Starting phenix.real_space_refine (version: dev) on Sat Apr 16 07:53:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/04_2022/5wdt_8813_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.009 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 91": "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 "F ASP 162": "OD1" <-> "OD2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ASP 14": "OD1" <-> "OD2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L GLU 10": "OE1" <-> "OE2" 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 GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 6": "NH1" <-> "NH2" Residue "M ARG 10": "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 GLU 82": "OE1" <-> "OE2" 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 GLU 46": "OE1" <-> "OE2" 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 GLU 8": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" 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 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "R GLU 16": "OE1" <-> "OE2" 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 11": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 16": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 44": "NH1" <-> "NH2" Residue "X PHE 45": "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 15": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 30": "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 "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 GLU 51": "OE1" <-> "OE2" Residue "b ARG 94": "NH1" <-> "NH2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b GLU 139": "OE1" <-> "OE2" Residue "b ASP 193": "OD1" <-> "OD2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c GLU 57": "OE1" <-> "OE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c GLU 151": "OE1" <-> "OE2" Residue "d GLU 77": "OE1" <-> "OE2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d ASP 173": "OD1" <-> "OD2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "g ARG 2": "NH1" <-> "NH2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "h ARG 113": "NH1" <-> "NH2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "k ARG 12": "NH1" <-> "NH2" Residue "k PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "k GLU 82": "OE1" <-> "OE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "l ARG 35": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 61": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "m ARG 70": "NH1" <-> "NH2" Residue "m ARG 89": "NH1" <-> "NH2" Residue "m ARG 108": "NH1" <-> "NH2" Residue "n GLU 9": "OE1" <-> "OE2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 90": "NH1" <-> "NH2" Residue "o ARG 71": "NH1" <-> "NH2" Residue "o ARG 83": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 25": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q GLU 17": "OE1" <-> "OE2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "q GLU 51": "OE1" <-> "OE2" Residue "q GLU 79": "OE1" <-> "OE2" Residue "r ARG 11": "NH1" <-> "NH2" Residue "r PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 15": "OE1" <-> "OE2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "s PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 72": "OE1" <-> "OE2" Residue "t GLU 14": "OE1" <-> "OE2" Residue "u GLU 7": "OE1" <-> "OE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 34": "NH1" <-> "NH2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u GLU 38": "OE1" <-> "OE2" Residue "u GLU 62": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 123": "NH1" <-> "NH2" Residue "z ASP 142": "OD1" <-> "OD2" Residue "z ARG 154": "NH1" <-> "NH2" Residue "z ARG 171": "NH1" <-> "NH2" Residue "z GLU 183": "OE1" <-> "OE2" Residue "z ARG 223": "NH1" <-> "NH2" Residue "z ARG 233": "NH1" <-> "NH2" Residue "z GLU 240": "OE1" <-> "OE2" Residue "z GLU 249": "OE1" <-> "OE2" Residue "z GLU 267": "OE1" <-> "OE2" Residue "z ARG 269": "NH1" <-> "NH2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z GLU 285": "OE1" <-> "OE2" Residue "z ARG 288": "NH1" <-> "NH2" Residue "z ARG 318": "NH1" <-> "NH2" Residue "z GLU 342": "OE1" <-> "OE2" Residue "z GLU 345": "OE1" <-> "OE2" Residue "z ARG 373": "NH1" <-> "NH2" Residue "z ARG 377": "NH1" <-> "NH2" Residue "z ARG 381": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 155275 Number of models: 1 Model: "" Number of chains: 125 Chain: "A" Number of atoms: 62277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62277 Classifications: {'RNA': 2900} Modifications used: {'rna3p': 17, 'rna2p_pyr': 120, 'p5*END': 1, 'rna3p_pur': 1414, 'rna2p': 7, 'rna3p_pyr': 1088, 'rna2p_pur': 253} Link IDs: {'rna3p': 2519, 'rna2p': 380} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 49, 'p5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 58, 'rna2p_pyr': 6} Link IDs: {'rna3p': 106, 'rna2p': 13} 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: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1557 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1544 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} 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: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1304 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} 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: "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: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1120 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} 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: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} 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: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} 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: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Chain: "R" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "S" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "T" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} 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: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 739 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "W" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 572 Classifications: {'peptide': 75} 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: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "1" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} 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: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} 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: 33050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33050 Classifications: {'RNA': 1540} Modifications used: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 753, 'rna3p_pyr': 592, 'rna2p_pur': 116, 'rna2p_pyr': 68} Link IDs: {'rna3p': 1354, 'rna2p': 185} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 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: 1164 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} bond proxies already assigned to first conformer: 1160 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: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} 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: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "v" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna3p': 3, 'rna2p': 1, 'p5*END': 1, 'rna3p_pur': 34, 'rna3p_pyr': 33, 'rna2p_pur': 5, 'rna2p_pyr': 1} Link IDs: {'rna3p': 70, 'rna2p': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna3p': 3, 'rna2p': 1, 'p5*END': 1, 'rna3p_pur': 33, 'rna3p_pyr': 30, 'rna2p_pur': 6, 'rna2p_pyr': 4} Link IDs: {'rna3p': 66, 