Starting phenix.real_space_refine on Wed Apr 17 16:55:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/04_2024/5mgp_3508.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/04_2024/5mgp_3508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/04_2024/5mgp_3508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/04_2024/5mgp_3508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/04_2024/5mgp_3508.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/04_2024/5mgp_3508.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.022 sd= 0.140 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: 5 Type Number sf(0) Gaussians P 4642 5.49 5 S 155 5.16 5 C 74160 2.51 5 N 27412 2.21 5 O 40786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" 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 "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" 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 "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" 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 "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 ARG 114": "NH1" <-> "NH2" 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 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 ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 77": "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 "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 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "b PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 147155 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 62261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62261 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p_pur': 222, 'rna2p_pyr': 103, 'rna3p_pur': 1452, 'rna3p_pyr': 1123} Link IDs: {'rna2p': 325, 'rna3p': 2574} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 61, 'rna3p_pyr': 52} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} 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: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} 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: "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: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} 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: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} 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: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} 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: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} 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: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 33016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33016 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p_pur': 97, 'rna2p_pyr': 56, 'rna3p_pur': 777, 'rna3p_pyr': 609} Link IDs: {'rna2p': 153, 'rna3p': 1385} Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, '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: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} 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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} 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: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} 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: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} 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: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "w" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 369 Classifications: {'peptide': 45} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 42} Chain: "x" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "z" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2846 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 351} Time building chain proxies: 55.21, per 1000 atoms: 0.38 Number of scatterers: 147155 At special positions: 0 Unit cell: (266.664, 279.672, 229.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 155 16.00 P 4642 15.00 O 40786 8.00 N 27412 7.00 C 74160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 18 " - pdb=" SG CYS 6 40 " 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: 53.79 Conformation dependent library (CDL) restraints added in 6.7 seconds 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11178 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 75 sheets defined 33.5% alpha, 17.4% beta 1376 base pairs and 2750 stacking pairs defined. Time for finding SS restraints: 51.53 Creating SS restraints... Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.505A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.651A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.517A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.596A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 102 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 24 through 38 removed outlier: 3.817A pdb=" N ALA E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.537A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.671A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 removed outlier: 3.605A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.558A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.596A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 10 removed outlier: 3.503A pdb=" N TYR F 7 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 19 removed outlier: 4.182A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.782A pdb=" N ALA F 44 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP F 45 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.953A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.858A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 100 " --> pdb=" O TRP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 171 removed outlier: 4.084A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.710A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 42 through 51 removed outlier: 3.940A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.821A pdb=" N GLU H 70 " --> pdb=" O ALA H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 96 through 104 removed outlier: 3.782A pdb=" N ALA H 102 " --> pdb=" O ASP H 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.239A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (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 98 through 107 removed outlier: 3.594A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 118 Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.552A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 132 through 136' Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.677A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.563A pdb=" N ALA L 72 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE L 73 " --> pdb=" O LYS L 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 69 through 73' Processing helix chain 'L' and resid 79 through 85 removed outlier: 3.967A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS L 84 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 136 removed outlier: 3.652A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 56 removed outlier: 3.558A pdb=" N ALA M 52 " --> pdb=" O ALA M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 121 removed outlier: 3.573A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 124 No H-bonds generated for 'chain 'M' and resid 122 through 124' Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.730A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.552A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 74 through 79 Processing helix chain 'O' and resid 4 through 22 removed outlier: 4.539A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.934A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.640A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 112 Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.537A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 removed outlier: 3.735A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 52 through 55' Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.514A pdb=" N LEU P 99 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 101' Processing helix chain 'Q' and resid 6 through 20 removed outlier: 3.568A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.845A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.268A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE Q 56 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 85 removed outlier: 3.527A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.595A pdb=" N GLU Q 110 " --> pdb=" O THR Q 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA Q 112 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 4.111A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.533A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 2 through 8 removed outlier: 3.547A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 26 removed outlier: 3.922A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.532A pdb=" N LEU V 20 " --> pdb=" O ALA V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 51 removed outlier: 3.976A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 57 removed outlier: 3.857A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 61 Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 11 through 20 removed outlier: 3.619A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 34 removed outlier: 3.504A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 61 removed outlier: 3.959A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.533A pdb=" N ALA Z 21 " --> pdb=" O PRO Z 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 50 removed outlier: 3.508A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 removed outlier: 3.703A pdb=" N ARG 0 15 " --> pdb=" O LYS 0 11 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 22 Processing helix chain '2' and resid 24 through 38 removed outlier: 3.578A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY 2 38 " --> pdb=" O ARG 2 34 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 removed outlier: 3.787A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 43 removed outlier: 3.595A pdb=" N HIS 3 42 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 53 No H-bonds generated for 'chain '3' and resid 51 through 53' Processing helix chain '3' and resid 54 through 61 Processing helix chain '4' and resid 30 through 34 Processing helix chain '6' and resid 56 through 65 removed outlier: 4.090A pdb=" N LYS 6 62 " --> pdb=" O ASP 6 58 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.749A pdb=" N LYS b 27 " --> pdb=" O PRO b 24 " (cutoff:3.500A) Proline residue: b 28 - end of helix Processing helix chain 'b' and resid 41 through 62 removed outlier: 3.782A pdb=" N VAL b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Proline residue: b 47 - end of helix removed outlier: 3.570A pdb=" N LYS b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE b 59 " --> pdb=" O GLU b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 87 removed outlier: 3.765A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP b 81 " --> pdb=" O GLU b 77 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU b 84 " --> pdb=" O LYS b 80 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 117 removed outlier: 3.621A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 117 through 122 removed outlier: 3.962A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 