Starting phenix.real_space_refine (version: dev) on Wed Apr 13 21:12:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zlu_6934/04_2022/5zlu_6934_neut_updated.pdb" } resolution = 3.6 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= 0.002 sd= 0.021 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 "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "F ARG 6": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 118": "NH1" <-> "NH2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "M ARG 3": "NH1" <-> "NH2" Residue "M ARG 6": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 93": "NH1" <-> "NH2" Residue "Z TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z ARG 263": "NH1" <-> "NH2" Residue "a ARG 13": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ARG 19": "NH1" <-> "NH2" Residue "a ARG 36": "NH1" <-> "NH2" Residue "a ARG 58": "NH1" <-> "NH2" Residue "a ARG 61": "NH1" <-> "NH2" Residue "a ARG 76": "NH1" <-> "NH2" Residue "a ARG 79": "NH1" <-> "NH2" Residue "a ARG 82": "NH1" <-> "NH2" Residue "a ARG 101": "NH1" <-> "NH2" Residue "a ARG 111": "NH1" <-> "NH2" Residue "a ARG 119": "NH1" <-> "NH2" Residue "a ARG 136": "NH1" <-> "NH2" Residue "a ARG 144": "NH1" <-> "NH2" Residue "a ARG 164": "NH1" <-> "NH2" Residue "b ARG 17": "NH1" <-> "NH2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b ARG 38": "NH1" <-> "NH2" Residue "b ARG 106": "NH1" <-> "NH2" Residue "b ARG 117": "NH1" <-> "NH2" Residue "b ARG 119": "NH1" <-> "NH2" Residue "b ARG 164": "NH1" <-> "NH2" Residue "b ARG 165": "NH1" <-> "NH2" Residue "b ARG 168": "NH1" <-> "NH2" Residue "b ARG 191": "NH1" <-> "NH2" Residue "b ARG 205": "NH1" <-> "NH2" Residue "c ARG 9": "NH1" <-> "NH2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 22": "NH1" <-> "NH2" Residue "c ARG 51": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ARG 91": "NH1" <-> "NH2" Residue "c ARG 95": "NH1" <-> "NH2" Residue "c ARG 98": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c ARG 115": "NH1" <-> "NH2" Residue "c ARG 118": "NH1" <-> "NH2" Residue "c ARG 153": "NH1" <-> "NH2" Residue "c ARG 181": "NH1" <-> "NH2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d GLU 18": "OE1" <-> "OE2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d ARG 54": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d ARG 60": "NH1" <-> "NH2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d ARG 130": "NH1" <-> "NH2" Residue "d ARG 132": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "f ARG 98": "NH1" <-> "NH2" Residue "h ARG 64": "NH1" <-> "NH2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "h ARG 97": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 50": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i ARG 102": "NH1" <-> "NH2" Residue "i ARG 111": "NH1" <-> "NH2" Residue "j ARG 51": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j ARG 101": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 13": "NH1" <-> "NH2" Residue "l ARG 15": "NH1" <-> "NH2" Residue "l ARG 17": "NH1" <-> "NH2" Residue "l ARG 20": "NH1" <-> "NH2" Residue "l ARG 23": "NH1" <-> "NH2" Residue "l ARG 25": "NH1" <-> "NH2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 67": "NH1" <-> "NH2" Residue "l ARG 71": "NH1" <-> "NH2" Residue "l ARG 89": "NH1" <-> "NH2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 51": "NH1" <-> "NH2" Residue "m ARG 53": "NH1" <-> "NH2" Residue "m ARG 54": "NH1" <-> "NH2" Residue "m ARG 93": "NH1" <-> "NH2" Residue "m ARG 95": "NH1" <-> "NH2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "n ARG 3": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n ARG 36": "NH1" <-> "NH2" Residue "n ARG 52": "NH1" <-> "NH2" Residue "n ARG 55": "NH1" <-> "NH2" Residue "n ARG 70": "NH1" <-> "NH2" Residue "n ARG 112": "NH1" <-> "NH2" Residue "o ARG 13": "NH1" <-> "NH2" Residue "o TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 11": "NH1" <-> "NH2" Residue "p ARG 15": "NH1" <-> "NH2" Residue "p ARG 18": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 42": "NH1" <-> "NH2" Residue "p ARG 68": "NH1" <-> "NH2" Residue "p TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 99": "NH1" <-> "NH2" Residue "r ARG 23": "NH1" <-> "NH2" Residue "r ARG 50": "NH1" <-> "NH2" Residue "r ARG 73": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 86": "NH1" <-> "NH2" Residue "t ARG 20": "NH1" <-> "NH2" Residue "t ARG 25": "NH1" <-> "NH2" Residue "t ARG 55": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "t ARG 77": "NH1" <-> "NH2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "u ARG 2": "NH1" <-> "NH2" Residue "u ARG 9": "NH1" <-> "NH2" Residue "u ARG 21": "NH1" <-> "NH2" Residue "u ARG 25": "NH1" <-> "NH2" Residue "u ARG 31": "NH1" <-> "NH2" Residue "u ARG 46": "NH1" <-> "NH2" Residue "u ARG 50": "NH1" <-> "NH2" Residue "u ARG 54": "NH1" <-> "NH2" Residue "u ARG 63": "NH1" <-> "NH2" Residue "u ARG 64": "NH1" <-> "NH2" Residue "v ARG 29": "NH1" <-> "NH2" Residue "v ARG 30": "NH1" <-> "NH2" Residue "v ARG 35": "NH1" <-> "NH2" Residue "v ARG 44": "NH1" <-> "NH2" Residue "v ARG 55": "NH1" <-> "NH2" Residue "w TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 15": "NH1" <-> "NH2" Residue "x ARG 16": "NH1" <-> "NH2" Residue "x ARG 19": "NH1" <-> "NH2" Residue "x ARG 20": "NH1" <-> "NH2" Residue "x ARG 55": "NH1" <-> "NH2" Residue "y ARG 18": "NH1" <-> "NH2" Residue "y ARG 37": "NH1" <-> "NH2" Residue "y ARG 44": "NH1" <-> "NH2" Residue "z ARG 47": "NH1" <-> "NH2" Residue "z ARG 49": "NH1" <-> "NH2" Residue "EE ARG 32": "NH1" <-> "NH2" Residue "EE ARG 63": "NH1" <-> "NH2" Residue "EE ARG 89": "NH1" <-> "NH2" Residue "EE TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EE ARG 208": "NH1" <-> "NH2" Residue "EE ARG 241": "NH1" <-> "NH2" Residue "EE ARG 265": "NH1" <-> "NH2" Residue "EE ARG 279": "NH1" <-> "NH2" Residue "EE ARG 282": "NH1" <-> "NH2" Residue "EE ARG 309": "NH1" <-> "NH2" Residue "EE ARG 345": "NH1" <-> "NH2" Residue "EE ARG 389": "NH1" <-> "NH2" Residue "EE GLU 413": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 150313 Number of models: 1 Model: "" Number of chains: 60 Chain: "W" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna3p_pyr': 2, 'rna2p_pur': 1, 'rna3p_pur': 3, 'rna2p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 2} Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 808 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 597 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "D" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 2 Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 794 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "F" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "G" Number of atoms: 32534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 32534 Classifications: {'RNA': 1514} Modifications used: {'rna3p_pyr': 611, 'rna2p_pur': 69, 'rna3p_pur': 786, 'rna2p_pyr': 48} Link IDs: {'rna3p': 1396, 'rna2p': 117} Chain: "H" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1810 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain: "I" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "J" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "K" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "L" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "M" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "N" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "O" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "P" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "Q" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "R" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "T" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "U" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 700 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "V" Number of atoms: 61917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2875, 61917 Classifications: {'RNA': 2875} Modifications used: {'rna3p_pyr': 1090, 'rna2p_pur': 174, 'rna3p_pur': 1509, 'rna2p_pyr': 102} Link IDs: {'rna3p': 2598, 'rna2p': 276} Chain: "X" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2641 Classifications: {'RNA': 123} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 54, 'p5*END': 1, 'rna3p_pur': 67, 'rna2p_pur': 1} Link IDs: {'rna3p': 121, 'rna2p': 1} Chain: "Y" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1742 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 214} Chain: "Z" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2126 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 19, 'TRANS': 251, 'PCIS': 2} Chain: "a" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1578 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "b" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1625 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "c" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1455 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1335 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 159} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 621 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 7, 'TRANS': 118} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 453 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 173 Chain: "f" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 10, 'TRANS': 123} Chain: "g" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 931 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "h" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "i" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1108 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 10, 'TRANS': 134} Chain: "j" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "k" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "l" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 877 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "m" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 976 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "n" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 964 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "o" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "p" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "q" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "r" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "s" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1435 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 15, 'TRANS': 164} Chain: "t" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 629 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "u" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 567 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "v" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 469 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "w" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 581 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "x" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 47} Chain: "y" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 422 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "z" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 430 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "AA" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 515 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "BB" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 307 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "CC" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 157 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 28} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "DD" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1648 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 28, 'rna2p_pur': 5, 'rna3p_pur': 34, 'rna2p_pyr': 5, 'rna3p': 5} Link IDs: {'rna3p': 66, 'rna2p': 10} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "EE" Number of atoms: 3841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3841 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 6, 'TRANS': 483} Chain: "Z" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "EE" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ANP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 470 residue: pdb=" N METEE 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE METEE 1 " occ=0.00 residue: pdb=" N SEREE 2 " occ=0.00 ... (4 atoms not shown) pdb=" OG SEREE 2 " occ=0.00 residue: pdb=" N LEUEE 3 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEUEE 3 " occ=0.00 residue: pdb=" N ILEEE 4 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILEEE 4 " occ=0.00 residue: pdb=" N ILEEE 5 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILEEE 5 " occ=0.00 residue: pdb=" N LYSEE 6 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYSEE 6 " occ=0.00 residue: pdb=" N ALAEE 7 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALAEE 7 " occ=0.00 residue: pdb=" N ARGEE 8 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARGEE 8 " occ=0.00 residue: pdb=" N ASNEE 9 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASNEE 9 " occ=0.00 residue: pdb=" N ILEEE 10 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILEEE 10 " occ=0.00 residue: pdb=" N ARGEE 11 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARGEE 11 " occ=0.00 residue: pdb=" N LEUEE 12 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEUEE 12 " occ=0.00 ... (remaining 458 not shown) Time building chain proxies: 61.72, per 1000 atoms: 0.41 Number of scatterers: 150313 At special positions: 0 Unit cell: (270.6, 294.8, 254.