Starting phenix.real_space_refine on Thu Dec 14 22:48:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvq_32857/12_2023/7wvq_32857.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvq_32857/12_2023/7wvq_32857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvq_32857/12_2023/7wvq_32857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvq_32857/12_2023/7wvq_32857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvq_32857/12_2023/7wvq_32857.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvq_32857/12_2023/7wvq_32857.pdb" } resolution = 4.04 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= 0.003 sd= 0.034 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 143 5.16 5 C 18895 2.51 5 N 4913 2.21 5 O 5576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29527 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 15.85, per 1000 atoms: 0.54 Number of scatterers: 29527 At special positions: 0 Unit cell: (148.648, 146.462, 238.274, 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 143 16.00 O 5576 8.00 N 4913 7.00 C 18895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 10.77 Conformation dependent library (CDL) restraints added in 4.9 seconds 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 61 sheets defined 25.8% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 746 through 752 removed outlier: 3.958A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 746 through 752' Processing helix chain 'D' and resid 753 through 757 removed outlier: 3.634A pdb=" N TYR D 756 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 772 Processing helix chain 'D' and resid 776 through 783 removed outlier: 4.040A pdb=" N GLU D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 removed outlier: 3.861A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 825 " --> pdb=" O LEU D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 883 removed outlier: 3.950A pdb=" N ALA D 876 " --> pdb=" O GLN D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.870A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 905 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 907 " --> pdb=" O ALA D 903 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 908 " --> pdb=" O TYR D 904 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.540A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 941 removed outlier: 4.067A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN D 926 " --> pdb=" O LEU D 922 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 929 " --> pdb=" O ASN D 925 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 930 " --> pdb=" O GLN D 926 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 931 " --> pdb=" O PHE D 927 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 940 " --> pdb=" O ASP D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 946 removed outlier: 3.515A pdb=" N LEU D 945 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY D 946 " --> pdb=" O SER D 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 942 through 946' Processing helix chain 'D' and resid 949 through 961 removed outlier: 3.516A pdb=" N ASN D 953 " --> pdb=" O GLN D 949 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS D 954 " --> pdb=" O ASP D 950 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 984 removed outlier: 4.030A pdb=" N PHE D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 983 " --> pdb=" O ASP D 979 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D 984 " --> pdb=" O ILE D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1031 removed outlier: 3.870A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 998 " --> pdb=" O ASP D 994 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D1003 " --> pdb=" O GLY D 999 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D1006 " --> pdb=" O GLN D1002 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D1009 " --> pdb=" O GLN D1005 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D1010 " --> pdb=" O THR D1006 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D1022 " --> pdb=" O ILE D1018 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.570A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.766A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 782 removed outlier: 3.858A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.570A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 883 removed outlier: 4.260A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.834A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.939A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 919' Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.755A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.553A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS C 954 " --> pdb=" O ASP C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 977 through 982 removed outlier: 4.202A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 977 through 982' Processing helix chain 'C' and resid 985 through 994 removed outlier: 3.924A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1032 removed outlier: 3.704A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 4.461A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.531A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.022A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.165A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 768 removed outlier: 3.735A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.795A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.883A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.934A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.878A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.567A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 965 removed outlier: 3.628A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1031 removed outlier: 3.766A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.965A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.874A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 52 " --> pdb=" O TRP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.725A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 60' Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.858A pdb=" N SER A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.734A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.694A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.851A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.667A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 4.034A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.870A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 4.220A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 194' Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.648A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 removed outlier: 3.887A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 243 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.984A pdb=" N LEU A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 267 " --> pdb=" O ALA A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.640A pdb=" N THR A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.659A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.985A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 4.160A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 331' Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.795A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.753A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.540A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.527A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.543A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.650A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.273A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 4.117A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 463 " --> pdb=" O TRP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.040A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 removed outlier: 4.029A pdb=" N SER A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.904A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 508' Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 533 removed outlier: 4.143A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.549A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.531A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.724A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.866A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS D 202 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR D 204 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN D 188 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 96 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.806A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 84 through 85 removed outlier: 4.041A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 84 through 85 removed outlier: 4.041A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN D 121 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL D 126 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 171 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE D 128 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU D 169 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 130 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 132 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASN D 165 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLN D 134 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA D 163 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.629A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 325 through 327 removed outlier: 5.940A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 585 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 576 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY D 566 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE D 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.982A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.982A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 391 through 392 removed outlier: 3.605A pdb=" N VAL D 524 " --> pdb=" O PHE D 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 448 through 454 removed outlier: 7.347A pdb=" N TYR D 451 " --> pdb=" O TYR D 495 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR D 495 " --> pdb=" O TYR D 451 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.671A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.784A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 693 " --> pdb=" O SER D 673 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 673 " --> pdb=" O ILE D 693 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.083A pdb=" N ALA D 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'D' and resid 718 through 723 removed outlier: 3.803A pdb=" N VAL D1068 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D1066 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D1064 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D1060 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU D 727 " --> pdb=" O VAL D1060 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 718 through 723 removed outlier: 3.803A pdb=" N VAL D1068 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D1066 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D1064 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D1061 " --> pdb=" O GLN D1054 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.471A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 735 " --> pdb=" O THR D 859 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR D 859 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 788 through 790 removed outlier: 5.856A pdb=" N ILE D 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 3.566A pdb=" N SER D1123 " --> pdb=" O ALA D1087 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1094 through 1097 removed outlier: 3.803A pdb=" N PHE D1103 " --> pdb=" O VAL D1096 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 22 through 23 removed outlier: 4.792A pdb=" N THR C 22 " --> pdb=" O PHE C 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.137A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.538A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.975A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.975A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 89 through 94 removed outlier: 3.561A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AD2, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.328A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.842A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.925A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.925A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD7, first strand: chain 'C' and resid 448 through 454 removed outlier: 7.331A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.651A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 566 through 567 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.616A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.785A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 718 through 724 removed outlier: 3.749A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 727 through 728 removed outlier: 4.673A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.502A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.895A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.874A pdb=" N VAL C1096 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C1103 " --> pdb=" O VAL C1096 