Starting phenix.real_space_refine on Sun Dec 10 01:00:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp4_11335/12_2023/6zp4_11335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp4_11335/12_2023/6zp4_11335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp4_11335/12_2023/6zp4_11335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp4_11335/12_2023/6zp4_11335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp4_11335/12_2023/6zp4_11335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp4_11335/12_2023/6zp4_11335_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 1788 5.49 5 Mg 1 5.21 5 S 377 5.16 5 C 67199 2.51 5 N 21464 2.21 5 O 26951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 13": "OE1" <-> "OE2" Residue "a GLU 213": "OE1" <-> "OE2" Residue "p GLU 122": "OE1" <-> "OE2" Residue "p PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 175": "OE1" <-> "OE2" Residue "d ARG 68": "NH1" <-> "NH2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 92": "OE1" <-> "OE2" Residue "d GLU 146": "OE1" <-> "OE2" Residue "q GLU 97": "OE1" <-> "OE2" Residue "q ARG 198": "NH1" <-> "NH2" Residue "q ARG 200": "NH1" <-> "NH2" Residue "q PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 252": "NH1" <-> "NH2" Residue "W ARG 2": "NH1" <-> "NH2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "r GLU 17": "OE1" <-> "OE2" Residue "r TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 91": "OE1" <-> "OE2" Residue "r GLU 165": "OE1" <-> "OE2" Residue "r ARG 170": "NH1" <-> "NH2" Residue "r GLU 208": "OE1" <-> "OE2" Residue "r GLU 219": "OE1" <-> "OE2" Residue "s GLU 50": "OE1" <-> "OE2" Residue "t GLU 163": "OE1" <-> "OE2" Residue "t GLU 194": "OE1" <-> "OE2" Residue "c GLU 89": "OE1" <-> "OE2" Residue "c ARG 162": "NH1" <-> "NH2" Residue "n TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 52": "OE1" <-> "OE2" Residue "y GLU 64": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "w GLU 37": "OE1" <-> "OE2" Residue "w GLU 75": "OE1" <-> "OE2" Residue "b GLU 31": "OE1" <-> "OE2" Residue "b ARG 54": "NH1" <-> "NH2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b ARG 116": "NH1" <-> "NH2" Residue "b GLU 128": "OE1" <-> "OE2" Residue "b ARG 178": "NH1" <-> "NH2" Residue "e GLU 43": "OE1" <-> "OE2" Residue "e ARG 55": "NH1" <-> "NH2" Residue "e GLU 176": "OE1" <-> "OE2" Residue "u GLU 60": "OE1" <-> "OE2" Residue "u GLU 74": "OE1" <-> "OE2" Residue "u GLU 88": "OE1" <-> "OE2" Residue "v ARG 36": "NH1" <-> "NH2" Residue "v GLU 37": "OE1" <-> "OE2" Residue "v GLU 58": "OE1" <-> "OE2" Residue "v GLU 87": "OE1" <-> "OE2" Residue "v GLU 117": "OE1" <-> "OE2" Residue "o GLU 31": "OE1" <-> "OE2" Residue "o GLU 66": "OE1" <-> "OE2" Residue "o PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 71": "NH1" <-> "NH2" Residue "g ARG 125": "NH1" <-> "NH2" Residue "k ARG 14": "NH1" <-> "NH2" Residue "k GLU 61": "OE1" <-> "OE2" Residue "k GLU 109": "OE1" <-> "OE2" Residue "k GLU 112": "OE1" <-> "OE2" Residue "x GLU 13": "OE1" <-> "OE2" Residue "x GLU 32": "OE1" <-> "OE2" Residue "x GLU 44": "OE1" <-> "OE2" Residue "h ARG 19": "NH1" <-> "NH2" Residue "h GLU 45": "OE1" <-> "OE2" Residue "h GLU 107": "OE1" <-> "OE2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "S ARG 66": "NH1" <-> "NH2" Residue "S ARG 67": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "U ARG 116": "NH1" <-> "NH2" Residue "U GLU 120": "OE1" <-> "OE2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "V ARG 100": "NH1" <-> "NH2" Residue "V GLU 145": "OE1" <-> "OE2" Residue "V GLU 262": "OE1" <-> "OE2" Residue "i ARG 104": "NH1" <-> "NH2" Residue "i ARG 121": "NH1" <-> "NH2" Residue "i ARG 146": "NH1" <-> "NH2" Residue "i ARG 150": "NH1" <-> "NH2" Residue "j ARG 11": "NH1" <-> "NH2" Residue "j GLU 96": "OE1" <-> "OE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B GLU 545": "OE1" <-> "OE2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C GLU 829": "OE1" <-> "OE2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C GLU 861": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H ASP 74": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H GLU 200": "OE1" <-> "OE2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H GLU 252": "OE1" <-> "OE2" Residue "H GLU 284": "OE1" <-> "OE2" Residue "H GLU 349": "OE1" <-> "OE2" Residue "K GLU 24": "OE1" <-> "OE2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K GLU 193": "OE1" <-> "OE2" Residue "L GLU 209": "OE1" <-> "OE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "L GLU 245": "OE1" <-> "OE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L GLU 384": "OE1" <-> "OE2" Residue "L GLU 392": "OE1" <-> "OE2" Residue "L GLU 410": "OE1" <-> "OE2" Residue "L GLU 483": "OE1" <-> "OE2" Residue "L PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 551": "OE1" <-> "OE2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "M GLU 194": "OE1" <-> "OE2" Residue "M ARG 206": "NH1" <-> "NH2" Residue "M GLU 271": "OE1" <-> "OE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M GLU 291": "OE1" <-> "OE2" Residue "M GLU 309": "OE1" <-> "OE2" Residue "M ARG 330": "NH1" <-> "NH2" Residue "M ARG 340": "NH1" <-> "NH2" Residue "N ARG 26": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 163": "OE1" <-> "OE2" Residue "N ARG 183": "NH1" <-> "NH2" Residue "N GLU 189": "OE1" <-> "OE2" Residue "N ARG 218": "NH1" <-> "NH2" Residue "N ARG 271": "NH1" <-> "NH2" Residue "N GLU 315": "OE1" <-> "OE2" Residue "N ARG 329": "NH1" <-> "NH2" Residue "N GLU 352": "OE1" <-> "OE2" Residue "N ARG 362": "NH1" <-> "NH2" Residue "N ARG 402": "NH1" <-> "NH2" Residue "N ARG 434": "NH1" <-> "NH2" Residue "N TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 462": "NH1" <-> "NH2" Residue "N GLU 475": "OE1" <-> "OE2" Residue "4 ARG 200": "NH1" <-> "NH2" Residue "4 ARG 211": "NH1" <-> "NH2" Residue "4 ARG 261": "NH1" <-> "NH2" Residue "4 ARG 285": "NH1" <-> "NH2" Residue "4 ARG 308": "NH1" <-> "NH2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 42": "OE1" <-> "OE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 74": "NH1" <-> "NH2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "O GLU 169": "OE1" <-> "OE2" Residue "O ARG 172": "NH1" <-> "NH2" Residue "Y GLU 74": "OE1" <-> "OE2" Residue "Z ARG 34": "NH1" <-> "NH2" Residue "J GLU 159": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 117784 Number of models: 1 Model: "" Number of chains: 59 Chain: "a" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "p" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "d" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "Q" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "q" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2031 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 14, 'TRANS': 240} Chain: "W" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "r" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1794 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "s" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1399 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 3 Chain: "t" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 1 Chain: "c" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "n" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1119 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 1 Chain: "m" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "z" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 999 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "R" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "T" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 354 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Chain: "2" Number of atoms: 36718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1721, 36718 Inner-chain residues flagged as termini: ['pdbres=" U 2 140 "', 'pdbres=" U 2 287 "', 'pdbres=" G 2 330 "', 'pdbres=" C 2 746 "', 'pdbres=" C 2 791 "', 'pdbres=" G 2 841 "', 'pdbres=" G 21424 "', 'pdbres=" A 21438 "', 'pdbres=" G 21771 "'] Classifications: {'RNA': 1721} Modifications used: {'5*END': 10, 'rna2p_pur': 139, 'rna2p_pyr': 119, 'rna3p_pur': 772, 'rna3p_pyr': 691} Link IDs: {'rna2p': 257, 'rna3p': 1463} Chain: "w" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1011 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "b" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1745 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "e" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "u" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "v" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "o" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 980 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "g" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1100 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "k" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1162 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "x" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1094 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "h" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 780 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 557 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "S" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "l" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 450 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "U" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "V" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2314 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 2 Chain: "i" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 939 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "j" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "G" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 712 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "I" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 1497 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 965 Unresolved non-hydrogen angles: 1241 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 21, 'TYR:plan': 10, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 11, 'PHE:plan': 18, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 570 Chain: "B" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 2966 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 509} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1526 Unresolved non-hydrogen angles: 1965 Unresolved non-hydrogen dihedrals: 1337 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 30, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 16, 'HIS:plan': 13, 'PHE:plan': 26, 'GLU:plan': 23, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 886 Chain: "A" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5380 Classifications: {'peptide': 692} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 454 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 22, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 220 Chain: "C" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5110 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 614} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3437 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 404} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2090 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain: "H" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2413 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 2 Chain: "K" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 3, 'TRANS': 210} Chain: "L" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3111 Classifications: {'peptide': 372} Link IDs: {'CIS': 5, 'PTRANS': 11, 'TRANS': 355} Chain: "M" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3617 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 19, 'TRANS': 427} Chain breaks: 2 Chain: "X" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 390 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "1" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1603 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 2, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "4" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1080 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 57 Chain: "O" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2138 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 9, 'TRANS': 286} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 138 Chain: "Y" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 2156 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 315} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1043 Unresolved non-hydrogen angles: 1328 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 133 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 15, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 8, 'GLU:plan': 23, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 444 Chain: "Z" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 106} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "J" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 31} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5272 SG CYS Q 23 83.819 186.775 114.025 1.00 17.83 S ATOM 5293 SG CYS Q 26 83.019 185.503 110.136 1.00 13.24 S ATOM 5676 SG CYS Q 74 85.835 183.491 112.331 1.00 17.62 S ATOM 5695 SG CYS Q 77 86.548 186.892 111.195 1.00 23.96 S ATOM 69956 SG CYS U 121 186.707 174.337 39.426 1.00 91.35 S ATOM 69992 SG CYS U 126 185.861 172.127 43.264 1.00100.85 S ATOM 70110 SG CYS U 141 183.623 172.368 40.047 1.00 66.64 S ATOM 70129 SG CYS U 144 183.884 175.621 41.726 1.00 74.70 S ATOM A09AI SG CYS 4 284 86.356 178.090 34.923 1.00 75.03 S ATOM A09ER SG CYS 4 302 86.262 182.093 34.946 1.00 82.38 S ATOM A09FD SG CYS 4 305 83.572 178.866 32.733 1.00 91.23 S Residues with excluded nonbonded symmetry interactions: 73 residue: pdb=" O5' A 1 1 " occ=0.00 ... (17 atoms not shown) pdb=" C4 A 1 1 " occ=0.00 residue: pdb=" P G 1 2 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 2 " occ=0.00 residue: pdb=" P C 1 3 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 1 3 " occ=0.00 residue: pdb=" P A 1 4 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 1 4 " occ=0.00 residue: pdb=" P G 1 5 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 5 " occ=0.00 residue: pdb=" P A 1 6 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 1 6 " occ=0.00 residue: pdb=" P G 1 7 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 7 " occ=0.00 residue: pdb=" P U 1 8 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U 1 8 " occ=0.00 residue: pdb=" P G 1 10 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 10 " occ=0.00 residue: pdb=" P C 1 11 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 1 11 " occ=0.00 residue: pdb=" P G 1 12 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 12 " occ=0.00 residue: pdb=" P C 1 13 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 1 13 " occ=0.00 ... (remaining 61 not shown) Time building chain proxies: 44.61, per 1000 atoms: 0.38 Number of scatterers: 117784 At special positions: 0 Unit cell: (227.685, 284.871, 312.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 377 16.00 P 1788 15.00 Mg 1 11.99 O 26951 8.00 N 21464 7.00 C 67199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.25 Conformation dependent library (CDL) restraints added in 11.