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 145 16.00 P 4602 15.00 Mg 2 11.99 O 40834 8.00 N 28306 7.00 C 76424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS J 9 " - pdb=" SG CYS J 12 " distance=2.06 Simple disulfide: pdb=" SG CYS J 9 " - pdb=" SG CYS J 26 " distance=2.14 Simple disulfide: pdb=" SG CYS J 9 " - pdb=" SG CYS J 31 " distance=1.91 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 26 " distance=1.91 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 31 " distance=2.14 Simple disulfide: pdb=" SG CYS J 26 " - pdb=" SG CYS J 31 " distance=2.07 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 43 " distance=2.67 Simple disulfide: pdb=" SG CYS r 76 " - pdb=" SG CYS r 99 " distance=2.05 Simple disulfide: pdb=" SG CYS x 33 " - pdb=" SG CYS x 36 " distance=1.66 Simple disulfide: pdb=" SG CYS x 33 " - pdb=" SG CYS x 49 " distance=2.05 Simple disulfide: pdb=" SG CYS x 36 " - pdb=" SG CYS x 49 " distance=2.14 Simple disulfide: pdb=" SG CYSBB 11 " - pdb=" SG CYSBB 14 " distance=2.02 Simple disulfide: pdb=" SG CYSBB 11 " - pdb=" SG CYSBB 27 " distance=2.03 Simple disulfide: pdb=" SG CYSBB 14 " - pdb=" SG CYSBB 27 " distance=2.04 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 Atom "ATOM A0BGM O4' A X 57 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 47.95 Conformation dependent library (CDL) restraints added in 6.1 seconds 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11930 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: 183 helices and 61 sheets defined 35.0% alpha, 13.5% beta 542 base pairs and 2054 stacking pairs defined. Time for finding SS restraints: 50.23 Creating SS restraints... Processing helix chain 'A' and resid 82 through 95 removed outlier: 5.474A pdb=" N GLU A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.855A pdb=" N THR B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 21 through 26' Processing helix chain 'B' and resid 36 through 45 removed outlier: 3.961A pdb=" N LEU B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 4.141A pdb=" N THR B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 77 removed outlier: 4.275A pdb=" N ILE B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 47 removed outlier: 4.151A pdb=" N HIS C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 30 " --> pdb=" O ASN C 26 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 45 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 removed outlier: 4.194A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 96 removed outlier: 5.606A pdb=" N ALA C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG C 79 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS C 87 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA C 94 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.658A pdb=" N GLU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS D 18 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 5.024A pdb=" N PHE D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Proline residue: D 76 - end of helix No H-bonds generated for 'chain 'D' and resid 70 through 76' Processing helix chain 'E' and resid 12 through 31 removed outlier: 4.845A pdb=" N ASP E 17 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER E 19 " --> pdb=" O THR E 15 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLU E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 88 removed outlier: 5.220A pdb=" N ILE E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 16 removed outlier: 4.329A pdb=" N ARG F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 65 removed outlier: 4.249A pdb=" N GLU H 49 " --> pdb=" O GLN H 45 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU H 50 " --> pdb=" O LYS H 46 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU H 52 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG H 53 " --> pdb=" O GLU H 49 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP H 60 " --> pdb=" O ARG H 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU H 61 " --> pdb=" O PHE H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 89 removed outlier: 5.103A pdb=" N ARG H 82 " --> pdb=" O GLN H 78 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N MET H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 105 removed outlier: 3.653A pdb=" N ASN H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE H 105 " --> pdb=" O MET H 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 100 through 105' Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.722A pdb=" N GLN H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU H 117 " --> pdb=" O HIS H 113 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALA H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 149 removed outlier: 3.954A pdb=" N TYR H 148 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU H 149 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 171 Processing helix chain 'H' and resid 172 through 181 removed outlier: 3.923A pdb=" N GLU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 180 " --> pdb=" O GLU H 176 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 198 removed outlier: 4.382A pdb=" N VAL H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP H 198 " --> pdb=" O PRO H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 198' Processing helix chain 'H' and resid 207 through 227 removed outlier: 3.568A pdb=" N GLN H 212 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU H 213 " --> pdb=" O ARG H 209 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE H 214 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA H 218 " --> pdb=" O ILE H 214 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL H 219 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP H 220 " --> pdb=" O SER H 216 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU H 221 " --> pdb=" O ARG H 217 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE H 222 " --> pdb=" O ALA H 218 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE H 223 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG H 226 " --> pdb=" O ILE H 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 12 removed outlier: 4.050A pdb=" N PHE I 10 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG I 11 " --> pdb=" O PRO I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 48 removed outlier: 6.114A pdb=" N ARG I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N HIS I 31 " --> pdb=" O LYS I 27 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU I 33 " --> pdb=" O TYR I 29 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU I 35 " --> pdb=" O HIS I 31 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLN I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU I 44 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS I 45 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU I 47 " --> pdb=" O LEU I 43 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR I 48 " --> pdb=" O GLU I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 78 removed outlier: 3.894A pdb=" N VAL I 76 " --> pdb=" O LYS I 72 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE I 77 " --> pdb=" O PRO I 73 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY I 78 " --> pdb=" O GLY I 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 78' Processing helix chain 'I' and resid 81 through 96 removed outlier: 4.773A pdb=" N ARG I 85 " --> pdb=" O GLY I 81 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 127 removed outlier: 3.627A pdb=" N ALA I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 145 removed outlier: 3.540A pdb=" N ALA I 133 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET I 142 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU I 143 " --> pdb=" O GLN I 139 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER I 144 " --> pdb=" O ARG I 140 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY I 145 " --> pdb=" O VAL I 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 15 removed outlier: 3.708A pdb=" N CYS J 12 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG J 13 " --> pdb=" O CYS J 9 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG J 14 " --> pdb=" O ARG J 10 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 8 through 15' Processing helix chain 'J' and resid 23 through 28 removed outlier: 4.143A pdb=" N TYR J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 69 removed outlier: 3.559A pdb=" N VAL J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE J 67 " --> pdb=" O LYS J 63 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY J 69 " --> pdb=" O ARG J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 85 removed outlier: 3.843A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 100 removed outlier: 3.792A pdb=" N GLY J 95 " --> pdb=" O SER J 91 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ARG J 100 " --> pdb=" O LEU J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 109 removed outlier: 5.035A pdb=" N GLY J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 124 removed outlier: 3.810A pdb=" N ALA J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN J 119 " --> pdb=" O ARG J 115 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG J 122 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 removed outlier: 3.704A pdb=" N ASN J 161 " --> pdb=" O LEU J 157 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA J 164 " --> pdb=" O GLN J 160 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET J 165 " --> pdb=" O ASN J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 209 removed outlier: 4.181A pdb=" N ILE J 204 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU J 205 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER J 208 " --> pdb=" O ILE J 204 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 200 through 209' Processing helix chain 'K' and resid 50 through 66 removed outlier: 3.889A pdb=" N VAL K 55 " --> pdb=" O VAL K 51 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN K 56 " --> pdb=" O PRO K 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG K 64 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 114 removed outlier: 3.997A pdb=" N ALA K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE K 109 " --> pdb=" O VAL K 105 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU K 112 " --> pdb=" O ALA K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 142 removed outlier: 4.663A pdb=" N ALA K 132 " --> pdb=" O PRO K 128 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA K 134 " --> pdb=" O ASN K 130 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR K 135 " --> pdb=" O ILE K 131 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET K 136 " --> pdb=" O ALA K 132 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU K 137 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG K 140 " --> pdb=" O MET K 136 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 153 removed outlier: 4.110A pdb=" N ARG K 150 " --> pdb=" O ALA K 146 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU K 151 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 34 removed outlier: 4.402A pdb=" N ALA L 20 " --> pdb=" O GLN L 16 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 83 removed outlier: 4.135A pdb=" N VAL L 72 " --> pdb=" O PRO L 68 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASP L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA L 76 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG L 77 " --> pdb=" O ASN L 73 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLU L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU L 79 " --> pdb=" O LEU L 75 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE L 81 " --> pdb=" O ARG L 77 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASP L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 32 removed outlier: 4.588A pdb=" N THR M 24 " --> pdb=" O ASP M 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS M 29 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE M 30 " --> pdb=" O PHE M 26 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG M 32 " --> pdb=" O ASN M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 54 removed outlier: 3.750A pdb=" N ALA M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE M 43 " --> pdb=" O ALA M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 70 removed outlier: 3.767A pdb=" N VAL M 61 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN M 68 " --> pdb=" O GLN M 64 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS M 70 " --> pdb=" O VAL M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 109 removed outlier: 3.789A pdb=" N SER M 98 " --> pdb=" O ARG M 94 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL M 105 " --> pdb=" O LEU M 101 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN M 109 " --> pdb=" O VAL M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 130 removed outlier: 4.250A pdb=" N HIS M 122 " --> pdb=" O VAL M 118 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU M 123 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU M 129 " --> pdb=" O MET M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 153 removed outlier: 4.172A pdb=" N VAL M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU M 146 " --> pdb=" O GLU M 142 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA M 147 " --> pdb=" O ARG M 143 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN M 148 " --> pdb=" O MET M 144 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG M 149 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA M 150 " --> pdb=" O GLU M 146 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR M 151 " --> pdb=" O ALA M 147 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA M 152 " --> pdb=" O ASN M 148 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS M 153 " --> pdb=" O ARG M 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 20 removed outlier: 3.897A pdb=" N LEU N 10 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG N 18 " --> pdb=" O ARG N 14 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL N 19 " --> pdb=" O ASN N 15 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR N 20 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 43 removed outlier: 4.024A pdb=" N GLU N 33 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE N 38 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU N 42 " --> pdb=" O ILE N 38 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLY N 43 " --> pdb=" O LEU N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 3.551A pdb=" N LYS N 126 " --> pdb=" O ARG N 122 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU N 127 " --> pdb=" O GLU N 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 38 removed outlier: 3.854A pdb=" N TYR O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE O 37 " --> pdb=" O PHE O 33 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN O 38 " --> pdb=" O ASN O 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 32 through 38' Processing helix chain 'O' and resid 70 through 90 removed outlier: 4.282A pdb=" N ILE O 74 " --> pdb=" O LYS O 70 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP O 75 " --> pdb=" O SER O 71 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN O 87 " --> pdb=" O ARG O 83 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN O 89 " --> pdb=" O LEU O 85 " (cutoff:3.500A) Proline residue: O 90 - end of helix Processing helix chain 