Starting phenix.real_space_refine (version: 1.21rc1) on Fri Sep 1 10:29:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/08_2023/5lze_4125_updated.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= 0.015 sd= 0.273 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4782 5.49 5 S 151 5.16 5 C 74201 2.51 5 N 27541 2.21 5 O 41341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 125": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 135": "NH1" <-> "NH2" Residue "d PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "n TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ASP 31": "OD1" <-> "OD2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 148018 Number of models: 1 Model: "" Number of chains: 59 Chain: "a" Number of atoms: 33029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33029 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 107, 'rna2p_pyr': 68, 'rna3p': 10, 'rna3p_pur': 761, 'rna3p_pyr': 592} Link IDs: {'rna2p': 175, 'rna3p': 1363} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "f" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 505 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "v" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p': 3, 'rna3p_pur': 35, 'rna3p_pyr': 32} Link IDs: {'rna2p': 6, 'rna3p': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "x" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1025 Classifications: {'RNA': 48} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 18} Link IDs: {'rna2p': 9, 'rna3p': 38} Chain: "y" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2031 Classifications: {'RNA': 95} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 7, 'rna2p_pyr': 11, 'rna3p': 3, 'rna3p_pur': 38, 'rna3p_pyr': 35} Link IDs: {'rna2p': 18, 'rna3p': 76} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 62274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62274 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 224, 'rna2p_pyr': 108, 'rna3p': 17, 'rna3p_pur': 1442, 'rna3p_pyr': 1102} Link IDs: {'rna2p': 339, 'rna3p': 2560} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 58, 'rna3p_pyr': 53} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "w" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A10G7 SG CYS 4 14 179.530 99.361 136.236 1.00114.73 S ATOM A10P5 SG CYS 6 16 114.070 107.170 228.386 1.00194.30 S ATOM A10TF SG CYS 6 37 117.340 107.398 226.831 1.00148.41 S ATOM A10U0 SG CYS 6 40 115.831 103.808 225.331 1.00193.31 S Time building chain proxies: 51.52, per 1000 atoms: 0.35 Number of scatterers: 148018 At special positions: 0 Unit cell: (237.8, 265.64, 248.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 151 16.00 P 4782 15.00 O 41341 8.00 N 27541 7.00 C 74201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.06 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: 57.96 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb=" ZN 6 100 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 40 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 37 " 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10684 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 176 helices and 66 sheets defined 38.1% alpha, 17.5% beta 1558 base pairs and 2451 stacking pairs defined. Time for finding SS restraints: 70.80 Creating SS restraints... Processing helix chain 'b' and resid 42 through 63 Proline residue: b 47 - end of helix removed outlier: 3.602A pdb=" N LYS b 63 " --> pdb=" O ILE b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 87 removed outlier: 4.758A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.663A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 128 removed outlier: 4.440A pdb=" N LYS b 127 " --> pdb=" O GLY b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 Processing helix chain 'b' and resid 164 through 169 removed outlier: 4.011A pdb=" N GLU b 168 " --> pdb=" O ASP b 164 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 164 through 169' Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.866A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 191 through 196 removed outlier: 4.433A pdb=" N VAL b 195 " --> pdb=" O ASP b 191 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP b 196 " --> pdb=" O PRO b 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 191 through 196' Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.710A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU b 222 " --> pdb=" O ALA b 218 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.821A pdb=" N ILE c 9 " --> pdb=" O HIS c 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 47 removed outlier: 4.132A pdb=" N ALA c 29 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.599A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.725A pdb=" N LYS c 85 " --> pdb=" O GLU c 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY c 95 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.777A pdb=" N ASP c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.972A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.664A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.666A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 109 through 120 removed outlier: 4.318A pdb=" N HIS d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 6.351A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.947A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.342A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.609A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 5.826A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.735A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET e 146 " --> pdb=" O GLY e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 156 Processing helix chain 'e' and resid 159 through 165 Processing helix chain 'f' and resid 11 through 19 removed outlier: 3.722A pdb=" N SER f 15 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 20 through 33 Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.844A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.539A pdb=" N GLN g 51 " --> pdb=" O GLU g 47 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 3.697A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 3.925A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.854A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN g 147 " --> pdb=" O MET g 143 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS g 148 " --> pdb=" O ALA g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 Processing helix chain 'i' and resid 33 through 38 Processing helix chain 'i' and resid 45 through 55 Proline residue: i 50 - end of helix removed outlier: 3.664A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 4.679A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 98 removed outlier: 4.997A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.326A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.971A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.247A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 74 removed outlier: 3.615A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 4.183A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.897A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY l 117 " --> pdb=" O ARG l 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 