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 284 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 302 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 26 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 77 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 74 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 23 " pdb=" ZN U 500 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 126 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 141 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 144 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 121 " Number of angles added : 12 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19620 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 346 helices and 111 sheets defined 47.4% alpha, 16.1% beta 508 base pairs and 970 stacking pairs defined. Time for finding SS restraints: 70.38 Creating SS restraints... Processing helix chain 'a' and resid 11 through 22 Processing helix chain 'a' and resid 34 through 39 removed outlier: 4.183A pdb=" N ILE a 38 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR a 39 " --> pdb=" O GLU a 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 34 through 39' Processing helix chain 'a' and resid 50 through 68 removed outlier: 4.151A pdb=" N ILE a 68 " --> pdb=" O ALA a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 95 removed outlier: 3.753A pdb=" N GLN a 84 " --> pdb=" O ARG a 80 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG a 85 " --> pdb=" O ASN a 81 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ALA a 86 " --> pdb=" O THR a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 131 removed outlier: 3.716A pdb=" N HIS a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 141 removed outlier: 4.010A pdb=" N SER a 138 " --> pdb=" O LEU a 134 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR a 139 " --> pdb=" O THR a 135 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN a 141 " --> pdb=" O ALA a 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 187 Processing helix chain 'a' and resid 199 through 204 removed outlier: 3.979A pdb=" N PHE a 203 " --> pdb=" O PRO a 199 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR a 204 " --> pdb=" O ASP a 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 199 through 204' Processing helix chain 'a' and resid 206 through 216 removed outlier: 4.616A pdb=" N GLN a 215 " --> pdb=" O GLU a 211 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA a 216 " --> pdb=" O LYS a 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 75 removed outlier: 3.760A pdb=" N ASP a 73 " --> pdb=" O ASN a 70 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL a 74 " --> pdb=" O PRO a 71 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER a 75 " --> pdb=" O ALA a 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 70 through 75' Processing helix chain 'p' and resid 23 through 29 removed outlier: 4.838A pdb=" N LYS p 27 " --> pdb=" O ASP p 23 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS p 28 " --> pdb=" O PRO p 24 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP p 29 " --> pdb=" O PHE p 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 23 through 29' Processing helix chain 'p' and resid 57 through 64 removed outlier: 3.549A pdb=" N GLY p 61 " --> pdb=" O ILE p 57 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS p 63 " --> pdb=" O SER p 59 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLY p 64 " --> pdb=" O ASP p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 76 removed outlier: 4.384A pdb=" N ASN p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 106 through 115 removed outlier: 3.628A pdb=" N MET p 113 " --> pdb=" O LYS p 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL p 114 " --> pdb=" O MET p 110 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS p 115 " --> pdb=" O CYS p 111 " (cutoff:3.500A) Processing helix chain 'p' and resid 157 through 179 removed outlier: 3.807A pdb=" N VAL p 176 " --> pdb=" O MET p 172 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR p 178 " --> pdb=" O ARG p 174 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASN p 179 " --> pdb=" O GLU p 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 180 through 191 Proline residue: p 190 - end of helix Processing helix chain 'p' and resid 192 through 203 removed outlier: 3.942A pdb=" N GLN p 202 " --> pdb=" O GLU p 198 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N SER p 203 " --> pdb=" O LYS p 199 " (cutoff:3.500A) Processing helix chain 'p' and resid 224 through 233 removed outlier: 3.529A pdb=" N LEU p 228 " --> pdb=" O GLU p 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 removed outlier: 4.151A pdb=" N ASP d 72 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N MET d 73 " --> pdb=" O LEU d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 85 removed outlier: 4.106A pdb=" N ILE d 81 " --> pdb=" O SER d 77 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE d 84 " --> pdb=" O GLU d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 98 Processing helix chain 'd' and resid 146 through 162 removed outlier: 3.775A pdb=" N ILE d 162 " --> pdb=" O ALA d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 207 through 218 removed outlier: 3.681A pdb=" N LEU d 213 " --> pdb=" O VAL d 209 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY d 218 " --> pdb=" O LEU d 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 250 removed outlier: 3.582A pdb=" N LYS d 246 " --> pdb=" O ASP d 242 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR d 247 " --> pdb=" O ALA d 243 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER d 249 " --> pdb=" O SER d 245 " (cutoff:3.500A) Processing helix chain 'd' and resid 252 through 257 removed outlier: 3.951A pdb=" N TRP d 256 " --> pdb=" O THR d 252 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LYS d 257 " --> pdb=" O PRO d 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 252 through 257' Processing helix chain 'd' and resid 264 through 270 removed outlier: 4.051A pdb=" N THR d 270 " --> pdb=" O TYR d 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 57 removed outlier: 5.372A pdb=" N ARG Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASP Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 82 Processing helix chain 'Q' and resid 88 through 94 removed outlier: 4.514A pdb=" N LYS Q 93 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP Q 94 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) Processing helix chain 'q' and resid 43 through 49 Processing helix chain 'q' and resid 57 through 68 removed outlier: 3.555A pdb=" N VAL q 61 " --> pdb=" O THR q 57 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN q 67 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG q 68 " --> pdb=" O ILE q 64 " (cutoff:3.500A) Processing helix chain 'q' and resid 115 through 122 removed outlier: 4.191A pdb=" N LYS q 120 " --> pdb=" O PRO q 116 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR q 121 " --> pdb=" O GLU q 117 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS q 122 " --> pdb=" O GLU q 118 " (cutoff:3.500A) Processing helix chain 'q' and resid 221 through 226 removed outlier: 3.954A pdb=" N ILE q 225 " --> pdb=" O ARG q 221 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE q 226 " --> pdb=" O LEU q 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 221 through 226' Processing helix chain 'q' and resid 247 through 256 Processing helix chain 'W' and resid 2 through 24 removed outlier: 3.628A pdb=" N ARG W 23 " --> pdb=" O LYS W 19 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER W 24 " --> pdb=" O MET W 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 29 removed outlier: 4.082A pdb=" N LEU r 24 " --> pdb=" O ASP r 20 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR r 26 " --> pdb=" O ARG r 22 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE r 27 " --> pdb=" O LYS r 23 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU r 29 " --> pdb=" O ARG r 25 " (cutoff:3.500A) Processing helix chain 'r' and resid 137 through 146 Processing helix chain 'r' and resid 152 through 157 removed outlier: 4.572A pdb=" N TYR r 156 " --> pdb=" O ASP r 152 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL r 157 " --> pdb=" O VAL r 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 152 through 157' Processing helix chain 'r' and resid 181 through 222 removed outlier: 4.558A pdb=" N GLU r 222 " --> pdb=" O LYS r 218 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 32 removed outlier: 4.385A pdb=" N GLY s 22 " --> pdb=" O GLU s 18 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE s 23 " --> pdb=" O PHE s 19 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU s 31 " --> pdb=" O LEU s 27 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N MET s 32 " --> pdb=" O LEU s 28 " (cutoff:3.500A) Processing helix chain 's' and resid 39 through 44 removed outlier: 4.480A pdb=" N LEU s 43 " --> pdb=" O GLN s 39 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN s 44 " --> pdb=" O LEU s 40 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 39 through 44' Processing helix chain 's' and resid 66 through 76 removed outlier: 4.377A pdb=" N LYS s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE s 75 " --> pdb=" O SER s 71 " (cutoff:3.500A) Processing helix chain 's' and resid 77 through 88 removed outlier: 4.948A pdb=" N SER s 88 " --> pdb=" O GLU s 84 " (cutoff:3.500A) Processing helix chain 's' and resid 121 through 135 removed outlier: 3.938A pdb=" N VAL s 134 " --> pdb=" O LEU s 130 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE s 135 " --> pdb=" O GLU s 131 " (cutoff:3.500A) Processing helix chain 's' and resid 159 through 167 removed outlier: 4.163A pdb=" N GLN s 163 " --> pdb=" O ASP s 159 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASN s 164 " --> pdb=" O LYS s 160 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN s 165 " --> pdb=" O ALA s 161 " (cutoff:3.500A) Processing helix chain 's' and resid 169 through 181 Processing helix chain 't' and resid 87 through 94 removed outlier: 4.472A pdb=" N VAL t 91 " --> pdb=" O ASN t 87 " (cutoff:3.500A) Processing helix chain 't' and resid 106 through 117 Processing helix chain 't' and resid 130 through 138 removed outlier: 3.710A pdb=" N GLU t 134 " --> pdb=" O THR t 130 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE t 136 " --> pdb=" O GLU t 132 " (cutoff:3.500A) Processing helix chain 't' and resid 142 through 157 removed outlier: 3.954A pdb=" N LYS t 154 " --> pdb=" O ASP t 150 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN t 155 " --> pdb=" O GLU t 151 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA t 156 " --> pdb=" O ARG t 152 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS t 157 " --> pdb=" O LYS t 153 " (cutoff:3.500A) Processing helix chain 't' and resid 159 through 169 removed outlier: 3.874A pdb=" N GLN t 167 " --> pdb=" O GLU t 163 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN t 168 " --> pdb=" O GLU t 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY t 169 " --> pdb=" O GLN t 165 " (cutoff:3.500A) Processing helix chain 't' and resid 192 through 206 removed outlier: 3.743A pdb=" N LYS t 206 " --> pdb=" O ILE t 202 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 36 Processing helix chain 'c' and resid 39 through 63 removed outlier: 4.051A pdb=" N VAL c 43 " --> pdb=" O ASN c 39 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL c 46 " --> pdb=" O GLU c 42 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR c 62 " --> pdb=" O ARG c 58 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU c 63 " --> pdb=" O GLU c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 85 removed outlier: 3.768A pdb=" N ASN c 75 " --> pdb=" O LEU c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 100 removed outlier: 4.076A pdb=" N ILE c 97 " --> pdb=" O LYS c 93 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU c 98 " --> pdb=" O LEU c 94 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY c 99 " --> pdb=" O ASP c 95 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 93 through 100' Processing helix chain 'c' and resid 101 through 109 removed outlier: 4.094A pdb=" N PHE c 105 " --> pdb=" O LYS c 101 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG c 108 " --> pdb=" O ASP c 104 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG c 109 " --> pdb=" O PHE c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 110 through 118 removed outlier: 3.604A pdb=" N GLY c 118 " --> pdb=" O VAL c 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 133 removed outlier: 3.955A pdb=" N ARG c 133 " --> pdb=" O LEU c 129 " (cutoff:3.500A) Processing helix chain 'c' and resid 150 through 155 removed outlier: 4.967A pdb=" N LYS c 155 " --> pdb=" O LEU c 151 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 180 removed outlier: 3.716A pdb=" N LYS c 179 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS c 180 " --> pdb=" O LYS c 176 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 53 Processing helix chain 'm' and resid 29 through 44 removed outlier: 3.958A pdb=" N LYS m 43 " --> pdb=" O LYS m 39 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY m 44 " --> pdb=" O LEU m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 57 Processing helix chain 'm' and resid 62 through 68 removed outlier: 3.681A pdb=" N VAL m 66 " --> pdb=" O GLN m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 79 removed outlier: 3.803A pdb=" N LYS m 78 " --> pdb=" O ILE m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 106 removed outlier: 4.316A pdb=" N ARG m 104 " --> pdb=" O LYS m 100 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG m 106 " --> pdb=" O LEU m 102 " (cutoff:3.500A) Processing helix chain 'm' and resid 108 through 133 removed outlier: 3.625A pdb=" N THR m 131 " --> pdb=" O ARG m 127 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS m 132 " --> pdb=" O TYR m 128 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG m 133 " --> pdb=" O TYR m 129 " (cutoff:3.500A) Processing helix chain 'm' and resid 145 through 150 removed outlier: 3.688A pdb=" N LEU m 149 " --> pdb=" O THR m 145 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL m 150 " --> pdb=" O ALA m 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 145 through 150' Processing helix chain 'y' and resid 56 through 63 Processing helix chain 'y' and resid 64 through 77 Processing helix chain 'D' and resid 5 through 21 Processing helix chain 'D' and resid 31 through 45 removed outlier: 3.782A pdb=" N HIS D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.625A pdb=" N LEU D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'z' and resid 36 through 49 Processing helix chain 'z' and resid 51 through 56 removed outlier: 4.586A pdb=" N ILE z 55 " --> pdb=" O THR z 51 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE z 56 " --> pdb=" O PRO z 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 51 through 56' Processing helix chain 'z' and resid 78 through 86 Processing helix chain 'z' and resid 87 through 95 removed outlier: 4.354A pdb=" N HIS z 94 " --> pdb=" O ARG z 90 " (cutoff:3.500A) Processing helix chain 'z' and resid 103 through 118 removed outlier: 5.517A pdb=" N ARG z 107 " --> pdb=" O SER z 103 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS z 116 " --> pdb=" O ASN z 112 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL z 117 " --> pdb=" O ARG z 113 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG z 118 " --> pdb=" O MET z 114 " (cutoff:3.500A) Processing helix chain 'z' and resid 119 through 125 removed outlier: 4.848A pdb=" N ALA z 123 " --> pdb=" O GLY z 119 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN z 124 " --> pdb=" O THR z 120 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL z 125 " --> pdb=" O ALA z 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 119 through 125' Processing helix chain 'R' and resid 11 through 19 removed outlier: 4.017A pdb=" N LYS R 18 " --> pdb=" O GLU R 14 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS R 19 " --> pdb=" O GLU R 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 16 removed outlier: 4.427A pdb=" N GLY T 14 " --> pdb=" O GLY T 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN T 15 " --> pdb=" O LYS T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 42 removed outlier: 3.503A pdb=" N ARG T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 6 through 20 removed outlier: 3.965A pdb=" N ALA w 12 " --> pdb=" O THR w 8 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG w 14 " --> pdb=" O LYS w 10 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR w 20 " --> pdb=" O ILE w 16 " (cutoff:3.500A) Processing helix chain 'w' and resid 27 through 39 removed outlier: 3.817A pdb=" N ARG w 33 " --> pdb=" O HIS w 29 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU w 36 " --> pdb=" O LYS w 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU w 37 " --> pdb=" O ARG w 33 " (cutoff:3.500A) Processing helix chain 'w' and resid 43 through 64 removed outlier: 3.845A pdb=" N ARG w 47 " --> pdb=" O SER w 43 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN w 62 " --> pdb=" O MET w 58 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG w 63 " --> pdb=" O LYS w 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY w 64 " --> pdb=" O ARG w 60 " (cutoff:3.500A) Processing helix chain 'w' and resid 71 through 81 removed outlier: 4.782A pdb=" N GLU w 75 " --> pdb=" O ILE w 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU w 76 " --> pdb=" O LYS w 72 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU w 79 " --> pdb=" O GLU w 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG w 81 " --> pdb=" O GLU w 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 99 through 110 Processing helix chain 'b' and resid 6 through 29 Processing helix chain 'b' and resid 54 through 60 removed outlier: 3.752A pdb=" N VAL b 58 " --> pdb=" O ARG b 54 " (cutoff:3.500A) Processing helix chain 'b' and resid 63 through 78 removed outlier: 3.645A pdb=" N GLY b 78 " --> pdb=" O GLN b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 98 removed outlier: 3.756A pdb=" N CYS b 97 " --> pdb=" O THR b 93 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA b 98 " --> pdb=" O ARG b 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 93 through 98' Processing helix chain 'b' and resid 99 through 112 removed outlier: 3.647A pdb=" N GLY b 112 " --> pdb=" O LYS b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 130 removed outlier: 3.597A pdb=" N GLY b 130 " --> pdb=" O ILE b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 162 through 167 removed outlier: 4.491A pdb=" N TYR b 166 " --> pdb=" O ASP b 162 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 40 removed outlier: 3.507A pdb=" N GLN e 36 " --> pdb=" O ASP e 32 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP e 37 " --> pdb=" O ILE e 33 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TYR e 38 " --> pdb=" O SER e 34 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE e 39 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ALA e 40 " --> pdb=" O GLN e 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 40' Processing helix chain 'e' and resid 61 through 67 removed outlier: 4.690A pdb=" N GLN e 65 " --> pdb=" O PHE e 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS e 66 " --> pdb=" O ARG e 62 " (cutoff:3.500A) Proline residue: e 67 - end of helix No H-bonds generated for 'chain 'e' and resid 61 through 67' Processing helix chain 'e' and resid 68 through 78 removed outlier: 3.993A pdb=" N MET e 77 " --> pdb=" O THR e 73 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N MET e 78 " --> pdb=" O ASN e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 104 removed outlier: 3.619A pdb=" N THR e 89 " --> pdb=" O LYS e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 120 removed outlier: 3.532A pdb=" N GLY e 120 " --> pdb=" O ILE e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 4.848A pdb=" N GLY e 157 " --> pdb=" O LEU e 153 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA e 158 " --> pdb=" O LEU e 154 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU e 160 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE e 163 " --> pdb=" O ARG e 159 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ARG e 164 " --> pdb=" O GLU e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 183 removed outlier: 3.511A pdb=" N LYS e 182 " --> pdb=" O ILE e 178 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY e 183 " --> pdb=" O ASN e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 187 through 204 removed outlier: 3.555A pdb=" N LYS e 191 " --> pdb=" O SER e 187 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA e 200 " --> pdb=" O LEU e 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG e 204 " --> pdb=" O ALA e 200 " (cutoff:3.500A) Processing helix chain 'u' and resid 4 through 19 Processing helix chain 'u' and resid 41 through 56 removed outlier: 3.645A pdb=" N VAL u 45 " --> pdb=" O PRO u 41 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG u 55 " --> pdb=" O SER u 51 " (cutoff:3.500A) Processing helix chain 'u' and resid 72 through 84 removed outlier: 4.433A pdb=" N HIS u 84 " --> pdb=" O ARG u 80 " (cutoff:3.500A) Processing helix chain 'v' and resid 15 through 29 removed outlier: 4.586A pdb=" N GLN v 19 " --> pdb=" O ASN v 15 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU v 20 " --> pdb=" O THR v 16 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU v 22 " --> pdb=" O LEU v 18 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR v 24 " --> pdb=" O GLU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 45 Processing helix chain 'v' and resid 58 through 73 removed outlier: 3.646A pdb=" N VAL v 62 " --> pdb=" O GLU v 58 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS v 63 " --> pdb=" O PRO v 59 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU v 64 " --> pdb=" O MET v 60 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL v 65 " --> pdb=" O TYR v 61 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLU v 66 " --> pdb=" O VAL v 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS v 69 " --> pdb=" O VAL v 65 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA v 70 " --> pdb=" O GLU v 66 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU v 71 " --> pdb=" O ALA v 67 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS v 72 " --> pdb=" O LEU v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 90 removed outlier: 3.847A pdb=" N LEU v 85 " --> pdb=" O ASP v 81 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY v 90 " --> pdb=" O GLY v 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 128 removed outlier: 4.619A pdb=" N ASP v 122 " --> pdb=" O SER v 118 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL v 123 " --> pdb=" O GLN v 119 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE v 128 " --> pdb=" O ILE v 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 21 through 29 removed outlier: 3.611A pdb=" N LEU o 26 " --> pdb=" O LEU o 22 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP o 27 " --> pdb=" O ASP o 23 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET o 28 " --> pdb=" O GLN o 24 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER o 29 " --> pdb=" O LEU o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 30 through 38 removed outlier: 4.195A pdb=" N GLN o 35 " --> pdb=" O GLU o 31 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU o 36 " --> pdb=" O GLN o 32 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER o 38 " --> pdb=" O MET o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 39 through 48 Processing helix chain 'o' and resid 50 through 67 removed outlier: 4.401A pdb=" N ALA o 67 " --> pdb=" O ALA o 63 " (cutoff:3.500A) Processing helix chain 'o' and resid 115 through 121 removed outlier: 4.405A pdb=" N PHE o 119 " --> pdb=" O TYR o 115 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER o 120 " --> pdb=" O LEU o 116 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE o 121 " --> pdb=" O GLY o 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 115 through 121' Processing helix chain 'g' and resid 44 through 59 removed outlier: 3.876A pdb=" N GLN g 48 " --> pdb=" O PRO g 44 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TYR g 49 " --> pdb=" O ARG g 45 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS g 50 " --> pdb=" O THR g 46 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) Proline residue: g 54 - end of helix Processing helix chain 'g' and resid 60 through 65 removed outlier: 3.688A pdb=" N ALA g 64 " --> pdb=" O LYS g 60 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLY g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 60 through 65' Processing helix chain 'g' and resid 76 through 99 removed outlier: 3.660A pdb=" N ILE g 81 " --> pdb=" O HIS g 77 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN g 86 " --> pdb=" O TYR g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 116 removed outlier: 3.632A pdb=" N LYS g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN g 114 " --> pdb=" O ASP g 110 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR g 115 " --> pdb=" O ILE g 111 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 32 removed outlier: 4.644A pdb=" N THR k 31 " --> pdb=" O ALA k 27 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA k 32 " --> pdb=" O PHE k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 49 removed outlier: 3.640A pdb=" N VAL k 43 " --> pdb=" O ARG k 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 74 Proline residue: k 74 - end of helix Processing helix chain 'k' and resid 100 through 118 removed outlier: 4.348A pdb=" N ASP k 104 " --> pdb=" O ALA k 100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN k 105 " --> pdb=" O ASN k 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 119 through 128 Processing helix chain 'x' and resid 5 through 10 removed outlier: 4.110A pdb=" N VAL x 9 " --> pdb=" O THR x 5 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASN x 10 " --> pdb=" O VAL x 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 5 through 10' Processing helix chain 'x' and resid 11 through 26 removed outlier: 3.884A pdb=" N ARG x 16 " --> pdb=" O GLN x 12 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY x 26 " --> pdb=" O LEU x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 67 removed outlier: 3.921A pdb=" N THR x 55 " --> pdb=" O ASN x 51 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 80 removed outlier: 3.989A pdb=" N LYS x 77 " --> pdb=" O GLY x 73 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY x 80 " --> pdb=" O THR x 76 " (cutoff:3.500A) Processing helix chain 'x' and resid 96 through 111 removed outlier: 3.620A pdb=" N ALA x 100 " --> pdb=" O SER x 96 " (cutoff:3.500A) Processing helix chain 'x' and resid 124 through 142 removed outlier: 4.336A pdb=" N ASN x 142 " --> pdb=" O VAL x 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 47 removed outlier: 3.779A pdb=" N LEU h 32 " --> pdb=" O ASN h 28 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS h 46 " --> pdb=" O GLY h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 104 removed outlier: 4.283A pdb=" N VAL h 98 " --> pdb=" O PRO h 94 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS h 99 " --> pdb=" O SER h 95 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN h 100 " --> pdb=" O GLU h 96 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER h 103 " --> pdb=" O LYS h 99 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE h 104 " --> pdb=" O GLN h 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 65 removed outlier: 4.502A pdb=" N LYS P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL P 62 " --> pdb=" O LEU P 58 " (cutoff:3.500A) Proline residue: P 63 - end of helix Processing helix chain 'P' and resid 69 through 78 removed outlier: 3.511A pdb=" N GLU P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 95 removed outlier: 3.601A pdb=" N SER P 93 " --> pdb=" O GLN P 89 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 removed outlier: 7.787A pdb=" N TRP l 8 " --> pdb=" O GLN l 4 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER l 9 " --> pdb=" O GLN l 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 4 through 9' Processing helix chain 'l' and resid 15 through 20 removed outlier: 3.840A pdb=" N ARG l 19 " --> pdb=" O GLY l 15 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER l 20 " --> pdb=" O GLN l 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 15 through 20' Processing helix chain 'l' and resid 39 through 51 removed outlier: 5.696A pdb=" N LYS l 48 " --> pdb=" O ARG l 44 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP l 49 " --> pdb=" O GLN l 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 107 removed outlier: 4.753A pdb=" N LYS U 104 " --> pdb=" O LEU U 100 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS U 107 " --> pdb=" O LEU U 103 " (cutoff:3.500A) Processing helix chain 'i' and resid 57 through 63 removed outlier: 4.036A pdb=" N LYS i 61 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL i 62 " --> pdb=" O GLY i 58 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS i 63 " --> pdb=" O GLY i 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 57 through 63' Processing helix chain 'i' and resid 64 through 69 removed outlier: 3.852A pdb=" N GLU i 68 " --> pdb=" O ALA i 64 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER i 69 " --> pdb=" O ASP i 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 64 through 69' Processing helix chain 'i' and resid 70 through 89 removed outlier: 3.776A pdb=" N GLU i 87 " --> pdb=" O GLN i 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU i 88 " --> pdb=" O ARG i 84 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY i 89 " --> pdb=" O CYS i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 123 removed outlier: 4.395A pdb=" N GLY i 123 " --> pdb=" O LEU i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 25 removed outlier: 4.104A pdb=" N TRP j 22 " --> pdb=" O ARG j 18 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS j 23 " --> pdb=" O ASP j 19 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP j 24 " --> pdb=" O GLN j 20 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS j 25 " --> pdb=" O LYS j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 32 Processing helix chain 'j' and resid 33 through 40 removed outlier: 3.719A pdb=" N ALA j 38 " --> pdb=" O THR j 34 " (cutoff:3.500A) Proline residue: j 40 - end of helix Processing helix chain 'j' and resid 89 through 95 removed outlier: 4.275A pdb=" N PHE j 93 " --> pdb=" O GLY j 89 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE j 94 " --> pdb=" O CYS j 90 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU j 95 " --> pdb=" O LEU j 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 89 through 95' Processing helix chain 'j' and resid 129 through 136 Processing helix chain 'G' and resid 96 through 107 Processing helix chain 'B' and resid 196 through 213 removed outlier: 4.883A pdb=" N GLU B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LYS B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 251 removed outlier: 3.563A pdb=" N ALA B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.897A pdb=" N LEU B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 289 through 295' Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.751A pdb=" N LYS B 463 " --> pdb=" O LYS B 459 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 464' Processing helix chain 'B' and resid 713 through 722 removed outlier: 4.035A pdb=" N ILE B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 718 " --> pdb=" O GLN B 714 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 744 removed outlier: 5.424A pdb=" N ARG B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 737 " --> pdb=" O GLN B 733 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 22 removed outlier: 3.976A pdb=" N ALA A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 37 removed outlier: 4.132A pdb=" N ALA A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 62 removed outlier: 4.811A pdb=" N GLU A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 83 through 116 removed outlier: 3.845A pdb=" N GLU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.887A pdb=" N VAL A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.546A pdb=" N LEU A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 189 removed outlier: 3.578A pdb=" N GLU A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 212 removed outlier: 4.881A pdb=" N HIS A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 244 Processing helix chain 'A' and resid 245 through 264 removed outlier: 4.745A pdb=" N LYS A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.556A pdb=" N MET A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 307 removed outlier: 4.811A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 removed outlier: 4.982A pdb=" N MET A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 5.188A pdb=" N ALA A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.925A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 removed outlier: 3.562A pdb=" N LEU A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.566A pdb=" N LYS A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASN A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 418 removed outlier: 5.421A pdb=" N CYS A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN A 417 " --> pdb=" O TRP A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 421 through 447 removed outlier: 3.884A pdb=" N GLN A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN A 426 " --> pdb=" O PRO A 422 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Proline residue: A 429 - end of helix removed outlier: 3.519A pdb=" N GLN A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 463 through 477 Processing helix chain 'A' and resid 514 through 522 removed outlier: 5.050A pdb=" N ASN A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 538 removed outlier: 3.871A pdb=" N LYS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 561 Processing helix chain 'A' and resid 562 through 600 removed outlier: 5.510A pdb=" N GLN A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 639 removed outlier: 3.583A pdb=" N GLU A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 685 Proline residue: A 669 - end of helix Processing helix chain 'A' and resid 707 through 725 removed outlier: 3.506A pdb=" N ARG A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 74 removed outlier: 3.775A pdb=" N LEU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 94 removed outlier: 3.800A pdb=" N GLU C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 94 " --> pdb=" O TYR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 4.744A pdb=" N GLU C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 124 removed outlier: 3.524A pdb=" N ILE C 109 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 149 removed outlier: 6.697A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 340 removed outlier: 3.859A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 330 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ARG C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 363 removed outlier: 3.674A pdb=" N ILE C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU C 363 " --> pdb=" O GLN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 3.915A pdb=" N ILE C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 416 removed outlier: 4.115A pdb=" N ASN C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Proline residue: C 416 - end of helix Processing helix chain 'C' and resid 443 through 463 removed outlier: 4.445A pdb=" N LEU C 447 " --> pdb=" O CYS C 443 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 491 removed outlier: 4.612A pdb=" N VAL C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 474 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU C 476 " --> pdb=" O HIS C 472 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN C 478 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 511 removed outlier: 3.568A pdb=" N ARG C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 504 " --> pdb=" O CYS C 500 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU C 505 " --> pdb=" O ARG C 501 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR C 510 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 558 Processing helix chain 'C' and resid 561 through 580 removed outlier: 4.941A pdb=" N ARG C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER C 580 " --> pdb=" O HIS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 removed outlier: 4.125A pdb=" N ALA C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS C 593 " --> pdb=" O MET C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 602 removed outlier: 5.158A pdb=" N GLN C 599 " --> pdb=" O GLN C 595 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N HIS C 600 " --> pdb=" O ASP C 596 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 624 removed outlier: 4.246A pdb=" N LEU C 608 " --> pdb=" O PRO C 604 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 624 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 removed outlier: 3.668A pdb=" N LEU C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP C 635 " --> pdb=" O ASN C 631 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 639 " --> pdb=" O ASP C 635 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY C 640 " --> pdb=" O ILE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 647 removed outlier: 4.237A pdb=" N LEU C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 647 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 670 removed outlier: 4.961A pdb=" N GLU C 663 " --> pdb=" O ASN C 659 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 664 " --> pdb=" O GLN C 660 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 665 " --> pdb=" O GLU C 661 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 668 " --> pdb=" O LYS C 664 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 702 removed outlier: 5.578A pdb=" N ILE C 677 " --> pdb=" O PHE C 673 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N ASN C 678 " --> pdb=" O HIS C 674 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N LEU C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N GLU C 680 " --> pdb=" O HIS C 676 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU C 681 " --> pdb=" O ILE C 677 " (cutoff:3.500A) Proline residue: C 696 - end of helix removed outlier: 3.529A pdb=" N GLU C 702 " --> pdb=" O MET C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 724 removed outlier: 3.534A pdb=" N ARG C 723 " --> pdb=" O ARG C 719 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN C 724 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 747 removed outlier: 3.792A pdb=" N MET C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 758 removed outlier: 4.374A pdb=" N CYS C 752 " --> pdb=" O ASP C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 765 removed outlier: 3.945A pdb=" N GLY C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 800 removed outlier: 3.640A pdb=" N VAL C 775 " --> pdb=" O GLU C 771 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER C 796 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER C 797 " --> pdb=" O PHE C 793 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 798 " --> pdb=" O THR C 794 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR C 799 " --> pdb=" O TYR C 795 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP C 800 " --> pdb=" O SER C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 812 Processing helix chain 'C' and resid 814 through 829 removed outlier: 3.975A pdb=" N ILE C 827 " --> pdb=" O SER C 823 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN C 828 " --> pdb=" O LYS C 824 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU C 829 " --> pdb=" O MET C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 878 removed outlier: 3.690A pdb=" N GLU C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 878 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 6.463A pdb=" N LYS C 128 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 129 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET C 130 " --> pdb=" O LYS C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 130' Processing helix chain 'E' and resid 6 through 15 removed outlier: 3.784A pdb=" N HIS E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 4.736A pdb=" N PHE E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Proline residue: E 21 - end of helix Processing helix chain 'E' and resid 33 through 49 removed outlier: 4.527A pdb=" N LEU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 62 Processing helix chain 'E' and resid 67 through 95 Proline residue: E 90 - end of helix Processing helix chain 'E' and resid 99 through 104 removed outlier: 4.494A pdb=" N GLN E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N MET E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 104' Processing helix chain 'E' and resid 110 through 121 removed outlier: 3.838A pdb=" N HIS E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 142 removed outlier: 4.280A pdb=" N LEU E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 158 Processing helix chain 'E' and resid 164 through 180 removed outlier: 3.528A pdb=" N GLN E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 199 removed outlier: 3.589A pdb=" N ASN E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 226 removed outlier: 4.389A pdb=" N ASN E 224 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS E 225 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Proline residue: E 226 - end of helix Processing helix chain 'E' and resid 227 through 236 removed outlier: 4.532A pdb=" N ASN E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 249 removed outlier: 4.554A pdb=" N ALA E 245 " --> pdb=" O GLN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 264 removed outlier: 4.971A pdb=" N TYR E 256 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN E 264 " --> pdb=" O ALA E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 285 removed outlier: 3.928A pdb=" N ARG E 270 " --> pdb=" O ASP E 266 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP E 276 " --> pdb=" O GLN E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 301 Processing helix chain 'E' and resid 305 through 320 removed outlier: 3.689A pdb=" N SER E 317 " --> pdb=" O ARG E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 348 removed outlier: 4.447A pdb=" N LEU E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU E 330 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE E 332 " --> pdb=" O CYS E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 361 removed outlier: 3.753A pdb=" N LEU E 356 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 removed outlier: 3.877A pdb=" N ASN E 377 " --> pdb=" O ASN E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 430 removed outlier: 4.916A pdb=" N SER E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 413 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 424 " --> pdb=" O MET E 420 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASN E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER E 430 " --> pdb=" O LEU E 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 109 removed outlier: 3.573A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 164 Processing helix chain 'F' and resid 180 through 194 removed outlier: 3.829A pdb=" N VAL F 184 " --> pdb=" O THR F 180 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA F 194 " --> pdb=" O TYR F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 259 removed outlier: 5.789A pdb=" N THR F 255 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS F 256 " --> pdb=" O ILE F 252 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER F 258 " --> pdb=" O LYS F 254 " (cutoff:3.500A) Proline residue: F 259 - end of helix Processing helix chain 'F' and resid 267 through 296 removed outlier: 3.685A pdb=" N SER F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 314 removed outlier: 4.266A pdb=" N GLN F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 357 removed outlier: 4.378A pdb=" N PHE F 323 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU F 357 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 56 removed outlier: 3.871A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 111 removed outlier: 3.662A pdb=" N VAL H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 144 removed outlier: 4.046A pdb=" N ILE H 144 " --> pdb=" O TYR H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 160 Processing helix chain 'H' and resid 170 through 180 Processing helix chain 'H' and resid 183 through 191 removed outlier: 3.558A pdb=" N ASN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 198 removed outlier: 4.408A pdb=" N MET H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE H 198 " --> pdb=" O PHE H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 198' Processing helix chain 'H' and resid 208 through 222 removed outlier: 3.857A pdb=" N SER H 222 " --> pdb=" O LEU H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 289 removed outlier: 5.899A pdb=" N LEU H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG H 288 " --> pdb=" O GLU H 284 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN H 289 " --> pdb=" O ASN H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 349 removed outlier: 4.930A pdb=" N LEU H 317 " --> pdb=" O ARG H 313 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 318 " --> pdb=" O MET H 314 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA H 346 " --> pdb=" O PHE H 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 Processing helix chain 'K' and resid 18 through 23 removed outlier: 4.683A pdb=" N ASN K 22 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Proline residue: K 23 - end of helix No H-bonds generated for 'chain 'K' and resid 18 through 23' Processing helix chain 'K' and resid 24 through 40 removed outlier: 4.691A pdb=" N THR K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN K 40 " --> pdb=" O GLN K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 58 removed outlier: 4.111A pdb=" N ASN K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Proline residue: K 58 - end of helix Processing helix chain 'K' and resid 62 through 77 removed outlier: 3.684A pdb=" N THR K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 89 removed outlier: 4.193A pdb=" N LEU K 84 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE K 89 " --> pdb=" O CYS K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 95 removed outlier: 3.574A pdb=" N GLN K 94 " --> pdb=" O ASP K 90 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU K 95 " --> pdb=" O GLN K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 95' Processing helix chain 'K' and resid 97 through 112 removed outlier: 7.816A pdb=" N GLN K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 119 removed outlier: 3.615A pdb=" N TRP K 118 " --> pdb=" O PHE K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.791A pdb=" N ILE K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR K 132 " --> pdb=" O LEU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 150 Processing helix chain 'K' and resid 154 through 163 removed outlier: 3.664A pdb=" N GLY K 163 " --> pdb=" O ALA K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 178 removed outlier: 4.550A pdb=" N VAL K 172 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR K 177 " --> pdb=" O TRP K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 211 removed outlier: 3.618A pdb=" N VAL K 210 " --> pdb=" O ASP K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 218 removed outlier: 3.927A pdb=" N SER K 216 " --> pdb=" O SER K 212 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN K 218 " --> pdb=" O MET K 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 203 removed outlier: 4.035A pdb=" N ILE L 187 " --> pdb=" O LEU L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 218 removed outlier: 4.984A pdb=" N ILE L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 247 removed outlier: 4.747A pdb=" N ASN L 229 " --> pdb=" O HIS L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 264 removed outlier: 3.997A pdb=" N TYR L 260 " --> pdb=" O VAL L 256 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG L 262 " --> pdb=" O GLY L 258 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N HIS L 263 " --> pdb=" O GLU L 259 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER L 264 " --> pdb=" O TYR L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 291 removed outlier: 3.629A pdb=" N ALA L 290 " --> pdb=" O ASP L 286 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE L 291 " --> pdb=" O TYR L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 302 removed outlier: 4.674A pdb=" N LYS L 302 " --> pdb=" O GLU L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 327 Processing helix chain 'L' and resid 328 through 341 removed outlier: 4.559A pdb=" N ARG L 334 " --> pdb=" O GLN L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 357 through 376 removed outlier: 4.027A pdb=" N THR L 376 " --> pdb=" O ALA L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 402 removed outlier: 4.352A pdb=" N LYS L 397 " --> pdb=" O LYS L 393 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET L 401 " --> pdb=" O LYS L 397 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN L 402 " --> pdb=" O MET L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 422 removed outlier: 4.404A pdb=" N GLU L 410 " --> pdb=" O PRO L 406 " (cutoff:3.500A) Proline residue: L 418 - end of helix removed outlier: 5.104A pdb=" N LEU L 421 " --> pdb=" O CYS L 417 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER L 422 " --> pdb=" O PRO L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 436 through 462 removed outlier: 4.684A pdb=" N PHE L 440 " --> pdb=" O HIS L 436 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS L 445 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL L 446 " --> pdb=" O GLN L 442 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP L 449 " --> pdb=" O LYS L 445 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU L 450 " --> pdb=" O VAL L 446 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL L 451 " --> pdb=" O PHE L 447 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN L 452 " --> pdb=" O SER L 448 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN L 453 " --> pdb=" O ASP L 449 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER L 458 " --> pdb=" O GLN L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 471 through 483 Processing helix chain 'L' and resid 489 through 498 removed outlier: 3.559A pdb=" N LYS L 494 " --> pdb=" O LEU L 490 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET L 497 " --> pdb=" O PHE L 493 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 551 removed outlier: 4.343A pdb=" N ILE L 528 " --> pdb=" O ASP L 524 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS L 549 " --> pdb=" O ARG L 545 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU L 551 " --> pdb=" O ILE L 547 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 26 removed outlier: 4.032A pdb=" N SER M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS M 25 " --> pdb=" O TYR M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 53 removed outlier: 5.144A pdb=" N VAL M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU M 53 " --> pdb=" O CYS M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 74 removed outlier: 4.650A pdb=" N ILE M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU M 74 " --> pdb=" O LEU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 95 removed outlier: 4.193A pdb=" N GLU M 95 " --> pdb=" O VAL M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 removed outlier: 4.398A pdb=" N MET M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP M 114 " --> pdb=" O PHE M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 134 removed outlier: 4.682A pdb=" N TYR M 121 " --> pdb=" O THR M 117 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR M 122 " --> pdb=" O PRO M 118 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER M 133 " --> pdb=" O LYS M 129 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS M 134 " --> pdb=" O VAL M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 154 Processing helix chain 'M' and resid 157 through 176 removed outlier: 3.662A pdb=" N LYS M 161 " --> pdb=" O THR M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 193 removed outlier: 3.565A pdb=" N LYS M 183 " --> pdb=" O ASP M 179 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 201 removed outlier: 4.661A pdb=" N SER M 198 " --> pdb=" O GLU M 194 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN M 199 " --> pdb=" O ASP M 195 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG M 201 " --> pdb=" O ALA M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 214 Processing helix chain 'M' and resid 220 through 226 removed outlier: 4.356A pdb=" N LEU M 224 " --> pdb=" O PHE M 220 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR M 225 " --> pdb=" O ASP M 221 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU M 226 " --> pdb=" O HIS M 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 220 through 226' Processing helix chain 'M' and resid 227 through 233 removed outlier: 5.010A pdb=" N GLU M 233 " --> pdb=" O VAL M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 246 removed outlier: 4.803A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 259 removed outlier: 3.788A pdb=" N PHE M 255 " --> pdb=" O SER M 251 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN M 259 " --> pdb=" O PHE M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 265 removed outlier: 4.046A pdb=" N ASP M 264 " --> pdb=" O LYS