Starting phenix.real_space_refine on Fri Dec 15 09:10:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6a_33019/12_2023/7x6a_33019.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6a_33019/12_2023/7x6a_33019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6a_33019/12_2023/7x6a_33019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6a_33019/12_2023/7x6a_33019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6a_33019/12_2023/7x6a_33019.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6a_33019/12_2023/7x6a_33019.pdb" } resolution = 3.5 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= -0.001 sd= 0.061 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 129 5.16 5 C 19682 2.51 5 N 5168 2.21 5 O 5900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 574": "OD1" <-> "OD2" Residue "D GLU 661": "OE1" <-> "OE2" Residue "D PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 780": "OE1" <-> "OE2" Residue "D GLU 988": "OE1" <-> "OE2" Residue "D GLU 1017": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 108": "OD1" <-> "OD2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30879 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8548 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8548 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 8551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8551 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 16.28, per 1000 atoms: 0.53 Number of scatterers: 30879 At special positions: 0 Unit cell: (175.48, 154.08, 208.65, 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 129 16.00 O 5900 8.00 N 5168 7.00 C 19682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - 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 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.76 Conformation dependent library (CDL) restraints added in 6.0 seconds 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7380 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 63 sheets defined 18.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.719A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.550A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.562A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.640A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.611A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.606A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.961A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.577A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.052A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.883A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.613A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.797A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.438A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 762 through 783 removed outlier: 3.883A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.589A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.563A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.743A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.837A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.657A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 3.760A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.665A pdb=" N ASN D 370 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.228A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.637A pdb=" N ASP D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR D 421 " --> pdb=" O ASN D 417 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 422' Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.779A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.823A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.634A pdb=" N LYS D 933 " --> pdb=" O SER D 929 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.868A pdb=" N GLN D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 956 " --> pdb=" O VAL D 952 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 957 " --> pdb=" O ASN D 953 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 958 " --> pdb=" O HIS D 954 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.347A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D1007 " --> pdb=" O SER D1003 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D1013 " --> pdb=" O THR D1009 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D1021 " --> pdb=" O GLU D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1150 removed outlier: 4.115A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.541A pdb=" N SER L 85 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.582A pdb=" N SER J 85 " --> pdb=" O SER J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.688A pdb=" N SER K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 31 removed outlier: 3.584A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.976A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.646A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.579A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.310A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.537A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.139A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.183A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 6.522A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.517A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.771A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.672A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.575A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.680A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.525A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.816A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 104 through 107 removed outlier: 3.622A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.561A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.158A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.060A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AC9, first strand: chain 'B' and resid 573 through 576 removed outlier: 6.385A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.448A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.635A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.617A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 861 " --> pdb=" O LYS B 733 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.886A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.392A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 51 through 55 removed outlier: 3.553A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 126 through 127 removed outlier: 3.562A pdb=" N PHE D 106 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 311 through 318 removed outlier: 3.609A pdb=" N THR D 315 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.637A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP D 398 " --> pdb=" O VAL D 512 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 512 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL D 510 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE D 402 " --> pdb=" O TYR D 508 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 508 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 539 through 540 Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 660 removed outlier: 3.506A pdb=" N ALA D 694 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL D 656 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR D 696 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 658 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 693 " --> pdb=" O SER D 673 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.702A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.989A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.746A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 861 " --> pdb=" O LYS D 733 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER D 735 " --> pdb=" O THR D 859 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.647A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU H 99 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA H 33 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.647A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 