'rna2p': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "x" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 7, 'rna2p_pur': 2, 'rna3p_pur': 3} Link IDs: {'rna3p': 10, 'rna2p': 1} Chain: "y" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1631 Classifications: {'RNA': 76} Modifications used: {'rna3p': 6, 'rna2p': 2, 'p5*END': 1, 'rna3p_pur': 31, 'rna3p_pyr': 28, 'rna2p_pur': 6, 'rna2p_pyr': 2} Link IDs: {'rna3p': 66, 'rna2p': 9} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 4 Chain: "z" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3031 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain: "A" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 1340 Unusual residues: {' K': 5, ' MG': 1325} Classifications: {'undetermined': 1330, 'peptide': 1} Link IDs: {None: 1330} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Unusual residues: {' MG': 36} Classifications: {'undetermined': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 481 Unusual residues: {' MG': 481} Classifications: {'undetermined': 481} Link IDs: {None: 480} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "z" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Unusual residues: {'GNP': 1, ' MG': 4} Classifications: {'undetermined': 5, 'peptide': 1} Link IDs: {None: 5} Chain: "A" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 653 Classifications: {'water': 653} Link IDs: {None: 652} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Classifications: {'water': 163} Link IDs: {None: 162} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 66.30, per 1000 atoms: 0.43 Number of scatterers: 155275 At special positions: 0 Unit cell: (278.32, 269.5, 241.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 5 19.00 S 171 16.00 P 4805 15.00 Mg 1904 11.99 O 43127 8.00 N 28328 7.00 C 76935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 53.62 Conformation dependent library (CDL) restraints added in 6.8 seconds 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11606 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: 195 helices and 74 sheets defined 38.3% alpha, 19.0% beta 1387 base pairs and 2405 stacking pairs defined. Time for finding SS restraints: 67.16 Creating SS restraints... Processing helix chain 'C' and resid 9 through 15 removed outlier: 7.803A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.667A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.057A 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 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.958A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.694A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.093A 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: 6.225A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.699A 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 'C' and resid 196 through 201 removed outlier: 4.046A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.277A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.683A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.169A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 105' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.596A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.758A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.452A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 4.109A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.649A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.736A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.531A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 1 through 20 removed outlier: 4.872A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.611A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 61 removed outlier: 4.718A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.544A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.777A 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 removed outlier: 4.054A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.280A 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: 3.545A pdb=" N LYS G 5 " --> pdb=" O SER G 1 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix No H-bonds generated for 'chain 'G' and resid 1 through 7' Processing helix chain 'G' and resid 59 through 80 removed outlier: 4.279A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.622A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.687A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 29 through 34' Processing helix chain 'H' and resid 40 through 50 removed outlier: 5.340A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.307A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.783A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.983A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.588A 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 'I' and resid 23 through 29 removed outlier: 5.212A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.558A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 3.550A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 3.768A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.746A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.582A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.228A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.073A 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: 3.836A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.468A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 109 through 120 removed outlier: 5.753A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.630A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.617A 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: 3.974A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.875A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 5.736A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.540A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.624A pdb=" N ARG M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.503A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 57 removed outlier: 4.581A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.643A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 5.565A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.579A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 89 removed outlier: 3.767A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.371A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.566A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.525A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.662A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 13 removed outlier: 3.560A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.605A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'P' and resid 104 through 109 removed outlier: 5.904A pdb=" N ILE P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.673A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.627A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.594A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.022A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 115 removed outlier: 4.112A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.820A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.575A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR S 37 " --> pdb=" O LEU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.007A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 11 removed outlier: 6.837A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 4 through 11' Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.744A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.866A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.011A 