M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 289 removed outlier: 3.959A pdb=" N ASN M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 302 removed outlier: 3.905A pdb=" N MET M 297 " --> pdb=" O SER M 293 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN M 302 " --> pdb=" O GLN M 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 319 removed outlier: 4.854A pdb=" N VAL M 308 " --> pdb=" O GLY M 304 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU M 309 " --> pdb=" O ALA M 305 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA M 310 " --> pdb=" O ASP M 306 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR M 318 " --> pdb=" O ASP M 314 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS M 319 " --> pdb=" O ALA M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 372 removed outlier: 3.944A pdb=" N TRP M 347 " --> pdb=" O GLY M 343 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER M 372 " --> pdb=" O LEU M 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 60 removed outlier: 3.888A pdb=" N LYS N 58 " --> pdb=" O ARG N 54 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR N 59 " --> pdb=" O TYR N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 183 removed outlier: 3.735A pdb=" N LEU N 179 " --> pdb=" O ASP N 175 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ARG N 183 " --> pdb=" O LEU N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 209 removed outlier: 4.721A pdb=" N ARG N 208 " --> pdb=" O LYS N 204 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE N 209 " --> pdb=" O ALA N 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 204 through 209' Processing helix chain 'N' and resid 232 through 240 removed outlier: 4.346A pdb=" N LYS N 240 " --> pdb=" O ARG N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 248 through 258 removed outlier: 3.990A pdb=" N LEU N 252 " --> pdb=" O THR N 248 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR N 254 " --> pdb=" O ALA N 250 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU N 255 " --> pdb=" O ILE N 251 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER N 257 " --> pdb=" O ALA N 253 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS N 258 " --> pdb=" O THR N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 327 removed outlier: 3.624A pdb=" N ALA N 313 " --> pdb=" O PRO N 309 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN N 325 " --> pdb=" O HIS N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 400 through 405 removed outlier: 4.277A pdb=" N CYS N 404 " --> pdb=" O ASP N 400 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASN N 405 " --> pdb=" O SER N 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 400 through 405' Processing helix chain 'N' and resid 408 through 413 Processing helix chain 'N' and resid 416 through 428 removed outlier: 3.928A pdb=" N VAL N 420 " --> pdb=" O GLN N 416 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS N 426 " --> pdb=" O ALA N 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 443 removed outlier: 3.690A pdb=" N THR N 436 " --> pdb=" O LEU N 432 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY N 443 " --> pdb=" O ALA N 439 " (cutoff:3.500A) Processing helix chain 'N' and resid 472 through 481 removed outlier: 3.505A pdb=" N ASN N 481 " --> pdb=" O ALA N 477 " (cutoff:3.500A) Processing helix chain 'N' and resid 483 through 502 removed outlier: 3.798A pdb=" N ILE N 497 " --> pdb=" O CYS N 493 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS N 500 " --> pdb=" O ASP N 496 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU N 501 " --> pdb=" O ILE N 497 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLU N 502 " --> pdb=" O CYS N 498 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 24 removed outlier: 3.574A pdb=" N ALA X 19 " --> pdb=" O ALA X 15 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 66 removed outlier: 3.830A pdb=" N ALA X 62 " --> pdb=" O ALA X 58 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA X 66 " --> pdb=" O ALA X 62 " (cutoff:3.500A) Processing helix chain '4' and resid 175 through 185 removed outlier: 4.605A pdb=" N ASN 4 185 " --> pdb=" O ASN 4 181 " (cutoff:3.500A) Processing helix chain '4' and resid 221 through 230 removed outlier: 4.526A pdb=" N ILE 4 225 " --> pdb=" O ASN 4 221 " (cutoff:3.500A) Processing helix chain '4' and resid 232 through 245 removed outlier: 3.647A pdb=" N LEU 4 236 " --> pdb=" O GLN 4 232 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY 4 245 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 278 removed outlier: 3.767A pdb=" N VAL 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG 4 273 " --> pdb=" O ASN 4 269 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU 4 277 " --> pdb=" O ARG 4 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 62 removed outlier: 3.657A pdb=" N LEU O 61 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 119 removed outlier: 3.726A pdb=" N ILE O 95 " --> pdb=" O PRO O 91 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS O 96 " --> pdb=" O GLU O 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR O 106 " --> pdb=" O THR O 102 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL O 107 " --> pdb=" O LYS O 103 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL O 117 " --> pdb=" O HIS O 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU O 118 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 133 removed outlier: 3.737A pdb=" N LEU O 126 " --> pdb=" O LYS O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 142 removed outlier: 5.131A pdb=" N ASP O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 158 removed outlier: 6.181A pdb=" N ALA O 148 " --> pdb=" O PRO O 144 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE O 152 " --> pdb=" O ALA O 148 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL O 156 " --> pdb=" O PHE O 152 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 165 removed outlier: 3.860A pdb=" N SER O 164 " --> pdb=" O SER O 160 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU O 165 " --> pdb=" O ILE O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 183 removed outlier: 3.561A pdb=" N GLU O 173 " --> pdb=" O GLU O 169 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL O 174 " --> pdb=" O ASP O 170 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE O 176 " --> pdb=" O ARG O 172 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN O 177 " --> pdb=" O GLU O 173 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG O 181 " --> pdb=" O ASN O 177 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU O 183 " --> pdb=" O ILE O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 202 through 218 removed outlier: 4.126A pdb=" N ALA O 206 " --> pdb=" O GLU O 202 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL O 207 " --> pdb=" O GLY O 203 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU O 209 " --> pdb=" O ASP O 205 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA O 210 " --> pdb=" O ALA O 206 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER O 218 " --> pdb=" O GLY O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 265 removed outlier: 4.076A pdb=" N SER O 248 " --> pdb=" O THR O 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL O 249 " --> pdb=" O GLU O 245 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA O 255 " --> pdb=" O SER O 251 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL O 256 " --> pdb=" O GLN O 252 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS O 264 " --> pdb=" O LYS O 260 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG O 265 " --> pdb=" O ILE O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 297 Processing helix chain 'Y' and resid 55 through 63 removed outlier: 4.472A pdb=" N LYS Y 59 " --> pdb=" O SER Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 145 Processing helix chain 'Y' and resid 165 through 179 removed outlier: 3.915A pdb=" N LEU Y 174 " --> pdb=" O THR Y 170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA Y 175 " --> pdb=" O SER Y 171 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA Y 176 " --> pdb=" O GLU Y 172 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE Y 177 " --> pdb=" O HIS Y 173 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU Y 178 " --> pdb=" O LEU Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 213 removed outlier: 3.971A pdb=" N GLN Y 203 " --> pdb=" O GLN Y 199 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR Y 204 " --> pdb=" O ALA Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 230 through 243 removed outlier: 3.587A pdb=" N VAL Y 234 " --> pdb=" O TYR Y 230 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS Y 236 " --> pdb=" O ILE Y 232 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU Y 237 " --> pdb=" O GLU Y 233 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR Y 238 " --> pdb=" O VAL Y 234 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL Y 240 " --> pdb=" O CYS Y 236 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS Y 241 " --> pdb=" O GLU Y 237 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS Y 242 " --> pdb=" O TYR Y 238 " (cutoff:3.500A) Processing helix chain 'Y' and resid 344 through 349 removed outlier: 3.574A pdb=" N CYS Y 348 " --> pdb=" O ASP Y 344 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 69 removed outlier: 3.799A pdb=" N ARG Y 68 " --> pdb=" O HIS Y 65 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE Y 69 " --> pdb=" O THR Y 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 19 removed outlier: 4.121A pdb=" N ASP Z 15 " --> pdb=" O ASP Z 11 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA Z 16 " --> pdb=" O PRO Z 12 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER Z 17 " --> pdb=" O PHE Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 68 removed outlier: 4.916A pdb=" N ALA Z 62 " --> pdb=" O LYS Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 89 through 101 removed outlier: 3.617A pdb=" N ILE Z 100 " --> pdb=" O PHE Z 96 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY Z 101 " --> pdb=" O LEU Z 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 160 Processing helix chain 'J' and resid 165 through 179 Processing sheet with id= 1, first strand: chain 'a' and resid 24 through 28 removed outlier: 5.398A pdb=" N HIS a 24 " --> pdb=" O ILE a 49 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TYR a 47 " --> pdb=" O GLY a 26 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR a 28 " --> pdb=" O GLY a 45 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY a 45 " --> pdb=" O THR a 28 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'a' and resid 121 through 125 Processing sheet with id= 3, first strand: chain 'p' and resid 45 through 48 removed outlier: 4.141A pdb=" N GLY p 45 " --> pdb=" O VAL p 33 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU p 97 " --> pdb=" O GLU p 89 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS p 85 " --> pdb=" O HIS p 101 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N MET p 103 " --> pdb=" O LYS p 83 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS p 83 " --> pdb=" O MET p 103 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU p 105 " --> pdb=" O PHE p 81 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE p 81 " --> pdb=" O LEU p 105 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARG p 65 " --> pdb=" O THR p 88 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'p' and resid 119 through 128 removed outlier: 5.431A pdb=" N THR p 119 " --> pdb=" O THR p 143 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU p 134 " --> pdb=" O LEU p 218 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'p' and resid 101 through 105 removed outlier: 8.305A pdb=" N HIS p 101 " --> pdb=" O MET p 217 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET p 217 " --> pdb=" O HIS p 101 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ARG p 213 " --> pdb=" O LEU p 105 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'd' and resid 107 through 116 removed outlier: 3.756A pdb=" N LYS d 108 " --> pdb=" O PHE d 127 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY d 119 " --> pdb=" O THR d 116 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS d 136 " --> pdb=" O ASP d 132 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'd' and resid 183 through 187 removed outlier: 4.368A pdb=" N ALA d 198 " --> pdb=" O ASP d 221 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP d 221 " --> pdb=" O ALA d 198 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'Q' and resid 20 through 23 removed outlier: 6.262A pdb=" N ILE Q 21 " --> pdb=" O CYS Q 29 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS Q 29 " --> pdb=" O ILE Q 21 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N CYS Q 23 " --> pdb=" O ALA Q 27 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'Q' and resid 36 through 43 Processing sheet with id= 10, first strand: chain 'q' and resid 88 through 93 removed outlier: 4.980A pdb=" N ASP q 88 " --> pdb=" O LEU q 101 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'q' and resid 123 through 126 removed outlier: 4.334A pdb=" N ASP q 158 " --> pdb=" O VAL q 126 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP q 171 " --> pdb=" O GLN q 161 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'q' and resid 128 through 131 Processing sheet with id= 13, first strand: chain 'q' and resid 197 through 200 Processing sheet with id= 14, first strand: chain 'r' and resid 12 through 17 removed outlier: 5.696A pdb=" N ASN r 110 " --> pdb=" O SER r 53 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL r 49 " --> pdb=" O VAL r 114 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR r 34 " --> pdb=" O ILE r 52 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'r' and resid 73 through 76 Processing sheet with id= 16, first strand: chain 'r' and resid 159 through 163 Processing sheet with id= 17, first strand: chain 's' and resid 46 through 53 removed outlier: 3.722A pdb=" N ARG s 57 " --> pdb=" O VAL s 53 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS s 91 " --> pdb=" O LYS s 58 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 's' and resid 141 through 146 removed outlier: 3.607A pdb=" N GLY s 141 " --> pdb=" O HIS s 157 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP s 184 " --> pdb=" O ARG s 152 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 't' and resid 42 through 47 removed outlier: 6.274A pdb=" N ARG t 42 " --> pdb=" O LEU t 58 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 't' and resid 72 through 75 removed outlier: 4.113A pdb=" N ASN t 64 " --> pdb=" O ALA t 185 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU t 172 " --> pdb=" O LEU t 190 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS t 100 " --> pdb=" O ILE t 175 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE t 101 " --> pdb=" O VAL t 82 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'n' and resid 71 through 76 removed outlier: 5.671A pdb=" N ARG n 71 " --> pdb=" O GLU n 130 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR n 127 " --> pdb=" O LEU n 143 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG n 139 " --> pdb=" O CYS n 131 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'n' and resid 85 through 97 removed outlier: 6.441A pdb=" N THR n 85 " --> pdb=" O HIS n 112 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS n 112 " --> pdb=" O THR n 85 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL n 87 " --> pdb=" O SER n 110 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER n 110 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG n 89 " --> pdb=" O ASN n 108 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN n 108 " --> pdb=" O ARG n 89 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP n 91 " --> pdb=" O HIS n 106 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N HIS n 106 " --> pdb=" O ASP n 91 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU n 93 " --> pdb=" O LYS n 104 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS n 104 " --> pdb=" O LEU n 93 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR n 95 " --> pdb=" O PHE n 102 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE n 102 " --> pdb=" O TYR n 95 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG n 97 " --> pdb=" O ASN n 100 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'n' and resid 124 through 127 removed outlier: 3.583A pdb=" N LYS n 144 " --> pdb=" O THR n 127 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'y' and resid 15 through 18 removed outlier: 4.568A pdb=" N ARG y 15 " --> pdb=" O ILE y 24 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG y 22 " --> pdb=" O CYS y 17 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'y' and resid 32 through 38 removed outlier: 4.917A pdb=" N GLN y 49 " --> pdb=" O GLU y 38 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 23 through 28 removed outlier: 5.249A pdb=" N ARG D 23 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU D 49 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 78 through 81 removed outlier: 4.338A pdb=" N PHE D 79 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 103 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'z' and resid 5 through 10 removed outlier: 4.088A