17 through 22 Processing sheet with id=AF6, first strand: chain 'L' and resid 3 through 7 removed outlier: 4.168A pdb=" N VAL L 3 " --> pdb=" O ARG L 26 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA L 19 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE L 73 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.540A pdb=" N GLN L 40 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.737A pdb=" N ALA G 5 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE G 83 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.750A pdb=" N ILE G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE G 51 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AG2, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.843A pdb=" N ALA J 19 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE J 77 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU J 75 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU J 72 " --> pdb=" O SER J 69 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 13 removed outlier: 4.024A pdb=" N VAL J 13 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU J 35 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR J 51 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP J 37 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.503A pdb=" N GLU I 10 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 117 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL I 116 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA I 92 " --> pdb=" O VAL I 116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA I 97 " --> pdb=" O HIS I 35 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.503A pdb=" N GLU I 10 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 117 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL I 116 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA I 92 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 18 through 22 removed outlier: 3.854A pdb=" N VAL I 18 " --> pdb=" O ILE I 83 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL I 69 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 3 through 7 removed outlier: 4.438A pdb=" N VAL K 3 " --> pdb=" O ARG K 26 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE K 73 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU K 72 " --> pdb=" O SER K 69 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.520A pdb=" N VAL K 13 " --> pdb=" O GLU K 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'K' and resid 47 through 51 removed outlier: 6.521A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TYR K 51 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU K 35 " --> pdb=" O TYR K 51 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2442 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: 13.33 Time building geometry restraints manager: 12.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9986 1.35 - 1.47: 8135 1.47 - 1.59: 13352 1.59 - 1.72: 0 1.72 - 1.84: 162 Bond restraints: 31635 Sorted by residual: bond pdb=" C VAL D 620 " pdb=" N PRO D 621 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.06e+00 bond pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.49e+00 bond pdb=" CA GLY D 257 " pdb=" C GLY D 257 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.32e+00 bond pdb=" C GLN D1142 " pdb=" N PRO D1143 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.28e+00 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 ... (remaining 31630 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.33: 890 106.33 - 113.25: 16782 113.25 - 120.18: 10687 120.18 - 127.10: 14404 127.10 - 134.02: 315 Bond angle restraints: 43078 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.46 -3.76 1.22e+00 6.72e-01 9.51e+00 angle pdb=" OG1 THR A 547 " pdb=" CB THR A 547 " pdb=" CG2 THR A 547 " ideal model delta sigma weight residual 109.30 103.28 6.02 2.00e+00 2.50e-01 9.05e+00 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 113.53 110.59 2.94 9.80e-01 1.04e+00 9.02e+00 angle pdb=" OG1 THR A 95 " pdb=" CB THR A 95 " pdb=" CG2 THR A 95 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.95e+00 angle pdb=" OG1 THR D 95 " pdb=" CB THR D 95 " pdb=" CG2 THR D 95 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.95e+00 ... (remaining 43073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 16852 17.60 - 35.21: 1539 35.21 - 52.81: 263 52.81 - 70.42: 58 70.42 - 88.02: 34 Dihedral angle restraints: 18746 sinusoidal: 7232 harmonic: 11514 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.23 -80.77 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CA TRP L 96 " pdb=" C TRP L 96 " pdb=" N PRO L 97 " pdb=" CA PRO L 97 " ideal model delta harmonic sigma weight residual 180.00 141.31 38.69 0 5.00e+00 4.00e-02 5.99e+01 dihedral pdb=" CA TRP K 96 " pdb=" C TRP K 96 " pdb=" N PRO K 97 " pdb=" CA PRO K 97 " ideal model delta harmonic sigma weight residual 180.00 146.41 33.59 0 5.00e+00 4.00e-02 4.51e+01 ... (remaining 18743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3429 0.039 - 0.078: 962 0.078 - 0.117: 383 0.117 - 0.156: 46 0.156 - 0.195: 9 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CB THR B 547 " pdb=" CA THR B 547 " pdb=" OG1 THR B 547 " pdb=" CG2 THR B 547 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 4826 not shown) Planarity restraints: 5588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 96 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO L 97 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A 412 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO B 621 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.032 5.00e-02 4.00e+02 ... (remaining 5585 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 213 2.56 - 3.15: 23728 3.15 - 3.73: 43913 3.73 - 4.32: 59934 4.32 - 4.90: 102976 Nonbonded interactions: 230764 Sorted by model distance: nonbonded pdb=" O ASN B 185 " pdb=" CD2 LEU B 212 " model vdw 1.981 3.460 nonbonded pdb=" O ALA B 67 " pdb=" OG1 THR B 250 " model vdw 2.177 2.440 nonbonded pdb=" O ALA B 292 " pdb=" OG1 THR B 632 " model vdw 2.179 2.440 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.197 2.440 nonbonded pdb=" O ALA D 67 " pdb=" OG1 THR D 250 " model vdw 2.203 2.440 ... (remaining 230759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 184 or (resid 185 and (name N or name CA or nam \ e C or name O or name CB )) or resid 186 through 1150)) selection = (chain 'B' and (resid 25 through 211 or (resid 212 and (name N or name CA or nam \ e C or name O or name CB )) or resid 213 through 1150)) selection = (chain 'D' and (resid 25 through 184 or (resid 185 and (name N or name CA or nam \ e C or name O or name CB )) or resid 186 through 211 or (resid 212 and (name N o \ r name CA or name C or name O or name CB )) or resid 213 through 1150)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.420 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: 0.060 Extract box with map and model: 11.460 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 81.750 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 0.038 31635 Z= 0.143 Angle : 0.523 7.180 43078 Z= 0.282 Chirality : 0.042 0.195 4829 Planarity : 0.004 0.089 5588 Dihedral : 14.042 88.023 11240 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.17 % Favored : 93.48 % Rotamer: Outliers : 0.06 % Allowed : 0.15 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3939 helix: 0.83 (0.22), residues: 636 sheet: -0.09 (0.18), residues: 928 loop : -1.73 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 64 HIS 0.004 0.000 HIS I 35 PHE 0.015 0.001 PHE D 562 TYR 0.011 0.001 TYR I 105 ARG 0.006 0.000 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 529 time to evaluate : 3.373 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 outliers start: 2 outliers final: 0 residues processed: 531 average time/residue: 0.4335 time to fit residues: 358.9353 Evaluate side-chains 271 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 10.0000 chunk 295 optimal weight: 0.1980 chunk 164 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 354 optimal weight: 40.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: