Starting phenix.real_space_refine on Sat Sep 28 18:07:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmm_36423/09_2024/8jmm_36423.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmm_36423/09_2024/8jmm_36423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmm_36423/09_2024/8jmm_36423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmm_36423/09_2024/8jmm_36423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmm_36423/09_2024/8jmm_36423.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmm_36423/09_2024/8jmm_36423.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 306 5.16 5 C 44894 2.51 5 N 11805 2.21 5 O 13626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 298 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 70631 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8103 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 6 Chain: "B" Number of atoms: 8112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8112 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 57, 'TRANS': 978} Chain breaks: 6 Chain: "C" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8103 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 6 Chain: "D" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8082 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 56, 'TRANS': 975} Chain breaks: 7 Chain: "E" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8103 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 6 Chain: "F" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8103 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 6 Chain: "H" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 1 Chain: "I" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1764 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "J" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 1 Chain: "K" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1764 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "M" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1764 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "N" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 1 Chain: "O" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1764 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "P" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1906 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1764 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 1 Chain: "G" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1764 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "L" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 1 Time building chain proxies: 30.21, per 1000 atoms: 0.43 Number of scatterers: 70631 At special positions: 0 Unit cell: (148.75, 154.7, 436.73, 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 306 16.00 O 13626 8.00 N 11805 7.00 C 44894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - 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 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.03 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 C 132 " - 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 379 " - pdb=" SG CYS C 432 " 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=2.03 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 D 132 " - 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 379 " - pdb=" SG CYS D 432 " distance=2.04 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 E 132 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 132 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 221 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 145 " - pdb=" SG CYS J 221 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 146 " - pdb=" SG CYS M 220 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 221 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 146 " - pdb=" SG CYS O 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 145 " - pdb=" SG CYS P 221 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 146 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS R 145 " - pdb=" SG CYS R 221 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 145 " - pdb=" SG CYS L 221 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.93 Conformation dependent library (CDL) restraints added in 6.9 seconds 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16794 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 185 sheets defined 14.5% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.805A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.735A pdb=" N PHE A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.689A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.698A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 782 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.653A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.401A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.595A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.791A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.557A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.748A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.709A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.952A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 782 removed outlier: 4.168A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.649A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.299A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.659A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.768A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 371 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.713A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.050A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 782 removed outlier: 3.672A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.616A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 941 removed outlier: 6.972A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.896A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.782A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.715A pdb=" N PHE D 371 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.903A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 754 " --> pdb=" O SER D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 782 Processing helix chain 'D' and resid 816 through 824 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 removed outlier: 3.641A pdb=" N ALA D 890 " --> pdb=" O THR D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 907 Processing helix chain 'D' and resid 913 through 941 removed outlier: 7.115A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 946 removed outlier: 4.041A pdb=" N LEU D 945 " --> pdb=" O PRO D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 949 through 965 removed outlier: 3.726A pdb=" N HIS D 954 " --> pdb=" O ASP D 950 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.502A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 998 " --> pdb=" O ASP D 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.689A pdb=" N PHE E 342 " --> pdb=" O PHE E 338 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN E 343 " --> pdb=" O HIS E 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 338 through 343' Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.805A pdb=" N TYR E 369 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE E 371 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.796A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 385 through 390' Processing helix chain 'E' and resid 403 through 410 removed outlier: 4.639A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 752 removed outlier: 3.672A pdb=" N ASN E 751 " --> pdb=" O THR E 747 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 752 " --> pdb=" O GLU E 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 747 through 752' Processing helix chain 'E' and resid 758 through 782 removed outlier: 4.197A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 763 " --> pdb=" O PHE E 759 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS E 764 " --> pdb=" O CYS E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 890 removed outlier: 3.667A pdb=" N ALA E 890 " --> pdb=" O THR E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 removed outlier: 3.522A pdb=" N GLY E 908 " --> pdb=" O TYR E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.337A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.844A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS E 954 " --> pdb=" O ASP E 950 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 983 removed outlier: 3.798A pdb=" N ARG E 983 " --> pdb=" O ASP E 979 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.393A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E1017 " --> pdb=" O ILE E1013 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.663A pdb=" N PHE F 371 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 389 removed outlier: 3.726A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP F 389 " --> pdb=" O LYS F 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 385 through 389' Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.704A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 754 removed outlier: 3.987A pdb=" N SER F 750 " --> pdb=" O SER F 746 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN F 751 " --> pdb=" O THR F 747 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU F 752 " --> pdb=" O GLU F 748 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 754 " --> pdb=" O SER F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 782 removed outlier: 3.685A pdb=" N ARG F 765 " --> pdb=" O THR F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 824 Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 886 through 890 removed outlier: 3.616A pdb=" N ALA F 890 " --> pdb=" O THR F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 907 Processing helix chain 'F' and resid 913 through 941 removed outlier: 6.954A pdb=" N LYS F 921 " --> pdb=" O TYR F 917 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) Processing helix chain 'F' and resid 949 through 965 removed outlier: 3.750A pdb=" N ASN F 953 " --> pdb=" O GLN F 949 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN F 955 " --> pdb=" O VAL F 951 " (cutoff:3.500A) Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.801A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP F 994 " --> pdb=" O GLU F 990 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 995 " --> pdb=" O VAL F 991 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU F1017 " --> pdb=" O ILE F1013 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F1033 " --> pdb=" O MET F1029 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 246 removed outlier: 3.660A pdb=" N PHE H 243 " --> pdb=" O GLY H 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 235 removed outlier: 4.429A pdb=" N GLY J 234 " --> pdb=" O ASP J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 246 removed outlier: 3.662A pdb=" N PHE J 243 " --> pdb=" O GLY J 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 235 removed outlier: 3.786A pdb=" N THR N 233 " --> pdb=" O TYR N 229 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY N 234 " --> pdb=" O ASP N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 246 Processing helix chain 'P' and resid 230 through 235 removed outlier: 4.427A pdb=" N GLY P 234 " --> pdb=" O ASP P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 246 removed outlier: 3.658A pdb=" N PHE P 243 " --> pdb=" O GLY P 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 246 removed outlier: 3.646A pdb=" N PHE R 243 " --> pdb=" O GLY R 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 246 removed outlier: 3.650A pdb=" N PHE L 243 " --> pdb=" O GLY L 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.662A pdb=" N THR A 30 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 61 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 7.659A pdb=" N VAL A 37 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 190 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.582A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.611A pdb=" N THR A 52 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A 275 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A 54 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 removed outlier: 4.344A pdb=" N GLY A 104 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA A 243 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 102 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 118 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.698A pdb=" N LEU A 244 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.812A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.830A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.538A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.616A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 565 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.131A pdb=" N ALA A 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 'A' and resid 712 through 728 removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 728 removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.162A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.560A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.586A pdb=" N THR B 30 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 61 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.680A pdb=" N THR B 52 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 275 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B 54 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 85 through 86 removed outlier: 4.375A pdb=" N GLY B 104 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA B 243 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 102 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.844A pdb=" N LEU B 244 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.605A pdb=" N ASN B 126 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.524A pdb=" N TYR B 170 