pdb=" N VAL z 24 " --> pdb=" O ARG z 10 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL z 24 " --> pdb=" O LYS z 11 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS z 11 " --> pdb=" O VAL z 24 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'z' and resid 60 through 63 removed outlier: 5.791A pdb=" N LYS z 68 " --> pdb=" O HIS z 63 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'z' and resid 19 through 29 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'R' and resid 43 through 47 removed outlier: 3.612A pdb=" N THR R 44 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N PHE R 32 " --> pdb=" O LYS R 82 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG R 80 " --> pdb=" O ASP R 34 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'b' and resid 35 through 41 removed outlier: 3.873A pdb=" N GLY b 36 " --> pdb=" O LEU b 51 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'b' and resid 148 through 154 removed outlier: 3.616A pdb=" N GLY b 133 " --> pdb=" O MET b 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY b 180 " --> pdb=" O LEU b 177 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 123 through 128 removed outlier: 4.101A pdb=" N ARG e 135 " --> pdb=" O ILE e 128 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'u' and resid 20 through 24 Processing sheet with id= 36, first strand: chain 'v' and resid 30 through 33 removed outlier: 7.064A pdb=" N GLY v 30 " --> pdb=" O LYS v 112 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL v 110 " --> pdb=" O ALA v 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU v 49 " --> pdb=" O VAL v 111 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'o' and resid 75 through 78 removed outlier: 4.622A pdb=" N SER o 92 " --> pdb=" O ILE o 107 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 9 through 15 removed outlier: 3.862A pdb=" N LEU g 31 " --> pdb=" O VAL g 66 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'x' and resid 81 through 84 Processing sheet with id= 40, first strand: chain 'x' and resid 113 through 116 removed outlier: 4.517A pdb=" N GLY x 120 " --> pdb=" O ASP x 116 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'h' and resid 53 through 56 removed outlier: 5.021A pdb=" N LYS h 86 " --> pdb=" O MET h 56 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG h 21 " --> pdb=" O THR h 115 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'h' and resid 58 through 66 Processing sheet with id= 43, first strand: chain 'P' and resid 97 through 100 removed outlier: 6.853A pdb=" N ILE P 108 " --> pdb=" O VAL P 100 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 18 through 22 removed outlier: 3.549A pdb=" N GLY S 19 " --> pdb=" O GLN S 29 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG S 31 " --> pdb=" O THR S 15 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP S 54 " --> pdb=" O VAL S 14 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 138 through 141 removed outlier: 3.676A pdb=" N HIS U 139 " --> pdb=" O TYR U 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU U 146 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'V' and resid 5 through 8 removed outlier: 6.591A pdb=" N VAL V 309 " --> pdb=" O ARG V 8 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY V 9 " --> pdb=" O VAL V 309 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 19 through 23 removed outlier: 6.241A pdb=" N ASP V 29 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU V 45 " --> pdb=" O ASP V 29 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE V 31 " --> pdb=" O TRP V 43 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET V 42 " --> pdb=" O GLN V 56 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR V 52 " --> pdb=" O THR V 46 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 67 through 72 removed outlier: 6.524A pdb=" N PHE V 77 " --> pdb=" O SER V 72 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR V 86 " --> pdb=" O SER V 82 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG V 99 " --> pdb=" O LEU V 89 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 109 through 114 removed outlier: 7.491A pdb=" N GLN V 119 " --> pdb=" O SER V 114 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 153 through 157 removed outlier: 3.613A pdb=" N SER V 157 " --> pdb=" O ILE V 164 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE V 164 " --> pdb=" O SER V 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER V 167 " --> pdb=" O LYS V 175 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS V 175 " --> pdb=" O SER V 167 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL V 176 " --> pdb=" O LYS V 185 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS V 183 " --> pdb=" O ASN V 178 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'V' and resid 196 through 201 removed outlier: 3.586A pdb=" N THR V 197 " --> pdb=" O GLY V 210 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA V 208 " --> pdb=" O THR V 199 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU V 206 " --> pdb=" O SER V 201 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLY V 211 " --> pdb=" O GLN V 215 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLN V 215 " --> pdb=" O GLY V 211 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY V 214 " --> pdb=" O GLY V 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR V 228 " --> pdb=" O LEU V 218 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'V' and resid 238 through 242 removed outlier: 3.552A pdb=" N ALA V 238 " --> pdb=" O ALA V 251 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N SER V 242 " --> pdb=" O TRP V 247 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TRP V 247 " --> pdb=" O SER V 242 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU V 248 " --> pdb=" O TRP V 259 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TRP V 259 " --> pdb=" O LEU V 248 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP V 268 " --> pdb=" O ILE V 258 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'V' and resid 288 through 292 removed outlier: 3.610A pdb=" N SER V 288 " --> pdb=" O GLY V 301 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N THR V 297 " --> pdb=" O SER V 292 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'V' and resid 39 through 42 Processing sheet with id= 55, first strand: chain 'V' and resid 173 through 176 removed outlier: 6.577A pdb=" N HIS V 188 " --> pdb=" O VAL V 174 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 296 through 302 removed outlier: 7.229A pdb=" N GLN V 296 " --> pdb=" O VAL V 312 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU V 306 " --> pdb=" O TYR V 302 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 40 through 46 removed outlier: 6.083A pdb=" N ILE i 95 " --> pdb=" O GLY i 127 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 46 through 50 removed outlier: 6.331A pdb=" N LEU j 101 " --> pdb=" O VAL j 123 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 52 through 59 removed outlier: 3.764A pdb=" N GLU j 53 " --> pdb=" O ARG j 71 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA j 65 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS j 79 " --> pdb=" O LEU j 74 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'G' and resid 33 through 37 removed outlier: 6.564A pdb=" N LEU G 78 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN G 87 " --> pdb=" O LYS G 56 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL G 55 " --> pdb=" O CYS G 51 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY G 45 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'I' and resid 1 through 6 removed outlier: 3.891A pdb=" N VAL I 309 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS I 298 " --> pdb=" O PHE I 314 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER I 299 " --> pdb=" O HIS I 294 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER I 290 " --> pdb=" O GLY I 303 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.820A pdb=" N GLN I 15 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU I 24 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP I 23 " --> pdb=" O SER I 39 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL I 36 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU I 43 " --> pdb=" O TYR I 38 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'I' and resid 56 through 60 removed outlier: 7.229A pdb=" N LYS I 65 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG I 77 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER I 71 " --> pdb=" O SER I 75 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'I' and resid 98 through 102 removed outlier: 4.310A pdb=" N THR I 98 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY I 100 " --> pdb=" O MET I 109 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE I 107 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN I 106 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N PHE I 121 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU I 137 " --> pdb=" O ASP I 126 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN I 135 " --> pdb=" O ARG I 128 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE I 133 " --> pdb=" O PRO I 130 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'I' and resid 151 through 155 removed outlier: 3.942A pdb=" N SER I 151 " --> pdb=" O GLY I 164 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N CYS I 160 " --> pdb=" O GLY I 155 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'I' and resid 169 through 172 removed outlier: 3.898A pdb=" N VAL I 182 " --> pdb=" O GLN I 172 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'I' and resid 193 through 197 removed outlier: 6.252A pdb=" N MET I 202 " --> pdb=" O SER I 197 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N THR I 201 " --> pdb=" O SER I 217 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 217 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS I 213 " --> pdb=" O THR I 205 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU I 214 " --> pdb=" O GLN I 223 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU I 221 " --> pdb=" O ASP I 216 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'I' and resid 234 through 237 removed outlier: 4.191A pdb=" N SER I 234 " --> pdb=" O GLY I 247 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ASP I 242 " --> pdb=" O LEU I 272 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE I 269 " --> pdb=" O PHE I 278 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU I 276 " --> pdb=" O HIS I 271 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'I' and resid 33 through 36 Processing sheet with id= 70, first strand: chain 'I' and resid 210 through 214 removed outlier: 5.812A pdb=" N ASN I 210 " --> pdb=" O THR I 228 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR I 228 " --> pdb=" O ASN I 210 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS I 224 " --> pdb=" O LEU I 214 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'I' and resid 266 through 269 removed outlier: 3.622A pdb=" N GLY I 279 " --> pdb=" O PHE I 269 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'B' and resid 187 through 190 removed outlier: 3.734A pdb=" N ARG B 262 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.776A pdb=" N ASN B 219 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 221 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'B' and resid 328 through 333 removed outlier: 4.512A pdb=" N GLN B 305 " --> pdb=" O ARG B 705 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU B 703 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'B' and resid 348 through 353 removed outlier: 4.030A pdb=" N ALA B 358 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS B 353 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 356 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 359 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'B' and resid 377 through 382 removed outlier: 6.276A pdb=" N TYR B 387 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG B 386 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE B 409 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP B 407 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 418 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'B' and resid 437 through 441 removed outlier: 4.767A pdb=" N SER B 447 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'B' and resid 470 through 473 removed outlier: 4.746A pdb=" N ILE B 478 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 496 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 481 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 483 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 492 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU B 485 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 491 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU B 509 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 495 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG B 505 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'B' and resid 513 through 520 removed outlier: 5.759A pdb=" N ASP B 514 " --> pdb=" O ASP B 531 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP B 531 " --> pdb=" O ASP B 514 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS B 518 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 527 " --> pdb=" O HIS B 518 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR B 525 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP B 524 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 545 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 530 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN B 543 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG B 532 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL B 541 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 561 " --> pdb=" O THR B 542 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 544 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'B' and resid 567 through 570 removed outlier: 5.396A pdb=" N SER B 575 " --> pdb=" O VAL B 594 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'B' and resid 613 through 616 removed outlier: 3.858A pdb=" N VAL B 624 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN B 621 " --> pdb=" O THR B 640 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA B 634 " --> pdb=" O GLY B 627 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'B' and resid 656 through 659 removed outlier: 3.749A pdb=" N ASP B 656 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 668 " --> pdb=" O TRP B 682 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA B 680 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'B' and resid 356 through 359 Processing sheet with id= 84, first strand: chain 'A' and resid 482 through 485 Processing sheet with id= 85, first strand: chain 'C' and resid 832 through 836 removed outlier: 8.807A pdb=" N MET C 832 " --> pdb=" O HIS C 845 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR C 841 " --> pdb=" O ASP C 836 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'E' and resid 381 through 385 removed outlier: 6.116A pdb=" N ASP E 381 " --> pdb=" O GLY E 394 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'F' and resid 90 through 94 removed outlier: 7.474A pdb=" N ARG F 90 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR F 236 " --> pdb=" O ARG F 90 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER F 212 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP F 203 " --> pdb=" O SER F 212 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS F 214 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'F' and resid 129 through 132 removed outlier: 6.739A pdb=" N LEU F 121 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE F 117 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'F' and resid 116 through 121 removed outlier: 5.356A pdb=" N VAL F 116 " --> pdb=" O THR F 175 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'H' and resid 37 through 41 removed outlier: 4.710A pdb=" N GLN H 38 " --> pdb=" O ASP H 74 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU H 68 " --> pdb=" O THR H 79 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N CYS H 81 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL H 66 " --> pdb=" O CYS H 81 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL H 63 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 122 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY H 65 " --> pdb=" O TYR H 120 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY H 118 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL H 148 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP H 119 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 150 " --> pdb=" O TRP H 119 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'K' and resid 179 through 182 removed outlier: 3.772A pdb=" N ASP K 182 " --> pdb=" O GLN K 186 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN K 186 " --> pdb=" O ASP K 182 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'M' and resid 322 through 327 removed outlier: 7.499A pdb=" N TYR M 322 " --> pdb=" O SER M 335 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'N' and resid 188 through 192 removed outlier: 4.158A pdb=" N GLU N 194 " --> pdb=" O TYR N 360 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'N' and