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.053A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.084A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.436A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 116 through 121 removed outlier: 5.649A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AF4, first strand: chain 'B' and resid 313 through 318 removed outlier: 6.451A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.662A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 376 through 378 removed outlier: 4.150A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 511 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 376 through 378 removed outlier: 4.150A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 511 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AG1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.541A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.639A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.813A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.613A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 861 " --> pdb=" O LYS B 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AG6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG7, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.399A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 738 hydrogen bonds defined for protein. 2055 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: 14.00 Time building geometry restraints manager: 11.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4893 1.31 - 1.44: 8417 1.44 - 1.57: 16733 1.57 - 1.71: 0 1.71 - 1.84: 194 Bond restraints: 30237 Sorted by residual: bond pdb=" C ASP A 335 " pdb=" N PRO A 336 " ideal model delta sigma weight residual 1.334 1.516 -0.183 2.34e-02 1.83e+03 6.09e+01 bond pdb=" CA SER B1003 " pdb=" C SER B1003 " ideal model delta sigma weight residual 1.524 1.428 0.095 1.29e-02 6.01e+03 5.45e+01 bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.337 1.417 -0.081 1.11e-02 8.12e+03 5.29e+01 bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.22e+01 bond pdb=" CA ILE B 997 " pdb=" C ILE B 997 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.27e-02 6.20e+03 4.94e+01 ... (remaining 30232 not shown) Histogram of bond angle deviations from ideal: 98.04 - 106.36: 920 106.36 - 114.69: 17134 114.69 - 123.01: 20443 123.01 - 131.34: 2546 131.34 - 139.66: 65 Bond angle restraints: 41108 Sorted by residual: angle pdb=" CA GLY B 526 " pdb=" C GLY B 526 " pdb=" O GLY B 526 " ideal model delta sigma weight residual 121.52 139.66 -18.14 1.43e+00 4.89e-01 1.61e+02 angle pdb=" N GLN B 957 " pdb=" CA GLN B 957 " pdb=" C GLN B 957 " ideal model delta sigma weight residual 111.28 98.04 13.24 1.09e+00 8.42e-01 1.48e+02 angle pdb=" N GLY B 526 " pdb=" CA GLY B 526 " pdb=" C GLY B 526 " ideal model delta sigma weight residual 112.34 133.74 -21.40 2.04e+00 2.40e-01 1.10e+02 angle pdb=" N ASP B 389 " pdb=" CA ASP B 389 " pdb=" C ASP B 389 " ideal model delta sigma weight residual 111.07 121.32 -10.25 1.07e+00 8.73e-01 9.17e+01 angle pdb=" N GLN C1002 " pdb=" CA GLN C1002 " pdb=" C GLN C1002 " ideal model delta sigma weight residual 112.38 100.82 11.56 1.22e+00 6.72e-01 8.98e+01 ... (remaining 41103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 17244 16.01 - 32.01: 611 32.01 - 48.02: 140 48.02 - 64.03: 26 64.03 - 80.04: 16 Dihedral angle restraints: 18037 sinusoidal: 7121 harmonic: 10916 Sorted by residual: dihedral pdb=" C CYS B 525 " pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta harmonic sigma weight residual -122.60 -140.16 17.56 0 2.50e+00 1.60e-01 4.93e+01 dihedral pdb=" N CYS B 525 " pdb=" C CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta harmonic sigma weight residual 122.80 137.77 -14.97 0 2.50e+00 1.60e-01 3.58e+01 dihedral pdb=" CA PRO A 389 " pdb=" C PRO A 389 " pdb=" N PHE A 390 " pdb=" CA PHE A 390 " ideal model delta harmonic sigma weight residual -180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 18034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 4429 0.132 - 0.265: 138 0.265 - 0.397: 17 0.397 - 0.529: 5 0.529 - 0.662: 3 Chirality restraints: 4592 Sorted by residual: chirality pdb=" CA CYS B 525 " pdb=" N CYS B 525 " pdb=" C CYS B 525 " pdb=" CB CYS B 525 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA ILE C 993 " pdb=" N ILE C 993 " pdb=" C ILE C 993 " pdb=" CB ILE C 993 " both_signs ideal model delta sigma weight residual False 2.43 1.85 0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" CA LEU B 966 " pdb=" N LEU B 966 " pdb=" C LEU B 966 " pdb=" CB LEU B 966 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 4589 not shown) Planarity restraints: 5321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 964 " 0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C LYS B 964 " -0.085 2.00e-02 2.50e+03 pdb=" O LYS B 964 " 0.033 2.00e-02 2.50e+03 pdb=" N GLN B 965 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO B 987 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 390 " -0.024 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C LEU B 390 " 0.080 2.00e-02 2.50e+03 pdb=" O LEU B 390 " -0.029 2.00e-02 2.50e+03 pdb=" N CYS B 391 " -0.027 2.00e-02 2.50e+03 ... (remaining 5318 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 9394 2.85 - 3.36: 22516 3.36 - 3.88: 47426 3.88 - 4.39: 49107 4.39 - 4.90: 86838 Nonbonded interactions: 215281 Sorted by model distance: nonbonded pdb=" O GLY B 526 " pdb=" CA PRO B 527 " model vdw 2.339 2.776 nonbonded pdb=" OG SER C 816 " pdb=" OE1 GLU C 819 " model vdw 2.349 2.440 nonbonded pdb=" N GLN B 957 " pdb=" N ALA B 958 " model vdw 2.356 2.560 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.367 2.440 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.371 2.440 ... (remaining 215276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 3.600 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: 0.040 Extract box with map and model: 11.650 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 79.370 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 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 : 0.007 0.183 30237 Z= 0.481 Angle : 1.050 21.404 41108 Z= 0.628 Chirality : 0.065 0.662 4592 Planarity : 0.008 0.122 5321 Dihedral : 9.787 80.037 10877 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.20 % Favored : 94.61 % Rotamer: Outliers : 0.46 % Allowed : 1.10 % Favored : 98.45 % Cbeta Deviations : 0.17 % 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: -3.46 (0.11), residues: 3691 helix: -4.60 (0.09), residues: 801 sheet: -0.63 (0.22), residues: 366 loop : -1.84 (0.10), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 461 HIS 0.012 0.001 HIS A 265 PHE 0.025 0.003 PHE D 275 TYR 0.030 0.002 TYR D 873 ARG 0.006 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 617 time to evaluate : 3.347 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 