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: 3.520A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.024A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.537A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.679A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 removed outlier: 3.811A pdb=" N ARG X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 8 removed outlier: 3.809A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.822A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 59 removed outlier: 4.481A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.514A pdb=" N LEU Z 23 " --> pdb=" O HIS Z 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 18 removed outlier: 4.988A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.262A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 3.514A pdb=" N LEU 2 31 " --> pdb=" O GLY 2 27 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 removed outlier: 3.536A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.728A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.140A 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: 4.829A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS 3 60 " --> pdb=" O LEU 3 56 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 3 through 21 removed outlier: 3.505A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 3.533A pdb=" N MET 5 38 " --> pdb=" O THR 5 34 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR 5 39 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA 5 44 " --> pdb=" O GLU 5 40 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY 5 45 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 70 removed outlier: 4.150A pdb=" N GLY 5 66 " --> pdb=" O ARG 5 62 " (cutoff:3.500A) Proline residue: 5 68 - end of helix Processing helix chain '5' and resid 73 through 79 removed outlier: 4.394A pdb=" N VAL 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY 5 78 " --> pdb=" O ASP 5 74 " (cutoff:3.500A) Proline residue: 5 79 - end of helix No H-bonds generated for 'chain '5' and resid 73 through 79' Processing helix chain '5' and resid 94 through 106 removed outlier: 3.749A pdb=" N GLU 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.590A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 53 removed outlier: 4.288A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 4.192A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 73 through 87 removed outlier: 4.304A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.562A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.609A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 169 Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.506A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.572A pdb=" N THR b 210 " --> pdb=" O ILE b 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.854A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.718A pdb=" N ALA c 47 " --> pdb=" O THR c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.994A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.617A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY c 95 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 4.141A pdb=" N ASP c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 5.805A 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 removed outlier: 3.780A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.917A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET c 141 " --> pdb=" O VAL c 137 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.070A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.516A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.531A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.761A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.715A 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: 4.208A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 3.569A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.955A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 186 through 191' Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.476A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.514A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.311A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.502A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 31 removed outlier: 3.701A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 3.552A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 3.560A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 6.093A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN g 27 " --> pdb=" O ALA g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.516A pdb=" N SER g 40 " --> pdb=" O SER g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 4.224A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.022A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.990A 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: 3.955A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.718A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.617A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 39 removed outlier: 4.251A pdb=" N GLY i 39 " --> pdb=" O GLU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 53 removed outlier: 4.651A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.682A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.987A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 98 removed outlier: 4.148A pdb=" N ARG i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 3.623A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.776A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.707A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.287A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 74 removed outlier: 3.706A pdb=" N ALA k 65 " --> pdb=" O ALA k 61 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.734A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN k 100 " --> pdb=" O ILE k 96 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 Processing helix chain 'l' and resid 112 through 117 removed outlier: 5.048A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 22 removed outlier: 3.785A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.608A pdb=" N SER m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.203A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.476A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 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 23 removed outlier: 3.500A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS n 11 " --> pdb=" O ALA n 7 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA n 21 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS n 22 " --> pdb=" O LYS n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.651A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.152A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.645A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 31 removed outlier: 4.251A pdb=" N ILE n 29 " --> pdb=" O ALA n 24 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER n 31 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 removed outlier: 4.013A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY o 15 " --> pdb=" O VAL o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.409A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.573A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.504A pdb=" N ARG o 83 " --> pdb=" O GLN o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.742A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA p 58 " --> pdb=" O LEU p 54 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP p 60 " --> pdb=" O