resid 214 through 217 removed outlier: 7.966A pdb=" N ARG N 462 " --> pdb=" O TYR N 455 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR N 451 " --> pdb=" O LEU N 466 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR N 446 " --> pdb=" O PHE N 390 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN N 392 " --> pdb=" O TYR N 446 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG N 454 " --> pdb=" O GLU N 398 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'N' and resid 244 through 247 Processing sheet with id= 96, first strand: chain 'N' and resid 276 through 280 removed outlier: 3.517A pdb=" N PHE N 277 " --> pdb=" O GLN N 270 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN N 270 " --> pdb=" O PHE N 277 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP N 265 " --> pdb=" O LYS N 510 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'N' and resid 356 through 364 removed outlier: 3.544A pdb=" N VAL N 373 " --> pdb=" O ARG N 361 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'N' and resid 447 through 451 removed outlier: 3.756A pdb=" N GLY N 467 " --> pdb=" O TYR N 451 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'X' and resid 30 through 33 removed outlier: 3.803A pdb=" N ALA X 32 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA X 2 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA X 74 " --> pdb=" O ALA X 7 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain '4' and resid 208 through 212 removed outlier: 3.695A pdb=" N GLN 4 208 " --> pdb=" O VAL 4 220 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS 4 216 " --> pdb=" O VAL 4 212 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain '4' and resid 289 through 293 removed outlier: 4.123A pdb=" N SER 4 307 " --> pdb=" O CYS 4 302 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'O' and resid 17 through 21 removed outlier: 4.261A pdb=" N ASP O 17 " --> pdb=" O VAL O 72 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL O 72 " --> pdb=" O ASP O 17 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'O' and resid 30 through 36 removed outlier: 3.512A pdb=" N GLY O 43 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE O 41 " --> pdb=" O LEU O 35 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'O' and resid 73 through 77 Processing sheet with id=105, first strand: chain 'O' and resid 223 through 229 removed outlier: 4.816A pdb=" N THR O 239 " --> pdb=" O PRO O 223 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG O 233 " --> pdb=" O ILE O 229 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR O 240 " --> pdb=" O VAL O 188 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL O 188 " --> pdb=" O THR O 240 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP O 193 " --> pdb=" O GLN O 271 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU O 195 " --> pdb=" O ASN O 269 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL O 267 " --> pdb=" O ALA O 197 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'Y' and resid 81 through 89 removed outlier: 3.580A pdb=" N PHE Y 132 " --> pdb=" O GLY Y 82 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU Y 126 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE Y 42 " --> pdb=" O VAL Y 127 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE Y 44 " --> pdb=" O HIS Y 129 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER Y 131 " --> pdb=" O ILE Y 44 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR Y 46 " --> pdb=" O SER Y 131 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL Y 133 " --> pdb=" O THR Y 46 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA Y 154 " --> pdb=" O ASN Y 43 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY Y 45 " --> pdb=" O ALA Y 154 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'Y' and resid 277 through 282 removed outlier: 5.412A pdb=" N GLY Y 277 " --> pdb=" O THR Y 341 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR Y 341 " --> pdb=" O GLY Y 277 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Y 279 " --> pdb=" O VAL Y 339 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL Y 339 " --> pdb=" O ALA Y 279 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'Y' and resid 313 through 318 removed outlier: 4.096A pdb=" N ILE Y 314 " --> pdb=" O VAL Y 296 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL Y 296 " --> pdb=" O ILE Y 314 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN Y 292 " --> pdb=" O ILE Y 318 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL Y 357 " --> pdb=" O ARG Y 297 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'Y' and resid 370 through 375 removed outlier: 5.704A pdb=" N ASP Y 423 " --> pdb=" O TYR Y 375 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU Y 424 " --> pdb=" O LYS Y 421 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA Y 419 " --> pdb=" O LYS Y 426 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'Y' and resid 412 through 416 removed outlier: 4.007A pdb=" N THR Y 413 " --> pdb=" O VAL Y 406 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY Y 415 " --> pdb=" O LEU Y 404 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU Y 404 " --> pdb=" O GLY Y 415 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N VAL Y 403 " --> pdb=" O ARG Y 446 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG Y 446 " --> pdb=" O VAL Y 403 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA Y 442 " --> pdb=" O ASN Y 407 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE Y 441 " --> pdb=" O TRP Y 456 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP Y 456 " --> pdb=" O ILE Y 441 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU Y 443 " --> pdb=" O ILE Y 454 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS Y 450 " --> pdb=" O VAL Y 447 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'Z' and resid 70 through 75 removed outlier: 5.227A pdb=" N ASN Z 70 " --> pdb=" O GLN Z 86 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS Z 42 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE Z 35 " --> pdb=" O HIS Z 111 " (cutoff:3.500A) 3667 hydrogen bonds defined for protein. 10905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1271 hydrogen bonds 2014 hydrogen bond angles 0 basepair planarities 508 basepair parallelities 970 stacking parallelities Total time for adding SS restraints: 79.70 Time building geometry restraints manager: 42.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 16397 1.32 - 1.44: 42252 1.44 - 1.57: 60776 1.57 - 1.70: 3568 1.70 - 1.82: 595 Bond restraints: 123588 Sorted by residual: bond pdb=" O3' U 2 367 " pdb=" P U 2 368 " ideal model delta sigma weight residual 1.607 1.514 0.093 1.50e-02 4.44e+03 3.84e+01 bond pdb=" O3' G 21206 " pdb=" P G 21207 " ideal model delta sigma weight residual 1.607 1.540 0.067 1.50e-02 4.44e+03 2.02e+01 bond pdb=" O3' U 21681 " pdb=" P C 21682 " ideal model delta sigma weight residual 1.607 1.542 0.065 1.50e-02 4.44e+03 1.88e+01 bond pdb=" O3' A 21850 " pdb=" P A 21851 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.50e-02 4.44e+03 1.84e+01 bond pdb=" O3' U 21848 " pdb=" P G 21849 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.50e+01 ... (remaining 123583 not shown) Histogram of bond angle deviations from ideal: 88.33 - 98.35: 7 98.35 - 108.36: 22388 108.36 - 118.37: 84248 118.37 - 128.39: 66364 128.39 - 138.40: 2707 Bond angle restraints: 175714 Sorted by residual: angle pdb=" O2' A 21850 " pdb=" C2' A 21850 " pdb=" C1' A 21850 " ideal model delta sigma weight residual 108.40 88.33 20.07 1.50e+00 4.44e-01 1.79e+02 angle pdb=" O2' G 21849 " pdb=" C2' G 21849 " pdb=" C1' G 21849 " ideal model delta sigma weight residual 108.40 92.31 16.09 1.50e+00 4.44e-01 1.15e+02 angle pdb=" O2' C 21683 " pdb=" C2' C 21683 " pdb=" C1' C 21683 " ideal model delta sigma weight residual 108.40 92.93 15.47 1.50e+00 4.44e-01 1.06e+02 angle pdb=" O2' A 21208 " pdb=" C2' A 21208 " pdb=" C1' A 21208 " ideal model delta sigma weight residual 108.40 96.48 11.92 1.50e+00 4.44e-01 6.32e+01 angle pdb=" C4' A 21208 " pdb=" C3' A 21208 " pdb=" O3' A 21208 " ideal model delta sigma weight residual 113.00 124.44 -11.44 1.50e+00 4.44e-01 5.82e+01 ... (remaining 175709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 71005 35.93 - 71.86: 4253 71.86 - 107.79: 595 107.79 - 143.72: 7 143.72 - 179.65: 32 Dihedral angle restraints: 75892 sinusoidal: 45652 harmonic: 30240 Sorted by residual: dihedral pdb=" CA HIS L 432 " pdb=" C HIS L 432 " pdb=" N PRO L 433 " pdb=" CA PRO L 433 " ideal model delta harmonic sigma weight residual 180.00 124.56 55.44 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA THR O 184 " pdb=" C THR O 184 " pdb=" N PRO O 185 " pdb=" CA PRO O 185 " ideal model delta harmonic sigma weight residual -180.00 -128.01 -51.99 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ALA Y 51 " pdb=" C ALA Y 51 " pdb=" N HIS Y 52 " pdb=" CA HIS Y 52 " ideal model delta harmonic sigma weight residual -180.00 -132.75 -47.25 0 5.00e+00 4.00e-02 8.93e+01 ... (remaining 75889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 19280 0.087 - 0.173: 1893 0.173 - 0.260: 129 0.260 - 0.346: 19 0.346 - 0.433: 6 Chirality restraints: 21327 Sorted by residual: chirality pdb=" C3' G 21849 " pdb=" C4' G 21849 " pdb=" O3' G 21849 " pdb=" C2' G 21849 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C3' A 21208 " pdb=" C4' A 21208 " pdb=" O3' A 21208 " pdb=" C2' A 21208 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C1' C 21682 " pdb=" O4' C 21682 " pdb=" C2' C 21682 " pdb=" N1 C 21682 " both_signs ideal model delta sigma weight residual False 2.45 2.02 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 21324 not shown) Planarity restraints: 15840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS L 432 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO L 433 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO L 433 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO L 433 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A 21850 " 0.037 2.00e-02 2.50e+03 2.67e-02 1.96e+01 pdb=" N9 A 21850 " -0.074 2.00e-02 2.50e+03 pdb=" C8 A 21850 " 0.016 2.00e-02 2.50e+03 pdb=" N7 A 21850 " 0.012 2.00e-02 2.50e+03 pdb=" C5 A 21850 " 0.009 2.00e-02 2.50e+03 pdb=" C6 A 21850 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A 21850 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A 21850 " 0.014 2.00e-02 2.50e+03 pdb=" C2 A 21850 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 21850 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A 21850 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21849 " 0.033 2.00e-02 2.50e+03 2.35e-02 1.66e+01 pdb=" N9 G 21849 " -0.059 2.00e-02 2.50e+03 pdb=" C8 G 21849 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 21849 " 0.022 2.00e-02 2.50e+03 pdb=" C5 G 21849 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 21849 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G 21849 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G 21849 " -0.029 2.00e-02 2.50e+03 pdb=" C2 G 21849 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G 21849 " 0.014 2.00e-02 2.50e+03 pdb=" N3 G 21849 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G 21849 " -0.012 2.00e-02 2.50e+03 ... (remaining 15837 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 2534 2.64 - 3.21: 94864 3.21 - 3.77: 211300 3.77 - 4.34: 284565 4.34 - 4.90: 413050 Nonbonded interactions: 1006313 Sorted by model distance: nonbonded pdb=" O3B GTP Y 501 " pdb="MG MG Y 502 " model vdw 2.079 2.170 nonbonded pdb=" OG SER Y 55 " pdb="MG MG Y 502 " model vdw 2.082 2.170 nonbonded pdb=" OG1 THR Y 78 " pdb="MG MG Y 502 " model vdw 2.098 2.170 nonbonded pdb=" O2A GTP Y 501 " pdb="MG MG Y 502 " model vdw 2.103 2.170 nonbonded pdb=" OG SER V 124 " pdb=" OD1 ASP V 126 " model vdw 2.192 2.440 ... (remaining 1006308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.060 Extract box with map and model: 13.500 Check model and map are aligned: 1.300 Set scattering table: 0.770 Process input model: 341.460 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 372.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.007 0.101 123588 Z= 0.407 Angle : 0.921 20.070 175714 Z= 0.478 Chirality : 0.052 0.433 21327 Planarity : 0.006 0.122 15840 Dihedral : 20.114 179.655 56272 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 0.33 % Allowed : 7.30 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.81 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.07), residues: 10224 helix: -2.78 (0.06), residues: 4048 sheet: -1.62 (0.12), residues: 1546 loop : -2.51 (0.08), residues: 4630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP k 82 HIS 0.013 0.001 HIS C 674 PHE 0.040 0.002 PHE d 236 TYR 0.025 0.002 TYR v 61 ARG 0.010 0.001 ARG e 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1067 time to evaluate : 7.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 1092 average time/residue: 2.0031 time to fit residues: 3002.3621 Evaluate side-chains 891 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 880 time to evaluate : 7.783 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 3 average time/residue: 1.0993 time to fit residues: 15.2095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 1009 optimal weight: 30.0000 chunk 905 optimal weight: 30.0000 chunk 502 optimal weight: 3.9990 chunk 309 optimal weight: 50.0000 chunk 610 optimal weight: 6.9990 chunk 483 optimal weight: 0.9990 chunk 936 optimal weight: 8.9990 chunk 362 optimal weight: 20.0000 chunk 569 optimal weight: 1.9990 chunk 697 optimal weight: 8.9990 chunk 1085 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 9 GLN a 132 GLN p 40 ASN p 149 GLN p 157 GLN p 160 GLN p 232 HIS ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 235 ASN Q 80 HIS q 8 HIS q 50 ASN q 209 HIS ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 56 ASN r 59 GLN r 110 ASN s 44 ASN s 73 GLN s 114 GLN s 126 HIS t 64 ASN c 132 GLN c 154 GLN n 13 GLN n 112 HIS m 58 HIS y 29 HIS y 35 ASN z 22 GLN R 26 GLN R 65 GLN T 15 GLN w 26 ASN w 29 HIS b 57 ASN e 31 ASN e 51 HIS e 74 ASN e 82 ASN e 83 ASN e 186 ASN u 32 HIS ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 15 ASN o 114 HIS g 24 HIS g 80 GLN g 86 GLN g 97 GLN g 114 GLN k 42 HIS k 85 ASN k 120 HIS x 11 GLN x 42 HIS x 117 GLN x 128 GLN ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 HIS l 26 ASN ** U 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 HIS ** V 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 ASN i 38 ASN i 79 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN B 518 HIS A 16 ASN A 25 GLN A 109 GLN A 166 ASN ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 433 ASN A 466 GLN A 477 HIS A 498 ASN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN C 364 ASN C 377 ASN C 430 ASN C 433 ASN C 467 GLN C 595 GLN C 600 HIS C 615 GLN C 648 GLN C 678 ASN C 715 HIS ** C 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 828 ASN C 870 ASN E 33 ASN E 39 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 125 GLN E 231 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 361 ASN E 373 ASN E 390 HIS ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 ASN F 140 ASN F 270 GLN F 280 GLN F 342 ASN F 351 ASN H 52 HIS ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 278 GLN ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 337 ASN K 10 ASN K 25 ASN ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN K 68 GLN L 223 ASN L 225 HIS L 263 HIS L 281 HIS L 300 ASN L 338 ASN L 363 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS M 108 ASN M 116 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 199 GLN ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 257 GLN M 259 ASN M 302 GLN N 57 ASN N 73 HIS N 178 GLN N 300 GLN N 336 ASN N 469 GLN N 474 ASN ** 4 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 235 HIS 4 266 GLN 4 301 GLN O 178 ASN Y 71 ASN Z 36 GLN Z 37 GLN ** Z 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 123588 Z= 0.290 Angle : 0.644 14.067 175714 Z= 0.333 Chirality : 0.042 0.318 21327 Planarity : 0.005 0.111 15840 Dihedral : 20.529 179.805 37778 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 2.39 % Allowed : 14.60 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.08), residues: 10224 helix: -0.83 (0.07), residues: 4149 sheet: -1.22 (0.13), residues: 1544 loop : -2.09 (0.08), residues: 4531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Y 451 HIS 0.010 0.001 HIS L 432 PHE 0.030 0.001 PHE q 86 TYR 0.017 0.001 TYR B 525 ARG 0.011 0.000 ARG G 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 915 time to evaluate : 7.829 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: 189 outliers final: 70 residues processed: 1015 average time/residue: 1.9221 time to fit residues: 2725.3272 Evaluate side-chains 935 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 865 time to evaluate : 7.760 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 43 residues processed: 29 average time/residue: 0.9981 time to fit residues: 60.7242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 603 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 chunk 903 optimal weight: 50.0000 chunk 738 optimal weight: 7.9990 chunk 299 optimal weight: 7.9990 chunk 1087 optimal weight: 9.9990 chunk 1174 optimal weight: 8.9990 chunk 968 optimal weight: 8.9990 chunk 1078 optimal