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.883A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.639A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.291A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.041A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.041A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.172A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.723A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.560A pdb=" N THR C 30 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 37 through 38 removed outlier: 7.645A pdb=" N VAL C 37 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 190 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 49 through 56 removed outlier: 3.614A pdb=" N THR C 52 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C 275 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP C 54 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 273 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 85 through 86 removed outlier: 4.261A pdb=" N GLY C 104 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA C 243 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE C 102 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 118 " --> pdb=" O PHE C 107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.734A pdb=" N LEU C 244 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.826A pdb=" N ASN C 123 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN C 126 " --> pdb=" O ASN C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.642A pdb=" N ILE C 129 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.582A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.582A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 326 through 327 removed outlier: 3.807A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.565A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.560A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 712 through 727 removed outlier: 7.063A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 712 through 727 removed outlier: 7.063A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.225A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.651A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.677A pdb=" N THR D 30 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER D 61 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 37 through 38 removed outlier: 7.574A pdb=" N VAL D 37 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N ALA D 222 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS D 207 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 206 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 190 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AG5, first strand: chain 'D' and resid 49 through 56 removed outlier: 3.603A pdb=" N THR D 52 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE D 275 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP D 54 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 273 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 85 through 86 removed outlier: 4.296A pdb=" N GLY D 104 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA D 243 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE D 102 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 118 " --> pdb=" O PHE D 107 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 85 through 86 removed outlier: 3.689A pdb=" N LEU D 244 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.596A pdb=" N ASN D 126 " --> pdb=" O ASN D 123 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.557A pdb=" N ILE D 129 " --> pdb=" O TYR D 170 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 311 through 319 removed outlier: 3.594A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR D 315 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 325 through 326 removed outlier: 3.516A pdb=" N GLY D 550 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 548 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N PHE D 565 " --> pdb=" O PHE E 44 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 376 through 379 removed outlier: 3.554A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 516 through 517 removed outlier: 7.446A pdb=" N GLU D 516 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AH6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.789A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.197A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.128A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.893A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D1068 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.893A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D1068 " --> pdb=" O THR D 719 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 787 through 789 Processing sheet with id=AI4, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.668A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 30 through 32 removed outlier: 3.593A pdb=" N THR E 30 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER E 61 " --> pdb=" O SER E 32 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 37 through 38 removed outlier: 7.674A pdb=" N VAL E 37 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS E 206 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG E 190 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 49 through 56 removed outlier: 3.878A pdb=" N PHE E 275 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP E 54 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG E 273 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 85 through 86 removed outlier: 4.326A pdb=" N GLY E 104 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA E 243 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE E 102 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 118 " --> pdb=" O PHE E 107 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 85 through 86 removed outlier: 3.697A pdb=" N LEU E 244 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.582A pdb=" N ASN E 126 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 129 through 130 removed outlier: 3.534A pdb=" N ILE E 129 " --> pdb=" O TYR E 170 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 310 through 313 removed outlier: 3.565A pdb=" N TYR E 313 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 597 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 650 " --> pdb=" O PHE E 643 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE E 643 " --> pdb=" O LEU E 650 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 325 through 328 removed outlier: 3.790A pdb=" N GLY E 550 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE E 565 " --> pdb=" O PHE F 44 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 376 through 380 removed outlier: 3.622A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AJ7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AJ8, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.053A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN E 675 " --> pdb=" O SER E 691 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 693 " --> pdb=" O SER E 673 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'E' and resid 701 through 704 removed outlier: 6.030A pdb=" N ALA E 701 " --> pdb=" O ILE F 788 