ARG p 56 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.735A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.463A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 25 removed outlier: 3.541A pdb=" N SER s 24 " --> pdb=" O LYS s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 75 removed outlier: 4.378A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.310A 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 7 through 39 removed outlier: 3.566A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU t 39 " --> pdb=" O TYR t 35 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 64 Proline residue: t 55 - end of helix removed outlier: 3.720A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 85 removed outlier: 4.206A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 3.787A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 61 Proline residue: u 40 - end of helix removed outlier: 3.553A pdb=" N LYS u 45 " --> pdb=" O THR u 41 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 32 removed outlier: 4.281A pdb=" N ARG u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 27 through 32' Processing helix chain 'z' and resid 24 through 39 removed outlier: 3.674A pdb=" N THR z 28 " --> pdb=" O LYS z 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS z 37 " --> pdb=" O THR z 33 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR z 38 " --> pdb=" O VAL z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 45 through 51 removed outlier: 4.121A pdb=" N ILE z 49 " --> pdb=" O ALA z 45 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP z 50 " --> pdb=" O PHE z 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN z 51 " --> pdb=" O ASP z 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 45 through 51' Processing helix chain 'z' and resid 52 through 57 removed outlier: 4.093A pdb=" N LYS z 56 " --> pdb=" O ALA z 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA z 57 " --> pdb=" O PRO z 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 52 through 57' Processing helix chain 'z' and resid 87 through 99 removed outlier: 3.791A pdb=" N THR z 93 " --> pdb=" O LYS z 89 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY z 94 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASP z 99 " --> pdb=" O ALA z 95 " (cutoff:3.500A) Processing helix chain 'z' and resid 112 through 126 removed outlier: 3.860A pdb=" N ARG z 116 " --> pdb=" O MET z 112 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN z 124 " --> pdb=" O LEU z 120 " (cutoff:3.500A) Processing helix chain 'z' and resid 136 through 141 removed outlier: 6.312A pdb=" N VAL z 140 " --> pdb=" O LYS z 136 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP z 141 " --> pdb=" O CYS z 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 136 through 141' Processing helix chain 'z' and resid 142 through 161 removed outlier: 4.277A pdb=" N LEU z 146 " --> pdb=" O ASP z 142 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU z 147 " --> pdb=" O GLU z 143 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL z 149 " --> pdb=" O LEU z 145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU z 150 " --> pdb=" O LEU z 146 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET z 151 " --> pdb=" O GLU z 147 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU z 152 " --> pdb=" O LEU z 148 " (cutoff:3.500A) Processing helix chain 'z' and resid 173 through 180 removed outlier: 3.583A pdb=" N ALA z 177 " --> pdb=" O SER z 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU z 179 " --> pdb=" O LEU z 175 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY z 180 " --> pdb=" O LYS z 176 " (cutoff:3.500A) Processing helix chain 'z' and resid 181 through 198 removed outlier: 3.541A pdb=" N ILE z 188 " --> pdb=" O TRP z 184 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU z 191 " --> pdb=" O LYS z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE z 286 " --> pdb=" O LYS z 282 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU z 287 " --> pdb=" O ARG z 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 282 through 287' Processing sheet with id= 1, first strand: chain 'C' and resid 1 through 4 Processing sheet with id= 2, first strand: chain 'C' and resid 72 through 77 removed outlier: 4.148A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.636A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.733A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.468A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.906A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.839A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.084A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.586A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 170 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.516A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 12, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 13, first strand: chain 'G' and resid 93 through 97 Processing sheet with id= 14, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.915A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LYS G 85 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 16 through 20 removed outlier: 5.563A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.323A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.229A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 6 through 9 removed outlier: 4.090A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 37 through 41 removed outlier: 4.303A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.362A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.687A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.181A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.990A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.501A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.465A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER P 84 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.748A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR P 75 " --> pdb=" O SER P 56 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.685A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.723A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.216A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.799A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.521A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.892A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.179A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG T 73 " --> pdb=" O HIS T 70 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS T 70 " --> pdb=" O ARG T 73 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'U' and resid 41 through 44 Processing sheet with id= 35, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.554A pdb=" N PHE U 94 " --> pdb=" O GLY U 83 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.346A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 25 through 28 removed outlier: 4.530A pdb=" N GLU W 25 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE W 78 " --> pdb=" O GLY W 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 46 through 50 removed outlier: 6.978A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.682A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 33 through 40 No H-bonds generated for sheet with id= 40 Processing sheet with id= 41, first strand: chain 'Z' and resid 33 through 38 removed outlier: 4.242A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '0' and resid 27 through 30 removed outlier: 6.420A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '1' and resid 19 through 23 