918 (m-40) cc_final: 0.8524 (m110)
REVERT: B  897 MET cc_start: 0.8320 (tpp) cc_final: 0.7973 (tpp)
REVERT: C   77 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.8016 (t0)
REVERT: C   81 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7301 (mm)
REVERT: C  339 PHE cc_start: 0.2520 (OUTLIER) cc_final: 0.2196 (t80)
REVERT: C  539 ASN cc_start: 0.7576 (t0) cc_final: 0.6804 (p0)
REVERT: C  728 MET cc_start: 0.8889 (ppp) cc_final: 0.7283 (ppp)
REVERT: C  748 ASN cc_start: 0.8437 (m110) cc_final: 0.8209 (m-40)
REVERT: C  803 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7961 (mp)
REVERT: C 1038 ASP cc_start: 0.6680 (t0) cc_final: 0.6441 (t0)
REVERT: D   74 LYS cc_start: 0.6183 (tptt) cc_final: 0.5144 (tptt)
REVERT: D   82 MET cc_start: 0.4529 (ppp) cc_final: 0.4186 (ppp)
REVERT: D  192 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7631 (tpm170)
REVERT: D  295 ASP cc_start: 0.8617 (t0) cc_final: 0.8118 (p0)
REVERT: D  318 VAL cc_start: 0.2912 (t) cc_final: 0.2640 (t)
REVERT: D  427 ASP cc_start: 0.5749 (OUTLIER) cc_final: 0.5419 (m-30)
REVERT: D  480 MET cc_start: 0.0906 (OUTLIER) cc_final: 0.0091 (ttp)
REVERT: D  506 VAL cc_start: 0.3494 (OUTLIER) cc_final: 0.3138 (p)
  outliers start: 151
  outliers final: 79
  residues processed: 351
  average time/residue: 0.4219
  time to fit residues: 255.6184
Evaluate side-chains
  278 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 190
  time to evaluate  : 3.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  718 SER
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1065 VAL
Chi-restraints excluded: chain A residue 1117 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain B residue  570 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  610 GLN
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  729 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 CYS
Chi-restraints excluded: chain B residue  777 GLU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  981 LEU
Chi-restraints excluded: chain B residue 1034 SER
Chi-restraints excluded: chain B residue 1046 LEU
Chi-restraints excluded: chain B residue 1073 THR
Chi-restraints excluded: chain B residue 1081 ASP
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   77 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  339 PHE
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 LYS
Chi-restraints excluded: chain C residue  607 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  614 CYS
Chi-restraints excluded: chain C residue  641 GLN
Chi-restraints excluded: chain C residue  648 ILE
Chi-restraints excluded: chain C residue  756 PHE
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  803 LEU
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  861 LEU
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  863 THR
Chi-restraints excluded: chain C residue  919 LEU
Chi-restraints excluded: chain C residue  920 ILE
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue  988 VAL
Chi-restraints excluded: chain C residue 1037 VAL
Chi-restraints excluded: chain C residue 1072 PHE
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain C residue 1113 THR
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  427 ASP
Chi-restraints excluded: chain D residue  480 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 174 optimal weight:    0.7980
   chunk 294 optimal weight:    2.9990
   chunk 223 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9990
   chunk 203 optimal weight:    3.9990
   chunk 240 optimal weight:   20.0000
   chunk 336 optimal weight:   10.0000
   chunk 343 optimal weight:    0.0020
   chunk 287 optimal weight:    9.9990
   chunk 138 optimal weight:    5.9990
   chunk 368 optimal weight:    8.9990
   overall best weight:    1.7594

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

Flipped N/Q/H residues before XYZ refinement:
A 419 ASN
** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 122 ASN
B 182 ASN
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 204 HIS
** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 388 GLN
** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 556 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.107892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.081079 restraints weight = 155158.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.079969 restraints weight = 108044.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.080072 restraints weight = 85564.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.4911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102  30584  Z= 0.164
  Angle     :  0.635  16.306  41640  Z= 0.318
  Chirality :  0.043   0.237   4633
  Planarity :  0.005   0.076   5380
  Dihedral  :  4.527  26.378   4060
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.73 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 32.19 %
    Favored  : 63.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.14), residues: 3742
  helix:  1.26 (0.17), residues: 987
  sheet: -1.22 (0.21), residues: 568
  loop : -2.01 (0.13), residues: 2187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 461 
 HIS   0.008   0.001   HIS D 228 
 PHE   0.026   0.001   PHE C 189 
 TYR   0.042   0.002   TYR A 492 
 ARG   0.031   0.001   ARG C 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 ( 1019)
  hydrogen bonds       : angle       4.80485 ( 2931)
  SS BOND              : bond        0.00251 (   40)
  SS BOND              : angle       1.01290 (   80)
  covalent geometry    : bond        0.00367 (30544)