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS F 790 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN E 703 " --> pdb=" O LYS F 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'E' and resid 712 through 728 removed outlier: 7.050A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E1068 " --> pdb=" O THR E 719 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E1056 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'E' and resid 712 through 728 removed outlier: 7.050A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E1068 " --> pdb=" O THR E 719 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 733 through 735 removed outlier: 4.316A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 1081 through 1082 removed outlier: 3.531A pdb=" N ILE E1081 " --> pdb=" O HIS E1088 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER E1123 " --> pdb=" O ALA E1087 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 30 through 32 removed outlier: 3.668A pdb=" N THR F 30 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER F 61 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 37 through 38 removed outlier: 7.612A pdb=" N VAL F 37 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ALA F 222 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N HIS F 207 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG F 190 " --> pdb=" O SER F 95 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'F' and resid 49 through 56 removed outlier: 3.885A pdb=" N THR F 52 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE F 275 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP F 54 " --> pdb=" O ARG F 273 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 85 through 86 removed outlier: 4.285A pdb=" N GLY F 104 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA F 243 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE F 102 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 118 " --> pdb=" O PHE F 107 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 85 through 86 removed outlier: 3.737A pdb=" N LEU F 244 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 122 through 123 removed outlier: 3.593A pdb=" N ASN F 126 " --> pdb=" O ASN F 123 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'F' and resid 129 through 130 removed outlier: 3.516A pdb=" N ILE F 129 " --> pdb=" O TYR F 170 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'F' and resid 311 through 313 removed outlier: 3.524A pdb=" N TYR F 313 " --> pdb=" O VAL F 597 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'F' and resid 311 through 313 removed outlier: 3.524A pdb=" N TYR F 313 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'F' and resid 325 through 326 removed outlier: 3.844A pdb=" N GLY F 550 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'F' and resid 376 through 380 removed outlier: 3.555A pdb=" N SER F 514 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'F' and resid 391 through 392 removed outlier: 3.568A pdb=" N VAL F 524 " --> pdb=" O PHE F 392 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AL9, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER F 691 " --> pdb=" O GLN F 675 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F 675 " --> pdb=" O SER F 691 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'F' and resid 712 through 727 removed outlier: 7.020A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F1068 " --> pdb=" O THR F 719 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F1056 " --> pdb=" O GLY F1059 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'F' and resid 712 through 727 removed outlier: 7.020A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F1068 " --> pdb=" O THR F 719 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.323A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.776A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.812A pdb=" N THR H 5 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.597A pdb=" N LEU H 11 " --> pdb=" O LYS H 104 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR H 36 " --> pdb=" O TYR H 87 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'H' and resid 48 through 49 Processing sheet with id=AM8, first strand: chain 'H' and resid 127 through 130 removed outlier: 3.617A pdb=" N SER H 130 " --> pdb=" O SER H 144 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU H 206 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER H 196 " --> pdb=" O TYR H 205 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'H' and resid 133 through 134 removed outlier: 6.149A pdb=" N GLY H 133 " --> pdb=" O THR H 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM9 Processing sheet with id=AN1, first strand: chain 'H' and resid 183 through 185 removed outlier: 3.948A pdb=" N GLU H 184 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE H 173 " --> pdb=" O GLU H 184 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU H 168 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA H 163 " --> pdb=" O LEU H 168 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP H 170 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG H 161 " --> pdb=" O TRP H 170 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY H 172 " --> pdb=" O TRP H 159 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET H 157 " --> pdb=" O ILE H 174 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.878A pdb=" N ALA I 10 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP I 86 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.878A pdb=" N ALA I 10 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AN5, first strand: chain 'I' and resid 193 through 197 removed outlier: 3.653A pdb=" N SER I 145 " --> pdb=" O SER I 131 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 129 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN I 243 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU I 130 " --> pdb=" O GLN I 243 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'I' and resid 182 through 184 removed outlier: 6.796A pdb=" N TRP I 160 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL I 174 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N MET I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL I 240 " --> pdb=" O LYS I 222 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'J' and resid 4 through 6 removed outlier: 4.046A pdb=" N THR J 5 " --> pdb=" O ARG J 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG J 24 " --> pdb=" O THR J 5 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.584A pdb=" N LEU J 11 " --> pdb=" O LYS J 104 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR J 36 " --> pdb=" O TYR J 87 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AO1, first strand: chain 'J' and resid 127 through 130 removed outlier: 3.554A pdb=" N SER J 130 " --> pdb=" O SER J 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 206 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'J' and resid 133 through 134 removed outlier: 6.160A pdb=" N GLY J 133 " --> pdb=" O THR J 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'J' and resid 183 through 185 removed