117 through 122' Processing helix chain 'b' and resid 129 through 147 removed outlier: 4.131A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU b 147 " --> pdb=" O LEU b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 178 removed outlier: 3.566A pdb=" N ILE b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 208 through 224 removed outlier: 3.579A pdb=" N LEU b 213 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA b 218 " --> pdb=" O GLY b 214 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR b 219 " --> pdb=" O ALA b 215 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 11 removed outlier: 3.793A pdb=" N LEU c 11 " --> pdb=" O GLY c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 29 through 46 removed outlier: 3.760A pdb=" N ASP c 35 " --> pdb=" O ASN c 31 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.007A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 91 removed outlier: 4.204A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.726A pdb=" N GLN c 122 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.595A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 15 removed outlier: 3.808A pdb=" N ARG d 12 " --> pdb=" O LEU d 8 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 65 removed outlier: 3.779A pdb=" N GLU d 56 " --> pdb=" O VAL d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 removed outlier: 3.797A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 95 removed outlier: 3.625A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 105 Processing helix chain 'd' and resid 109 through 119 Processing helix chain 'd' and resid 153 through 161 Processing helix chain 'd' and resid 162 through 164 No H-bonds generated for 'chain 'd' and resid 162 through 164' Processing helix chain 'd' and resid 196 through 203 removed outlier: 3.538A pdb=" N VAL d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU d 201 " --> pdb=" O HIS d 197 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 68 removed outlier: 3.511A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 removed outlier: 3.520A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY e 118 " --> pdb=" O LEU e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 145 removed outlier: 3.688A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE e 140 " --> pdb=" O VAL e 136 " (cutoff:3.500A) Processing helix chain 'e' and resid 151 through 155 removed outlier: 3.576A pdb=" N LYS e 155 " --> pdb=" O VAL e 152 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 164 removed outlier: 3.594A pdb=" N LEU e 164 " --> pdb=" O VAL e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 16 removed outlier: 4.711A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 31 removed outlier: 3.987A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.655A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE f 80 " --> pdb=" O THR f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.695A pdb=" N ASN g 27 " --> pdb=" O ALA g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.559A pdb=" N SER g 40 " --> pdb=" O SER g 36 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE g 41 " --> pdb=" O THR g 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 67 removed outlier: 3.663A pdb=" N VAL g 63 " --> pdb=" O GLU g 59 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 109 removed outlier: 4.164A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL g 104 " --> pdb=" O MET g 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 128 removed outlier: 3.691A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 144 removed outlier: 3.557A pdb=" N ASP g 139 " --> pdb=" O LYS g 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 19 removed outlier: 3.641A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 42 removed outlier: 3.510A pdb=" N ALA h 34 " --> pdb=" O LYS h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 98 removed outlier: 4.303A pdb=" N ALA h 96 " --> pdb=" O LYS h 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU h 98 " --> pdb=" O MET h 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.526A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 38 removed outlier: 3.803A pdb=" N PHE i 38 " --> pdb=" O LEU i 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 34 through 38' Processing helix chain 'i' and resid 48 through 54 removed outlier: 3.538A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.540A pdb=" N THR i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 89 through 94 Processing helix chain 'i' and resid 95 through 100 Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.920A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 50 removed outlier: 3.736A pdb=" N GLY k 50 " --> pdb=" O GLY k 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 47 through 50' Processing helix chain 'k' and resid 54 through 57 removed outlier: 3.560A pdb=" N SER k 57 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 57' Processing helix chain 'k' and resid 58 through 71 removed outlier: 3.608A pdb=" N ALA k 62 " --> pdb=" O THR k 58 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 95 through 101 Processing helix chain 'l' and resid 4 through 9 removed outlier: 3.824A pdb=" N ARG l 8 " --> pdb=" O ASN l 4 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS l 9 " --> pdb=" O GLN l 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 4 through 9' Processing helix chain 'm' and resid 13 through 19 removed outlier: 3.618A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 37 Processing helix chain 'm' and resid 48 through 57 removed outlier: 4.169A pdb=" N ASP m 53 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 68 through 83 