  covalent geometry    : angle       0.63389 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 137
    poor density    : 195
  time to evaluate  : 6.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LEU cc_start: 0.7961 (mm) cc_final: 0.7360 (tp)
REVERT: A  174 MET cc_start: 0.0065 (tpp) cc_final: -0.0160 (tpp)
REVERT: A  402 ASN cc_start: 0.3978 (OUTLIER) cc_final: 0.2931 (p0)
REVERT: A  723 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8952 (pt)
REVERT: A  866 MET cc_start: 0.7942 (mtt) cc_final: 0.7664 (mtt)
REVERT: A  982 ASP cc_start: 0.8648 (t0) cc_final: 0.8312 (m-30)
REVERT: B  187 ARG cc_start: 0.7386 (mtt180) cc_final: 0.6757 (ptp-170)
REVERT: B  198 PHE cc_start: 0.7582 (m-80) cc_final: 0.7366 (m-80)
REVERT: B  477 CYS cc_start: 0.1119 (OUTLIER) cc_final: -0.2449 (p)
REVERT: B  744 THR cc_start: 0.8352 (t) cc_final: 0.8132 (t)
REVERT: B  975 ASN cc_start: 0.8428 (m-40) cc_final: 0.7841 (t0)
REVERT: B  976 ASP cc_start: 0.7725 (p0) cc_final: 0.7518 (p0)
REVERT: C   21 ARG cc_start: 0.1075 (OUTLIER) cc_final: -0.0496 (mtp85)
REVERT: C   77 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8446 (t0)
REVERT: C   81 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7365 (mm)
REVERT: C  339 PHE cc_start: 0.2494 (OUTLIER) cc_final: 0.2020 (t80)
REVERT: C  515 LEU cc_start: 0.8900 (tp) cc_final: 0.8547 (tt)
REVERT: C  728 MET cc_start: 0.8912 (ppp) cc_final: 0.7440 (ppp)
REVERT: C  748 ASN cc_start: 0.8368 (m110) cc_final: 0.8095 (m-40)
REVERT: C  777 GLU cc_start: 0.7933 (pm20) cc_final: 0.7675 (pm20)
REVERT: C 1047 MET cc_start: 0.8606 (tpp) cc_final: 0.8054 (mmm)
REVERT: D   74 LYS cc_start: 0.6067 (tptt) cc_final: 0.5131 (tptt)
REVERT: D   82 MET cc_start: 0.4468 (ppp) cc_final: 0.4124 (ppp)
REVERT: D  192 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7651 (tpm170)
REVERT: D  295 ASP cc_start: 0.8630 (t0) cc_final: 0.8261 (p0)
REVERT: D  332 MET cc_start: -0.1915 (tmm) cc_final: -0.2747 (ptm)
REVERT: D  480 MET cc_start: 0.0725 (OUTLIER) cc_final: -0.0050 (ttp)
REVERT: D  506 VAL cc_start: 0.3614 (OUTLIER) cc_final: 0.3220 (p)
REVERT: D  578 ASN cc_start: 0.6685 (t0) cc_final: 0.6234 (t0)
  outliers start: 137
  outliers final: 75
  residues processed: 318
  average time/residue: 0.4746
  time to fit residues: 260.1553
Evaluate side-chains
  255 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 171
  time to evaluate  : 3.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  718 SER
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1117 THR
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  191 PHE
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  411 GLN
Chi-restraints excluded: chain B residue  441 LYS
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  570 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  729 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 CYS
Chi-restraints excluded: chain B residue  764 LEU
Chi-restraints excluded: chain B residue  777 GLU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  820 PHE
Chi-restraints excluded: chain B residue  875 LEU
Chi-restraints excluded: chain B residue  981 LEU
Chi-restraints excluded: chain B residue 1034 SER
Chi-restraints excluded: chain B residue 1046 LEU
Chi-restraints excluded: chain B residue 1073 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   21 ARG
Chi-restraints excluded: chain C residue   77 ASP
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  339 PHE
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  522 CYS
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 LYS
Chi-restraints excluded: chain C residue  607 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  641 GLN
Chi-restraints excluded: chain C residue  719 VAL
Chi-restraints excluded: chain C residue  757 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  791 ILE
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  861 LEU
Chi-restraints excluded: chain C residue  920 ILE
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue 1065 VAL
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  461 TRP
Chi-restraints excluded: chain D residue  480 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 332 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 106 optimal weight:   20.0000
   chunk 76 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 359 optimal weight:   20.0000
   chunk 163 optimal weight:    8.9990
   chunk 203 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 327 optimal weight:   20.0000
   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  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 HIS
** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
A 923 GLN
A 954 GLN
A 962 GLN
A 975 ASN
A1105 ASN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 706 ASN
** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 904 ASN
** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 131 GLN
** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 340 GLN
** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 556 ASN
D 580 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.101765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.068080 restraints weight = 160188.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.069419 restraints weight = 98036.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.069813 restraints weight = 57809.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.7981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.119  30584  Z= 0.419