outlier: 3.878A pdb=" N GLU J 184 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE J 173 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU J 168 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA J 163 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP J 170 " --> pdb=" O ARG J 161 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG J 161 " --> pdb=" O TRP J 170 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY J 172 " --> pdb=" O TRP J 159 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY K 12 " --> pdb=" O THR K 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO4 Processing sheet with id=AO5, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.526A pdb=" N VAL K 18 " --> pdb=" O ILE K 76 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'K' and resid 46 through 49 removed outlier: 6.684A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR K 88 " --> pdb=" O TYR K 37 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP K 86 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'K' and resid 90 through 93 removed outlier: 4.012A pdb=" N ASN K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'K' and resid 130 through 131 removed outlier: 3.838A pdb=" N SER K 145 " --> pdb=" O SER K 131 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 142 " --> pdb=" O MET K 207 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET K 207 " --> pdb=" O LEU K 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU K 144 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'K' and resid 182 through 184 removed outlier: 3.502A pdb=" N TYR K 183 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP K 160 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL K 174 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N MET K 158 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA K 221 " --> pdb=" O HIS K 159 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.760A pdb=" N GLY M 12 " --> pdb=" O THR M 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP1 Processing sheet with id=AP2, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AP3, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.667A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'M' and resid 90 through 93 removed outlier: 3.996A pdb=" N ASN M 97 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'M' and resid 141 through 142 removed outlier: 3.546A pdb=" N LEU M 142 " --> pdb=" O MET M 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET M 207 " --> pdb=" O LEU M 142 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER M 202 " --> pdb=" O ASP M 197 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'M' and resid 141 through 142 removed outlier: 3.546A pdb=" N LEU M 142 " --> pdb=" O MET M 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET M 207 " --> pdb=" O LEU M 142 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER M 145 " --> pdb=" O SER M 131 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL M 129 " --> pdb=" O ALA M 147 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN M 243 " --> pdb=" O LEU M 128 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU M 130 " --> pdb=" O GLN M 243 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'M' and resid 160 through 163 removed outlier: 6.960A pdb=" N TRP M 160 " --> pdb=" O VAL M 172 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'M' and resid 222 through 223 removed outlier: 3.886A pdb=" N VAL M 240 " --> pdb=" O LYS M 222 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.709A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS N 23 " --> pdb=" O PHE N 71 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.566A pdb=" N LEU N 11 " --> pdb=" O LYS N 104 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'N' and resid 33 through 34 Processing sheet with id=AQ3, first strand: chain 'N' and resid 48 through 49 removed outlier: 3.798A pdb=" N ASN N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'N' and resid 127 through 130 Processing sheet with id=AQ5, first strand: chain 'N' and resid 133 through 134 removed outlier: 6.215A pdb=" N GLY N 133 " --> pdb=" O THR N 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ5 Processing sheet with id=AQ6, first strand: chain 'N' and resid 183 through 185 removed outlier: 4.187A pdb=" N GLU N 184 " --> pdb=" O PHE N 173 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE N 173 " --> pdb=" O GLU N 184 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU N 168 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA N 163 " --> pdb=" O LEU N 168 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TRP N 170 " --> pdb=" O ARG N 161 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ARG N 161 " --> pdb=" O TRP N 170 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY N 172 " --> pdb=" O TRP N 159 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER N 158 " --> pdb=" O THR N 222 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.672A pdb=" N GLY O 12 " --> pdb=" O THR O 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ7 Processing sheet with id=AQ8, first strand: chain 'O' and resid 18 through 23 removed outlier: 3.526A pdb=" N VAL O 18 " --> pdb=" O ILE O 76 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'O' and resid 46 through 49 removed outlier: 6.612A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP O 86 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'O' and resid 90 through 93 removed outlier: 3.984A pdb=" N ASN O 97 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'O' and resid 192 through 197 removed outlier: 3.552A pdb=" N SER O 195 " --> pdb=" O TYR O 204 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER O 145 " --> pdb=" O SER O 131 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL O 129 " --> pdb=" O ALA O 147 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LEU O 128 " --> pdb=" O GLN O 243 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'O' and resid 182 through 184 removed outlier: 6.744A pdb=" N TRP O 160 " --> pdb=" O VAL O 172 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL O 174 " --> pdb=" O MET O 158 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N MET O 158 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA O 221 " --> pdb=" O HIS O 159 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL O 240 " --> pdb=" O LYS O 222 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'P' and resid 4 through 6 removed outlier: 3.729A pdb=" N THR P 5 " --> pdb=" O ARG P 24 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'P' and resid 10 through 11 removed outlier: 3.516A pdb=" N LEU P 11 " --> pdb=" O LYS P 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA P 84 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR P 36 " --> pdb=" O TYR P 87 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'P' and resid 127 through 130 removed outlier: 3.604A pdb=" N SER P 130 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU P 206 " --> pdb=" O LEU P 143 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'P' and resid 133 through 134 removed outlier: 6.097A pdb=" N