removed outlier: 3.886A pdb=" N MET m 74 " --> pdb=" O ARG m 70 " (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 19 removed outlier: 3.588A pdb=" N LYS n 6 " --> pdb=" O LYS n 2 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG n 12 " --> pdb=" O ARG n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 29 removed outlier: 3.710A pdb=" N ALA n 28 " --> pdb=" O ALA n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 43 removed outlier: 3.773A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 51 removed outlier: 4.251A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 60 Processing helix chain 'n' and resid 82 through 91 Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.577A pdb=" N LYS o 9 " --> pdb=" O GLU o 5 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 42 removed outlier: 4.613A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.509A pdb=" N ARG o 53 " --> pdb=" O HIS o 49 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 85 removed outlier: 3.564A pdb=" N GLN o 79 " --> pdb=" O ALA o 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU o 80 " --> pdb=" O ARG o 76 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU o 82 " --> pdb=" O THR o 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 76 Processing helix chain 'r' and resid 11 through 16 removed outlier: 3.859A pdb=" N GLY r 16 " --> pdb=" O PHE r 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 29 Processing helix chain 'r' and resid 30 through 32 No H-bonds generated for 'chain 'r' and resid 30 through 32' Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 64 Processing helix chain 's' and resid 11 through 24 removed outlier: 3.865A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU s 23 " --> pdb=" O GLU s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 44 Processing helix chain 's' and resid 70 through 74 Processing helix chain 't' and resid 4 through 6 No H-bonds generated for 'chain 't' and resid 4 through 6' Processing helix chain 't' and resid 7 through 41 removed outlier: 3.601A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 63 removed outlier: 3.636A pdb=" N ALA t 46 " --> pdb=" O ASP t 42 " (cutoff:3.500A) Proline residue: t 55 - end of helix Processing helix chain 't' and resid 69 through 83 removed outlier: 3.877A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR t 79 " --> pdb=" O LYS t 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE t 82 " --> pdb=" O LEU t 78 " (cutoff:3.500A) Processing helix chain 'u' and resid 25 through 30 removed outlier: 3.605A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 60 removed outlier: 4.272A pdb=" N ARG u 44 " --> pdb=" O PRO u 40 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS u 53 " --> pdb=" O ALA u 49 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS u 57 " --> pdb=" O LYS u 53 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS u 58 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 22 through 26 removed outlier: 3.852A pdb=" N ARG w 26 " --> pdb=" O PRO w 23 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 24 removed outlier: 3.594A pdb=" N ILE z 11 " --> pdb=" O VAL z 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR z 15 " --> pdb=" O ILE z 11 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU z 16 " --> pdb=" O GLN z 12 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG z 17 " --> pdb=" O ASP z 13 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER z 18 " --> pdb=" O LEU z 14 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP z 19 " --> pdb=" O THR z 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL z 20 " --> pdb=" O GLU z 16 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU z 21 " --> pdb=" O ARG z 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG z 22 " --> pdb=" O SER z 18 " (cutoff:3.500A) Processing helix chain 'z' and resid 26 through 42 removed outlier: 4.092A pdb=" N LYS z 31 " --> pdb=" O TYR z 27 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU z 32 " --> pdb=" O ASP z 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA z 39 " --> pdb=" O GLU z 35 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU z 40 " --> pdb=" O GLU z 36 " (cutoff:3.500A) Processing helix chain 'z' and resid 43 through 48 removed outlier: 4.155A pdb=" N VAL z 46 " --> pdb=" O GLN z 43 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP z 47 " --> pdb=" O PRO z 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN z 48 " --> pdb=" O ASP z 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 43 through 48' Processing helix chain 'z' and resid 49 through 87 removed outlier: 4.034A pdb=" N ALA z 55 " --> pdb=" O GLU z 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL z 67 " --> pdb=" O LEU z 63 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU z 70 " --> pdb=" O VAL z 66 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN z 75 " --> pdb=" O ASP z 71 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU z 78 " --> pdb=" O LYS z 74 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL z 80 " --> pdb=" O GLY z 76 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER z 81 " --> pdb=" O LEU z 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU z 84 " --> pdb=" O VAL z 80 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU z 86 " --> pdb=" O GLY z 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA z 87 " --> pdb=" O LEU z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 92 through 118 removed outlier: 3.749A pdb=" N PHE z 96 " --> pdb=" O ASP z 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL z 100 " --> pdb=" O PHE z 96 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA z 101 " --> pdb=" O ASN z 