'O' and resid 92 through 99 removed outlier: 4.790A pdb=" N LEU O 96 " --> pdb=" O TYR O 92 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS O 97 " --> pdb=" O ARG O 93 " (cutoff:3.500A) Proline residue: O 98 - end of helix No H-bonds generated for 'chain 'O' and resid 92 through 99' Processing helix chain 'O' and resid 40 through 47 removed outlier: 3.682A pdb=" N VAL O 44 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA O 46 " --> pdb=" O ALA O 43 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU O 47 " --> pdb=" O VAL O 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 49 removed outlier: 4.320A pdb=" N ILE P 48 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY P 49 " --> pdb=" O GLY P 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 44 through 49' Processing helix chain 'P' and resid 52 through 57 removed outlier: 4.456A pdb=" N GLY P 56 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR P 57 " --> pdb=" O SER P 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 52 through 57' Processing helix chain 'P' and resid 58 through 76 removed outlier: 5.430A pdb=" N GLN P 62 " --> pdb=" O PRO P 58 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU P 63 " --> pdb=" O TYR P 59 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA P 69 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS P 71 " --> pdb=" O ASP P 67 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA P 72 " --> pdb=" O ALA P 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA P 74 " --> pdb=" O LYS P 70 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.643A pdb=" N ALA P 94 " --> pdb=" O GLY P 90 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE P 95 " --> pdb=" O ARG P 91 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG P 96 " --> pdb=" O GLU P 92 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN P 99 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA P 100 " --> pdb=" O ARG P 96 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER P 101 " --> pdb=" O ALA P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 127 Processing helix chain 'Q' and resid 6 through 13 removed outlier: 3.959A pdb=" N LEU Q 10 " --> pdb=" O THR Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 121 removed outlier: 5.243A pdb=" N TYR Q 120 " --> pdb=" O SER Q 116 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 116 through 121' Processing helix chain 'R' and resid 15 through 20 removed outlier: 3.999A pdb=" N THR R 20 " --> pdb=" O ASP R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 38 removed outlier: 6.531A pdb=" N LYS R 31 " --> pdb=" O LYS R 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU R 32 " --> pdb=" O ALA R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 62 removed outlier: 6.073A pdb=" N VAL R 54 " --> pdb=" O GLU R 50 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASN R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 83 removed outlier: 3.761A pdb=" N ILE R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU R 81 " --> pdb=" O ASN R 77 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP R 83 " --> pdb=" O LYS R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 95 removed outlier: 4.687A pdb=" N LEU R 90 " --> pdb=" O CYS R 86 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG R 91 " --> pdb=" O TYR R 87 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 112 removed outlier: 5.338A pdb=" N LYS R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY R 112 " --> pdb=" O ARG R 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 107 through 112' Processing helix chain 'S' and resid 3 through 8 removed outlier: 3.665A pdb=" N ILE S 7 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU S 8 " --> pdb=" O LYS S 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 3 through 8' Processing helix chain 'S' and resid 40 through 51 removed outlier: 4.201A pdb=" N LEU S 44 " --> pdb=" O CYS S 40 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG S 45 " --> pdb=" O ARG S 41 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU S 46 " --> pdb=" O ILE S 42 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU S 47 " --> pdb=" O CYS S 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 16 removed outlier: 4.080A pdb=" N LYS T 8 " --> pdb=" O THR T 4 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN T 13 " --> pdb=" O GLN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 47 removed outlier: 4.188A pdb=" N VAL T 29 " --> pdb=" O THR T 25 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA T 30 " --> pdb=" O GLU T 26 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU T 41 " --> pdb=" O ASN T 37 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU T 43 " --> pdb=" O LEU T 39 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS T 44 " --> pdb=" O SER T 40 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL T 45 " --> pdb=" O GLU T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 74 removed outlier: 3.635A pdb=" N MET T 59 " --> pdb=" O GLY T 55 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY T 61 " --> pdb=" O LEU T 57 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG T 65 " --> pdb=" O GLY T 61 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR T 69 " --> pdb=" O ARG T 65 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG T 72 " --> pdb=" O ARG T 68 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU T 73 " --> pdb=" O TYR T 69 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP T 74 " --> pdb=" O LEU T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 86 removed outlier: 3.900A pdb=" N LEU T 81 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE T 82 " --> pdb=" O TYR T 78 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU T 83 " --> pdb=" O ARG T 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 63 removed outlier: 5.072A pdb=" N ALA U 56 " --> pdb=" O ASP U 52 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG U 57 " --> pdb=" O VAL U 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL U 62 " --> pdb=" O TYR U 58 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY U 63 " --> pdb=" O TRP U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 78 removed outlier: 4.023A pdb=" N ARG U 72 " --> pdb=" O ASP U 68 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU U 73 " --> pdb=" O THR U 69 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA U 77 " --> pdb=" O LEU U 73 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 15 removed outlier: 4.884A pdb=" N ALA Y 9 " --> pdb=" O LYS Y 5 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU Y 10 " --> pdb=" O ARG Y 6 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS Y 13 " --> pdb=" O ALA Y 9 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP Y 15 " --> pdb=" O LEU Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 33 Processing helix chain 'Y' and resid 53 through 58 removed outlier: 6.011A pdb=" N VAL Y 58 " --> pdb=" O SER Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 90 Processing helix chain 'Y' and resid 96 through 106 Processing helix chain 'Y' and resid 116 through 126 removed outlier: 3.790A pdb=" N MET Y 120 " --> pdb=" O THR Y 116 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLY Y 121 " --> pdb=" O PRO Y 117 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA Y 122 " --> pdb=" O ASP Y 118 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 158 removed outlier: 3.887A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 153 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA Y 158 " --> pdb=" O ARG Y 154 " (cutoff:3.500A) Processing helix chain 'Y' and resid 181 through 200 removed outlier: 4.401A pdb=" N LEU Y 185 " --> pdb=" O PRO Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 132 removed outlier: 4.312A pdb=" N GLY Y 132 " --> pdb=" O LEU Y 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 127 through 132' Processing helix chain 'Z' and resid 12 through 17 removed outlier: 4.684A pdb=" N MET Z 16 " --> pdb=" O SER Z 12 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR Z 17 " --> pdb=" O ARG Z 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 12 through 17' Processing helix chain 'Z' and resid 132 through 137 removed outlier: 4.072A pdb=" N ILE Z 136 " --> pdb=" O PRO Z 132 " (cutoff:3.500A) Proline residue: Z 137 - end of helix No H-bonds generated for 'chain 'Z' and resid 132 through 137' Processing helix chain 'Z' and resid 208 through 216 removed outlier: 4.389A pdb=" N SER Z 212 " --> pdb=" O LYS Z 208 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG Z 213 " --> pdb=" O ALA Z 209 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU Z 215 " --> pdb=" O ARG Z 211 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY Z 216 " --> pdb=" O SER Z 212 " (cutoff:3.500A) Processing helix chain 'Z' and resid 266 through 271 removed outlier: 4.763A pdb=" N ILE Z 270 " --> pdb=" O SER Z 266 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE Z 271 " --> pdb=" O SER Z 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 266 through 271' Processing helix chain 'Z' and resid 198 through 203 removed outlier: 3.816A pdb=" N HIS Z 201 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS Z 202 " --> pdb=" O ALA Z 199 " (cutoff:3.500A) Processing helix chain 'a' and resid 59 through 68 removed outlier: 4.478A pdb=" N HIS a 66 " --> pdb=" O PRO a 62 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 96 removed outlier: 4.390A pdb=" N ILE a 95 " --> pdb=" O VAL a 91 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE a 96 " --> pdb=" O THR a 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 91 through 96' Processing helix chain 'a' and resid 115 through 120 Processing helix chain 'b' and resid 29 through 45 removed outlier: 4.462A pdb=" N LEU b 33 " --> pdb=" O ASN b 29 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG b 44 " --> pdb=" O GLN b 40 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG b 45 " --> pdb=" O LEU b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 121 removed outlier: 3.806A pdb=" N ARG b 106 " --> pdb=" O PRO b 102 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS b 107 " --> pdb=" O LYS b 103 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU b 110 " --> pdb=" O ARG b 106 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG b 119 " --> pdb=" O ALA b 115 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU b 120 " --> pdb=" O ASP b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 147 removed outlier: 4.509A pdb=" N PHE b 139 " --> pdb=" O LYS b 135 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU b 140 " --> pdb=" O THR b 136 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS b 144 " --> pdb=" O LEU b 140 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU b 145 " --> pdb=" O ALA b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 160 through 165 Processing helix chain 'b' and resid 182 through 190 removed outlier: 4.194A pdb=" N ILE b 186 " --> pdb=" O ASN b 182 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL b 187 " --> pdb=" O VAL b 183 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG b 188 " --> pdb=" O TYR b 184 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU b 190 " --> pdb=" O ILE b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 210 removed outlier: 4.611A pdb=" N GLU b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL b 201 " --> pdb=" O ASP b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 20 removed outlier: 3.569A pdb=" N TYR c 11 " --> pdb=" O LEU c 7 " (cutoff:3.500A) Proline residue: c 17 - end of helix Processing helix chain 'c' and resid 50 through 64 removed outlier: 4.809A pdb=" N GLU c 54 " --> pdb=" O ALA c 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA c 57 " --> pdb=" O LEU c 53 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN c 58 " --> pdb=" O GLU c 54 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU c 59 " --> pdb=" O LYS c 55 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU c 60 " --> pdb=" O ALA c 56 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU c 62 " --> pdb=" O GLN c 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 108 removed outlier: 3.959A pdb=" N TRP c 100 " --> pdb=" O ARG c 96 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU c 104 " --> pdb=" O TRP c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 165 through 177 removed outlier: 4.139A pdb=" N ALA c 169 " --> pdb=" O THR c 165 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU c 172 " --> pdb=" O GLU c 168 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 49 removed outlier: 5.771A pdb=" N ALA c 46 " --> pdb=" O LEU c 43 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS c 47 " --> pdb=" O GLY c 44 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU c 48 " --> pdb=" O GLU c 45 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP c 49 " --> pdb=" O ALA c 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 43 through 49' Processing helix chain 'c' and resid 110 through 115 removed outlier: 5.592A pdb=" N ARG c 115 " --> pdb=" O PRO c 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 82 removed outlier: 5.434A pdb=" N SER d 63 " --> pdb=" O ARG d 59 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY d 66 " --> pdb=" O LYS d 62 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU d 67 " --> pdb=" O SER d 63 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE d 72 " --> pdb=" O THR d 68 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN d 74 " --> pdb=" O THR d 70 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA d 75 " --> pdb=" O LEU d 71 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS d 77 " --> pdb=" O ALA d 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY d 78 " --> pdb=" O ASN d 74 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER d 80 " --> pdb=" O VAL d 76 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU d 81 " --> pdb=" O LYS d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 151 removed outlier: 4.960A pdb=" N VAL d 141 " --> pdb=" O ASP d 137 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY d 142 " --> pdb=" O LYS d 138 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN d 143 " --> pdb=" O GLN d 139 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG d 149 " --> pdb=" O ALA d 145 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE d 151 " --> pdb=" O ASN d 147 