weight: 8.9990 chunk 370 optimal weight: 9.9990 chunk 872 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 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 HIS q 188 ASN ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN m 105 ASN z 94 HIS e 29 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 19 GLN g 114 GLN k 85 ASN h 85 HIS ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN U 135 HIS V 14 HIS V 104 HIS ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 522 ASN ** B 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 GLN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 HIS ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 ASN H 58 GLN ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 GLN ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 ASN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 257 GLN M 259 ASN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 ASN 4 221 ASN ** O 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 111 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.136 123588 Z= 0.498 Angle : 0.725 13.593 175714 Z= 0.370 Chirality : 0.047 0.363 21327 Planarity : 0.005 0.109 15840 Dihedral : 20.536 179.883 37778 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.46 % Favored : 94.48 % Rotamer: Outliers : 3.23 % Allowed : 16.60 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.81 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.08), residues: 10224 helix: -0.05 (0.08), residues: 4164 sheet: -1.11 (0.13), residues: 1550 loop : -1.90 (0.08), residues: 4510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP u 64 HIS 0.010 0.001 HIS t 22 PHE 0.039 0.002 PHE l 14 TYR 0.037 0.002 TYR V 228 ARG 0.008 0.001 ARG F 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 881 time to evaluate : 7.804 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: 255 outliers final: 144 residues processed: 1043 average time/residue: 1.8306 time to fit residues: 2702.3395 Evaluate side-chains 995 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 851 time to evaluate : 7.782 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 103 residues processed: 46 average time/residue: 1.0737 time to fit residues: 93.8579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 1074 optimal weight: 5.9990 chunk 817 optimal weight: 6.9990 chunk 564 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 518 optimal weight: 4.9990 chunk 730 optimal weight: 20.0000 chunk 1091 optimal weight: 10.0000 chunk 1155 optimal weight: 40.0000 chunk 570 optimal weight: 0.1980 chunk 1034 optimal weight: 50.0000 chunk 311 optimal weight: 50.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 29 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 ASN g 114 GLN ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 117 GLN ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 ASN ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 226 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 876 HIS ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 344 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 123588 Z= 0.287 Angle : 0.630 13.377 175714 Z= 0.323 Chirality : 0.042 0.363 21327 Planarity : 0.004 0.106 15840 Dihedral : 20.461 179.924 37778 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 3.28 % Allowed : 18.01 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.54 % Twisted General : 0.04 % 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: -1.11 (0.08), residues: 10224 helix: 0.42 (0.08), residues: 4151 sheet: -0.99 (0.13), residues: 1578 loop : -1.73 (0.09), residues: 4495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 482 HIS 0.010 0.001 HIS E 225 PHE 0.034 0.001 PHE q 86 TYR 0.028 0.001 TYR V 228 ARG 0.009 0.000 ARG s 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 883 time to evaluate : 7.926 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: 259 outliers final: 147 residues processed: 1071 average time/residue: 1.8261 time to fit residues: 2781.4714 Evaluate side-chains 1006 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 859 time to evaluate : 7.802 Switching outliers to nearest non-outliers outliers start: 147 outliers final: 120 residues processed: 31 average time/residue: 1.1532 time to fit residues: 68.9866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 962 optimal weight: 20.0000 chunk 655 optimal weight: 6.9990 chunk 16 optimal weight: 0.1980 chunk 860 optimal weight: 20.0000 chunk 476 optimal weight: 10.0000 chunk 985 optimal weight: 8.9990 chunk 798 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 589 optimal weight: 10.0000 chunk 1036 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 26 ASN w 62 GLN e 29 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 GLN ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 85 ASN x 10 ASN ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 ASN ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN B 538 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 221 ASN ** O 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 95 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 123588 Z= 0.260 Angle : 0.618 19.954 175714 Z= 0.316 Chirality : 0.041 0.389 21327 Planarity : 0.004 0.108 15840 Dihedral : 20.390 179.537 37778 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 3.41 % Allowed : 18.80 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -0.85 (0.08), residues: 10224 helix: 0.67 (0.08), residues: 4158 sheet: -0.92 (0.13), residues: 1597 loop : -1.60 (0.09), residues: 4469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 482 HIS 0.019 0.001 HIS C 876 PHE 0.031 0.001 PHE q 86 TYR 0.025 0.001 TYR V 228 ARG 0.011 0.000 ARG r 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 890 time to evaluate : 7.846 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 outliers start: 269 outliers final: 165 residues processed: 1089 average time/residue: 1.8215 time to fit residues: 2831.4905 Evaluate side-chains 1009 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 844 time to evaluate : 7.826 Switching outliers to nearest non-outliers outliers start: 165 outliers final: 127 residues processed: 41 average time/residue: 1.0881 time to fit residues: 86.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 388 optimal weight: 10.0000 chunk 1040 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 678 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 1156 optimal weight: 20.0000 chunk 959 optimal weight: 40.0000 chunk 535 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 382 optimal weight: 8.9990 chunk 606 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 HIS c 154 GLN w 26 ASN w 62 GLN e 29 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 104 GLN g 114 GLN ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 85 ASN ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 339 HIS Y 85 ASN Z 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 123588 Z= 0.402 Angle : 0.686 14.834 175714 Z= 0.348 Chirality : 0.045 0.419 21327 Planarity : 0.005 0.107 15840 Dihedral : 20.407 179.910 37778 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 3.30 % Allowed : 19.90 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.54 % Twisted General : 0.04 % 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: -0.82 (0.08), residues: 10224 helix: 0.72 (0.08), residues: 4171 sheet: -0.95 (0.13), residues: 1587 loop : -1.59 (0.09), residues: 4466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 363 HIS 0.009 0.001 HIS t 22 PHE 0.034 0.002 PHE U 136 TYR 0.020 0.001 TYR V 228 ARG 0.011 0.001 ARG s 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 861 time to evaluate : 7.899 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: 261 outliers final: 176 residues processed: 1053 average time/residue: 1.7792 time to fit residues: 2665.8630 Evaluate side-chains 1024 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 848 time to evaluate : 7.786 Switching outliers to nearest non-outliers outliers start: 176 outliers final: 143 residues processed: 37 average time/residue: 1.0607 time to fit residues: 77.3336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 1114 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 658 optimal weight: 10.0000 chunk 844 optimal weight: 4.9990 chunk 654 optimal weight: 50.0000 chunk 973 optimal weight: 20.0000 chunk 645 optimal weight: 8.9990 chunk 1151 optimal weight: 40.0000 chunk 720 optimal weight: 6.9990 chunk 702 optimal weight: 2.9990 chunk 531 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 HIS b 174 HIS ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 GLN k 85 ASN U 91 ASN V 117 ASN ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 HIS ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 225 HIS L 229 ASN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN 4 221 ASN O 125 GLN ** O 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 ASN Z 95 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 123588 Z= 0.340 Angle : 0.664 14.363 175714 Z= 0.336 Chirality : 0.043 0.421 21327 Planarity : 0.004 0.109 15840 Dihedral : 20.400 179.862 37778 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 3.27 % Allowed : 20.46 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -0.69 (0.08), residues: 10224 helix: 0.83 (0.08), residues: 4169 sheet: -0.91 (0.13), residues: 1572 loop : -1.53 (0.09), residues: 4483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 582 HIS 0.007 0.001 HIS t 22 PHE 0.042 0.001 PHE F 307 TYR 0.018 0.001 TYR V 228 ARG 0.012 0.000 ARG G 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 867 time to evaluate : 7.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 258 outliers final: 193 residues processed: 1067 average time/residue: 1.8149 time to fit residues: 2762.5877 Evaluate side-chains 1045 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 852 time to evaluate : 7.824 Switching outliers to nearest non-outliers outliers start: 193 outliers final: 160 residues processed: 38 average time/residue: 1.0835 time to fit residues: 81.0945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 712 optimal weight: 10.0000 chunk 459 optimal weight: 3.9990 chunk 687 optimal weight: 50.0000 chunk 346 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 732 optimal weight: 20.0000 chunk 784 optimal weight: 50.0000 chunk 569 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 905 optimal weight: 40.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 HIS g 114 GLN k 85 ASN U 91 ASN V 117 ASN V 188 HIS ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN B 538 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN L 241 ASN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN Y 85 ASN Z 95 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 123588 Z= 0.196 Angle : 0.619 13.975 175714 Z= 0.312 Chirality : 0.040 0.416 21327 Planarity : 0.004 0.107 15840 Dihedral : 20.330 179.188 37778 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 2.89 % Allowed : 21.22 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -0.50 (0.08), residues: 10224 helix: 1.01 (0.08), residues: 4161 sheet: -0.82 (0.13), residues: 1584 loop : -1.43 (0.09), residues: 4479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 482 HIS 0.005 0.001 HIS C 876 PHE 0.031 0.001 PHE U 136 TYR 0.034 0.001 TYR M 192 ARG 0.014 0.000 ARG s 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 880 time to evaluate : 7.839 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: 228 outliers final: 170 residues processed: 1062 average time/residue: 1.8836 time to fit residues: 2877.8250 Evaluate side-chains 1019 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 849 time to evaluate : 7.824 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 153 residues processed: 20 average time/residue: 1.0274 time to fit residues: 46.8491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 1047 optimal weight: 30.0000 chunk 1103 optimal weight: 9.9990 chunk 1006 optimal weight: 50.0000 chunk 1073 optimal weight: 20.0000 chunk 646 optimal weight: 40.0000 chunk 467 optimal weight: 9.9990 chunk 842 optimal weight: 5.9990 chunk 329 optimal weight: 10.0000 chunk 969 optimal weight: 40.0000 chunk 1015 optimal weight: 9.9990 chunk 1069 optimal weight: 0.2980 overall best weight: 7.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 HIS c 154 GLN g 114 GLN k 85 ASN U 91 ASN V 117 ASN ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN B 538 GLN A 159 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 235 HIS O 125 GLN O 178 ASN Z 95 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 123588 Z= 0.426 Angle : 0.715 15.179 175714 Z= 0.360 Chirality : 0.046 0.403 21327 Planarity : 0.005 0.110 15840 Dihedral : 20.375 179.957 37778 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 2.89 % Allowed : 21.84 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -0.56 (0.08), residues: 10224 helix: 0.94 (0.08), residues: 4185 sheet: -0.83 (0.13), residues: 1597 loop : -1.46 (0.09), residues: 4442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 182 HIS 0.007 0.001 HIS t 22 PHE 0.044 0.002 PHE F 307 TYR 0.021 0.001 TYR M 192 ARG 0.020 0.001 ARG G 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 853 time to evaluate : 7.965 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: 228 outliers final: 177 residues processed: 1036 average time/residue: 1.8670 time to fit residues: 2746.8897 Evaluate side-chains 1024 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 847 time to evaluate : 7.828 Switching outliers to nearest non-outliers outliers start: 177 outliers final: 157 residues processed: 23 average time/residue: 1.1059 time to fit residues: 53.1416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 704 optimal weight: 50.0000 chunk 1134 optimal weight: 20.0000 chunk 692 optimal weight: 6.9990 chunk 538 optimal weight: 2.9990 chunk 788 optimal weight: 40.0000 chunk 1190 optimal weight: 3.9990 chunk 1095 optimal weight: 20.0000 chunk 948 optimal weight: 50.0000 chunk 98 optimal weight: 0.9980 chunk 732 optimal weight: 10.0000 chunk 581 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 GLN k 85 ASN U 91 ASN V 117 ASN ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN L 229 ASN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 221 ASN O 125 GLN O 178 ASN Z 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 123588 Z= 0.271 Angle : 0.665 16.799 175714 Z= 0.335 Chirality : 0.042 0.441 21327 Planarity : 0.004 0.110 15840 Dihedral : 20.349 179.449 37778 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 2.33 % Allowed : 22.48 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -0.45 (0.08), residues: 10224 helix: 1.03 (0.08), residues: 4169 sheet: -0.75 (0.13), residues: 1595 loop : -1.40 (0.09), residues: 4460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP E 170 HIS 0.007 0.001 HIS U 139 PHE 0.031 0.001 PHE q 86 TYR 0.021 0.001 TYR v 114 ARG 0.017 0.000 ARG B 505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20448 Ramachandran restraints generated. 10224 Oldfield, 0 Emsley, 10224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 866 time to evaluate : 7.898 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 outliers start: 184 outliers final: 161 residues processed: 1029 average time/residue: 1.8858 time to fit residues: 2743.0555 Evaluate side-chains 1012 residues out of total 9096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 851 time to evaluate : 7.820 Switching outliers to nearest non-outliers outliers start: 161 outliers final: 152 residues processed: 12 average time/residue: 1.0124 time to fit residues: 31.3224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1195 random chunks: chunk 753 optimal weight: 50.0000 chunk 1009 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 874 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 949 optimal weight: 8.9990 chunk 397 optimal weight: 10.0000 chunk 975 optimal weight: 50.0000 chunk 120 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 179 ASN ** d 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 GLN k 85 ASN U 91 ASN ** V 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN B 538 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 355 ASN ** 4 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN O 178 ASN Z 95 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.109979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087789 restraints weight = 293949.472| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.06 r_work: 0.2597 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 123588 Z= 0.395 Angle : 0.718 21.462 175714 Z= 0.361 Chirality : 0.045 0.445 21327 Planarity : 0.005 0.112 15840 Dihedral : 20.367 179.934 37778 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 2.51 % Allowed : 22.45 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.10 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -0.51 (0.08), residues: 10224 helix: 0.96 (0.08), residues: 4186 sheet: -0.78 (0.13), residues: 1595 loop : -1.42 (0.09), residues: 4443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP E 182 HIS 0.010 0.001 HIS U 139 PHE 0.044 0.002 PHE F 307 TYR 0.027 0.001 TYR H 99 ARG 0.022 0.001 ARG G 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38900.35 seconds wall clock time: 674 minutes 48.31 seconds (40488.31 seconds total)