Processing sheet with id= 44, first strand: chain '3' and resid 21 through 24 removed outlier: 5.694A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '4' and resid 13 through 19 removed outlier: 8.499A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '5' and resid 24 through 28 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain '6' and resid 20 through 25 removed outlier: 4.621A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER 6 15 " --> pdb=" O LEU 6 32 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU 6 34 " --> pdb=" O SER 6 15 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 29 through 33 removed outlier: 6.685A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN b 41 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.929A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.696A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE c 63 " --> pdb=" O PRO c 97 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.712A pdb=" N VAL c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU c 169 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE c 148 " --> pdb=" O GLU c 169 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE c 202 " --> pdb=" O GLY c 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.534A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 11 through 15 removed outlier: 3.971A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.547A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY e 86 " --> pdb=" O VAL e 93 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL e 122 " --> pdb=" O GLY e 103 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 31 through 39 removed outlier: 4.663A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 38 through 43 removed outlier: 3.749A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 44 through 47 removed outlier: 6.305A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 59, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.174A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU h 59 " --> pdb=" O LYS h 49 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS h 49 " --> pdb=" O GLU h 59 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.703A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.594A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.852A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'k' and resid 29 through 34 removed outlier: 4.519A pdb=" N ASN k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.032A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.935A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.968A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN p 40 " --> pdb=" O GLY p 49 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 6 through 10 removed outlier: 7.374A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 's' and resid 29 through 33 removed outlier: 4.194A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN s 55 " --> pdb=" O ASN s 52 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'z' and resid 64 through 70 removed outlier: 3.536A pdb=" N SER z 65 " --> pdb=" O ASP z 80 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR z 69 " --> pdb=" O TYR z 76 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS z 81 " --> pdb=" O THR z 16 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY z 18 " --> pdb=" O CYS z 81 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY z 15 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL z 105 " --> pdb=" O PHE z 133 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN z 135 " --> pdb=" O VAL z 105 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'z' and resid 210 through 214 removed outlier: 6.666A pdb=" N PHE z 210 " --> pdb=" O LYS z 294 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN z 290 " --> pdb=" O ILE z 214 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'z' and resid 216 through 220 removed outlier: 3.867A pdb=" N ASP z 216 " --> pdb=" O THR z 228 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'z' and resid 234 through 237 removed outlier: 7.302A pdb=" N GLY z 234 " --> pdb=" O ALA z 270 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'z' and resid 336 through 340 removed outlier: 3.730A pdb=" N GLY z 339 " --> pdb=" O PRO z 328 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU z 372 " --> pdb=" O VAL z 387 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL z 387 " --> pdb=" O LEU z 372 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE z 374 " --> pdb=" O ALA z 385 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA z 385 " --> pdb=" O PHE z 374 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE z 376 " --> pdb=" O VAL z 383 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG z 381 " --> pdb=" O GLU z 378 " (cutoff:3.500A) 1780 hydrogen bonds defined for protein. 5240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3440 hydrogen bonds 5536 hydrogen bond angles 0 basepair planarities 1387 basepair parallelities 2405 stacking parallelities Total time for adding SS restraints: 531.68 Time building geometry restraints manager: 60.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 62089 1.40 - 1.62: 103036 1.62 - 1.84: 352 1.84 - 2.06: 0 2.06 - 2.28: 1 Bond restraints: 165478 Sorted by residual: bond pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " ideal model delta sigma weight residual 1.607 2.280 -0.673 1.50e-02 4.44e+03 2.01e+03 bond pdb=" O4' 3TD A1915 " pdb=" C1' 3TD A1915 " ideal model delta sigma weight residual 1.412 1.663 -0.251 1.50e-02 4.44e+03 2.80e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.805 1.481 0.324 2.00e-02 2.50e+03 2.62e+02 bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.805 1.484 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.805 1.489 0.316 2.00e-02 2.50e+03 2.49e+02 ... (remaining 165473 not shown) Histogram of bond angle deviations from ideal: 62.92 - 83.68: 3 83.68 - 104.44: 20235 104.44 - 125.21: 207793 125.21 - 145.97: 19173 145.97 - 166.73: 2 Bond angle restraints: 247206 Sorted by residual: angle pdb=" O3' C w 17 " pdb=" P U w 117 " pdb=" O5' U w 117 " ideal model delta sigma weight residual 104.00 148.04 -44.04 1.50e+00 4.44e-01 8.62e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" OP1 A A2031 " ideal model delta sigma weight residual 108.00 166.73 -58.73 3.00e+00 1.11e-01 3.83e+02 angle pdb=" N3 MIA y 37 " pdb=" C2 MIA y 37 " pdb=" S10 MIA y 37 " ideal model delta sigma weight residual 164.14 118.09 46.05 3.00e+00 1.11e-01 2.36e+02 angle pdb=" C1' MIA y 37 " pdb=" N9 MIA y 37 " pdb=" C8 MIA y 37 " ideal model delta sigma weight residual 81.43 127.45 -46.02 3.00e+00 1.11e-01 2.35e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" OP2 A A2031 " ideal model delta sigma weight residual 108.00 62.92 45.08 3.00e+00 1.11e-01 2.26e+02 ... (remaining 247201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 83538 35.82 - 71.64: 4439 71.64 - 107.46: 385 107.46 - 143.27: 44 143.27 - 179.09: 43 Dihedral angle restraints: 88449 sinusoidal: 70448 harmonic: 18001 Sorted by residual: dihedral pdb=" C5' G a1305 " pdb=" C4' G a1305 " pdb=" C3' G a1305 " pdb=" O3' G a1305 " ideal model delta sinusoidal sigma weight residual 147.00 70.00 77.00 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" C5' G a1432 " pdb=" C4' G a1432 " pdb=" C3' G a1432 " pdb=" O3' G a1432 " ideal model delta sinusoidal sigma weight residual 147.00 70.25 76.75 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" C5' U w 27 " pdb=" C4' U w 27 " pdb=" C3' U w 27 " pdb=" O3' U w 27 " ideal model delta sinusoidal sigma weight residual 147.00 74.06 72.94 1 8.00e+00 