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU z 102 " --> pdb=" O GLU z 98 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA z 105 " --> pdb=" O ALA z 101 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG z 117 " --> pdb=" O LEU z 113 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET z 118 " --> pdb=" O GLU z 114 " (cutoff:3.500A) Processing helix chain 'z' and resid 138 through 156 removed outlier: 3.558A pdb=" N GLN z 142 " --> pdb=" O GLY z 138 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 193 removed outlier: 3.586A pdb=" N TRP z 191 " --> pdb=" O TYR z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 194 through 196 No H-bonds generated for 'chain 'z' and resid 194 through 196' Processing helix chain 'z' and resid 235 through 237 No H-bonds generated for 'chain 'z' and resid 235 through 237' Processing helix chain 'z' and resid 252 through 256 removed outlier: 4.017A pdb=" N ARG z 256 " --> pdb=" O HIS z 253 " (cutoff:3.500A) Processing helix chain 'z' and resid 279 through 310 removed outlier: 3.519A pdb=" N GLU z 306 " --> pdb=" O LYS z 302 " (cutoff:3.500A) Processing helix chain 'z' and resid 310 through 316 removed outlier: 3.639A pdb=" N LYS z 314 " --> pdb=" O MET z 310 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER z 315 " --> pdb=" O GLU z 311 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP z 316 " --> pdb=" O ASP z 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 310 through 316' Processing helix chain 'z' and resid 344 through 349 removed outlier: 3.623A pdb=" N VAL z 348 " --> pdb=" O ASN z 344 " (cutoff:3.500A) Processing helix chain 'z' and resid 353 through 362 removed outlier: 3.776A pdb=" N ALA z 359 " --> pdb=" O GLN z 355 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS z 362 " --> pdb=" O GLU z 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.228A pdb=" N LEU C 94 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL C 77 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 130 removed outlier: 5.705A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 170 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 16 removed outlier: 3.767A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE D 15 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 20 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 33 through 38 removed outlier: 5.530A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.714A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'F' and resid 65 through 68 removed outlier: 3.654A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 8 through 9 Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 19 Processing sheet with id=AB4, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AB5, first strand: chain 'G' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'H' and resid 127 through 133 Processing sheet with id=AB8, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.443A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AC1, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.775A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.932A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS P 36 " --> pdb=" O GLU P 33 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 89 through 90 removed outlier: 5.739A pdb=" N VAL L 90 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.628A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 39 through 42 removed outlier: 5.801A pdb=" N VAL M 89 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU M 75 " --> pdb=" O VAL M 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.647A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 47 through 50 removed outlier: 3.505A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.510A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.657A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE R 101 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL R 58 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 74 through 78 removed outlier: 4.114A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 4 through 10 removed outlier: 5.074A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD4, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.738A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 69 through 70 removed outlier: 3.662A pdb=" N ARG T 73 " --> pdb=" O HIS T 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.346A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AD8, first strand: chain 'U' and resid 82 through 85 Processing sheet with id=AD9, first strand: chain 'V' and resid 78 through 79 removed outlier: 3.600A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.929A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 26 through 27 Processing sheet with id=AE3, first strand: chain 'X' and resid 12 through 17 removed outlier: 3.631A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.719A pdb=" N VAL X 50 " --> pdb=" O HIS X 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AE6, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AE7, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AE8, first strand: chain '1' and resid 19 through 24 removed outlier: 3.736A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '3' and resid 14 through 15 Processing sheet with id=AF1, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AF2, first strand: chain '6' and resid 20 through 26 removed outlier: 4.108A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU 6 32 " --> pdb=" O THR 6 13 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 30 through 32 Processing sheet with id=AF4, first strand: chain 'b' and resid 89 through 91 removed outlier: 5.885A pdb=" N ILE b 66 