  Angle     :  0.937  13.401  41640  Z= 0.486
  Chirality :  0.052   0.247   4633
  Planarity :  0.006   0.066   5380
  Dihedral  :  6.041  32.668   4060
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 24.03
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.02 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 30.71 %
    Favored  : 63.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

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: -2.23 (0.13), residues: 3742
  helix:  0.38 (0.16), residues: 978
  sheet: -1.57 (0.21), residues: 550
  loop : -2.45 (0.12), residues: 2214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP C 101 
 HIS   0.015   0.002   HIS C1098 
 PHE   0.037   0.004   PHE D 390 
 TYR   0.057   0.003   TYR A 492 
 ARG   0.011   0.001   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04670 ( 1019)
  hydrogen bonds       : angle       5.87043 ( 2931)
  SS BOND              : bond        0.00541 (   40)
  SS BOND              : angle       1.84980 (   80)
  covalent geometry    : bond        0.00919 (30544)
  covalent geometry    : angle       0.93391 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 200
    poor density    : 149
  time to evaluate  : 3.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8310 (tttt) cc_final: 0.8065 (mtpt)
REVERT: A  161 ASN cc_start: 0.8991 (m-40) cc_final: 0.8782 (t0)
REVERT: A  174 MET cc_start: 0.1794 (tpp) cc_final: 0.1518 (tpp)
REVERT: A  220 LEU cc_start: 0.7623 (tp) cc_final: 0.6956 (tp)
REVERT: A  389 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6638 (m-80)
REVERT: A  694 MET cc_start: 0.8500 (mmt) cc_final: 0.8290 (mmt)
REVERT: A  735 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7290 (p)
REVERT: A  954 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8642 (pp30)
REVERT: A  962 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.9166 (tp40)
REVERT: A 1130 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8926 (t)
REVERT: B  198 PHE cc_start: 0.8436 (m-80) cc_final: 0.7770 (m-80)
REVERT: B  201 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6506 (m-80)
REVERT: B  477 CYS cc_start: 0.1954 (OUTLIER) cc_final: -0.0120 (p)
REVERT: B  570 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8598 (p)
REVERT: B  706 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8500 (t0)
REVERT: B  975 ASN cc_start: 0.9041 (m-40) cc_final: 0.8383 (t0)
REVERT: C   81 LEU cc_start: 0.8398 (tt) cc_final: 0.7612 (mm)
REVERT: C  102 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7785 (tp)
REVERT: C  156 VAL cc_start: 0.5608 (OUTLIER) cc_final: 0.5373 (p)
REVERT: C  339 PHE cc_start: 0.4477 (OUTLIER) cc_final: 0.3662 (t80)
REVERT: C  661 ILE cc_start: 0.9262 (mm) cc_final: 0.8910 (mm)
REVERT: C  694 MET cc_start: 0.8830 (mmm) cc_final: 0.8594 (tpt)
REVERT: C  893 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8858 (mt)
REVERT: D   82 MET cc_start: 0.5375 (ppp) cc_final: 0.5162 (ppp)
REVERT: D  192 ARG cc_start: 0.8363 (mtt180) cc_final: 0.8084 (tpm170)
REVERT: D  295 ASP cc_start: 0.8601 (t0) cc_final: 0.8177 (p0)
REVERT: D  332 MET cc_start: -0.1624 (tmm) cc_final: -0.2350 (ptm)
REVERT: D  506 VAL cc_start: 0.3493 (OUTLIER) cc_final: 0.3147 (p)
REVERT: D  557 MET cc_start: 0.2343 (ttt) cc_final: 0.1306 (ttt)
  outliers start: 200
  outliers final: 119
  residues processed: 335
  average time/residue: 0.3666
  time to fit residues: 207.3224
Evaluate side-chains
  268 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 133
    poor density    : 135
  time to evaluate  : 3.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  583 ASP
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  778 VAL
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  812 ARG
Chi-restraints excluded: chain A residue  898 GLN
Chi-restraints excluded: chain A residue  928 ILE
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  951 HIS
Chi-restraints excluded: chain A residue  954 GLN
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  962 GLN
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1117 THR
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  411 GLN
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  525 LYS
Chi-restraints excluded: chain B residue  548 VAL
Chi-restraints excluded: chain B residue  570 THR
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  706 ASN
Chi-restraints excluded: chain B residue  719 VAL
Chi-restraints excluded: chain B residue  731 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 CYS
Chi-restraints excluded: chain B residue  777 GLU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  852 PHE
Chi-restraints excluded: chain B residue  863 THR
Chi-restraints excluded: chain B residue  867 ILE
Chi-restraints excluded: chain B residue  875 LEU
Chi-restraints excluded: chain B residue  948 VAL
Chi-restraints excluded: chain B residue  951 HIS
Chi-restraints excluded: chain B residue  952 ASN
Chi-restraints excluded: chain B residue 1046 LEU
Chi-restraints excluded: chain B residue 1073 THR
Chi-restraints excluded: chain B residue 1136 ASP
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  339 PHE
Chi-restraints excluded: chain C residue  350 TRP
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  415 ILE
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  522 CYS
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 LYS
Chi-restraints excluded: chain C residue  594 VAL
Chi-restraints excluded: chain C residue  601 THR