1.56e-02 1.06e+02 ... (remaining 88446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 26596 0.158 - 0.315: 4770 0.315 - 0.473: 25 0.473 - 0.631: 12 0.631 - 0.788: 11 Chirality restraints: 31414 Sorted by residual: chirality pdb=" C3' G A 242 " pdb=" C4' G A 242 " pdb=" O3' G A 242 " pdb=" C2' G A 242 " both_signs ideal model delta sigma weight residual False -2.74 -1.96 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" C3' G a1305 " pdb=" C4' G a1305 " pdb=" O3' G a1305 " pdb=" C2' G a1305 " both_signs ideal model delta sigma weight residual False -2.74 -2.02 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C3' G A 859 " pdb=" C4' G A 859 " pdb=" O3' G A 859 " pdb=" C2' G A 859 " both_signs ideal model delta sigma weight residual False -2.74 -2.05 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 31411 not shown) Planarity restraints: 13504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2069 " 0.037 2.00e-02 2.50e+03 6.24e-01 8.77e+03 pdb=" C4' 7MG A2069 " 0.450 2.00e-02 2.50e+03 pdb=" O4' 7MG A2069 " 0.728 2.00e-02 2.50e+03 pdb=" C3' 7MG A2069 " -0.622 2.00e-02 2.50e+03 pdb=" O3' 7MG A2069 " -0.644 2.00e-02 2.50e+03 pdb=" C2' 7MG A2069 " -0.170 2.00e-02 2.50e+03 pdb=" O2' 7MG A2069 " 0.973 2.00e-02 2.50e+03 pdb=" C1' 7MG A2069 " 0.223 2.00e-02 2.50e+03 pdb=" N9 7MG A2069 " -0.974 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " -0.038 2.00e-02 2.50e+03 6.13e-01 8.45e+03 pdb=" C4' 5MC a1407 " -0.442 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.661 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.655 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.153 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.992 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.225 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " -0.020 2.00e-02 2.50e+03 6.09e-01 8.34e+03 pdb=" C4' 2MG A2445 " -0.466 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.794 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.599 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.592 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.211 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.867 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.221 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.967 2.00e-02 2.50e+03 ... (remaining 13501 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.25: 331 2.25 - 2.97: 64183 2.97 - 3.69: 321451 3.69 - 4.42: 542585 4.42 - 5.14: 752947 Nonbonded interactions: 1681497 Sorted by model distance: nonbonded pdb=" O6 G B 21 " pdb=" N3 C B 62 " model vdw 1.527 2.496 nonbonded pdb=" N1 A A1021 " pdb=" O4 U A1141 " model vdw 1.536 2.496 nonbonded pdb=" O6 G A 283 " pdb=" O6 G A 356 " model vdw 1.569 3.040 nonbonded pdb=" O2 U A2489 " pdb=" O4 U A2491 " model vdw 1.616 3.040 nonbonded pdb=" N1 G A1867 " pdb=" N3 C A1874 " model vdw 1.677 2.600 ... (remaining 1681492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'v' and (resid 0 through 76 or resid 101)) selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 5 8.98 5 P 4805 5.49 5 Mg 1904 5.21 5 S 171 5.16 5 C 76935 2.51 5 N 28328 2.21 5 O 43127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.410 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: 0.160 Extract box with map and model: 24.030 Check model and map are aligned: 1.730 Convert atoms to be neutral: 1.020 Process input model: 836.690 Find NCS groups from input model: 4.250 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 885.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.008 0.673 165478 Z= 0.504 Angle : 1.149 58.733 247206 Z= 0.746 Chirality : 0.098 0.788 31414 Planarity : 0.024 0.624 13504 Dihedral : 17.676 179.093 76843 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 2.25 % Allowed : 9.68 % Favored : 88.07 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.08), residues: 6219 helix: -2.60 (0.09), residues: 1774 sheet: -2.92 (0.13), residues: 965 loop : -2.75 (0.09), residues: 3480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1998 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1828 time to evaluate : 6.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 170 outliers final: 16 residues processed: 1945 average time/residue: 2.4717 time to fit residues: 6961.1093 Evaluate side-chains 1186 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1170 time to evaluate : 6.800 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 2.4892 time to fit residues: 28.6907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 917 optimal weight: 4.9990 chunk 823 optimal weight: 10.0000 chunk 457 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 555 optimal weight: 1.9990 chunk 440 optimal weight: 7.9990 chunk 851 optimal weight: 0.5980 chunk 329 optimal weight: 8.9990 chunk 518 optimal weight: 3.9990 chunk 634 optimal weight: 7.9990 chunk 987 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 HIS C 85 ASN C 116 GLN C 141 HIS E 136 GLN E 156 ASN E 165 HIS E 195 GLN F 36 ASN G 63 GLN G 87 GLN J 77 HIS J 128 ASN K 9 ASN L 54 GLN N 62 ASN Q 19 GLN Q 80 ASN R 6 GLN R 66 HIS R 82 HIS R 86 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS V 49 ASN W 72 ASN Z 8 GLN Z 19 HIS 6 41 HIS ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 102 ASN c 7 ASN ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN d 70 GLN d 115 GLN d 197 HIS e 121 ASN f 3 HIS f 81 ASN g 67 ASN h 75 GLN i 74 GLN k 23 HIS k 80 ASN m 51 GLN n 60 GLN o 27 GLN p 40 ASN p 79 ASN t 69 ASN ** z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.115 165478 Z= 0.262 Angle : 0.796 18.830 247206 Z= 0.423 Chirality : 0.042 0.402 31414 Planarity : 0.008 0.130 13504 Dihedral : 16.356 179.599 64475 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.49 % Favored : 91.65 % Rotamer Outliers : 7.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.09), residues: 6219 helix: -0.46 (0.11), residues: 1900 sheet: -2.28 (0.13), residues: 1125 loop : -2.34 (0.10), residues: 3194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1629 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 1262 time to evaluate : 6.826 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 outliers start: 367 outliers final: 126 residues processed: 1456 average time/residue: 2.2896 time to fit residues: 4866.3359 Evaluate side-chains 1216 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1090 time to evaluate : 6.759 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 75 residues processed: 55 average time/residue: 1.5026 time to fit residues: 148.2591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 548 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 821 optimal weight: 5.9990 chunk 672 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 988 optimal weight: 0.0770 chunk 1068 optimal weight: 6.9990 chunk 880 optimal weight: 5.9990 chunk 980 optimal weight: 8.9990 chunk 337 optimal weight: 8.9990 chunk 793 optimal weight: 8.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN C 199 HIS ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN F 62 GLN F 134 GLN G 103 ASN H 43 ASN I 42 ASN J 40 HIS J 76 HIS K 89 ASN N 18 GLN N 62 ASN ** O 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS S 31 GLN U 26 ASN U 73 ASN V 87 GLN W 8 ASN W 72 ASN Y 20 ASN Y 45 GLN Z 33 HIS 0 4 GLN ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 37 GLN 5 4 ASN b 108 GLN c 138 GLN d 88 ASN e 60 GLN e 77 ASN e 121 ASN f 63 ASN f 81 ASN g 67 ASN g 147 ASN k 23 HIS l 5 GLN n 43 ASN p 40 ASN s 51 HIS t 2 ASN z 11 HIS ** z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 124 GLN z 135 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.187 165478 Z= 0.400 Angle : 0.844 17.560 247206 Z= 0.445 Chirality : 0.045 0.382 31414 Planarity : 0.009 0.143 13504 Dihedral : 16.243 179.602 64475 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.62 % Favored : 90.58 % Rotamer Outliers : 9.