626 average time/residue: 0.4486 time to fit residues: 438.5264 Evaluate side-chains 445 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 439 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3235 time to fit residues: 8.0625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 290 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS D 99 ASN D 218 GLN D 234 ASN ** D 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN D 957 GLN D1088 HIS D1108 ASN C 49 HIS C 173 GLN C 675 GLN C 872 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C 935 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1010 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 137 ASN B 394 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN A 81 GLN A 96 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30237 Z= 0.272 Angle : 0.697 11.872 41108 Z= 0.363 Chirality : 0.045 0.182 4592 Planarity : 0.006 0.087 5321 Dihedral : 5.227 22.044 4011 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.94 % Rotamer: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.20 % 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: -2.44 (0.11), residues: 3691 helix: -2.81 (0.13), residues: 818 sheet: -0.23 (0.23), residues: 425 loop : -1.49 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 459 HIS 0.009 0.002 HIS A 378 PHE 0.021 0.002 PHE B 515 TYR 0.031 0.002 TYR B 495 ARG 0.007 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 510 time to evaluate : 3.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 511 average time/residue: 0.4153 time to fit residues: 338.3075 Evaluate side-chains 445 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 3.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 337 optimal weight: 5.9990 chunk 364 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN D 394 ASN D 506 GLN ** D 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN ** D 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 218 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1058 HIS ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN A 102 GLN A 277 ASN A 330 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 30237 Z= 0.385 Angle : 0.859 15.930 41108 Z= 0.452 Chirality : 0.050 0.281 4592 Planarity : 0.007 0.073 5321 Dihedral : 5.988 24.989 4011 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 0.30 % Allowed : 3.66 % Favored : 96.04 % 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 (0.12), residues: 3691 helix: -1.67 (0.15), residues: 863 sheet: -0.83 (0.20), residues: 550 loop : -1.39 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 461 HIS 0.010 0.002 HIS B 207 PHE 0.038 0.003 PHE C 906 TYR 0.035 0.003 TYR B 707 ARG 0.011 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 531 time to evaluate : 3.494 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 outliers start: 10 outliers final: 4 residues processed: 538 average time/residue: 0.4196 time to fit residues: 362.4153 Evaluate side-chains 465 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 461 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2717 time to fit residues: 6.6379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 7.9990 chunk 253 optimal weight: 0.8980 chunk 175 optimal weight: 0.0270 chunk 37 optimal weight: 0.0030 chunk 161 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 338 optimal weight: 0.9980 chunk 358 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.5850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN D 17 ASN D 207 HIS D 314 GLN D 532 ASN D 606 ASN D 690 GLN D 779 GLN D1011 GLN D1088 HIS D1119 ASN C 779 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30237 Z= 0.156 Angle : 0.580 12.834 41108 Z= 0.294 Chirality : 0.044 0.206 4592 Planarity : 0.005 0.091 5321 Dihedral : 5.002 22.393 4011 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % 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: 3691 helix: -0.74 (0.17), residues: 833 sheet: -0.55 (0.21), residues: 541 loop : -1.22 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 461 HIS 0.007 0.001 HIS A 374 PHE 0.040 0.002 PHE B 797 TYR 0.022 0.001 TYR C1007 ARG 0.005 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 523 time to evaluate : 3.453 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 524 average time/residue: 0.4225 time to fit residues: 355.3793 Evaluate side-chains 450 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 3.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 0.4980 chunk 203 optimal weight: 0.7980 chunk 5 optimal weight: 0.0470 chunk 267 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 306 optimal weight: 0.3980 chunk 247 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 321 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 992 GLN D1010 GLN D1088 HIS C 49 HIS ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C 949 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 872 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30237 Z= 0.138 Angle : 0.544 11.818 41108 Z= 0.271 Chirality : 0.043 0.250 4592 Planarity : 0.004 0.083 5321 Dihedral : 4.611 22.496 4011 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 0.03 % Allowed : 1.62 % Favored : 98.35 % 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: -1.21 (0.13), residues: 3691 helix: -0.22 (0.18), residues: 841 sheet: -0.47 (0.21), residues: 549 loop : -1.13 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.007 0.001 HIS A 374 PHE 0.023 0.001 PHE C 759 TYR 0.017 0.001 TYR C1007 ARG 0.006 0.000 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 505 time to evaluate : 3.237 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.4181 time to fit residues: 339.4944 Evaluate side-chains 437 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 6.9990 chunk 322 optimal weight: 8.9990 chunk 70 optimal weight: 0.4980 chunk 210 optimal weight: 4.9990 chunk 88 optimal weight: 0.0050 chunk 358 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 overall best weight: 2.