Chi-restraints excluded: chain C residue  607 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  614 CYS
Chi-restraints excluded: chain C residue  719 VAL
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  756 PHE
Chi-restraints excluded: chain C residue  757 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  791 ILE
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  863 THR
Chi-restraints excluded: chain C residue  893 ILE
Chi-restraints excluded: chain C residue  920 ILE
Chi-restraints excluded: chain C residue  949 VAL
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  970 ILE
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue  988 VAL
Chi-restraints excluded: chain C residue 1040 CYS
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  266 LEU
Chi-restraints excluded: chain D residue  323 MET
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  461 TRP
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  555 PHE
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 337 optimal weight:   10.0000
   chunk 157 optimal weight:    4.9990
   chunk 351 optimal weight:    8.9990
   chunk 79 optimal weight:    0.8980
   chunk 345 optimal weight:   20.0000
   chunk 55 optimal weight:    7.9990
   chunk 369 optimal weight:    6.9990
   chunk 152 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1033 GLN
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 484 ASN
B 706 ASN
B 892 GLN
** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 904 ASN
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1085 HIS
C 641 GLN
** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 580 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.098897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.066114 restraints weight = 139389.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.067580 restraints weight = 78667.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.067568 restraints weight = 53073.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.8207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  30584  Z= 0.221
  Angle     :  0.699  11.577  41640  Z= 0.356
  Chirality :  0.045   0.254   4633
  Planarity :  0.005   0.056   5380
  Dihedral  :  5.346  32.546   4060
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.59 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 31.98 %
    Favored  : 63.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

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: -1.97 (0.13), residues: 3742
  helix:  0.77 (0.16), residues: 977
  sheet: -1.55 (0.21), residues: 549
  loop : -2.34 (0.12), residues: 2216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 461 
 HIS   0.009   0.001   HIS C 336 
 PHE   0.026   0.002   PHE B 397 
 TYR   0.038   0.002   TYR D  50 
 ARG   0.009   0.001   ARG C 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 ( 1019)
  hydrogen bonds       : angle       5.25817 ( 2931)
  SS BOND              : bond        0.00346 (   40)
  SS BOND              : angle       1.53943 (   80)
  covalent geometry    : bond        0.00493 (30544)
  covalent geometry    : angle       0.69674 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 155
    poor density    : 146
  time to evaluate  : 3.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASN cc_start: 0.8973 (m-40) cc_final: 0.8701 (t0)
REVERT: A  389 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6453 (m-80)
REVERT: A  987 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8625 (mp0)
REVERT: B  150 MET cc_start: 0.7378 (mmp) cc_final: 0.7135 (mmt)
REVERT: B  198 PHE cc_start: 0.8302 (m-80) cc_final: 0.7478 (m-80)
REVERT: B  201 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6245 (m-80)
REVERT: B  230 ILE cc_start: 0.5017 (OUTLIER) cc_final: 0.4645 (tt)
REVERT: B  272 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7637 (m-80)
REVERT: B  477 CYS cc_start: 0.1187 (OUTLIER) cc_final: -0.1568 (p)
REVERT: B  570 THR cc_start: 0.8667 (p) cc_final: 0.8408 (p)
REVERT: B  957 ASN cc_start: 0.8968 (m-40) cc_final: 0.8745 (t0)
REVERT: B  975 ASN cc_start: 0.8935 (m-40) cc_final: 0.8193 (t0)
REVERT: C   81 LEU cc_start: 0.8316 (tt) cc_final: 0.7747 (mm)
REVERT: C  339 PHE cc_start: 0.4224 (OUTLIER) cc_final: 0.3740 (t80)
REVERT: C  694 MET cc_start: 0.8992 (mmm) cc_final: 0.8760 (tpt)
REVERT: C  728 MET cc_start: 0.9128 (ppp) cc_final: 0.7942 (ppp)
REVERT: C  893 ILE cc_start: 0.9380 (pt) cc_final: 0.8908 (mt)
REVERT: C 1047 MET cc_start: 0.8435 (tpp) cc_final: 0.8235 (mmm)
REVERT: D   82 MET cc_start: 0.4876 (ppp) cc_final: 0.4654 (ppp)
REVERT: D  192 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7990 (tpm170)
REVERT: D  295 ASP cc_start: 0.8650 (t0) cc_final: 0.8171 (p0)
REVERT: D  332 MET cc_start: -0.1514 (tmm) cc_final: -0.2311 (ptm)
REVERT: D  455 MET cc_start: -0.1993 (ttm) cc_final: -0.2245 (tmm)
REVERT: D  506 VAL cc_start: 0.3777 (OUTLIER) cc_final: 0.3419 (p)
REVERT: D  557 MET cc_start: 0.2522 (ttt) cc_final: 0.1446 (ttt)
  outliers start: 155
  outliers final: 101
  residues processed: 287
  average time/residue: 0.4068
  time to fit residues: 197.2782
Evaluate side-chains
  244 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 109
    poor density    : 135
  time to evaluate  : 3.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  778 VAL
Chi-restraints excluded: chain A residue  848 CYS
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1117 THR
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  272 PHE
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain B residue  525 LYS