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.10), residues: 6219 helix: -0.25 (0.11), residues: 1946 sheet: -1.88 (0.14), residues: 1159 loop : -2.19 (0.10), residues: 3114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1712 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 471 poor density : 1241 time to evaluate : 6.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 471 outliers final: 186 residues processed: 1520 average time/residue: 2.2721 time to fit residues: 5082.6736 Evaluate side-chains 1276 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1090 time to evaluate : 6.682 Switching outliers to nearest non-outliers outliers start: 186 outliers final: 117 residues processed: 71 average time/residue: 1.4351 time to fit residues: 181.2268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 977 optimal weight: 8.9990 chunk 743 optimal weight: 30.0000 chunk 513 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 471 optimal weight: 6.9990 chunk 664 optimal weight: 20.0000 chunk 992 optimal weight: 5.9990 chunk 1050 optimal weight: 0.9990 chunk 518 optimal weight: 0.6980 chunk 940 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN C 114 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS D 150 GLN E 41 GLN E 165 HIS E 195 GLN F 36 ASN G 87 GLN J 138 GLN K 3 GLN N 18 GLN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN T 15 HIS W 72 ASN Y 31 GLN 0 4 GLN ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 ASN e 72 ASN e 77 ASN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN f 81 ASN g 67 ASN g 129 ASN g 147 ASN h 37 ASN h 75 GLN j 20 GLN j 35 GLN k 118 ASN o 19 ASN ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.204 165478 Z= 0.311 Angle : 0.754 16.712 247206 Z= 0.402 Chirality : 0.040 0.404 31414 Planarity : 0.008 0.134 13504 Dihedral : 15.943 179.357 64475 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.67 % Favored : 91.69 % Rotamer Outliers : 8.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.10), residues: 6219 helix: 0.12 (0.12), residues: 1941 sheet: -1.66 (0.14), residues: 1202 loop : -2.02 (0.10), residues: 3076 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1577 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 429 poor density : 1148 time to evaluate : 6.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 429 outliers final: 224 residues processed: 1378 average time/residue: 2.2413 time to fit residues: 4580.1713 Evaluate side-chains 1292 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1068 time to evaluate : 6.747 Switching outliers to nearest non-outliers outliers start: 224 outliers final: 140 residues processed: 87 average time/residue: 1.5552 time to fit residues: 234.6002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 875 optimal weight: 3.9990 chunk 596 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 782 optimal weight: 10.0000 chunk 433 optimal weight: 0.0870 chunk 896 optimal weight: 7.9990 chunk 726 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 536 optimal weight: 7.9990 chunk 943 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 HIS E 195 GLN F 36 ASN G 87 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 138 GLN N 18 GLN P 11 GLN R 11 GLN S 61 ASN U 73 ASN 0 4 GLN ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 65 ASN b 102 ASN b 176 ASN b 177 ASN c 138 GLN e 77 ASN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN h 37 ASN h 75 GLN j 20 GLN k 108 ASN o 34 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.097 165478 Z= 0.427 Angle : 0.830 17.414 247206 Z= 0.435 Chirality : 0.044 0.393 31414 Planarity : 0.008 0.140 13504 Dihedral : 16.048 179.832 64475 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.17 % Favored : 90.19 % Rotamer Outliers : 8.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.10), residues: 6219 helix: -0.04 (0.12), residues: 1932 sheet: -1.60 (0.14), residues: 1192 loop : -1.99 (0.10), residues: 3095 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 422 poor density : 1109 time to evaluate : 6.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 422 outliers final: 249 residues processed: 1360 average time/residue: 2.2439 time to fit residues: 4515.2727 Evaluate side-chains 1322 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1073 time to evaluate : 6.838 Switching outliers to nearest non-outliers outliers start: 249 outliers final: 163 residues processed: 89 average time/residue: 1.5860 time to fit residues: 243.0744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 353 optimal weight: 0.9980 chunk 946 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 616 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 chunk 1051 optimal weight: 0.9990 chunk 873 optimal weight: 5.9990 chunk 486 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 347 optimal weight: 0.8980 chunk 552 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN F 36 ASN G 103 ASN G 127 GLN J 138 GLN N 18 GLN P 11 GLN P 40 GLN W 8 ASN Y 31 GLN 0 4 GLN 0 5 ASN b 176 ASN b 177 ASN e 77 ASN e 121 ASN f 81 ASN h 37 ASN h 75 GLN ** i 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN o 34 GLN p 63 GLN s 68 HIS z 63 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.090 165478 Z= 0.153 Angle : 0.678 16.850 247206 Z= 0.367 Chirality : 0.035 0.456 31414 Planarity : 0.007 0.123 13504 Dihedral : 15.606 179.778 64475 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.19 % Favored : 92.22 % Rotamer Outliers : 6.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.10), residues: 6219 helix: 0.46 (0.12), residues: 1947 sheet: -1.37 (0.14), residues: 1162 loop : -1.82 (0.10), residues: 3110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1480 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1168 time to evaluate : 6.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 312 outliers final: 181 residues processed: 1373 average time/residue: 2.2607 time to fit residues: 4624.0008 Evaluate side-chains 1248 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1067 time to evaluate : 6.945 Switching outliers to nearest non-outliers outliers start: 181 outliers final: 153 residues processed: 34 average time/residue: 1.4552 time to fit residues: 93.9728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 1013 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 599 optimal weight: 5.9990 chunk 768 optimal weight: 10.0000 chunk 595 optimal weight: 1.9990 chunk 885 optimal weight: 0.9990 chunk 587 optimal weight: 8.9990 chunk 1047 optimal weight: 10.0000 chunk 655 optimal weight: 10.0000 chunk 638 optimal weight: 6.9990 chunk 483 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN F 36 ASN G 21 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN J 138 GLN L 104 GLN N 18 GLN P 11 GLN 0 4 GLN 2 29 GLN b 41 ASN b 88 GLN b 176 ASN b 177 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN e 121 ASN f 81 ASN g 129 ASN h 37 ASN h 75 GLN ** i 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN o 34 GLN t 12 GLN z 75 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 165478 Z= 0.356 Angle : 0.763 16.907 247206 Z= 0.402 Chirality : 0.040 0.373 31414 Planarity : 0.008 0.135 13504 Dihedral : 15.666 179.738 64475 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.49 % Favored : 90.91 % Rotamer Outliers : 6.