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 20 removed outlier: 4.408A pdb=" N THR e 12 " --> pdb=" O GLU e 8 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU e 13 " --> pdb=" O LEU e 9 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN e 16 " --> pdb=" O THR e 12 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA e 20 " --> pdb=" O ASN e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 42 removed outlier: 4.675A pdb=" N LEU e 40 " --> pdb=" O GLU e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 43 through 48 Processing helix chain 'e' and resid 59 through 70 removed outlier: 5.640A pdb=" N LEU e 63 " --> pdb=" O ILE e 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY e 67 " --> pdb=" O LEU e 63 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU e 68 " --> pdb=" O LYS e 64 " (cutoff:3.500A) Proline residue: e 69 - end of helix Processing helix chain 'e' and resid 94 through 107 removed outlier: 3.965A pdb=" N LYS e 98 " --> pdb=" O VAL e 94 " (cutoff:3.500A) Proline residue: e 101 - end of helix Proline residue: e 105 - end of helix Processing helix chain 'e' and resid 124 through 130 Proline residue: e 129 - end of helix Processing helix chain 'f' and resid 26 through 31 removed outlier: 4.678A pdb=" N HIS f 30 " --> pdb=" O ALA f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 49 removed outlier: 3.630A pdb=" N ALA f 43 " --> pdb=" O LYS f 39 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA f 44 " --> pdb=" O ALA f 40 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA f 46 " --> pdb=" O ASN f 42 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN f 47 " --> pdb=" O ALA f 43 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET f 48 " --> pdb=" O ALA f 44 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY f 49 " --> pdb=" O THR f 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 74 through 80 Processing helix chain 'f' and resid 100 through 109 Processing helix chain 'f' and resid 121 through 126 removed outlier: 4.298A pdb=" N ARG f 125 " --> pdb=" O GLU f 121 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET f 126 " --> pdb=" O ALA f 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 121 through 126' Processing helix chain 'f' and resid 127 through 135 removed outlier: 3.781A pdb=" N ARG f 132 " --> pdb=" O ALA f 128 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 36 removed outlier: 3.511A pdb=" N LEU g 26 " --> pdb=" O THR g 22 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS g 29 " --> pdb=" O ARG g 25 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY g 36 " --> pdb=" O THR g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 94 removed outlier: 4.175A pdb=" N MET g 90 " --> pdb=" O PRO g 86 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA g 92 " --> pdb=" O GLU g 88 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS g 94 " --> pdb=" O MET g 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 108 removed outlier: 4.605A pdb=" N LEU g 99 " --> pdb=" O PRO g 95 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU g 107 " --> pdb=" O VAL g 103 " (cutoff:3.500A) Proline residue: g 108 - end of helix Processing helix chain 'g' and resid 110 through 117 removed outlier: 4.581A pdb=" N ARG g 115 " --> pdb=" O PRO g 111 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE g 117 " --> pdb=" O GLY g 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 118 removed outlier: 4.940A pdb=" N VAL h 115 " --> pdb=" O PHE h 111 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 89 removed outlier: 3.596A pdb=" N ALA i 89 " --> pdb=" O LEU i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 104 removed outlier: 4.488A pdb=" N LEU i 100 " --> pdb=" O THR i 96 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG i 102 " --> pdb=" O GLU i 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 131 through 140 removed outlier: 3.723A pdb=" N LEU i 138 " --> pdb=" O ALA i 134 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA i 140 " --> pdb=" O GLU i 136 " (cutoff:3.500A) Processing helix chain 'j' and resid 43 through 59 removed outlier: 4.218A pdb=" N ILE j 47 " --> pdb=" O THR j 43 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU j 48 " --> pdb=" O ALA j 44 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL j 55 " --> pdb=" O ARG j 51 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE j 58 " --> pdb=" O MET j 54 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG j 59 " --> pdb=" O VAL j 55 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 126 removed outlier: 4.364A pdb=" N ALA j 117 " --> pdb=" O GLN j 113 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU j 118 " --> pdb=" O ALA j 114 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG j 119 " --> pdb=" O MET j 115 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY j 122 " --> pdb=" O LEU j 118 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS j 124 " --> pdb=" O ILE j 120 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU j 125 " --> pdb=" O ALA j 121 " (cutoff:3.500A) Proline residue: j 126 - end of helix Processing helix chain 'k' and resid 14 through 32 removed outlier: 5.547A pdb=" N LEU k 18 " --> pdb=" O SER k 14 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA k 19 " --> pdb=" O SER k 15 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS k 26 " --> pdb=" O ARG k 22 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER k 27 " --> pdb=" O ASN k 23 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU k 28 " --> pdb=" O GLN k 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU k 29 " --> pdb=" O ALA k 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR k 30 " --> pdb=" O LYS k 26 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 58 removed outlier: 4.661A pdb=" N GLU k 43 " --> pdb=" O PRO k 39 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG k 45 " --> pdb=" O ALA k 41 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY k 46 " --> pdb=" O LYS k 42 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE k 47 " --> pdb=" O GLU k 43 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP k 49 " --> pdb=" O ARG k 45 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS k 50 " --> pdb=" O GLY k 46 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE k 52 " --> pdb=" O VAL k 48 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS k 53 " --> pdb=" O ASP k 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU k 54 " --> pdb=" O HIS k 50 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS k 56 " --> pdb=" O ILE k 52 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG k 57 " --> pdb=" O HIS k 53 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY k 58 " --> pdb=" O LEU k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 71 removed outlier: 4.046A pdb=" N LEU k 65 " --> pdb=" O HIS k 61 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU k 67 " --> pdb=" O ARG k 63 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG k 68 " --> pdb=" O ARG k 64 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP k 69 " --> pdb=" O LEU k 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 72 through 88 removed outlier: 4.091A pdb=" N ARG k 77 " --> pdb=" O VAL k 73 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP k 81 " --> pdb=" O ARG k 77 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA k 84 " --> pdb=" O PHE k 80 " (cutoff:3.500A) Proline residue: k 85 - end of helix removed outlier: 4.819A pdb=" N ARG k 88 " --> pdb=" O ALA k 84 " (cutoff:3.500A) Processing helix chain 'l' and resid 7 through 21 removed outlier: 4.345A pdb=" N LYS l 11 " --> pdb=" O TYR l 7 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG l 15 " --> pdb=" O LYS l 11 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS l 19 " --> pdb=" O ARG l 15 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG l 20 " --> pdb=" O ASN l 16 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR l 21 " --> pdb=" O ARG l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 63 through 81 removed outlier: 4.330A pdb=" N ARG l 67 " --> pdb=" O THR l 63 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY l 70 " --> pdb=" O ALA l 66 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU l 75 " --> pdb=" O ARG l 71 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU l 80 " --> pdb=" O LYS l 76 " (cutoff:3.500A) Processing helix chain 'l' and resid 96 through 109 removed outlier: 4.647A pdb=" N LEU l 101 " --> pdb=" O ARG l 97 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA l 102 " --> pdb=" O VAL l 98 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU l 107 " --> pdb=" O GLU l 103 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY l 108 " --> pdb=" O GLY l 104 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY l 109 " --> pdb=" O ALA l 105 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 16 removed outlier: 5.333A pdb=" N LYS m 8 " --> pdb=" O GLY m 4 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU m 9 " --> pdb=" O ALA m 5 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL m 10 " --> pdb=" O LEU m 6 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER m 12 " --> pdb=" O LYS m 8 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG m 13 " --> pdb=" O LEU m 9 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR m 14 " --> pdb=" O VAL m 10 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG m 16 " --> pdb=" O SER m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 103 through 109 removed outlier: 4.845A pdb=" N ASP m 107 " --> pdb=" O ARG m 103 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU m 109 " --> pdb=" O LEU m 105 " (cutoff:3.500A) Processing helix chain 'm' and resid 110 through 117 removed outlier: 3.688A pdb=" N ARG m 115 " --> pdb=" O ARG m 111 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA m 116 " --> pdb=" O ARG m 112 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP m 117 " --> pdb=" O LYS m 113 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 22 removed outlier: 3.732A pdb=" N HIS n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS n 16 " --> pdb=" O ARG n 12 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE n 17 " --> pdb=" O LYS n 13 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU n 20 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS n 22 " --> pdb=" O LEU n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 25 through 31 removed outlier: 3.663A pdb=" N SER n 29 " --> pdb=" O TRP n 25 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER n 31 " --> pdb=" O LEU n 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 25 through 31' Processing helix chain 'n' and resid 32 through 37 removed outlier: 4.169A pdb=" N ARG n 36 " --> pdb=" O PHE n 32 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU n 37 " --> pdb=" O ARG n 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 32 through 37' Processing helix chain 'n' and resid 39 through 54 removed outlier: 4.153A pdb=" N GLY n 43 " --> pdb=" O LEU n 39 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN n 44 " --> pdb=" O PHE n 40 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA n 46 " --> pdb=" O ALA n 42 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR n 47 " --> pdb=" O GLY n 43 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA n 48 " --> pdb=" O ASN n 44 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG n 50 " --> pdb=" O ALA n 46 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS n 51 " --> pdb=" O TYR n 47 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS n 54 " --> pdb=" O ARG n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 removed outlier: 3.527A pdb=" N LEU n 60 " --> pdb=" O ASP n 56 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL n 63 " --> pdb=" O ARG n 59 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA n 68 " --> pdb=" O ARG n 64 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN n 71 " --> pdb=" O ALA n 67 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS n 72 " --> pdb=" O ALA n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 87 removed outlier: 3.957A pdb=" N PHE n 79 " --> pdb=" O ASN n 75 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY n 87 " --> pdb=" O LEU n 83 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 102 removed outlier: 4.052A pdb=" N ALA n 96 " --> pdb=" O ARG n 92 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP n 97 " --> pdb=" O LYS n 93 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL n 100 " --> pdb=" O ALA n 96 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG n 101 " --> pdb=" O ASP n 97 " (cutoff:3.500A) Processing helix chain 'n' and resid 103 through 117 removed outlier: 5.149A pdb=" N GLU n 108 " --> pdb=" O GLN n 104 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU n 109 " --> pdb=" O VAL n 105 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA n 113 " --> pdb=" O LEU n 109 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA n 115 " --> pdb=" O GLU n 111 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA n 116 " --> pdb=" O ARG n 112 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN n 117 " --> pdb=" O ALA n 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 13 through 25 removed outlier: 4.412A pdb=" N VAL p 17 " --> pdb=" O SER p 13 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG p 18 " --> pdb=" O PRO p 14 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU p 19 " --> pdb=" O ARG p 15 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL p 20 " --> pdb=" O LYS p 16 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP p 22 " --> pdb=" O ARG p 18 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU p 23 " --> pdb=" O LEU p 19 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE p 24 " --> pdb=" O VAL p 20 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG p 25 " --> pdb=" O VAL p 21 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 removed outlier: 3.839A pdb=" N ARG p 33 " --> pdb=" O LEU p 29 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE p 35 " --> pdb=" O GLU p 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU p 36 " --> pdb=" O ALA p 32 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR p 38 " --> pdb=" O ASN p 34 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR p 39 " --> pdb=" O ILE p 35 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 60 removed outlier: 4.816A pdb=" N TYR p 45 " --> pdb=" O LYS p 41 