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN D 115 GLN D 606 ASN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1106 GLN A 330 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 30237 Z= 0.330 Angle : 0.751 16.363 41108 Z= 0.391 Chirality : 0.048 0.230 4592 Planarity : 0.006 0.080 5321 Dihedral : 5.496 23.207 4011 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % 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: -1.63 (0.13), residues: 3691 helix: -0.78 (0.17), residues: 860 sheet: -0.75 (0.22), residues: 519 loop : -1.30 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 473 HIS 0.010 0.002 HIS B1064 PHE 0.026 0.003 PHE D 906 TYR 0.024 0.002 TYR C 396 ARG 0.014 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 531 time to evaluate : 3.434 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: 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 outliers start: 1 outliers final: 0 residues processed: 532 average time/residue: 0.4121 time to fit residues: 350.7346 Evaluate side-chains 458 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 3.190 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 302 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 357 optimal weight: 0.5980 chunk 223 optimal weight: 0.0070 chunk 218 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN D 564 GLN D 606 ASN D1011 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1106 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.7152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30237 Z= 0.210 Angle : 0.622 15.622 41108 Z= 0.316 Chirality : 0.045 0.202 4592 Planarity : 0.005 0.080 5321 Dihedral : 5.108 23.636 4011 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -1.47 (0.13), residues: 3691 helix: -0.52 (0.17), residues: 846 sheet: -0.81 (0.21), residues: 545 loop : -1.21 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 328 HIS 0.007 0.001 HIS A 374 PHE 0.023 0.002 PHE D 906 TYR 0.025 0.002 TYR C 796 ARG 0.014 0.001 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 3.276 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.4373 time to fit residues: 376.5127 Evaluate side-chains 462 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 3.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 227 optimal weight: 0.0040 chunk 243 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 GLN ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 218 GLN C 613 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1106 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30237 Z= 0.187 Angle : 0.612 14.354 41108 Z= 0.308 Chirality : 0.045 0.220 4592 Planarity : 0.006 0.246 5321 Dihedral : 4.958 26.037 4011 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 0.03 % Allowed : 0.76 % Favored : 99.21 % 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: -1.35 (0.13), residues: 3691 helix: -0.31 (0.18), residues: 852 sheet: -0.63 (0.22), residues: 505 loop : -1.20 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 104 HIS 0.006 0.001 HIS B1064 PHE 0.029 0.001 PHE D1052 TYR 0.021 0.001 TYR C 796 ARG 0.024 0.001 ARG D 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 532 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: 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 outliers start: 1 outliers final: 0 residues processed: 532 average time/residue: 0.4168 time to fit residues: 356.4102 Evaluate side-chains 464 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 3.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 6.9990 chunk 342 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 394 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 675 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1023 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 330 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.8720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 30237 Z= 0.444 Angle : 0.901 20.223 41108 Z= 0.474 Chirality : 0.053 0.258 4592 Planarity : 0.007 0.091 5321 Dihedral : 6.306 29.818 4011 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 31.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.15 % Favored : 92.82 % Rotamer: Outliers : 0.06 % Allowed : 0.98 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.13 (0.13), residues: 3691 helix: -1.14 (0.16), residues: 845 sheet: -1.06 (0.23), residues: 495 loop : -1.65 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 473 HIS 0.010 0.003 HIS C1088 PHE 0.061 0.003 PHE C 906 TYR 0.039 0.003 TYR D 200 ARG 0.036 0.002 ARG D 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 559 time to evaluate : 3.197 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: 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 outliers start: 2 outliers final: 0 residues processed: 560 average time/residue: 0.4379 time to fit residues: 391.1087 Evaluate side-chains 469 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 0.9980 chunk 352 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 244 optimal weight: 0.0000 chunk 369 optimal weight: 9.9990 chunk 340 optimal weight: 20.0000 chunk 294 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 GLN D 81 ASN D 183 GLN D 207 HIS D 239 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 928 ASN C 960 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.8524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30237 Z= 0.198 Angle : 0.656 17.138 41108 Z= 0.331 Chirality : 0.046 0.198 4592 Planarity : 0.005 0.076 5321 Dihedral : 5.437 27.695 4011 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.74 (0.13), residues: 3691 helix: -0.58 (0.18), residues: 838 sheet: -1.07 (0.21), residues: 549 loop : -1.42 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 203 HIS 0.008 0.001 HIS A 374 PHE 0.031 0.002 PHE C1089 TYR 0.026 0.002 TYR A 199 ARG 0.024 0.001 ARG D 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 3.215 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 549 average time/residue: 0.4278 time to fit residues: 375.8569 Evaluate side-chains 468 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 3.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 271 optimal weight: 3.9990 chunk 43 optimal weight: 50.0000 chunk 81 optimal weight: 0.9980 chunk 294 optimal weight: 0.0770 chunk 123 optimal weight: 0.0170 chunk 302 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 GLN D 606 ASN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 314 GLN C 777 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 314 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1106 GLN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.182386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.145959 restraints weight = 100625.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.149113 restraints weight = 69619.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.151410 restraints weight = 51816.164| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.8406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30237 Z= 0.167 Angle : 0.618 14.842 41108 Z= 0.309 Chirality : 0.045 0.221 4592 Planarity : 0.006 0.269 5321 Dihedral : 4.972 31.548 4011 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 0.03 % Allowed : 0.18 % Favored : 99.79 % 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: -1.44 (0.13), residues: 3691 helix: -0.15 (0.18), residues: 814 sheet: -0.82 (0.21), residues: 560 loop : -1.32 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1102 HIS 0.008 0.001 HIS B 49 PHE 0.023 0.001 PHE D 817 TYR 0.025 0.001 TYR B1007 ARG 0.008 0.001 ARG D1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7269.82 seconds wall clock time: 132 minutes 29.63 seconds (7949.63 seconds total)