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 6219 helix: 0.26 (0.12), residues: 1945 sheet: -1.37 (0.14), residues: 1190 loop : -1.85 (0.11), residues: 3084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1067 time to evaluate : 6.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 339 outliers final: 219 residues processed: 1289 average time/residue: 2.2165 time to fit residues: 4267.2543 Evaluate side-chains 1261 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1042 time to evaluate : 6.885 Switching outliers to nearest non-outliers outliers start: 219 outliers final: 163 residues processed: 59 average time/residue: 1.5036 time to fit residues: 161.4119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 648 optimal weight: 10.0000 chunk 418 optimal weight: 4.9990 chunk 625 optimal weight: 7.9990 chunk 315 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 666 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 517 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 823 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN F 36 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN G 127 GLN J 138 GLN N 18 GLN P 11 GLN U 98 ASN 0 4 GLN 2 29 GLN b 176 ASN b 177 ASN e 121 ASN f 81 ASN h 37 ASN h 75 GLN ** i 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 HIS o 34 GLN t 12 GLN z 63 ASN z 75 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 165478 Z= 0.289 Angle : 0.728 16.967 247206 Z= 0.388 Chirality : 0.038 0.390 31414 Planarity : 0.007 0.131 13504 Dihedral : 15.653 179.962 64475 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.64 % Favored : 90.82 % Rotamer Outliers : 5.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.10), residues: 6219 helix: 0.21 (0.12), residues: 1975 sheet: -1.30 (0.14), residues: 1166 loop : -1.88 (0.10), residues: 3078 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1083 time to evaluate : 6.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 297 outliers final: 210 residues processed: 1285 average time/residue: 2.1982 time to fit residues: 4184.3645 Evaluate side-chains 1266 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1056 time to evaluate : 6.651 Switching outliers to nearest non-outliers outliers start: 210 outliers final: 167 residues processed: 47 average time/residue: 1.5359 time to fit residues: 130.3203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 953 optimal weight: 2.9990 chunk 1003 optimal weight: 0.7980 chunk 915 optimal weight: 20.0000 chunk 976 optimal weight: 6.9990 chunk 587 optimal weight: 2.9990 chunk 425 optimal weight: 0.8980 chunk 766 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 882 optimal weight: 7.9990 chunk 923 optimal weight: 0.0010 chunk 972 optimal weight: 0.7980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN F 36 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN J 138 GLN N 18 GLN P 11 GLN P 40 GLN U 98 ASN 0 4 GLN ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 HIS 2 29 GLN b 176 ASN b 177 ASN e 131 ASN f 81 ASN g 129 ASN h 37 ASN h 75 GLN ** i 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 GLN o 27 GLN o 34 GLN s 68 HIS z 75 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.077 165478 Z= 0.144 Angle : 0.660 16.846 247206 Z= 0.358 Chirality : 0.033 0.461 31414 Planarity : 0.007 0.122 13504 Dihedral : 15.396 179.506 64475 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.62 % Favored : 91.89 % Rotamer Outliers : 4.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.10), residues: 6219 helix: 0.50 (0.12), residues: 1969 sheet: -1.11 (0.15), residues: 1156 loop : -1.75 (0.11), residues: 3094 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1101 time to evaluate : 6.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 238 outliers final: 173 residues processed: 1284 average time/residue: 2.0471 time to fit residues: 3939.6386 Evaluate side-chains 1227 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1054 time to evaluate : 6.340 Switching outliers to nearest non-outliers outliers start: 173 outliers final: 150 residues processed: 28 average time/residue: 1.3682 time to fit residues: 73.5325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 641 optimal weight: 0.9980 chunk 1032 optimal weight: 10.0000 chunk 630 optimal weight: 7.9990 chunk 489 optimal weight: 0.5980 chunk 717 optimal weight: 10.0000 chunk 1082 optimal weight: 6.9990 chunk 996 optimal weight: 0.9980 chunk 862 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 666 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN J 138 GLN N 18 GLN P 11 GLN P 40 GLN 2 29 GLN b 176 ASN b 177 ASN c 138 GLN e 131 ASN f 81 ASN g 67 ASN g 147 ASN h 37 ASN h 75 GLN ** i 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN o 27 GLN o 34 GLN q 44 HIS t 12 GLN z 75 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 165478 Z= 0.238 Angle : 0.691 16.814 247206 Z= 0.370 Chirality : 0.035 0.404 31414 Planarity : 0.007 0.130 13504 Dihedral : 15.379 178.624 64475 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.17 % Favored : 91.32 % Rotamer Outliers : 4.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.10), residues: 6219 helix: 0.48 (0.12), residues: 1968 sheet: -1.10 (0.15), residues: 1162 loop : -1.73 (0.11), residues: 3089 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1069 time to evaluate : 6.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 211 outliers final: 176 residues processed: 1229 average time/residue: 2.0630 time to fit residues: 3776.0361 Evaluate side-chains 1212 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1036 time to evaluate : 6.182 Switching outliers to nearest non-outliers outliers start: 176 outliers final: 153 residues processed: 27 average time/residue: 1.2540 time to fit residues: 67.1737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 684 optimal weight: 10.0000 chunk 918 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 795 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 863 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 886 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN G 103 ASN J 138 GLN M 3 GLN N 18 GLN V 12 GLN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN b 88 GLN b 176 ASN b 177 ASN c 138 GLN ** d 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN e 131 ASN h 37 ASN h 75 GLN ** i 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 34 GLN t 12 GLN z 75 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105764 restraints weight = 249824.292| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 0.99 r_work: 0.3271 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 1.01 restraints_weight: 0.2500 r_work: 0.3247 rms_B_bonded: 1.16 restraints_weight: 0.1250 r_work: 0.3232 rms_B_bonded: 1.37 restraints_weight: 0.0625 r_work: 0.3214 rms_B_bonded: 1.67 restraints_weight: 0.0312 r_work: 0.3193 rms_B_bonded: 2.06 restraints_weight: 0.0156 r_work: 0.3167 rms_B_bonded: 2.57 restraints_weight: 0.0078 r_work: 0.3134 rms_B_bonded: 3.24 restraints_weight: 0.0039 r_work: 0.3092 rms_B_bonded: 4.16 restraints_weight: 0.0020 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.096 165478 Z= 0.540 Angle : 0.900 18.717 247206 Z= 0.463 Chirality : 0.048 0.424 31414 Planarity : 0.008 0.145 13504 Dihedral : 15.962 179.804 64475 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.59 % Favored : 89.87 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.10), residues: 6219 helix: -0.11 (0.12), residues: 1966 sheet: -1.23 (0.14), residues: 1175 loop : -1.98 (0.10), residues: 3078 =============================================================================== Job complete usr+sys time: 58191.68 seconds wall clock time: 995 minutes 41.08 seconds (59741.08 seconds total)