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 VAL
Chi-restraints excluded: chain B residue  720 THR
Chi-restraints excluded: chain B residue  729 THR
Chi-restraints excluded: chain B residue  731 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 CYS
Chi-restraints excluded: chain B residue  777 GLU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  848 CYS
Chi-restraints excluded: chain B residue  863 THR
Chi-restraints excluded: chain B residue  875 LEU
Chi-restraints excluded: chain B residue  909 THR
Chi-restraints excluded: chain B residue  951 HIS
Chi-restraints excluded: chain B residue  956 LEU
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue 1046 LEU
Chi-restraints excluded: chain B residue 1073 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  339 PHE
Chi-restraints excluded: chain C residue  350 TRP
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  415 ILE
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  522 CYS
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  554 LYS
Chi-restraints excluded: chain C residue  607 VAL
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  641 GLN
Chi-restraints excluded: chain C residue  671 TYR
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain C residue  757 CYS
Chi-restraints excluded: chain C residue  778 VAL
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  791 ILE
Chi-restraints excluded: chain C residue  808 LYS
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  861 LEU
Chi-restraints excluded: chain C residue  863 THR
Chi-restraints excluded: chain C residue  920 ILE
Chi-restraints excluded: chain C residue  956 LEU
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  970 ILE
Chi-restraints excluded: chain C residue  973 VAL
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue  988 VAL
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  461 TRP
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 354 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0020
   chunk 266 optimal weight:    7.9990
   chunk 145 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 314 optimal weight:    3.9990
   chunk 242 optimal weight:    4.9990
   chunk 219 optimal weight:    1.9990
   chunk 328 optimal weight:    0.6980
   chunk 296 optimal weight:    0.0980
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A 242 HIS
A 314 ASN
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN
A 923 GLN
A 962 GLN
B 314 ASN
** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 951 HIS
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 367 ASN
C 641 GLN
** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 962 GLN
** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 556 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.100293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.066518 restraints weight = 139380.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.067915 restraints weight = 73118.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.068790 restraints weight = 46806.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.8243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  30584  Z= 0.124
  Angle     :  0.637   9.945  41640  Z= 0.320
  Chirality :  0.044   0.272   4633
  Planarity :  0.005   0.061   5380
  Dihedral  :  4.959  29.206   4060
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  7.43 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 32.73 %
    Favored  : 63.53 %
  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: -1.73 (0.13), residues: 3742
  helix:  0.98 (0.17), residues: 992
  sheet: -1.54 (0.21), residues: 565
  loop : -2.17 (0.12), residues: 2185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP D 461 
 HIS   0.012   0.001   HIS C 336 
 PHE   0.022   0.001   PHE B1072 
 TYR   0.030   0.001   TYR A 492 
 ARG   0.012   0.001   ARG C 631 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03054 ( 1019)
  hydrogen bonds       : angle       4.96110 ( 2931)
  SS BOND              : bond        0.00287 (   40)
  SS BOND              : angle       1.28639 (   80)
  covalent geometry    : bond        0.00281 (30544)
  covalent geometry    : angle       0.63521 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 124
    poor density    : 150
  time to evaluate  : 3.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7865 (tttt) cc_final: 0.7597 (mtpp)
REVERT: A  161 ASN cc_start: 0.8772 (m-40) cc_final: 0.8415 (t0)
REVERT: A  389 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6594 (m-80)
REVERT: A  735 CYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7114 (p)
REVERT: A  987 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8619 (mp0)
REVERT: B  150 MET cc_start: 0.7150 (mmp) cc_final: 0.6713 (mmt)
REVERT: B  198 PHE cc_start: 0.7932 (m-80) cc_final: 0.7114 (m-80)
REVERT: B  201 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.5846 (m-80)
REVERT: B  230 ILE cc_start: 0.4841 (OUTLIER) cc_final: 0.4527 (tt)
REVERT: B  477 CYS cc_start: 0.1217 (OUTLIER) cc_final: -0.1514 (p)
REVERT: B  570 THR cc_start: 0.8677 (p) cc_final: 0.8421 (p)
REVERT: B  737 MET cc_start: 0.8034 (mmm) cc_final: 0.7822 (mmm)
REVERT: B  957 ASN cc_start: 0.9079 (m-40) cc_final: 0.8634 (t0)
REVERT: B  975 ASN cc_start: 0.8761 (m-40) cc_final: 0.8201 (t0)
REVERT: C   77 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8460 (t0)
REVERT: C   81 LEU cc_start: 0.8342 (tt) cc_final: 0.7512 (mm)
REVERT: C  412 THR cc_start: 0.6188 (OUTLIER) cc_final: 0.5933 (p)