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE p 46 " --> pdb=" O ARG p 42 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL p 47 " --> pdb=" O GLY p 43 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA p 48 " --> pdb=" O ALA p 44 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS p 49 " --> pdb=" O TYR p 45 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL p 50 " --> pdb=" O PHE p 46 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU p 51 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLU p 52 " --> pdb=" O ALA p 48 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA p 56 " --> pdb=" O GLU p 52 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 24 removed outlier: 4.862A pdb=" N TYR q 18 " --> pdb=" O SER q 14 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA q 19 " --> pdb=" O GLU q 15 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY q 20 " --> pdb=" O LYS q 16 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU q 23 " --> pdb=" O ALA q 19 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY q 24 " --> pdb=" O GLY q 20 " (cutoff:3.500A) Processing helix chain 'q' and resid 35 through 47 removed outlier: 3.877A pdb=" N ASN q 41 " --> pdb=" O THR q 37 " (cutoff:3.500A) Processing helix chain 'q' and resid 89 through 96 removed outlier: 4.176A pdb=" N GLU q 93 " --> pdb=" O ILE q 89 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU q 95 " --> pdb=" O ALA q 91 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE q 96 " --> pdb=" O LEU q 92 " (cutoff:3.500A) Processing helix chain 's' and resid 14 through 22 removed outlier: 4.712A pdb=" N ARG s 19 " --> pdb=" O PRO s 15 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG s 20 " --> pdb=" O SER s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 50 removed outlier: 3.893A pdb=" N ASP s 45 " --> pdb=" O LEU s 41 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL s 47 " --> pdb=" O GLU s 43 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE s 48 " --> pdb=" O PHE s 44 " (cutoff:3.500A) Processing helix chain 's' and resid 110 through 115 Processing helix chain 'u' and resid 1 through 12 removed outlier: 4.554A pdb=" N LEU u 5 " --> pdb=" O MET u 1 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU u 7 " --> pdb=" O LYS u 3 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG u 9 " --> pdb=" O LEU u 5 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS u 10 " --> pdb=" O GLU u 6 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU u 11 " --> pdb=" O GLU u 7 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER u 12 " --> pdb=" O ALA u 8 " (cutoff:3.500A) Processing helix chain 'u' and resid 14 through 34 removed outlier: 4.049A pdb=" N LYS u 18 " --> pdb=" O VAL u 14 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL u 20 " --> pdb=" O LEU u 16 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU u 22 " --> pdb=" O LYS u 18 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS u 23 " --> pdb=" O LEU u 19 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU u 27 " --> pdb=" O LYS u 23 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU u 29 " --> pdb=" O ARG u 25 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU u 30 " --> pdb=" O GLU u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 41 through 67 removed outlier: 7.314A pdb=" N ILE u 45 " --> pdb=" O GLN u 41 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG u 46 " --> pdb=" O ASN u 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU u 48 " --> pdb=" O LYS u 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS u 49 " --> pdb=" O ILE u 45 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG u 50 " --> pdb=" O ARG u 46 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA u 53 " --> pdb=" O LYS u 49 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU u 55 " --> pdb=" O GLN u 51 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL u 58 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU u 59 " --> pdb=" O LEU u 55 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN u 60 " --> pdb=" O LEU u 56 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG u 63 " --> pdb=" O LEU u 59 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASN u 66 " --> pdb=" O LYS u 62 " (cutoff:3.500A) Processing helix chain 'v' and resid 16 through 27 Processing helix chain 'v' and resid 40 through 51 removed outlier: 3.906A pdb=" N GLY v 45 " --> pdb=" O PRO v 41 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN v 46 " --> pdb=" O ALA v 42 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU v 48 " --> pdb=" O ARG v 44 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL v 50 " --> pdb=" O ASN v 46 " (cutoff:3.500A) Processing helix chain 'w' and resid 59 through 71 removed outlier: 3.862A pdb=" N TYR w 63 " --> pdb=" O PHE w 59 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP w 65 " --> pdb=" O ARG w 61 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER w 66 " --> pdb=" O ARG w 62 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR w 67 " --> pdb=" O TYR w 63 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG w 68 " --> pdb=" O GLY w 64 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 24 removed outlier: 4.434A pdb=" N ALA x 18 " --> pdb=" O ALA x 14 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG x 19 " --> pdb=" O ARG x 15 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG x 20 " --> pdb=" O ARG x 16 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER x 21 " --> pdb=" O ASP x 17 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N HIS x 22 " --> pdb=" O ALA x 18 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS x 23 " --> pdb=" O ARG x 19 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA x 24 " --> pdb=" O ARG x 20 " (cutoff:3.500A) Processing helix chain 'z' and resid 8 through 16 removed outlier: 4.137A pdb=" N ARG z 12 " --> pdb=" O ASN z 8 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA z 13 " --> pdb=" O ARG z 9 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR z 15 " --> pdb=" O LYS z 11 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS z 16 " --> pdb=" O ARG z 12 " (cutoff:3.500A) Processing helix chain 'z' and resid 17 through 24 removed outlier: 4.352A pdb=" N ARG z 21 " --> pdb=" O GLY z 17 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR z 24 " --> pdb=" O ALA z 20 " (cutoff:3.500A) Processing helix chain 'z' and resid 25 through 37 removed outlier: 5.155A pdb=" N LYS z 29 " --> pdb=" O PRO z 25 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL z 30 " --> pdb=" O GLY z 26 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU z 31 " --> pdb=" O GLY z 27 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN z 36 " --> pdb=" O LYS z 32 " (cutoff:3.500A) Processing helix chain 'AA' and resid 6 through 12 removed outlier: 4.711A pdb=" N ALAAA 10 " --> pdb=" O THRAA 6 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYSAA 11 " --> pdb=" O HISAA 7 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYSAA 12 " --> pdb=" O LYSAA 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 6 through 12' Processing helix chain 'AA' and resid 37 through 45 removed outlier: 4.181A pdb=" N ILEAA 41 " --> pdb=" O SERAA 37 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYSAA 44 " --> pdb=" O GLUAA 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLYAA 45 " --> pdb=" O ILEAA 41 " (cutoff:3.500A) Processing helix chain 'AA' and resid 52 through 61 removed outlier: 3.560A pdb=" N GLUAA 56 " --> pdb=" O LYSAA 52 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARGAA 57 " --> pdb=" O PROAA 53 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEUAA 60 " --> pdb=" O GLUAA 56 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEUAA 61 " --> pdb=" O ARGAA 57 " (cutoff:3.500A) Processing helix chain 'CC' and resid 15 through 20 removed outlier: 7.234A pdb=" N GLYCC 19 " --> pdb=" O ILECC 15 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASNCC 20 " --> pdb=" O CYSCC 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 15 through 20' Processing helix chain 'EE' and resid 42 through 52 removed outlier: 3.645A pdb=" N LEUEE 50 " --> pdb=" O LEUEE 46 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASNEE 51 " --> pdb=" O LEUEE 47 " (cutoff:3.500A) Processing helix chain 'EE' and resid 102 through 114 removed outlier: 3.873A pdb=" N THREE 106 " --> pdb=" O GLYEE 102 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARGEE 107 " --> pdb=" O GLYEE 103 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALAEE 108 " --> pdb=" O GLUEE 104 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALAEE 112 " --> pdb=" O ALAEE 108 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALAEE 113 " --> pdb=" O LYSEE 109 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHEEE 114 " --> pdb=" O ILEEE 110 " (cutoff:3.500A) Processing helix chain 'EE' and resid 131 through 145 removed outlier: 4.503A pdb=" N GLNEE 141 " --> pdb=" O LEUEE 137 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYSEE 143 " --> pdb=" O ILEEE 139 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALAEE 144 " --> pdb=" O GLYEE 140 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHEEE 145 " --> pdb=" O GLNEE 141 " (cutoff:3.500A) Processing helix chain 'EE' and resid 155 through 163 removed outlier: 4.187A pdb=" N LEUEE 159 " --> pdb=" O ASPEE 155 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASPEE 160 " --> pdb=" O ARGEE 156 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N METEE 161 " --> pdb=" O TYREE 157 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VALEE 163 " --> pdb=" O LEUEE 159 " (cutoff:3.500A) Processing helix chain 'EE' and resid 181 through 224 removed outlier: 3.645A pdb=" N ARGEE 186 " --> pdb=" O SEREE 182 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLNEE 187 " --> pdb=" O ASPEE 183 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYSEE 188 " --> pdb=" O TYREE 184 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLUEE 189 " --> pdb=" O LEUEE 185 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLUEE 190 " --> pdb=" O ARGEE 186 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLUEE 191 " --> pdb=" O GLNEE 187 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARGEE 192 " --> pdb=" O LYSEE 188 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLNEE 193 " --> pdb=" O GLUEE 189 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N HISEE 194 " --> pdb=" O GLUEE 190 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLNEE 195 " --> pdb=" O GLUEE 191 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALAEE 196 " --> pdb=" O ARGEE 192 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLUEE 198 " --> pdb=" O HISEE 194 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYREE 199 " --> pdb=" O GLNEE 195 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLUEE 200 " --> pdb=" O ALAEE 196 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEUEE 201 " --> pdb=" O VALEE 197 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N METEE 202 " --> pdb=" O GLUEE 198 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N METEE 203 " --> pdb=" O TYREE 199 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARGEE 206 " --> pdb=" O METEE 202 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLUEE 207 " --> pdb=" O METEE 203 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEUEE 209 " --> pdb=" O GLUEE 205 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUEE 210 " --> pdb=" O ARGEE 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SEREE 211 " --> pdb=" O GLUEE 207 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALAEE 212 " --> pdb=" O ARGEE 208 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VALEE 213 " --> pdb=" O LEUEE 209 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLNEE 214 " --> pdb=" O GLUEE 210 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLUEE 215 " --> pdb=" O SEREE 211 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYSEE 216 " --> pdb=" O ALAEE 212 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARGEE 217 " --> pdb=" O VALEE 213 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLNEE 218 " --> pdb=" O GLNEE 214 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLNEE 219 " --> pdb=" O GLUEE 215 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAEE 220 " --> pdb=" O LYSEE 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASNEE 221 " --> pdb=" O ARGEE 217 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARGEE 222 " --> pdb=" O GLNEE 218 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEUEE 223 " --> pdb=" O GLNEE 219 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASPEE 224 " --> pdb=" O ALAEE 220 " (cutoff:3.500A) Processing helix chain 'EE' and resid 247 through 265 removed outlier: 3.790A pdb=" N LYSEE 251 " --> pdb=" O METEE 247 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARGEE 253 " --> pdb=" O GLYEE 249 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYSEE 254 " --> pdb=" O THREE 250 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEUEE 255 " --> pdb=" O LYSEE 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYREE 256 " --> pdb=" O GLNEE 252 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLNEE 257 " --> pdb=" O ARGEE 253 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALAEE 258 " --> pdb=" O LYSEE 254 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALAEE 259 " --> pdb=" O LEUEE 255 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYSEE 260 " --> pdb=" O TYREE 256 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SEREE 261 " --> pdb=" O GLNEE 257 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLUEE 263 " --> pdb=" O ALAEE 259 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYSEE 264 " --> pdb=" O LYSEE 260 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARGEE 265 " --> pdb=" O SEREE 261 " (cutoff:3.500A) Processing helix chain 'EE' and resid 334 through 343 removed outlier: 4.584A pdb=" N LEUEE 338 " --> pdb=" O GLYEE 334 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEUEE 339 " --> pdb=" O LYSEE 335 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N METEE 341 " --> pdb=" O SEREE 337 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILEEE 342 " --> pdb=" O LEUEE 338 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SEREE 343 " --> pdb=" O LEUEE 339 " (cutoff:3.500A) Processing helix chain 'EE' and resid 387 through 396 