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL b 91 " --> pdb=" O ILE b 66 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE b 68 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU b 67 " --> pdb=" O PHE b 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'b' and resid 184 through 186 Processing sheet with id=AF6, first strand: chain 'c' and resid 19 through 20 removed outlier: 7.100A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE c 54 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE c 56 " --> pdb=" O ARG c 64 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR c 69 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.625A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 127 through 128 Processing sheet with id=AF9, first strand: chain 'e' and resid 13 through 14 Processing sheet with id=AG1, first strand: chain 'e' and resid 18 through 21 Processing sheet with id=AG2, first strand: chain 'e' and resid 84 through 85 Processing sheet with id=AG3, first strand: chain 'f' and resid 2 through 3 Processing sheet with id=AG4, first strand: chain 'f' and resid 41 through 44 removed outlier: 4.619A pdb=" N ASP f 41 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU f 61 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL f 7 " --> pdb=" O SER f 87 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER f 87 " --> pdb=" O VAL f 7 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET f 9 " --> pdb=" O ILE f 85 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 72 through 79 removed outlier: 3.841A pdb=" N ARG g 77 " --> pdb=" O TYR g 84 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR g 84 " --> pdb=" O ARG g 77 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER g 82 " --> pdb=" O VAL g 79 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 23 through 27 removed outlier: 4.113A pdb=" N THR h 61 " --> pdb=" O ASP h 47 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 74 through 76 removed outlier: 3.702A pdb=" N GLN h 75 " --> pdb=" O TYR h 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR h 127 " --> pdb=" O ILE h 100 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE h 100 " --> pdb=" O TYR h 127 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'i' and resid 5 through 7 removed outlier: 3.834A pdb=" N THR i 65 " --> pdb=" O ARG i 17 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL i 28 " --> pdb=" O ILE i 64 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL i 66 " --> pdb=" O VAL i 28 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.661A pdb=" N THR j 69 " --> pdb=" O ARG j 45 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.661A pdb=" N THR j 69 " --> pdb=" O ARG j 45 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'k' and resid 40 through 45 removed outlier: 6.580A pdb=" N ILE k 33 " --> pdb=" O LEU k 41 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TRP k 43 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL k 31 " --> pdb=" O TRP k 43 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR k 45 " --> pdb=" O THR k 29 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR k 29 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL k 83 " --> pdb=" O THR k 107 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE k 109 " --> pdb=" O VAL k 83 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL k 85 " --> pdb=" O ILE k 109 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP k 111 " --> pdb=" O VAL k 85 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'l' and resid 28 through 31 Processing sheet with id=AH4, first strand: chain 'l' and resid 36 through 39 Processing sheet with id=AH5, first strand: chain 'p' and resid 32 through 35 removed outlier: 6.949A pdb=" N VAL p 21 " --> pdb=" O ILE p 33 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'p' and resid 9 through 11 removed outlier: 3.665A pdb=" N ARG p 14 " --> pdb=" O ALA p 11 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'p' and resid 37 through 39 removed outlier: 3.639A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 6 through 13 removed outlier: 16.593A pdb=" N THR q 6 " --> pdb=" O PHE q 27 " (cutoff:3.500A) removed outlier: 12.898A pdb=" N PHE q 27 " --> pdb=" O THR q 6 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN q 8 " --> pdb=" O GLU q 25 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU q 25 " --> pdb=" O GLN q 8 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL q 21 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP q 72 " --> pdb=" O HIS q 44 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 's' and resid 31 through 32 Processing sheet with id=AI1, first strand: chain 'w' and resid 28 through 29 Processing sheet with id=AI2, first strand: chain 'z' and resid 162 through 170 removed outlier: 6.822A pdb=" N THR z 163 " --> pdb=" O ILE z 183 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE z 183 " --> pdb=" O THR z 163 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE z 165 " --> pdb=" O ILE z 181 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE z 181 " --> pdb=" O ILE z 165 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU z 167 " --> pdb=" O VAL z 179 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL z 179 " --> pdb=" O GLU z 167 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER z 169 " --> pdb=" O LYS z 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG z 203 " --> pdb=" O HIS z 214 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR z 326 " --> pdb=" O VAL z 198 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG z 200 " --> pdb=" O TYR z 326 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'z' and resid 239 through 242 1644 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3406 hydrogen bonds 5400 hydrogen bond angles 0 basepair planarities 1376 basepair parallelities 2750 stacking parallelities Total time for adding SS restraints: 235.04 Time building geometry restraints manager: 58.