REVERT: C  694 MET cc_start: 0.9032 (mmm) cc_final: 0.8807 (tpt)
REVERT: C  728 MET cc_start: 0.9082 (ppp) cc_final: 0.7876 (ppp)
REVERT: C  756 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7628 (t80)
REVERT: C  893 ILE cc_start: 0.9362 (pt) cc_final: 0.8922 (mt)
REVERT: D   82 MET cc_start: 0.4738 (ppp) cc_final: 0.4418 (ppp)
REVERT: D  192 ARG cc_start: 0.8372 (mtt180) cc_final: 0.8073 (tpm170)
REVERT: D  295 ASP cc_start: 0.8647 (t0) cc_final: 0.8288 (p0)
REVERT: D  332 MET cc_start: -0.1690 (tmm) cc_final: -0.2287 (ptm)
REVERT: D  506 VAL cc_start: 0.3858 (OUTLIER) cc_final: 0.3617 (p)
REVERT: D  523 PHE cc_start: 0.6008 (OUTLIER) cc_final: 0.5662 (t80)
REVERT: D  557 MET cc_start: 0.2377 (ttt) cc_final: 0.1451 (ttt)
  outliers start: 124
  outliers final: 81
  residues processed: 259
  average time/residue: 0.3767
  time to fit residues: 164.4694
Evaluate side-chains
  227 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 135
  time to evaluate  : 4.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 PHE
Chi-restraints excluded: chain A residue  243 ARG
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  987 GLU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1117 THR
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain B residue  525 LYS
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 VAL
Chi-restraints excluded: chain B residue  729 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 CYS
Chi-restraints excluded: chain B residue  777 GLU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  909 THR
Chi-restraints excluded: chain B residue  951 HIS
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1046 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   77 ASP
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  274 LEU
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  336 HIS
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  522 CYS
Chi-restraints excluded: chain C residue  554 LYS
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  641 GLN
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain C residue  756 PHE
Chi-restraints excluded: chain C residue  757 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  791 ILE
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  861 LEU
Chi-restraints excluded: chain C residue  863 THR
Chi-restraints excluded: chain C residue  920 ILE
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  970 ILE
Chi-restraints excluded: chain C residue  973 VAL
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue  988 VAL
Chi-restraints excluded: chain C residue 1065 VAL
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  461 TRP
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  523 PHE
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 345 optimal weight:   20.0000
   chunk 198 optimal weight:    0.8980
   chunk 118 optimal weight:    8.9990
   chunk 247 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0980
   chunk 22 optimal weight:    3.9990
   chunk 170 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 146 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 904 ASN
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
C 641 GLN
** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.099318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.065529 restraints weight = 138869.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.066884 restraints weight = 73161.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.067775 restraints weight = 47160.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.8493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  30584  Z= 0.177
  Angle     :  0.650  10.744  41640  Z= 0.327
  Chirality :  0.044   0.219   4633
  Planarity :  0.005   0.058   5380
  Dihedral  :  4.905  29.205   4060
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  7.62 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 32.61 %
    Favored  : 64.01 %
  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: -1.68 (0.13), residues: 3742
  helix:  1.08 (0.17), residues: 993
  sheet: -1.55 (0.21), residues: 532
  loop : -2.16 (0.12), residues: 2217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP D 461 
 HIS   0.044   0.001   HIS B 951 
 PHE   0.024   0.001   PHE B  83 
 TYR   0.030   0.002   TYR A 492 
 ARG   0.008   0.001   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03125 ( 1019)
  hydrogen bonds       : angle       4.96711 ( 2931)
  SS BOND              : bond        0.00318 (   40)
  SS BOND              : angle       1.26684 (   80)
  covalent geometry    : bond        0.00405 (30544)
  covalent geometry    : angle       0.64811 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 112
    poor density    : 141
  time to evaluate  : 3.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASN cc_start: 0.8709 (m-40) cc_final: 0.8382 (t0)
REVERT: A  389 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6897 (m-80)
REVERT: A  735 CYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7030 (p)
REVERT: B  150 MET cc_start: 0.7333 (mmp) cc_final: 0.6994 (mmt)
REVERT: B  198 PHE cc_start: 0.8026 (m-80) cc_final: 0.7260 (m-80)
REVERT: B  201 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.6128 (m-80)
REVERT: B  230 ILE cc_start: 0.4532 (OUTLIER) cc_final: 0.4279 (tt)
REVERT: B  477 CYS cc_start: 0.1193 (OUTLIER) cc_final: -0.1611 (p)
REVERT: B  570 THR cc_start: 0.8709 (p) cc_final: 0.8475 (p)
REVERT: B  957 ASN cc_start: 0.8996 (m-40) cc_final: 0.8747 (t0)
REVERT: B  975 ASN cc_start: 0.8773 (m-40) cc_final: 0.8250 (t0)
REVERT: C   77 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8532 (t0)
REVERT: C   81 LEU cc_start: 0.8285 (tt) cc_final: 0.7543 (mm)
REVERT: C  728 MET cc_start: 0.9164 (ppp) cc_final: 0.7868 (ppp)
REVERT: C  756 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7699 (t80)
REVERT: C  893 ILE cc_start: 0.9373 (pt) cc_final: 0.8915 (mt)
REVERT: D   82 MET cc_start: 0.4782 (ppp) cc_final: 0.4459 (ppp)
REVERT: D  192 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8187 (tpm170)
REVERT: D  295 ASP cc_start: 0.8635 (t0) cc_final: 0.8256 (p0)
REVERT: D  332 MET cc_start: -0.1486 (tmm) cc_final: -0.2119 (ptm)
REVERT: D  506 VAL cc_start: 0.3898 (OUTLIER) cc_final: 0.3611 (p)
REVERT: D  523 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.5722 (t80)
REVERT: D  557 MET cc_start: 0.2427 (ttt) cc_final: 0.1505 (ttt)
  outliers start: 112
  outliers final: 91
  residues processed: 238
  average time/residue: 0.3688
  time to fit residues: 150.0465
Evaluate side-chains
  238 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 100
    poor density    : 138
  time to evaluate  : 3.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 PHE
Chi-restraints excluded: chain A residue  243 ARG
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  805 ASP
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1079 CYS
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1117 THR
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain B residue  525 LYS
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 VAL
Chi-restraints excluded: chain B residue  720 THR
Chi-restraints excluded: chain B residue  729 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 CYS
Chi-restraints excluded: chain B residue  777 GLU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  863 THR
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1046 LEU
Chi-restraints excluded: chain B residue 1136 ASP
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   77 ASP
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  336 HIS
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  498 TYR
Chi-restraints excluded: chain C residue  522 CYS
Chi-restraints excluded: chain C residue  601 THR
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  641 GLN
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain C residue  756 PHE
Chi-restraints excluded: chain C residue  757 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  791 ILE
Chi-restraints excluded: chain C residue  808 LYS
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  861 LEU
Chi-restraints excluded: chain C residue  863 THR
Chi-restraints excluded: chain C residue  875 LEU
Chi-restraints excluded: chain C residue  897 MET
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  970 ILE
Chi-restraints excluded: chain C residue  973 VAL
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue  988 VAL
Chi-restraints excluded: chain C residue 1065 VAL
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  461 TRP
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  523 PHE
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 348 optimal weight:    0.9980
   chunk 180 optimal weight:    0.2980
   chunk 322 optimal weight:    3.9990
   chunk 274 optimal weight:    5.9990
   chunk 75 optimal weight:    0.1980
   chunk 157 optimal weight:    7.9990
   chunk 357 optimal weight:    5.9990
   chunk 155 optimal weight:    5.9990
   chunk 216 optimal weight:    0.9990
   chunk 346 optimal weight:   10.0000
   chunk 287 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 311 GLN
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 GLN
** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 962 GLN
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 641 GLN
** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.099647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.065870 restraints weight = 139670.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.067279 restraints weight = 73620.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.068191 restraints weight = 47211.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.8612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  30584  Z= 0.132
  Angle     :  0.629   9.840  41640  Z= 0.314
  Chirality :  0.044   0.225   4633
  Planarity :  0.004   0.060   5380
  Dihedral  :  4.775  28.678   4060
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  7.51 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 32.85 %
    Favored  : 64.01 %
  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: -1.61 (0.13), residues: 3742
  helix:  1.16 (0.17), residues: 990
  sheet: -1.54 (0.21), residues: 532
  loop : -2.11 (0.12), residues: 2220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP D 461 
 HIS   0.011   0.001   HIS C 336 
 PHE   0.024   0.001   PHE C 389 
 TYR   0.021   0.001   TYR C 420 
 ARG   0.008   0.001   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02982 ( 1019)
  hydrogen bonds       : angle       4.87141 ( 2931)
  SS BOND              : bond        0.00331 (   40)
  SS BOND              : angle       1.21211 (   80)
  covalent geometry    : bond        0.00302 (30544)
  covalent geometry    : angle       0.62725 (41560)

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

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

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7484 Ramachandran restraints generated.