removed outlier: 4.378A pdb=" N VALEE 391 " --> pdb=" O GLUEE 387 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALAEE 393 " --> pdb=" O ARGEE 389 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N METEE 395 " --> pdb=" O VALEE 391 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLYEE 396 " --> pdb=" O LEUEE 392 " (cutoff:3.500A) Processing helix chain 'EE' and resid 413 through 425 removed outlier: 4.862A pdb=" N GLYEE 425 " --> pdb=" O LYSEE 421 " (cutoff:3.500A) Processing helix chain 'EE' and resid 441 through 454 removed outlier: 3.889A pdb=" N THREE 449 " --> pdb=" O ALAEE 445 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N METEE 450 " --> pdb=" O ALAEE 446 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N METEE 451 " --> pdb=" O LEUEE 447 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYSEE 452 " --> pdb=" O GLUEE 448 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SEREE 453 " --> pdb=" O THREE 449 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYREE 454 " --> pdb=" O METEE 450 " (cutoff:3.500A) Processing helix chain 'EE' and resid 465 through 471 removed outlier: 6.801A pdb=" N ASPEE 469 " --> pdb=" O LYSEE 465 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASNEE 470 " --> pdb=" O GLNEE 466 " (cutoff:3.500A) Processing helix chain 'EE' and resid 231 through 236 removed outlier: 6.176A pdb=" N SEREE 235 " --> pdb=" O SEREE 232 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.722A pdb=" N GLU A 58 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 74 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 17 through 28 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.424A pdb=" N THR D 48 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE D 31 " --> pdb=" O THR D 48 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 42 through 48 removed outlier: 3.758A pdb=" N ARG E 43 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS E 7 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG E 9 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU E 95 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'H' and resid 90 through 94 removed outlier: 4.451A pdb=" N VAL H 165 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR H 199 " --> pdb=" O VAL H 184 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'I' and resid 19 through 22 removed outlier: 6.156A pdb=" N GLU I 19 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG I 59 " --> pdb=" O ARG I 21 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG I 54 " --> pdb=" O HIS I 69 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU I 58 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA I 100 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL I 66 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL I 106 " --> pdb=" O VAL I 70 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'I' and resid 148 through 153 removed outlier: 3.791A pdb=" N GLY I 148 " --> pdb=" O PHE I 203 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE I 152 " --> pdb=" O LYS I 199 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL I 198 " --> pdb=" O ALA I 187 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA I 187 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA I 200 " --> pdb=" O GLY I 185 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY I 185 " --> pdb=" O ALA I 200 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'J' and resid 143 through 147 removed outlier: 3.508A pdb=" N GLY J 183 " --> pdb=" O ILE J 146 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'K' and resid 7 through 11 removed outlier: 3.986A pdb=" N LEU K 31 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU K 12 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'K' and resid 79 through 83 removed outlier: 4.168A pdb=" N ALA K 94 " --> pdb=" O ASP K 117 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASP K 117 " --> pdb=" O ALA K 94 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR K 120 " --> pdb=" O ILE K 101 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'K' and resid 28 through 35 Processing sheet with id= 12, first strand: chain 'L' and resid 39 through 44 removed outlier: 5.443A pdb=" N LYS L 39 " --> pdb=" O GLN L 64 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN L 64 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP L 62 " --> pdb=" O GLU L 41 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU L 43 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N PHE L 60 " --> pdb=" O LEU L 43 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE L 8 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR L 63 " --> pdb=" O VAL L 6 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL L 6 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL L 65 " --> pdb=" O TYR L 4 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR L 4 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG L 3 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'L' and resid 45 through 48 Processing sheet with id= 14, first strand: chain 'M' and resid 73 through 79 Processing sheet with id= 15, first strand: chain 'N' and resid 45 through 53 removed outlier: 7.131A pdb=" N ILE N 45 " --> pdb=" O LYS N 64 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS N 64 " --> pdb=" O ILE N 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY N 47 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL N 51 " --> pdb=" O TYR N 58 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'N' and resid 82 through 86 removed outlier: 7.368A pdb=" N ILE N 134 " --> pdb=" O ILE N 86 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.597A pdb=" N VAL O 14 " --> pdb=" O ARG O 66 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG O 16 " --> pdb=" O THR O 64 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR O 64 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS O 25 " --> pdb=" O PHE O 59 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'P' and resid 40 through 43 removed outlier: 3.792A pdb=" N THR P 41 " --> pdb=" O ILE P 32 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE P 32 " --> pdb=" O THR P 41 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA P 23 " --> pdb=" O ARG P 85 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP P 111 " --> pdb=" O VAL P 84 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Q' and resid 32 through 37 removed outlier: 4.665A pdb=" N SER Q 81 " --> pdb=" O CYS Q 37 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 39 through 44 removed outlier: 3.765A pdb=" N VAL Q 39 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS Q 54 " --> pdb=" O ILE Q 70 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.869A pdb=" N ARG U 18 " --> pdb=" O ALA U 7 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY U 37 " --> pdb=" O ILE U 19 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Y' and resid 59 through 64 removed outlier: 4.307A pdb=" N GLY Y 60 " --> pdb=" O PHE Y 163 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL Y 62 " --> pdb=" O ILE Y 161 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE Y 161 " --> pdb=" O VAL Y 62 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU Y 64 " --> pdb=" O GLY Y 159 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Y' and resid 73 through 77 Processing sheet with id= 24, first strand: chain 'Y' and resid 169 through 175 removed outlier: 4.736A pdb=" N GLY Y 169 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL Y 41 " --> pdb=" O VAL Y 175 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Z' and resid 35 through 38 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'Z' and resid 81 through 84 removed outlier: 4.052A pdb=" N ALA Z 81 " --> pdb=" O LEU Z 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU Z 94 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN Z 115 " --> pdb=" O VAL Z 79 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY Z 128 " --> pdb=" O GLN Z 116 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL Z 118 " --> pdb=" O GLY Z 128 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Z' and resid 163 through 166 removed outlier: 6.918A pdb=" N ILE Z 174 " --> pdb=" O GLN Z 166 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU Z 181 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Z' and resid 92 through 97 removed outlier: 4.301A pdb=" N GLU Z 101 " --> pdb=" O TYR Z 97 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'a' and resid 1 through 6 removed outlier: 7.694A pdb=" N MET a 1 " --> pdb=" O GLU a 200 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU a 200 " --> pdb=" O MET a 1 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU a 100 " --> pdb=" O VAL a 172 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL a 172 " --> pdb=" O GLU a 100 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.772A pdb=" N VAL a 9 " --> pdb=" O THR a 24 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'a' and resid 45 through 50 removed outlier: 4.899A pdb=" N ALA a 46 " --> pdb=" O GLU a 80 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU a 80 " --> pdb=" O ALA a 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN a 48 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU a 78 " --> pdb=" O GLN a 48 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG a 76 " --> pdb=" O GLY a 50 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'b' and resid 122 through 125 removed outlier: 4.043A pdb=" N MET b 194 " --> pdb=" O LEU b 123 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU b 125 " --> pdb=" O MET b 194 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU b 155 " --> pdb=" O ARG b 191 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL b 157 " --> pdb=" O VAL b 193 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR b 158 " --> pdb=" O LEU b 176 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'c' and resid 90 through 95 removed outlier: 6.913A pdb=" N LEU c 90 " --> pdb=" O GLN c 41 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN c 41 " --> pdb=" O LEU c 90 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG c 136 " --> pdb=" O MET c 155 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE c 157 " --> pdb=" O GLY c 134 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY c 134 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL c 159 " --> pdb=" O ASN c 132 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN c 132 " --> pdb=" O VAL c 159 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR c 161 " --> pdb=" O ASN c 130 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASN c 130 " --> pdb=" O THR c 161 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'd' and resid 83 through 88 Processing sheet with id= 35, first strand: chain 'd' and resid 102 through 106 removed outlier: 3.734A pdb=" N LEU d 103 " --> pdb=" O VAL d 115 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL d 115 " --> pdb=" O LEU d 103 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'e' and resid 26 through 29 removed outlier: 5.465A pdb=" N LEU e 26 " --> pdb=" O GLY e 114 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY e 114 " --> pdb=" O LEU e 26 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 12 through 17 removed outlier: 3.918A pdb=" N PHE g 51 " --> pdb=" O ARG g 12 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL g 14 " --> pdb=" O PHE g 51 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'h' and resid 5 through 9 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'h' and resid 37 through 42 removed outlier: 4.575A pdb=" N ASP h 37 " --> pdb=" O VAL h 61 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL h 61 " --> pdb=" O ASP h 37 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL h 58 " --> pdb=" O ILE h 86 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'i' and resid 80 through 83 Processing sheet with id= 41, first strand: chain 'j' and resid 32 through 37 removed outlier: 3.853A pdb=" N GLY j 33 " --> pdb=" O VAL j 132 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL j 132 " --> pdb=" O GLY j 33 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS j 128 " --> pdb=" O LEU j 37 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 64 through 67 removed outlier: 6.566A pdb=" N ARG j 67 " --> pdb=" O MET j 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET j 103 " --> pdb=" O ARG j 67 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'k' and resid 33 through 36 removed outlier: 4.691A pdb=" N LEU k 111 " --> pdb=" O LEU k 100 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU k 100 " --> pdb=" O LEU k 111 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR k 94 " --> pdb=" O VAL k 117 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'l' and resid 48 through 53 removed outlier: 6.528A pdb=" N TYR l 36 " --> pdb=" O PHE l 29 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU l 26 " --> pdb=" O PHE l 87 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL l 28 " --> pdb=" O ARG l 89 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'm' and resid 42 through 50 removed outlier: 3.738A pdb=" N GLU m 36 " --> pdb=" O ASP m 44 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG m 29 " --> pdb=" O ARG m 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL m 89 " --> pdb=" O SER m 31 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'm' and resid 64 through 69 removed outlier: 4.250A pdb=" N ARG m 64 " --> pdb=" O LEU m 78 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU m 78 " --> pdb=" O ARG m 64 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL m 66 " --> pdb=" O PHE m 76 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'o' and resid 16 through 22 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'p' and resid 2 through 8 removed outlier: 4.567A pdb=" N THR p 100 " --> pdb=" O GLY p 79 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY p 79 " --> pdb=" O THR p 100 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'q' and resid 25 through 29 Processing sheet with id= 50, first strand: chain 'r' and resid 11 through 15 removed outlier: 4.020A pdb=" N LYS r 21 " --> pdb=" O LEU r 14 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 's' and resid 4 through 7 removed outlier: 4.619A pdb=" N LYS s 36 " --> pdb=" O ALA s 7 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL s 37 " --> pdb=" O GLY s 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL s 86 " --> pdb=" O PRO s 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR s 29 " --> pdb=" O PHE s 88 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 's' and resid 58 through 61 Processing sheet with id= 53, first strand: chain 'v' and resid 2 through 9 removed outlier: 8.135A pdb=" N LEU v 53 " --> pdb=" O VAL v 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'w' and resid 13 through 18 removed outlier: 3.782A pdb=" N ILE w 14 " --> pdb=" O SER w 37 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS w 18 " --> pdb=" O VAL w 33 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL w 33 " --> pdb=" O CYS w 18 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'y' and resid 10 through 14 removed outlier: 5.108A pdb=" N CYS y 13 " --> pdb=" O ALA y 22 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BB' and resid 14 through 18 removed outlier: 6.669A pdb=" N VALBB 23 " --> pdb=" O GLNBB 36 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLNBB 34 " --> pdb=" O VALBB 25 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'EE' and resid 5 through 8 removed outlier: 3.670A pdb=" N ILEEE 5 " --> pdb=" O ILEEE 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILEEE 27 " --> pdb=" O ILEEE 5 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'EE' and resid 67 through 70 removed outlier: 4.132A pdb=" N ALAEE 148 " --> pdb=" O HISEE 119 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEUEE 150 " --> pdb=" O ILEEE 121 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALAEE 123 " --> pdb=" O LEUEE 150 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILEEE 152 " --> pdb=" O ALAEE 123 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASPEE 31 " --> pdb=" O GLYEE 147 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILEEE 33 " --> pdb=" O LEUEE 149 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VALEE 151 " --> pdb=" O ILEEE 33 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEUEE 35 " --> pdb=" O VALEE 151 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYSEE 165 " --> pdb=" O ARGEE 32 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'EE' and resid 297 through 300 removed outlier: 4.051A pdb=" N ILEEE 297 " --> pdb=" O ILEEE 319 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'EE' and resid 324 through 328 removed outlier: 4.827A pdb=" N ILEEE 474 " --> pdb=" O LYSEE 324 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYREE 476 " --> pdb=" O ALAEE 326 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'EE' and resid 356 through 360 removed outlier: 5.315A pdb=" N ASPEE 433 " --> pdb=" O PHEEE 360 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEUEE 430 " --> pdb=" O THREE 457 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N METEE 432 " --> pdb=" O ILEEE 459 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1454 hydrogen bonds 2484 hydrogen bond angles 0 basepair planarities 542 basepair parallelities 2054 stacking parallelities Total time for adding SS restraints: 180.05 Time building geometry restraints manager: 53.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 29260 1.33 - 1.48: 76036 1.48 - 1.63: 57413 1.63 - 1.77: 36 1.77 - 1.92: 249 Bond restraints: 162994 Sorted by residual: bond pdb=" C2' ANPEE 501 " pdb=" C3' ANPEE 501 " ideal model delta sigma weight residual 1.238 1.527 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C2' ANPEE 502 " pdb=" C3' ANPEE 502 " ideal model delta sigma weight residual 1.238 1.526 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C5 5MUDD 55 " pdb=" C6 5MUDD 55 " ideal model delta sigma weight residual 1.150 1.414 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" O3' G V1449A" pdb=" P C V1450 " ideal model delta sigma weight residual 1.607 1.420 0.187 1.50e-02 4.44e+03 1.56e+02 bond pdb=" C4 5MUDD 55 " pdb=" C5 5MUDD 55 " ideal model delta sigma weight residual 1.805 1.607 0.198 2.00e-02 2.50e+03 9.78e+01 ... (remaining 162989 not shown) Histogram of bond angle deviations from ideal: 67.18 - 84.57: 7 84.57 - 101.95: 3932 101.95 - 119.34: 162147 119.34 - 136.72: 76948 136.72 - 154.11: 17 Bond angle restraints: 243051 Sorted by residual: angle pdb=" O3' G V1449A" pdb=" P C V1450 " pdb=" O5' C V1450 " ideal model delta sigma weight residual 104.00 67.18 36.82 1.50e+00 4.44e-01 6.02e+02 angle pdb=" O3' C V 155 " pdb=" P U V 161 " pdb=" O5' U V 161 " ideal model delta sigma weight residual 104.00 69.77 34.23 1.50e+00 4.44e-01 5.21e+02 angle pdb=" C VAL d 11 " pdb=" N PRO d 12 " pdb=" CD PRO d 12 " ideal model delta sigma weight residual 125.00 72.92 52.08 4.10e+00 5.95e-02 1.61e+02 angle pdb=" C ARG Z 244 " pdb=" N PRO Z 245 " pdb=" CD PRO Z 245 " ideal model delta sigma weight residual 120.60 94.76 25.84 2.20e+00 2.07e-01 1.38e+02 angle pdb=" C ARG Z 244 " pdb=" N PRO Z 245 " pdb=" CA PRO Z 245 " ideal model delta sigma weight residual 127.00 154.11 -27.11 2.40e+00 1.74e-01 1.28e+02 ... (remaining 243046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 82440 35.95 - 71.90: 4571 71.90 - 107.85: 417 107.85 - 143.80: 79 143.80 - 179.75: 74 Dihedral angle restraints: 87581 sinusoidal: 68984 harmonic: 18597 Sorted by residual: dihedral pdb=" CA GLY i 34 " pdb=" C GLY i 34 " pdb=" N HIS i 35 " pdb=" CA HIS i 35 " ideal model delta harmonic sigma weight residual -180.00 -103.96 -76.04 0 5.00e+00 4.00e-02 2.31e+02 dihedral pdb=" CA LYS q 88 " pdb=" C LYS q 88 " pdb=" N ILE q 89 " pdb=" CA ILE q 89 " ideal model delta harmonic sigma weight residual -180.00 -108.73 -71.27 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA GLU d 40 " pdb=" C GLU d 40 " pdb=" N MET d 41 " pdb=" CA MET d 41 " ideal model delta harmonic sigma weight residual -180.00 -113.62 -66.38 0 5.00e+00 4.00e-02 1.76e+02 ... (remaining 87578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.427: 30653 0.427 - 0.854: 17 0.854 - 1.280: 0 1.280 - 1.707: 1 1.707 - 2.134: 1 Chirality restraints: 30672 Sorted by residual: chirality pdb=" P G V 921 " pdb=" OP1 G V 921 " pdb=" OP2 G V 921 " pdb=" O5' G V 921 " both_signs ideal model delta sigma weight residual True 2.41 0.28 2.13 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" P U V1061 " pdb=" OP1 U V1061 " pdb=" OP2 U V1061 " pdb=" O5' U V1061 " both_signs ideal model delta sigma weight residual True 2.41 0.97 1.44 2.00e-01 2.50e+01 5.19e+01 chirality pdb=" C3' U V 403 " pdb=" C4' U V 403 " pdb=" O3' U V 403 " pdb=" C2' U V 403 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 30669 not shown) Planarity restraints: 13687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MUDD 55 " 0.029 2.00e-02 2.50e+03 5.42e-01 6.62e+03 pdb=" C4' 5MUDD 55 " 0.419 2.00e-02 2.50e+03 pdb=" O4' 5MUDD 55 " 0.569 2.00e-02 2.50e+03 pdb=" C3' 5MUDD 55 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 5MUDD 55 " -0.524 2.00e-02 2.50e+03 pdb=" C2' 5MUDD 55 " -0.223 2.00e-02 2.50e+03 pdb=" O2' 5MUDD 55 " 0.879 2.00e-02 2.50e+03 pdb=" C1' 5MUDD 55 " 0.243 2.00e-02 2.50e+03 pdb=" N1 5MUDD 55 " -0.803 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MGDD 47 " -0.465 2.00e-02 2.50e+03 4.53e-01 4.61e+03 pdb=" C4' 7MGDD 47 " 0.365 2.00e-02 2.50e+03 pdb=" O4' 7MGDD 47 " 0.818 2.00e-02 2.50e+03 pdb=" C3' 7MGDD 47 " -0.454 2.00e-02 2.50e+03 pdb=" O3' 7MGDD 47 " 0.148 2.00e-02 2.50e+03 pdb=" C2' 7MGDD 47 " -0.451 2.00e-02 2.50e+03 pdb=" O2' 7MGDD 47 " 0.160 2.00e-02 2.50e+03 pdb=" C1' 7MGDD 47 " 0.365 2.00e-02 2.50e+03 pdb=" N9 7MGDD 47 " -0.485 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANPEE 502 " 0.370 2.00e-02 2.50e+03 4.46e-01 4.48e+03 pdb=" C2' ANPEE 502 " -0.434 2.00e-02 2.50e+03 pdb=" C3' ANPEE 502 " -0.432 2.00e-02 2.50e+03 pdb=" C4' ANPEE 502 " 0.364 2.00e-02 2.50e+03 pdb=" C5' ANPEE 502 " -0.481 2.00e-02 2.50e+03 pdb=" N9 ANPEE 502 " -0.483 2.00e-02 2.50e+03 pdb=" O2' ANPEE 502 " 0.140 2.00e-02 2.50e+03 pdb=" O3' ANPEE 502 " 0.155 2.00e-02 2.50e+03 pdb=" O4' ANPEE 502 " 0.801 2.00e-02 2.50e+03 ... (remaining 13684 not shown) Histogram of nonbonded interaction distances: 0.40 - 1.30: 18 1.30 - 2.20: 232 2.20 - 3.10: 93360 3.10 - 4.00: 408730 4.00 - 4.90: 711143 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1213483 Sorted by model distance: nonbonded pdb=" CD1 LEUEE 374 " pdb=" C ILEEE 402 " model vdw 0.401 3.690 nonbonded pdb=" CG LEUEE 374 " pdb=" O ILEEE 402 " model vdw 0.712 3.470 nonbonded pdb=" CD1 LEUEE 374 " pdb=" O ILEEE 402 " model vdw 0.915 3.460 nonbonded pdb=" N3 U V 271B" pdb=" N4 C V 404 " model vdw 1.046 2.560 nonbonded pdb=" O3' A V1084 " pdb=" OP1 G V1106 " model vdw 1.139 3.040 ... (remaining 1213478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4602 5.49 5 Mg 2 5.21 5 S 145 5.16 5 C 76424 2.51 5 N 28306 2.21 5 O 40834 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 20.430 Check model and map are aligned: 1.640 Convert atoms to be neutral: 0.960 Process input model: 444.090 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 475.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 0.289 162994 Z= 0.471 Angle : 1.260 52.080 243051 Z= 0.644 Chirality : 0.069 2.134 30672 Planarity : 0.013 0.542 13687 Dihedral : 18.680 179.754 75609 Min Nonbonded Distance : 0.401 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 1.91 % Allowed : 18.94 % Favored : 79.14 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.46 % Twisted General : 1.75 % 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: -5.90 (0.08), residues: 6424 helix: -4.16 (0.07), residues: 1605 sheet: -2.73 (0.15), residues: 882 loop : -4.35 (0.07), residues: 3937 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1636 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1503 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 34 residues processed: 1599 average time/residue: 1.4001 time to fit residues: 3794.3893 Evaluate side-chains 1155 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1121 time to evaluate : 6.520 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 6 residues processed: 34 average time/residue: 1.2419 time to fit residues: 82.4959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 917 optimal weight: 4.9990 chunk 823 optimal weight: 2.9990 chunk 456 optimal weight: 6.9990 chunk 281 optimal weight: 9.9990 chunk 555 optimal weight: 10.0000 chunk 439 optimal weight: 4.9990 chunk 851 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 chunk 517 optimal weight: 8.9990 chunk 633 optimal weight: 8.9990 chunk 986 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 HIS C 73 HIS D 23 ASN E 62 HIS E 69 ASN H 95 GLN H 113 HIS ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 HIS I 110 ASN J 77 ASN J 123 HIS J 129 ASN M 96 GLN M 122 HIS O 3 GLN O 89 ASN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN Q 99 HIS ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN T 46 HIS T 53 HIS U 65 GLN Y 139 ASN ** Y 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 44 ASN Z 186 HIS a 85 ASN b 40 GLN b 75 HIS c 123 ASN d 158 HIS ** f 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 ASN f 103 GLN ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 HIS ** k 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 ASN p 57 ASN ** p 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 102 HIS q 31 HIS r 68 HIS s 75 ASN t 80 HIS ** u 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 66 ASN v 19 GLN x 23 HIS y 20 ASN z 16 HIS AA 31 HIS ** AA 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 285 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 162994 Z= 0.288 Angle : 0.887 28.668 243051 Z= 0.450 Chirality : 0.048 1.977 30672 Planarity : 0.008 0.157 13687 Dihedral : 18.825 179.889 62563 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.95 % Allowed : 18.91 % Favored : 80.14 % Rotamer Outliers : 4.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.50 % Twisted General : 1.04 % 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: -5.37 (0.08), residues: 6424 helix: -3.40 (0.10), residues: 1603 sheet: -2.36 (0.16), residues: 862 loop : -4.17 (0.08), residues: 3959 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1210 time to evaluate : 6.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 261 outliers final: 148 residues processed: 1369 average time/residue: 1.4175 time to fit residues: 3359.2463 Evaluate side-chains 1227 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1079 time to evaluate : 6.720 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 148 outliers final: 1 residues processed: 148 average time/residue: 1.1371 time to fit residues: 328.5434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 548 optimal weight: 10.0000 chunk 306 optimal weight: 0.4980 chunk 820 optimal weight: 8.9990 chunk 671 optimal weight: 20.0000 chunk 272 optimal weight: 0.9990 chunk 987 optimal weight: 2.9990 chunk 1067 optimal weight: 0.9990 chunk 879 optimal weight: 8.9990 chunk 979 optimal weight: 0.0870 chunk 336 optimal weight: 6.9990 chunk 792 optimal weight: 9.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 HIS E 69 ASN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN J 45 GLN K 65 ASN N 78 GLN ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 GLN a 85 ASN d 158 HIS ** f 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN i 13 ASN j 57 HIS ** k 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 94 ASN o 80 GLN ** p 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 43 HIS v 19 GLN w 46 GLN x 43 HIS AA 35 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.133 162994 Z= 0.163 Angle : 0.736 27.304 243051 Z= 0.377 Chirality : 0.041 1.991 30672 Planarity : 0.006 0.157 13687 Dihedral : 18.242 179.486 62563 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.78 % Allowed : 16.39 % Favored : 82.83 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.62 % 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: -4.84 (0.09), residues: 6424 helix: -2.76 (0.11), residues: 1606 sheet: -2.09 (0.16), residues: 894 loop : -3.93 (0.08), residues: 3924 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1256 time to evaluate : 6.