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 18069 1.32 - 1.45: 68313 1.45 - 1.57: 63811 1.57 - 1.69: 9278 1.69 - 1.82: 277 Bond restraints: 159748 Sorted by residual: bond pdb=" C PHE X 28 " pdb=" N LEU X 29 " ideal model delta sigma weight residual 1.331 1.228 0.103 2.07e-02 2.33e+03 2.45e+01 bond pdb=" C VAL c 96 " pdb=" N PRO c 97 " ideal model delta sigma weight residual 1.331 1.380 -0.049 1.31e-02 5.83e+03 1.41e+01 bond pdb=" C THR O 31 " pdb=" N PRO O 32 " ideal model delta sigma weight residual 1.335 1.376 -0.042 1.28e-02 6.10e+03 1.06e+01 bond pdb=" C ALA O 41 " pdb=" N PRO O 42 " ideal model delta sigma weight residual 1.335 1.371 -0.037 1.19e-02 7.06e+03 9.44e+00 bond pdb=" CA ARG i 17 " pdb=" CB ARG i 17 " ideal model delta sigma weight residual 1.524 1.566 -0.041 1.46e-02 4.69e+03 8.03e+00 ... (remaining 159743 not shown) Histogram of bond angle deviations from ideal: 95.12 - 103.38: 11158 103.38 - 111.63: 91818 111.63 - 119.89: 69761 119.89 - 128.14: 58201 128.14 - 136.40: 7732 Bond angle restraints: 238670 Sorted by residual: angle pdb=" C THR b 45 " pdb=" N VAL b 46 " pdb=" CA VAL b 46 " ideal model delta sigma weight residual 120.24 124.67 -4.43 6.30e-01 2.52e+00 4.95e+01 angle pdb=" C HIS w 21 " pdb=" N ASP w 22 " pdb=" CA ASP w 22 " ideal model delta sigma weight residual 120.51 130.41 -9.90 1.45e+00 4.76e-01 4.67e+01 angle pdb=" O3' G A1930 " pdb=" C3' G A1930 " pdb=" C2' G A1930 " ideal model delta sigma weight residual 109.50 119.66 -10.16 1.50e+00 4.44e-01 4.59e+01 angle pdb=" C GLU u 35 " pdb=" N PHE u 36 " pdb=" CA PHE u 36 " ideal model delta sigma weight residual 121.54 133.66 -12.12 1.91e+00 2.74e-01 4.02e+01 angle pdb=" C PHE z 119 " pdb=" N SER z 120 " pdb=" CA SER z 120 " ideal model delta sigma weight residual 121.70 132.74 -11.04 1.80e+00 3.09e-01 3.76e+01 ... (remaining 238665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 90593 35.94 - 71.89: 10404 71.89 - 107.83: 1244 107.83 - 143.77: 16 143.77 - 179.72: 44 Dihedral angle restraints: 102301 sinusoidal: 84971 harmonic: 17330 Sorted by residual: dihedral pdb=" CA ASN f 52 " pdb=" C ASN f 52 " pdb=" N LYS f 53 " pdb=" CA LYS f 53 " ideal model delta harmonic sigma weight residual -180.00 -106.61 -73.39 0 5.00e+00 4.00e-02 2.15e+02 dihedral pdb=" CA HIS b 17 " pdb=" C HIS b 17 " pdb=" N GLN b 18 " pdb=" CA GLN b 18 " ideal model delta harmonic sigma weight residual -180.00 -113.43 -66.57 0 5.00e+00 4.00e-02 1.77e+02 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 -123.61 -56.39 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 102298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 29768 0.121 - 0.242: 604 0.242 - 0.363: 51 0.363 - 0.484: 11 0.484 - 0.605: 1 Chirality restraints: 30435 Sorted by residual: chirality pdb=" C3' G A1930 " pdb=" C4' G A1930 " pdb=" O3' G A1930 " pdb=" C2' G A1930 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C3' G A 858 " pdb=" C4' G A 858 " pdb=" O3' G A 858 " pdb=" C2' G A 858 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C3' G a 86 " pdb=" C4' G a 86 " pdb=" O3' G a 86 " pdb=" C2' G a 86 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 30432 not shown) Planarity restraints: 13013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA m 4 " -0.032 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C ALA m 4 " 0.112 2.00e-02 2.50e+03 pdb=" O ALA m 4 " -0.042 2.00e-02 2.50e+03 pdb=" N GLY m 5 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS w 44 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C LYS w 44 " 0.075 2.00e-02 2.50e+03 pdb=" O LYS w 44 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS w 45 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS l 76 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C HIS l 76 " 0.065 2.00e-02 2.50e+03 pdb=" O HIS l 76 " -0.024 2.00e-02 2.50e+03 pdb=" N SER l 77 " -0.022 2.00e-02 2.50e+03 ... (remaining 13010 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 11782 2.70 - 3.25: 120681 3.25 - 3.80: 295391 3.80 - 4.35: 396558 4.35 - 4.90: 523318 Nonbonded interactions: 1347730 Sorted by model distance: nonbonded pdb=" N ALA w 15 " pdb=" OE1 GLU z 311 " model vdw 2.151 2.520 nonbonded pdb=" O2 C A 948 " pdb=" O2' A A 984 " model vdw 2.228 2.440 nonbonded pdb=" O GLY w 35 " pdb=" N GLY w 37 " model vdw 2.232 2.520 nonbonded pdb=" O ASP w 13 " pdb=" OE1 GLU z 311 " model vdw 2.233 3.040 nonbonded pdb=" O2' G A1136 " pdb=" O2' G A2038 " model vdw 2.234 2.440 ... (remaining 1347725 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 individual isotropic 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 9.070 Check model and map are aligned: 1.460 Set scattering table: 1.000 Process input model: 498.870 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.320 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 516.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 290, in __init__ self.caller(self.show_stats) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 346, in show_stats self.structure_monitor.show(prefix="",log=self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/__init__.py", line 150, in show self.update_statistics(prefix = prefix, log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/__init__.py", line 157, in update_statistics gs.show(prefix=prefix, log=log, uppercase=False) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/model/statistics.py", line 327, in show res = self.resul