    3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 104
    poor density    : 147
  time to evaluate  : 3.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7976 (tttt) cc_final: 0.7751 (mtpp)
REVERT: A  161 ASN cc_start: 0.8740 (m-40) cc_final: 0.8431 (t0)
REVERT: A  735 CYS cc_start: 0.7331 (OUTLIER) cc_final: 0.7035 (p)
REVERT: B  150 MET cc_start: 0.7288 (mmp) cc_final: 0.6944 (mmt)
REVERT: B  198 PHE cc_start: 0.7977 (m-80) cc_final: 0.7198 (m-80)
REVERT: B  201 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6040 (m-80)
REVERT: B  230 ILE cc_start: 0.4340 (OUTLIER) cc_final: 0.4112 (tt)
REVERT: B  477 CYS cc_start: 0.1315 (OUTLIER) cc_final: -0.1360 (p)
REVERT: B  552 SER cc_start: 0.7618 (t) cc_final: 0.7186 (p)
REVERT: B  570 THR cc_start: 0.8791 (p) cc_final: 0.8560 (p)
REVERT: B  957 ASN cc_start: 0.9094 (m-40) cc_final: 0.8810 (t0)
REVERT: B  975 ASN cc_start: 0.8769 (m-40) cc_final: 0.8227 (t0)
REVERT: C   81 LEU cc_start: 0.8342 (tt) cc_final: 0.7633 (mm)
REVERT: C  728 MET cc_start: 0.9137 (ppp) cc_final: 0.7845 (ppp)
REVERT: C  756 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7733 (t80)
REVERT: C  893 ILE cc_start: 0.9395 (pt) cc_final: 0.8943 (mt)
REVERT: D   74 LYS cc_start: 0.7380 (tptt) cc_final: 0.6931 (mmmt)
REVERT: D   82 MET cc_start: 0.4741 (ppp) cc_final: 0.4422 (ppp)
REVERT: D  192 ARG cc_start: 0.8480 (mtt180) cc_final: 0.8188 (tpm170)
REVERT: D  295 ASP cc_start: 0.8631 (t0) cc_final: 0.8260 (p0)
REVERT: D  332 MET cc_start: -0.1497 (tmm) cc_final: -0.2045 (ptm)
REVERT: D  506 VAL cc_start: 0.3930 (OUTLIER) cc_final: 0.3645 (p)
REVERT: D  523 PHE cc_start: 0.6131 (OUTLIER) cc_final: 0.5740 (t80)
REVERT: D  557 MET cc_start: 0.2428 (ttt) cc_final: 0.1519 (ttt)
  outliers start: 104
  outliers final: 89
  residues processed: 240
  average time/residue: 0.3807
  time to fit residues: 156.1423
Evaluate side-chains
  233 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 137
  time to evaluate  : 3.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 PHE
Chi-restraints excluded: chain A residue  243 ARG
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  311 GLN
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  735 CYS
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1079 CYS
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1117 THR
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  376 CYS
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain B residue  485 CYS
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain B residue  525 LYS
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  642 THR
Chi-restraints excluded: chain B residue  648 ILE
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 VAL
Chi-restraints excluded: chain B residue  720 THR
Chi-restraints excluded: chain B residue  729 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 CYS
Chi-restraints excluded: chain B residue  777 GLU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  863 THR
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1046 LEU
Chi-restraints excluded: chain B residue 1136 ASP
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  336 HIS
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  498 TYR
Chi-restraints excluded: chain C residue  601 THR
Chi-restraints excluded: chain C residue  608 LEU
Chi-restraints excluded: chain C residue  641 GLN
Chi-restraints excluded: chain C residue  671 TYR
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain C residue  756 PHE
Chi-restraints excluded: chain C residue  757 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  791 ILE
Chi-restraints excluded: chain C residue  858 LEU
Chi-restraints excluded: chain C residue  861 LEU
Chi-restraints excluded: chain C residue  863 THR
Chi-restraints excluded: chain C residue  897 MET
Chi-restraints excluded: chain C residue  958 THR
Chi-restraints excluded: chain C residue  970 ILE
Chi-restraints excluded: chain C residue  973 VAL
Chi-restraints excluded: chain C residue  976 ASP
Chi-restraints excluded: chain C residue  988 VAL
Chi-restraints excluded: chain C residue 1065 VAL
Chi-restraints excluded: chain C residue 1098 HIS
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  461 TRP
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  523 PHE
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 376
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 300 optimal weight:    0.0050
   chunk 67 optimal weight:    0.7980
   chunk 155 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0270
   chunk 330 optimal weight:    7.9990
   chunk 69 optimal weight:    8.9990
   chunk 321 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 148 optimal weight:    3.9990
   overall best weight:    1.7656

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

Flipped N/Q/H residues before XYZ refinement:
A 311 GLN
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 962 GLN
** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.100027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.064300 restraints weight = 139700.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.065673 restraints weight = 76547.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.066582 restraints weight = 50265.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.8610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.235  30584  Z= 0.177
  Angle     :  0.752  59.146  41640  Z= 0.406
  Chirality :  0.044   0.432   4633
  Planarity :  0.005   0.153   5380
  Dihedral  :  4.774  28.686   4060
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  7.51 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 32.82 %
    Favored  : 63.95 %
  Cbeta Deviations :  0.03 %
  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: -1.61 (0.13), residues: 3742
  helix:  1.16 (0.17), residues: 990
  sheet: -1.54 (0.21), residues: 532
  loop : -2.11 (0.12), residues: 2220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP D 461 
 HIS   0.011   0.001   HIS C 336 
 PHE   0.020   0.001   PHE C 389 
 TYR   0.065   0.001   TYR D  50 
 ARG   0.007   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02984 ( 1019)
  hydrogen bonds       : angle       4.87199 ( 2931)
  SS BOND              : bond        0.00285 (   40)
  SS BOND              : angle       1.19275 (   80)
  covalent geometry    : bond        0.00390 (30544)
  covalent geometry    : angle       0.75132 (41560)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12463.21 seconds
wall clock time: 223 minutes 53.02 seconds (13433.02 seconds total)