112 through 117' Processing helix chain 'm' and resid 13 through 21 removed outlier: 3.812A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 48 through 63 removed outlier: 3.779A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 3.555A pdb=" N GLY m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 23 through 29 removed outlier: 4.914A pdb=" N LYS n 27 " --> pdb=" O ARG n 23 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 50 removed outlier: 3.658A pdb=" N TRP n 41 " --> pdb=" O ASP n 37 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR n 49 " --> pdb=" O LEU n 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU n 50 " --> pdb=" O LYS n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 79 through 90 removed outlier: 3.743A pdb=" N ARG n 89 " --> pdb=" O GLU n 85 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.171A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.577A pdb=" N MET o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.589A pdb=" N GLN o 79 " --> pdb=" O ALA o 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.790A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 5.064A pdb=" N ASN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 removed outlier: 6.237A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 5.157A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.783A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 25 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.369A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 6 through 41 removed outlier: 4.720A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS t 15 " --> pdb=" O ILE t 11 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 64 Proline residue: t 55 - end of helix Processing helix chain 't' and resid 67 through 86 Processing helix chain 'u' and resid 16 through 23 removed outlier: 4.346A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU u 23 " --> pdb=" O LYS u 19 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 34 removed outlier: 4.381A pdb=" N LEU u 28 " --> pdb=" O LYS u 24 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 62 removed outlier: 4.176A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU u 62 " --> pdb=" O LYS u 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 16 removed outlier: 7.157A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.710A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.690A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.348A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.602A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 5.625A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.765A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.230A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.529A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 removed outlier: 4.115A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.724A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.719A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 19 removed outlier: 4.411A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 47 through 60 removed outlier: 4.989A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 4.043A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.192A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 removed outlier: 4.029A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.743A pdb=" N ALA G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.689A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.233A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 4.082A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 4.500A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.550A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 removed outlier: 4.897A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 72 removed outlier: 5.561A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.792A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY H 107 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.277A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.620A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.131A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.838A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 120 removed outlier: 4.807A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.835A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.117A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.851A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.387A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.370A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.958A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 58 removed outlier: 4.155A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.301A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.315A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.401A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 88 Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.088A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.069A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 4.041A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.702A pdb=" N LYS P 5 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 103 removed outlier: 3.956A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 98 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.650A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.209A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 60 removed outlier: 3.677A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 Processing helix chain 'Q' and resid 74 through 86 removed outlier: 3.661A pdb=" N ALA Q 85 " --> pdb=" O GLY Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 removed outlier: 3.619A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.619A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 4.013A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.243A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 11 removed outlier: 4.061A pdb=" N GLU T 5 " --> pdb=" O MET T 1 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.534A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.745A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.929A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.731A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.188A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.819A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.881A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 1 through 7 removed outlier: 3.722A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 25 through 35 removed outlier: 3.922A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 62 removed outlier: 4.058A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 20 removed outlier: 3.892A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.356A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 31 through 36 removed outlier: 4.991A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.159A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '6' and resid 45 through 54 removed outlier: 4.192A pdb=" N ARG 6 49 " --> pdb=" O THR 6 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP 6 50 