GLY P 133 " --> pdb=" O THR P 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR7 Processing sheet with id=AR8, first strand: chain 'P' and resid 183 through 185 removed outlier: 4.008A pdb=" N GLU P 184 " --> pdb=" O PHE P 173 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE P 173 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU P 168 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA P 163 " --> pdb=" O LEU P 168 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TRP P 170 " --> pdb=" O ARG P 161 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG P 161 " --> pdb=" O TRP P 170 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY P 172 " --> pdb=" O TRP P 159 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET P 157 " --> pdb=" O ILE P 174 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.635A pdb=" N GLY Q 12 " --> pdb=" O THR Q 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR9 Processing sheet with id=AS1, first strand: chain 'Q' and resid 18 through 23 removed outlier: 3.504A pdb=" N VAL Q 18 " --> pdb=" O ILE Q 76 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'Q' and resid 46 through 49 removed outlier: 6.619A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR Q 88 " --> pdb=" O TYR Q 37 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'Q' and resid 90 through 93 removed outlier: 4.017A pdb=" N ASN Q 97 " --> pdb=" O ASP Q 93 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'Q' and resid 193 through 197 removed outlier: 3.534A pdb=" N SER Q 195 " --> pdb=" O TYR Q 204 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER Q 202 " --> pdb=" O ASP Q 197 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU Q 144 " --> pdb=" O LEU Q 205 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET Q 207 " --> pdb=" O LEU Q 142 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU Q 142 " --> pdb=" O MET Q 207 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER Q 145 " --> pdb=" O SER Q 131 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL Q 129 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LEU Q 128 " --> pdb=" O GLN Q 243 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'Q' and resid 182 through 184 removed outlier: 3.516A pdb=" N TYR Q 183 " --> pdb=" O VAL Q 174 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP Q 160 " --> pdb=" O VAL Q 172 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL Q 174 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N MET Q 158 " --> pdb=" O VAL Q 174 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'R' and resid 4 through 6 removed outlier: 3.857A pdb=" N THR R 5 " --> pdb=" O ARG R 24 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.616A pdb=" N LEU R 11 " --> pdb=" O LYS R 104 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'R' and resid 44 through 46 Processing sheet with id=AS9, first strand: chain 'R' and resid 48 through 49 Processing sheet with id=AT1, first strand: chain 'R' and resid 127 through 130 removed outlier: 3.543A pdb=" N SER R 130 " --> pdb=" O SER R 144 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU R 206 " --> pdb=" O LEU R 143 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'R' and resid 133 through 134 removed outlier: 6.080A pdb=" N GLY R 133 " --> pdb=" O THR R 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT2 Processing sheet with id=AT3, first strand: chain 'R' and resid 183 through 185 removed outlier: 4.048A pdb=" N GLU R 184 " --> pdb=" O PHE R 173 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE R 173 " --> pdb=" O GLU R 184 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU R 168 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA R 163 " --> pdb=" O LEU R 168 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP R 170 " --> pdb=" O ARG R 161 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG R 161 " --> pdb=" O TRP R 170 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY R 172 " --> pdb=" O TRP R 159 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET R 157 " --> pdb=" O ILE R 174 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.742A pdb=" N ALA G 10 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G 86 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR G 88 " --> pdb=" O TYR G 37 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AT6, first strand: chain 'G' and resid 90 through 93 removed outlier: 4.017A pdb=" N ASN G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'G' and resid 193 through 197 removed outlier: 3.513A pdb=" N LEU G 144 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET G 207 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 142 " --> pdb=" O MET G 207 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER G 145 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 129 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LEU G 128 " --> pdb=" O GLN G 243 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'G' and resid 182 through 184 removed outlier: 6.815A pdb=" N TRP G 160 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL G 174 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N MET G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.961A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.643A pdb=" N LEU L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AU3, first strand: chain 'L' and resid 127 through 130 removed outlier: 3.619A pdb=" N SER L 130 " --> pdb=" O SER L 144 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 206 " --> pdb=" O LEU L 143 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'L' and resid 133 through 134 removed outlier: 6.185A pdb=" N GLY L 133 " --> pdb=" O THR L 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU4 Processing sheet with id=AU5, first strand: chain 'L' and resid 183 through 185 removed outlier: 3.985A pdb=" N GLU L 184 " --> pdb=" O PHE L 173 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE L 173 " --> pdb=" O GLU L 184 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU L 168 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA L 163 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TRP L 170 " --> pdb=" O ARG L 161 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ARG L 161 " --> pdb=" O TRP L 170 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY L 172 " --> pdb=" O TRP L 159 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET L 157 " --> pdb=" O ILE L 174 " (cutoff:3.500A) 2112 hydrogen bonds defined for protein. 5727 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: 42.87 Time building geometry restraints manager: 14.