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 62 residues processed: 1383 average time/residue: 1.4647 time to fit residues: 3515.8442 Evaluate side-chains 1136 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1074 time to evaluate : 6.697 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 2 residues processed: 62 average time/residue: 1.2562 time to fit residues: 151.5680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 976 optimal weight: 7.9990 chunk 742 optimal weight: 6.9990 chunk 512 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 471 optimal weight: 9.9990 chunk 663 optimal weight: 10.0000 chunk 991 optimal weight: 9.9990 chunk 1049 optimal weight: 8.9990 chunk 518 optimal weight: 10.0000 chunk 939 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 HIS D 69 HIS E 69 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN J 45 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 GLN ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 GLN P 116 HIS Q 8 ASN R 101 GLN S 49 HIS T 62 GLN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 121 ASN ** c 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS ** f 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 38 HIS g 45 ASN ** i 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 84 GLN ** p 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 41 GLN v 52 HIS AA 31 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.136 162994 Z= 0.524 Angle : 1.088 29.317 243051 Z= 0.541 Chirality : 0.057 1.965 30672 Planarity : 0.009 0.141 13687 Dihedral : 19.109 179.526 62563 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 1.12 % Allowed : 20.98 % Favored : 77.90 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.18 % Twisted General : 0.99 % 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: -5.07 (0.09), residues: 6424 helix: -2.93 (0.10), residues: 1592 sheet: -2.18 (0.16), residues: 906 loop : -4.11 (0.08), residues: 3926 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1466 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1140 time to evaluate : 6.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 326 outliers final: 196 residues processed: 1342 average time/residue: 1.3499 time to fit residues: 3126.1592 Evaluate side-chains 1253 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1057 time to evaluate : 6.531 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 3 residues processed: 196 average time/residue: 1.0882 time to fit residues: 408.5824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 874 optimal weight: 0.8980 chunk 595 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 781 optimal weight: 7.9990 chunk 433 optimal weight: 7.9990 chunk 895 optimal weight: 2.9990 chunk 725 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 536 optimal weight: 10.0000 chunk 942 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN K 130 ASN N 78 GLN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 112 GLN b 40 GLN c 41 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS f 103 GLN i 70 GLN ** k 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 16 HIS AA 33 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 162994 Z= 0.207 Angle : 0.787 27.543 243051 Z= 0.401 Chirality : 0.044 1.980 30672 Planarity : 0.007 0.150 13687 Dihedral : 18.375 179.414 62563 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.75 % Allowed : 17.05 % Favored : 82.21 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.58 % 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: -4.69 (0.09), residues: 6424 helix: -2.50 (0.11), residues: 1596 sheet: -2.04 (0.17), residues: 831 loop : -3.86 (0.08), residues: 3997 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1119 time to evaluate : 6.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 72 residues processed: 1228 average time/residue: 1.4266 time to fit residues: 3019.4551 Evaluate side-chains 1112 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1040 time to evaluate : 6.721 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 3 residues processed: 72 average time/residue: 1.1872 time to fit residues: 167.9727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 353 optimal weight: 9.9990 chunk 945 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 616 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 1050 optimal weight: 2.9990 chunk 872 optimal weight: 5.9990 chunk 486 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 347 optimal weight: 0.8980 chunk 551 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN J 45 GLN K 130 ASN L 64 GLN N 78 GLN P 99 GLN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS ** f 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 123 HIS ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 57 GLN w 46 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.144 162994 Z= 0.301 Angle : 0.844 27.827 243051 Z= 0.428 Chirality : 0.046 1.976 30672 Planarity : 0.007 0.149 13687 Dihedral : 18.422 179.652 62563 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.79 % Allowed : 19.44 % Favored : 79.76 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.91 % Twisted General : 0.68 % 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: -4.65 (0.09), residues: 6424 helix: -2.41 (0.11), residues: 1604 sheet: -1.89 (0.17), residues: 902 loop : -3.93 (0.08), residues: 3918 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1081 time to evaluate : 6.784 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 outliers start: 170 outliers final: 101 residues processed: 1182 average time/residue: 1.3860 time to fit residues: 2815.6124 Evaluate side-chains 1144 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1043 time to evaluate : 6.863 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 2 residues processed: 101 average time/residue: 1.1269 time to fit residues: 219.6704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 1013 optimal weight: 0.0370 chunk 118 optimal weight: 10.0000 chunk 598 optimal weight: 9.9990 chunk 767 optimal weight: 20.0000 chunk 594 optimal weight: 30.0000 chunk 884 optimal weight: 2.9990 chunk 586 optimal weight: 10.0000 chunk 1046 optimal weight: 6.9990 chunk 655 optimal weight: 10.0000 chunk 638 optimal weight: 10.0000 chunk 483 optimal weight: 10.0000 overall best weight: 6.0068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 HIS E 69 ASN H 224 GLN J 45 GLN N 78 GLN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 GLN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 115 GLN ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS ** f 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 123 HIS ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.503 162994 Z= 0.388 Angle : 0.932 49.049 243051 Z= 0.468 Chirality : 0.050 1.972 30672 Planarity : 0.008 0.163 13687 Dihedral : 18.617 179.983 62563 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.78 % Allowed : 20.59 % Favored : 78.63 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.55 % Twisted General : 0.73 % 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: -4.73 (0.09), residues: 6424 helix: -2.48 (0.11), residues: 1603 sheet: -2.05 (0.17), residues: 899 loop : -3.94 (0.08), residues: 3922 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1071 time to evaluate : 6.554 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 outliers start: 158 outliers final: 76 residues processed: 1176 average time/residue: 1.4046 time to fit residues: 2847.0149 Evaluate side-chains 1110 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1034 time to evaluate : 6.721 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 2 residues processed: 76 average time/residue: 1.2154 time to fit residues: 184.6571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 647 optimal weight: 10.0000 chunk 418 optimal weight: 10.0000 chunk 625 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 665 optimal weight: 10.0000 chunk 713 optimal weight: 0.8980 chunk 517 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 822 optimal weight: 30.0000 overall best weight: 7.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN H 224 GLN J 45 GLN K 130 ASN M 97 GLN N 78 GLN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 115 GLN ** c 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS ** f 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 HIS ** i 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 46 HIS ** AA 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.568 162994 Z= 0.469 Angle : 0.972 73.900 243051 Z= 0.485 Chirality : 0.051 1.969 30672 Planarity : 0.008 0.224 13687 Dihedral : 18.618 179.952 62563 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.86 % Allowed : 20.50 % Favored : 78.64 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.23 % Twisted General : 0.76 % 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: -4.75 (0.09), residues: 6424 helix: -2.51 (0.11), residues: 1611 sheet: -2.04 (0.17), residues: 896 loop : -3.95 (0.08), residues: 3917 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1051 time to evaluate : 6.793 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 outliers start: 108 outliers final: 79 residues processed: 1100 average time/residue: 1.4115 time to fit residues: 2653.3173 Evaluate side-chains 1111 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1032 time to evaluate : 6.482 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 2 residues processed: 79 average time/residue: 1.2349 time to fit residues: 183.6617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 952 optimal weight: 8.9990 chunk 1002 optimal weight: 0.9990 chunk 914 optimal weight: 0.9990 chunk 975 optimal weight: 20.0000 chunk 587 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 765 optimal weight: 4.9990 chunk 299 optimal weight: 0.0060 chunk 881 optimal weight: 1.9990 chunk 922 optimal weight: 1.9990 chunk 972 optimal weight: 0.6980 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 HIS E 69 ASN J 45 GLN K 130 ASN N 78 GLN ** P 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 115 GLN ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS ** f 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 34 HIS ** p 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.995 162994 Z= 0.346 Angle : 0.977 106.089 243051 Z= 0.487 Chirality : 0.048 1.973 30672 Planarity : 0.008 0.225 13687 Dihedral : 18.618 179.978 62563 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.83 % Allowed : 20.52 % Favored : 78.66 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.87 % Twisted General : 0.76 % 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: -4.73 (0.09), residues: 6424 helix: -2.47 (0.11), residues: 1603 sheet: -2.05 (0.17), residues: 896 loop : -3.94 (0.08), residues: 3925 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1038 time to evaluate : 6.662 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 outliers start: 49 outliers final: 37 residues processed: 1060 average time/residue: 1.4006 time to fit residues: 2547.2643 Evaluate side-chains 1058 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1021 time to evaluate : 6.715 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 2 residues processed: 37 average time/residue: 1.1446 time to fit residues: 87.2525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 640 optimal weight: 10.0000 chunk 1031 optimal weight: 20.0000 chunk 629 optimal weight: 10.0000 chunk 489 optimal weight: 30.0000 chunk 717 optimal weight: 0.0470 chunk 1081 optimal weight: 1.9990 chunk 995 optimal weight: 2.9990 chunk 861 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 665 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 overall best weight: 4.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 ASN H 94 ASN ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN N 78 GLN ** P 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 115 GLN ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS ** f 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.969 162994 Z= 0.373 Angle : 0.985 87.827 243051 Z= 0.492 Chirality : 0.049 1.975 30672 Planarity : 0.008 0.249 13687 Dihedral : 18.621 179.943 62563 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.87 % Allowed : 20.47 % Favored : 78.66 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.50 % Twisted General : 0.76 % 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: -4.73 (0.09), residues: 6424 helix: -2.47 (0.11), residues: 1603 sheet: -2.04 (0.17), residues: 896 loop : -3.95 (0.08), residues: 3925 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12848 Ramachandran restraints generated. 6424 Oldfield, 0 Emsley, 6424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1025 time to evaluate : 6.700 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 outliers start: 22 outliers final: 19 residues processed: 1032 average time/residue: 1.4215 time to fit residues: 2501.4770 Evaluate side-chains 1040 residues out of total 5408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1021 time to evaluate : 6.691 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 1.4846 time to fit residues: 59.8786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 684 optimal weight: 9.9990 chunk 917 optimal weight: 20.0000 chunk 263 optimal weight: 9.9990 chunk 794 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 862 optimal weight: 2.9990 chunk 361 optimal weight: 8.9990 chunk 886 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 ASN ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN N 78 GLN ** P 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 115 GLN ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS ** f 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.163905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136293 restraints weight = 270840.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134628 restraints weight = 213589.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135968 restraints weight = 178707.620| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3711 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3711 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.969 162994 Z= 0.402 Angle : 0.990 87.817 243051 Z= 0.497 Chirality : 0.049 1.975 30672 Planarity : 0.008 0.249 13687 Dihedral : 18.621 179.943 62563 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.87 % Allowed : 20.47 % Favored : 78.66 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.50 % Twisted General : 0.76 % 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: -4.73 (0.09), residues: 6424 helix: -2.47 (0.11), residues: 1603 sheet: -2.04 (0.17), residues: 896 loop : -3.95 (0.08), residues: 3925 =============================================================================== Job complete usr+sys time: 40051.05 seconds wall clock time: 688 minutes 16.56 seconds (41296.56 seconds total)