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY 6 54 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 5.901A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 29 through 33 removed outlier: 7.103A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE b 39 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.810A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 53 through 58 Processing sheet with id= 4, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.539A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR c 190 " --> pdb=" O GLY c 193 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 170 through 173 removed outlier: 5.047A pdb=" N ASP d 173 " --> pdb=" O GLU d 178 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 10 through 15 removed outlier: 3.967A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.551A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'f' and resid 39 through 42 removed outlier: 4.477A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP f 42 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET f 90 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.696A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 11, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.315A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS h 49 " --> pdb=" O GLU h 59 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.855A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.057A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.526A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE j 67 " --> pdb=" O GLU j 47 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'k' and resid 29 through 34 Processing sheet with id= 16, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.081A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.744A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.898A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'q' and resid 6 through 10 removed outlier: 4.675A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL q 58 " --> pdb=" O GLY q 9 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL q 75 " --> pdb=" O GLU q 59 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 's' and resid 46 through 51 removed outlier: 4.710A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 79 through 82 removed outlier: 4.001A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.802A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.448A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.560A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.405A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.008A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.501A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 1 through 5 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'E' and resid 44 through 47 removed outlier: 7.419A pdb=" N ARG E 44 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ALA E 87 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.653A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 147 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE E 149 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.566A pdb=" N VAL F 88 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN F 36 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 151 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR F 157 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY F 125 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 34, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 35, first strand: chain 'G' and resid 81 through 88 removed outlier: 6.438A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'G' and resid 93 through 97 removed outlier: 3.550A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'H' and resid 2 through 6 removed outlier: 5.466A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.813A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.877A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.258A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU K 86 " --> pdb=" O ALA K 11 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.502A pdb=" N ASP M 106 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.510A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.651A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'O' and resid 49 through 53 removed outlier: 4.123A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 37 through 44 removed outlier: 5.983A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 56 through 63 removed outlier: 8.064A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.559A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R' and resid 18 through 21 removed outlier: 3.948A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL R 72 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLN R 91 " --> pdb=" O GLU R 70 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLU R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE R 93 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG R 68 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R' and resid 32 through 36 Processing sheet with id= 51, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.322A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 29 through 33 removed outlier: 5.038A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'U' and resid 39 through 44 removed outlier: 4.582A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'U' and resid 81 through 86 removed outlier: 5.004A pdb=" N ARG U 81 " --> pdb=" O LYS U 96 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 69 through 73 removed outlier: 7.157A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA V 6 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG V 9 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 47 through 50 removed outlier: 4.296A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'W' and resid 61 through 67 Processing sheet with id= 58, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.611A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG X 26 " --> pdb=" O GLY X 14 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 60, first strand: chain 'Z' and resid 33 through 38 removed outlier: 4.930A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain '0' and resid 27 through 30 removed outlier: 6.277A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '1' and resid 6 through 11 Processing sheet with id= 63, first strand: chain '1' and resid 33 through 36 removed outlier: 6.636A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '3' and resid 21 through 24 removed outlier: 5.662A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '4' and resid 23 through 27 removed outlier: 6.911A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '6' and resid 20 through 25 removed outlier: 4.097A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) 1683 hydrogen bonds defined for protein. 4998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3922 hydrogen bonds 6242 hydrogen bond angles 0 basepair planarities 1558 basepair parallelities 2451 stacking parallelities Total time for adding SS restraints: 234.13 Time building geometry restraints manager: 62.