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22671 1.34 - 1.46: 14486 1.46 - 1.58: 34743 1.58 - 1.70: 0 1.70 - 1.82: 402 Bond restraints: 72302 Sorted by residual: bond pdb=" N GLY B 268 " pdb=" CA GLY B 268 " ideal model delta sigma weight residual 1.445 1.481 -0.036 9.20e-03 1.18e+04 1.56e+01 bond pdb=" N PHE F 329 " pdb=" CA PHE F 329 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.56e+01 bond pdb=" N PHE D 329 " pdb=" CA PHE D 329 " ideal model delta sigma weight residual 1.453 1.485 -0.032 8.30e-03 1.45e+04 1.50e+01 bond pdb=" N GLY E 268 " pdb=" CA GLY E 268 " ideal model delta sigma weight residual 1.445 1.480 -0.035 9.20e-03 1.18e+04 1.43e+01 bond pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 1.445 1.479 -0.034 9.20e-03 1.18e+04 1.38e+01 ... (remaining 72297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 95178 1.27 - 2.54: 2501 2.54 - 3.82: 556 3.82 - 5.09: 69 5.09 - 6.36: 10 Bond angle restraints: 98314 Sorted by residual: angle pdb=" CA PHE F 329 " pdb=" C PHE F 329 " pdb=" N PRO F 330 " ideal model delta sigma weight residual 117.67 123.53 -5.86 1.08e+00 8.57e-01 2.94e+01 angle pdb=" CA PHE F 329 " pdb=" C PHE F 329 " pdb=" O PHE F 329 " ideal model delta sigma weight residual 120.64 115.57 5.07 9.90e-01 1.02e+00 2.63e+01 angle pdb=" N VAL E1128 " pdb=" CA VAL E1128 " pdb=" C VAL E1128 " ideal model delta sigma weight residual 113.71 109.38 4.33 9.50e-01 1.11e+00 2.07e+01 angle pdb=" CA GLY B 268 " pdb=" C GLY B 268 " pdb=" O GLY B 268 " ideal model delta sigma weight residual 122.33 117.36 4.97 1.11e+00 8.12e-01 2.01e+01 angle pdb=" CA GLY E 268 " pdb=" C GLY E 268 " pdb=" O GLY E 268 " ideal model delta sigma weight residual 122.33 117.47 4.86 1.11e+00 8.12e-01 1.91e+01 ... (remaining 98309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 41270 17.62 - 35.24: 1305 35.24 - 52.86: 244 52.86 - 70.48: 50 70.48 - 88.09: 14 Dihedral angle restraints: 42883 sinusoidal: 16600 harmonic: 26283 Sorted by residual: dihedral pdb=" C THR C 323 " pdb=" N THR C 323 " pdb=" CA THR C 323 " pdb=" CB THR C 323 " ideal model delta harmonic sigma weight residual -122.00 -130.92 8.92 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" CB GLU E 324 " pdb=" CG GLU E 324 " pdb=" CD GLU E 324 " pdb=" OE1 GLU E 324 " ideal model delta sinusoidal sigma weight residual 0.00 -84.13 84.13 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" CA ALA C 124 " pdb=" C ALA C 124 " pdb=" N THR C 125 " pdb=" CA THR C 125 " ideal model delta harmonic sigma weight residual 180.00 164.53 15.47 0 5.00e+00 4.00e-02 9.57e+00 ... (remaining 42880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 8533 0.044 - 0.088: 1690 0.088 - 0.133: 666 0.133 - 0.177: 28 0.177 - 0.221: 11 Chirality restraints: 10928 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA THR C 323 " pdb=" N THR C 323 " pdb=" C THR C 323 " pdb=" CB THR C 323 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE F 326 " pdb=" N ILE F 326 " pdb=" C ILE F 326 " pdb=" CB ILE F 326 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 10925 not shown) Planarity restraints: 12753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 265 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C TYR D 265 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR D 265 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR D 266 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 329 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO F 330 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 330 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 330 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 986 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.018 5.00e-02 4.00e+02 ... (remaining 12750 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4474 2.74 - 3.28: 67271 3.28 - 3.82: 114316 3.82 - 4.36: 133669 4.36 - 4.90: 232189 Nonbonded interactions: 551919 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.196 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.205 3.040 nonbonded pdb=" OG SER F 758 " pdb=" OG1 THR F 761 " model vdw 2.214 3.040 nonbonded pdb=" O GLY E 880 " pdb=" OG SER E 884 " model vdw 2.215 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.216 3.040 ... (remaining 551914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 517 or resid 522 through 1147)) selection = (chain 'B' and (resid 28 through 517 or resid 522 through 676 or resid 689 throu \ gh 1147)) selection = (chain 'C' and (resid 28 through 517 or resid 522 through 1147)) selection = (chain 'D' and (resid 28 through 676 or resid 689 through 1147)) selection = (chain 'E' and (resid 28 through 517 or resid 522 through 1147)) selection = (chain 'F' and (resid 28 through 517 or resid 522 through 1147)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = (chain 'H' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or resid 2 through 260)) selection = (chain 'J' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or resid 2 through 260)) selection = (chain 'L' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or resid 2 through 260)) selection = (chain 'N' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or resid 2 through 260)) selection = chain 'P' selection = (chain 'R' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or resid 2 through 260)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 51.960 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: 0.090 Extract box with map and model: 2.040 Check model and map are aligned: 0.400 Set scattering table: 0.500 Process input model: 140.200 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.390 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: 0.020 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 200.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4218 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 : 0.002 0.039 72302 Z= 0.149 Angle : 0.503 6.362 98314 Z= 0.312 Chirality : 0.041 0.221 10928 Planarity : 0.003 0.037 12753 Dihedral : 8.684 88.095 25837 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 3.80 % Allowed : 6.89 % Favored : 89.31 % 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: -3.47 (0.08), residues: 8966 helix: -0.42 (0.14), residues: 1247 sheet: -2.16 (0.10), residues: 2091 loop : -2.98 (0.07), residues: 5628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 94 HIS 0.002 0.000 HIS D 339 PHE 0.011 0.001 PHE C 318 TYR 0.015 0.001 TYR E 269 ARG 0.004 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 7811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 466 time to evaluate : 6.005 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 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 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 TARDY: cannot create tardy model for: "GLU P 1 " (corrupted residue). Skipping it. 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: F 458 LYS cc_start: 0.3656 (OUTLIER) cc_final: 0.3001 (mmtm) REVERT: H 211 LEU cc_start: -0.1600 (OUTLIER) cc_final: -0.2046 (mt) REVERT: J 58 ILE cc_start: -0.4739 (OUTLIER) cc_final: -0.5169 (pt) REVERT: K 249 VAL cc_start: -0.1006 (OUTLIER) cc_final: -0.1211 (p) REVERT: P 58 ILE cc_start: -0.3839 (OUTLIER) cc_final: -0.4142 (pt) REVERT: Q 207 MET cc_start: 0.0171 (mtm) cc_final: -0.0430 (mmm) REVERT: R 208 MET cc_start: -0.1652 (mtt) cc_final: -0.2405 (mmt) REVERT: R 211 LEU cc_start: -0.3058 (OUTLIER) cc_final: -0.4208 (tm) outliers start: 297 outliers final: 62 residues processed: 746 average time/residue: 0.7335 time to fit residues: 902.4012 Evaluate side-chains 287 residues out of total 7811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 219 time to evaluate : 5.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 1041 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 1129 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain I residue 89 CYS Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain Q residue 89 CYS Chi-restraints excluded: chain Q residue 189 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 0.0030 chunk 682 optimal weight: 0.9990 chunk 378 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 460 optimal weight: 6.9990 chunk 364 optimal weight: 9.9990 chunk 705 optimal weight: 0.6980 chunk 272 optimal weight: 0.7980 chunk 428 optimal weight: 8.9990 chunk 525 optimal weight: 20.0000 chunk 817 optimal weight: 20.0000 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 70 HIS A 146 GLN A 188 ASN A 474 GLN A 544 ASN A 607 GLN A 613 GLN A 657 ASN A 784 GLN A 901 GLN A 949 GLN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1054 GLN B 53 GLN B 67 HIS B 146 GLN B 474 GLN B 493 GLN B 540 ASN B 563 GLN B 564 GLN B 607 GLN B 613 GLN B 677 GLN B 690 GLN B 784 GLN B 901 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1088 HIS B1108 ASN C 53 GLN C 70 HIS C 82 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 188 ASN C 354 ASN C 394 ASN C 417 ASN C 439 ASN C 474 GLN C 544 ASN C 563 GLN C 607 GLN C 690 GLN C 784 GLN C 901 GLN C1002 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN C1048 HIS ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 146 GLN D 173 GLN D 188 ASN D 439 ASN D 474 GLN D 493 GLN D 544 ASN D 563 GLN D 564 GLN D 607 GLN D 677 GLN D 690 GLN D 710 ASN D 784 GLN D 901 GLN D 913 GLN D 949 GLN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN D1048 HIS D1088 HIS E 53 GLN E 146 GLN E 164 ASN E 173 GLN E 188 ASN E 339 HIS E 439 ASN E 474 GLN E 493 GLN E 544 ASN E 563 GLN E 564 GLN E 607 GLN E 784 GLN E 901 GLN E 913 GLN E 949 GLN ** E1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1010 GLN E1011 GLN E1048 HIS E1054 GLN F 53 GLN F 75 ASN F 146 GLN F 173 GLN F 188 ASN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 439 ASN F 474 GLN F 563 GLN F 564 GLN F 607 GLN F 613 GLN F 690 GLN F 784 GLN F 901 GLN F 913 GLN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1011 GLN F1048 HIS ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 96 GLN H 126 GLN H 207 GLN I 80 GLN I 97 ASN I 159 HIS I 206 GLN J 37 GLN J 89 GLN J 96 GLN J 126 GLN J 207 GLN K 16 GLN K 80 GLN K 97 ASN K 159 HIS K 206 GLN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN M 80 GLN ** M 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 GLN N 37 GLN N 96 GLN N 126 GLN N 207 GLN O 80 GLN O 97 ASN O 206 GLN O 208 ASN P 37 GLN P 96 GLN P 126 GLN P 207 GLN Q 80 GLN Q 97 ASN Q 206 GLN Q 208 ASN R 37 GLN R 96 GLN R 126 GLN R 207 GLN G 80 GLN G 97 ASN G 159 HIS G 206 GLN L 37 GLN L 96 GLN L 126 GLN L 207 GLN Total number of N/Q/H flips: 160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4388 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 72302 Z= 0.180 Angle : 0.571 11.759 98314 Z= 0.287 Chirality : 0.043 0.248 10928 Planarity : 0.004 0.109 12753 Dihedral : 4.043 58.516 9989 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.09 % Allowed : 10.36 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.08), residues: 8966 helix: 0.64 (0.15), residues: 1293 sheet: -1.82 (0.10), residues: 2179 loop : -2.55 (0.07), residues: 5494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 159 HIS 0.006 0.001 HIS Q 159 PHE 0.019 0.001 PHE F 927 TYR 0.033 0.001 TYR R 245 ARG 0.010 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 7811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 226 time to evaluate : 6.071 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 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 TARDY: cannot create tardy model for: "GLU P 1 " (corrupted residue). Skipping it. 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: F 458 LYS cc_start: 0.3699 (OUTLIER) cc_final: 0.2666 (mmtm) REVERT: H 211 LEU cc_start: -0.1969 (OUTLIER) cc_final: -0.2253 (mt) REVERT: J 58 ILE cc_start: -0.5038 (OUTLIER) cc_final: -0.5443 (pt) REVERT: K 249 VAL cc_start: -0.0758 (OUTLIER) cc_final: -0.1043 (p) REVERT: M 207 MET cc_start: -0.0527 (mpp) cc_final: -0.1007 (mpp) REVERT: N 208 MET cc_start: -0.0098 (OUTLIER) cc_final: -0.0394 (mpp) REVERT: N 211 LEU cc_start: -0.2820 (OUTLIER) cc_final: -0.3079 (mt) REVERT: P 58 ILE cc_start: -0.3742 (OUTLIER) cc_final: -0.4044 (pt) REVERT: P 208 MET cc_start: -0.1023 (mmt) cc_final: -0.1239 (mmt) REVERT: Q 207 MET cc_start: 0.0560 (mtm) cc_final: -0.0158 (mmm) REVERT: R 211 LEU cc_start: -0.3492 (OUTLIER) cc_final: -0.3885 (tm) outliers start: 163 outliers final: 80 residues processed: 376 average time/residue: 0.7372 time to fit residues: 466.0298 Evaluate side-chains 265 residues out of total 7811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 177 time to evaluate : 6.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain E residue 1041 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 1129 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 208 MET Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 89 CYS Chi-restraints excluded: chain Q residue 189 LYS Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 211 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4652 > 50: distance: 5 - 15: 25.485 distance: 15 - 16: 14.002 distance: 16 - 17: 22.887 distance: 16 - 19: 17.437 distance: 17 - 18: 31.063 distance: 17 - 24: 21.923 distance: 19 - 20: 10.195 distance: 20 - 21: 8.705 distance: 21 - 22: 10.009 distance: 21 - 23: 12.717 distance: 24 - 25: 13.078 distance: 25 - 26: 23.432 distance: 26 - 27: 19.300 distance: 26 - 29: 15.364 distance: 29 - 30: 11.738 distance: 31 - 32: 5.751 distance: 31 - 33: 8.860 distance: 33 - 34: 28.580 distance: 34 - 35: 15.521 distance: 34 - 37: 21.586 distance: 35 - 36: 29.992 distance: 35 - 41: 28.258 distance: 37 - 38: 8.441 distance: 38 - 39: 22.683 distance: 38 - 40: 26.449 distance: 41 - 42: 28.704 distance: 42 - 43: 25.795 distance: 42 - 45: 41.938 distance: 43 - 44: 41.277 distance: 43 - 50: 9.163 distance: 45 - 46: 34.341 distance: 46 - 47: 18.063 distance: 47 - 48: 14.282 distance: 48 - 49: 13.050 distance: 50 - 51: 16.885 distance: 50 - 56: 10.877 distance: 51 - 52: 23.033 distance: 51 - 54: 25.372 distance: 52 - 53: 12.730 distance: 52 - 57: 37.914 distance: 54 - 55: 22.078 distance: 55 - 56: 35.575 distance: 57 - 58: 15.308 distance: 58 - 59: 30.659 distance: 58 - 61: 6.433 distance: 59 - 60: 15.485 distance: 59 - 63: 28.287 distance: 61 - 62: 19.928 distance: 62 - 101: 5.180 distance: 63 - 64: 21.411 distance: 64 - 65: 25.862 distance: 64 - 67: 19.388 distance: 65 - 66: 24.929 distance: 65 - 71: 20.223 distance: 67 - 68: 6.694 distance: 68 - 69: 15.038 distance: 68 - 70: 18.561 distance: 71 - 72: 6.650 distance: 72 - 73: 24.538 distance: 73 - 74: 23.386 distance: 73 - 75: 5.044 distance: 75 - 76: 10.882 distance: 76 - 77: 16.285 distance: 76 - 79: 14.544 distance: 77 - 78: 13.338 distance: 77 - 82: 15.485 distance: 79 - 80: 6.736 distance: 79 - 81: 13.269