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.53: 148098 1.53 - 1.90: 12816 1.90 - 2.26: 2 2.26 - 2.63: 0 2.63 - 3.00: 4 Bond restraints: 160920 Sorted by residual: bond pdb=" O3' U y 67A" pdb=" P C y 68 " ideal model delta sigma weight residual 1.607 2.997 -1.390 1.50e-02 4.44e+03 8.59e+03 bond pdb=" O3' G y 5 " pdb=" P A y 5A" ideal model delta sigma weight residual 1.607 2.992 -1.385 1.50e-02 4.44e+03 8.53e+03 bond pdb=" O3' A y 67 " pdb=" P U y 67A" ideal model delta sigma weight residual 1.607 2.991 -1.384 1.50e-02 4.44e+03 8.52e+03 bond pdb=" O3' G y 47 " pdb=" P G y 47A" ideal model delta sigma weight residual 1.607 2.967 -1.360 1.50e-02 4.44e+03 8.22e+03 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.469 0.333 2.00e-02 2.50e+03 2.78e+02 ... (remaining 160915 not shown) Histogram of bond angle deviations from ideal: 69.27 - 83.57: 12 83.57 - 97.87: 18 97.87 - 112.17: 110010 112.17 - 126.48: 116513 126.48 - 140.78: 14409 Bond angle restraints: 240962 Sorted by residual: angle pdb=" O3' U y 67A" pdb=" P C y 68 " pdb=" O5' C y 68 " ideal model delta sigma weight residual 104.00 71.70 32.30 1.50e+00 4.44e-01 4.64e+02 angle pdb=" O3' G y 5 " pdb=" P A y 5A" pdb=" O5' A y 5A" ideal model delta sigma weight residual 104.00 73.08 30.92 1.50e+00 4.44e-01 4.25e+02 angle pdb=" O3' A y 67 " pdb=" P U y 67A" pdb=" O5' U y 67A" ideal model delta sigma weight residual 104.00 76.44 27.56 1.50e+00 4.44e-01 3.38e+02 angle pdb=" O3' G y 47 " pdb=" P G y 47A" pdb=" O5' G y 47A" ideal model delta sigma weight residual 104.00 79.25 24.75 1.50e+00 4.44e-01 2.72e+02 angle pdb=" O3' A y 67 " pdb=" P U y 67A" pdb=" OP1 U y 67A" ideal model delta sigma weight residual 108.00 69.27 38.73 3.00e+00 1.11e-01 1.67e+02 ... (remaining 240957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 82959 35.91 - 71.81: 2490 71.81 - 107.72: 261 107.72 - 143.63: 31 143.63 - 179.54: 23 Dihedral angle restraints: 85764 sinusoidal: 69202 harmonic: 16562 Sorted by residual: dihedral pdb=" CA ILE m 3 " pdb=" C ILE m 3 " pdb=" N ALA m 4 " pdb=" CA ALA m 4 " ideal model delta harmonic sigma weight residual 180.00 -120.88 -59.12 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA HIS 3 30 " pdb=" C HIS 3 30 " pdb=" N ILE 3 31 " pdb=" CA ILE 3 31 " ideal model delta harmonic sigma weight residual -180.00 -126.94 -53.06 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" C5' U a1301 " pdb=" C4' U a1301 " pdb=" C3' U a1301 " pdb=" O3' U a1301 " ideal model delta sinusoidal sigma weight residual 147.00 77.28 69.72 1 8.00e+00 1.56e-02 9.80e+01 ... (remaining 85761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.946: 30720 0.946 - 1.891: 0 1.891 - 2.837: 0 2.837 - 3.782: 0 3.782 - 4.728: 4 Chirality restraints: 30724 Sorted by residual: chirality pdb=" C4' G7M A2069 " pdb=" C5' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C3' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.50 2.23 -4.73 2.00e-01 2.50e+01 5.59e+02 chirality pdb=" C4' G7M a 527 " pdb=" C5' G7M a 527 " pdb=" O4' G7M a 527 " pdb=" C3' G7M a 527 " both_signs ideal model delta sigma weight residual False -2.50 2.05 -4.55 2.00e-01 2.50e+01 5.17e+02 chirality pdb=" C3' G7M A2069 " pdb=" C4' G7M A2069 " pdb=" O3' G7M A2069 " pdb=" C2' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.48 1.77 -4.25 2.00e-01 2.50e+01 4.51e+02 ... (remaining 30721 not shown) Planarity restraints: 12791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.089 2.00e-02 2.50e+03 6.21e-01 8.67e+03 pdb=" C4' OMG A2251 " 0.430 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " 0.609 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " -0.612 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " -0.691 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " -0.158 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " 1.062 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " 0.197 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " -0.928 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.073 2.00e-02 2.50e+03 6.08e-01 8.33e+03 pdb=" C4' 5MC a1407 " 0.440 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " 0.575 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " -0.688 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " -0.140 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " 1.028 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " 0.228 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " -0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " -0.041 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' 2MG a1207 " -0.461 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " -0.708 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " 0.584 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " 0.590 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " 0.224 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " -0.896 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " -0.209 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " 0.918 2.00e-02 2.50e+03 ... (remaining 12788 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 12535 2.71 - 3.25: 132462 3.25 - 3.80: 309715 3.80 - 4.35: 387829 4.35 - 4.90: 508462 Nonbonded interactions: 1351003 Sorted by model distance: nonbonded pdb=" O2' U a 407 " pdb=" OE1 GLU d 112 " model vdw 2.158 2.440 nonbonded pdb=" O2' C a1097 " pdb=" O2' A a1169 " model vdw 2.175 2.440 nonbonded pdb=" N2 G A1171 " pdb=" O2 C A1178 " model vdw 2.178 2.496 nonbonded pdb=" OG SER r 35 " pdb=" OE2 GLU u 23 " model vdw 2.200 2.440 nonbonded pdb=" O2' A a 749 " pdb=" OD1 ASN o 19 " model vdw 2.202 2.440 ... (remaining 1350998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 14.500 Check model and map are aligned: 1.570 Set scattering table: 0.980 Process input model: 527.960 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.330 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 552.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.012 1.390 160920 Z= 0.720 Angle : 1.240 38.729 240962 Z= 0.643 Chirality : 0.077 4.728 30724 Planarity : 0.022 0.621 12791 Dihedral : 14.187 179.537 75077 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 2.22 % Allowed : 7.68 % Favored : 90.10 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.34 (0.10), residues: 5717 helix: -2.77 (0.09), residues: 1820 sheet: -3.26 (0.13), residues: 957 loop : -1.31 (0.11), residues: 2940 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2325 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 2291 time to evaluate : 5.886 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 outliers start: 34 outliers final: 10 residues processed: 2312 average time/residue: 1.5449 time to fit residues: 5967.7770 Evaluate side-chains 1604 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1594 time to evaluate : 5.328 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 1.0768 time to fit residues: 26.9086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 873 optimal weight: 7.9990 chunk 783 optimal weight: 20.0000 chunk 434 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 528 optimal weight: 0.9990 chunk 418 optimal weight: 20.0000 chunk 810 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 chunk 492 optimal weight: 10.0000 chunk 603 optimal weight: 0.9990 chunk 938 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: