Starting phenix.real_space_refine on Mon Mar 11 20:57:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egc_31112/03_2024/7egc_31112_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egc_31112/03_2024/7egc_31112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egc_31112/03_2024/7egc_31112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egc_31112/03_2024/7egc_31112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egc_31112/03_2024/7egc_31112_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egc_31112/03_2024/7egc_31112_updated.pdb" } resolution = 3.9 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= -0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 16 6.06 5 P 142 5.49 5 Mg 1 5.21 5 S 638 5.16 5 C 71327 2.51 5 N 19733 2.21 5 O 21268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 254": "OE1" <-> "OE2" Residue "0 ARG 295": "NH1" <-> "NH2" Residue "1 PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 361": "OE1" <-> "OE2" Residue "4 GLU 189": "OE1" <-> "OE2" Residue "4 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 419": "NH1" <-> "NH2" Residue "6 GLU 422": "OE1" <-> "OE2" Residue "6 GLU 434": "OE1" <-> "OE2" Residue "6 GLU 619": "OE1" <-> "OE2" Residue "6 ARG 678": "NH1" <-> "NH2" Residue "8 GLU 68": "OE1" <-> "OE2" Residue "8 PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 99": "OE1" <-> "OE2" Residue "8 GLU 126": "OE1" <-> "OE2" Residue "8 GLU 147": "OE1" <-> "OE2" Residue "8 GLU 227": "OE1" <-> "OE2" Residue "9 GLU 16": "OE1" <-> "OE2" Residue "9 GLU 49": "OE1" <-> "OE2" Residue "9 ARG 77": "NH1" <-> "NH2" Residue "9 GLU 185": "OE1" <-> "OE2" Residue "9 GLU 240": "OE1" <-> "OE2" Residue "9 GLU 263": "OE1" <-> "OE2" Residue "9 GLU 269": "OE1" <-> "OE2" Residue "9 ARG 279": "NH1" <-> "NH2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A ARG 1181": "NH1" <-> "NH2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ARG 966": "NH1" <-> "NH2" Residue "B TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 881": "NH1" <-> "NH2" Residue "D GLU 884": "OE1" <-> "OE2" Residue "D ARG 909": "NH1" <-> "NH2" Residue "D GLU 954": "OE1" <-> "OE2" Residue "D GLU 960": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "E ARG 450": "NH1" <-> "NH2" Residue "E ARG 452": "NH1" <-> "NH2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "E PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 607": "NH1" <-> "NH2" Residue "E GLU 763": "OE1" <-> "OE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ARG 284": "NH1" <-> "NH2" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 330": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "I TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 119": "NH1" <-> "NH2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "P GLU 320": "OE1" <-> "OE2" Residue "P GLU 326": "OE1" <-> "OE2" Residue "Q GLU 317": "OE1" <-> "OE2" Residue "R ARG 28": "NH1" <-> "NH2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 112": "NH1" <-> "NH2" Residue "R ARG 127": "NH1" <-> "NH2" Residue "R ARG 248": "NH1" <-> "NH2" Residue "R ARG 290": "NH1" <-> "NH2" Residue "T GLU 134": "OE1" <-> "OE2" Residue "T ARG 177": "NH1" <-> "NH2" Residue "U ARG 111": "NH1" <-> "NH2" Residue "U ARG 113": "NH1" <-> "NH2" Residue "U ARG 174": "NH1" <-> "NH2" Residue "U GLU 182": "OE1" <-> "OE2" Residue "U ARG 192": "NH1" <-> "NH2" Residue "V GLU 169": "OE1" <-> "OE2" Residue "V GLU 172": "OE1" <-> "OE2" Residue "V GLU 173": "OE1" <-> "OE2" Residue "V GLU 230": "OE1" <-> "OE2" Residue "d GLU 847": "OE1" <-> "OE2" Residue "d GLU 848": "OE1" <-> "OE2" Residue "d ARG 851": "NH1" <-> "NH2" Residue "d GLU 858": "OE1" <-> "OE2" Residue "d ARG 865": "NH1" <-> "NH2" Residue "d GLU 870": "OE1" <-> "OE2" Residue "d ARG 881": "NH1" <-> "NH2" Residue "d ARG 909": "NH1" <-> "NH2" Residue "d GLU 954": "OE1" <-> "OE2" Residue "d ARG 1057": "NH1" <-> "NH2" Residue "e TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 250": "OE1" <-> "OE2" Residue "e GLU 257": "OE1" <-> "OE2" Residue "e GLU 335": "OE1" <-> "OE2" Residue "e ARG 365": "NH1" <-> "NH2" Residue "e ARG 450": "NH1" <-> "NH2" Residue "e ARG 452": "NH1" <-> "NH2" Residue "e ARG 607": "NH1" <-> "NH2" Residue "e ARG 634": "NH1" <-> "NH2" Residue "e GLU 706": "OE1" <-> "OE2" Residue "f GLU 17": "OE1" <-> "OE2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 109": "OE1" <-> "OE2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f GLU 229": "OE1" <-> "OE2" Residue "f ARG 239": "NH1" <-> "NH2" Residue "f ARG 258": "NH1" <-> "NH2" Residue "f ARG 284": "NH1" <-> "NH2" Residue "f GLU 303": "OE1" <-> "OE2" Residue "f ARG 315": "NH1" <-> "NH2" Residue "f ARG 373": "NH1" <-> "NH2" Residue "f ARG 395": "NH1" <-> "NH2" Residue "i ARG 34": "NH1" <-> "NH2" Residue "i GLU 41": "OE1" <-> "OE2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i ARG 119": "NH1" <-> "NH2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 167": "OE1" <-> "OE2" Residue "k GLU 174": "OE1" <-> "OE2" Residue "k ARG 192": "NH1" <-> "NH2" Residue "k ARG 193": "NH1" <-> "NH2" Residue "l GLU 121": "OE1" <-> "OE2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ASP 45": "OD1" <-> "OD2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "m GLU 109": "OE1" <-> "OE2" Residue "o GLU 30": "OE1" <-> "OE2" Residue "o GLU 38": "OE1" <-> "OE2" Residue "o GLU 89": "OE1" <-> "OE2" Residue "o ARG 743": "NH1" <-> "NH2" Residue "o ARG 749": "NH1" <-> "NH2" Residue "o PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 869": "OE1" <-> "OE2" Residue "o GLU 1097": "OE1" <-> "OE2" Residue "o GLU 1349": "OE1" <-> "OE2" Residue "o TYR 1482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 1485": "OE1" <-> "OE2" Residue "p TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p GLU 266": "OE1" <-> "OE2" Residue "p GLU 346": "OE1" <-> "OE2" Residue "p GLU 381": "OE1" <-> "OE2" Residue "p GLU 609": "OE1" <-> "OE2" Residue "p GLU 647": "OE1" <-> "OE2" Residue "p ARG 770": "NH1" <-> "NH2" Residue "q ARG 10": "NH1" <-> "NH2" Residue "q PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 207": "OE1" <-> "OE2" Residue "r GLU 15": "OE1" <-> "OE2" Residue "r GLU 54": "OE1" <-> "OE2" Residue "r GLU 106": "OE1" <-> "OE2" Residue "t GLU 86": "OE1" <-> "OE2" Residue "w GLU 19": "OE1" <-> "OE2" Residue "y GLU 97": "OE1" <-> "OE2" Residue "y GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 113129 Number of models: 1 Model: "" Number of chains: 63 Chain: "0" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1774 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 11, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 81 Chain: "1" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2634 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 777 Unresolved non-hydrogen dihedrals: 504 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 318 Chain: "2" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2534 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "3" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2065 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "4" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3579 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain: "5" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 428 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "6" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4880 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "7" Number of atoms: 5833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5833 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 32, 'TRANS': 701} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "8" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2370 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain: "9" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 271} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4511 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 510} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 7796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7796 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 45, 'TRANS': 917} Chain breaks: 1 Chain: "D" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1322 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4364 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3109 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "G" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1180 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 2 Chain: "H" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1633 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 188} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 720 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 6, 'TRANS': 83} Chain breaks: 1 Chain: "L" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 614 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "O" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 771 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1412 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "Q" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 996 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1929 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 872 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain breaks: 1 Chain: "T" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "U" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1476 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain breaks: 1 Chain: "V" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1404 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "X" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1464 Classifications: {'DNA': 71} Link IDs: {'rna3p': 70} Chain: "Y" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1447 Classifications: {'DNA': 71} Link IDs: {'rna3p': 70} Chain: "c" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1011 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "d" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1307 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "e" Number of atoms: 4327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4327 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3081 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 24, 'TRANS': 378} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "i" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 759 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Chain: "k" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 785 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "l" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "m" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 724 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "o" Number of atoms: 11308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11308 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 70, 'TRANS': 1356} 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: "p" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "q" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "r" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "s" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "t" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "u" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "v" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "w" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "x" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "y" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "z" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "0" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "R" 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: "o" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 30 SG CYS 0 6 229.065 130.757 178.661 1.00200.73 S ATOM 48 SG CYS 0 9 230.681 128.519 175.974 1.00206.24 S ATOM 166 SG CYS 0 31 229.760 127.142 180.059 1.00212.05 S ATOM 182 SG CYS 0 34 232.175 129.762 179.361 1.00219.26 S ATOM 243 SG CYS 0 46 240.084 135.336 183.368 1.00221.32 S ATOM 6620 SG CYS 2 345 127.830 121.654 246.343 1.00 75.65 S ATOM 6642 SG CYS 2 348 124.873 120.172 243.618 1.00 64.83 S ATOM 6799 SG CYS 2 368 129.824 119.577 243.701 1.00 71.71 S ATOM 6820 SG CYS 2 371 127.851 122.937 243.255 1.00 71.32 S ATOM 6740 SG CYS 2 360 133.762 132.526 248.660 1.00 84.88 S ATOM 6758 SG CYS 2 363 130.487 131.888 251.125 1.00 87.91 S ATOM 6907 SG CYS 2 382 130.068 131.935 247.159 1.00 71.58 S ATOM 6924 SG CYS 2 385 130.800 135.524 248.897 1.00 74.09 S ATOM 6184 SG CYS 2 291 121.175 156.707 216.092 1.00 79.05 S ATOM 6206 SG CYS 2 294 120.511 158.083 213.034 1.00 89.45 S ATOM 6295 SG CYS 2 305 123.851 156.406 213.943 1.00 81.96 S ATOM 6318 SG CYS 2 308 123.413 160.076 213.678 1.00 86.60 S ATOM 8828 SG CYS 3 268 134.456 155.731 234.311 1.00 65.95 S ATOM 8847 SG CYS 3 271 132.042 154.249 236.366 1.00 64.03 S ATOM 8932 SG CYS 3 282 132.873 157.637 237.438 1.00 77.32 S ATOM 8952 SG CYS 3 285 135.317 154.863 238.464 1.00 82.61 S ATOM 18826 SG CYS 7 116 200.685 151.594 217.838 1.00 57.98 S ATOM 19135 SG CYS 7 155 206.220 155.357 218.819 1.00 71.14 S ATOM 18966 SG CYS 7 134 206.570 149.531 218.880 1.00 58.64 S ATOM 19424 SG CYS 7 190 203.987 153.335 223.594 1.00 60.71 S ATOM 57838 SG CYS R 15 264.065 111.415 123.828 1.00 0.00 S ATOM 57985 SG CYS R 34 264.680 111.850 120.378 1.00 0.00 S ATOM 58007 SG CYS R 37 265.612 108.774 121.203 1.00 0.00 S ATOM 63289 SG CYS U 129 257.451 129.606 148.307 1.00 0.00 S ATOM 63309 SG CYS U 132 255.163 128.089 145.811 1.00 0.00 S ATOM 63481 SG CYS U 154 257.142 125.871 147.987 1.00 0.00 S ATOM 63505 SG CYS U 157 258.906 127.753 145.393 1.00 0.00 S ATOM 82499 SG CYS o 71 244.837 117.362 135.427 1.00215.08 S ATOM 82568 SG CYS o 81 243.978 114.200 133.459 1.00201.81 S ATOM 82803 SG CYS o 111 199.819 111.278 155.730 1.00291.01 S ATOM 82831 SG CYS o 114 202.241 111.059 159.521 1.00287.14 S ATOM 83144 SG CYS o 154 199.010 109.086 158.862 1.00287.91 S ATOM A01IV SG CYS p1119 237.892 102.856 147.831 1.00179.27 S ATOM A01JH SG CYS p1122 234.909 104.356 147.009 1.00181.25 S ATOM A01MO SG CYS p1137 238.383 106.365 147.824 1.00194.80 S ATOM A01N9 SG CYS p1140 235.068 106.008 150.096 1.00200.53 S ATOM A02EG SG CYS q 90 279.308 99.213 79.827 1.00126.45 S ATOM A02FF SG CYS q 94 280.287 99.369 76.585 1.00113.16 S ATOM A02G1 SG CYS q 97 277.233 97.501 77.410 1.00107.06 S ATOM A0814 SG CYS w 17 153.986 112.685 95.087 1.00165.50 S ATOM A081S SG CYS w 20 156.235 114.765 96.970 1.00166.36 S ATOM A0869 SG CYS w 39 155.513 111.958 99.402 1.00170.94 S ATOM A086Y SG CYS w 42 152.928 114.219 98.041 1.00174.09 S ATOM A08GQ SG CYS w 86 171.113 84.554 62.528 1.00138.72 S ATOM A08HE SG CYS w 89 171.194 86.266 59.276 1.00141.27 S ATOM A08N2 SG CYS w 114 174.179 87.085 61.528 1.00129.58 S ATOM A08O1 SG CYS w 119 170.711 88.227 62.251 1.00136.89 S ATOM A08R3 SG CYS x 7 248.466 87.897 65.749 1.00 65.12 S ATOM A08RR SG CYS x 10 250.305 83.728 64.287 1.00 73.64 S ATOM A08Z3 SG CYS x 44 247.099 84.545 64.678 1.00 74.53 S ATOM A08Z9 SG CYS x 45 248.808 86.321 62.126 1.00 74.88 S ATOM A09UU SG CYS z 19 245.597 131.872 75.767 1.00111.16 S ATOM A09VD SG CYS z 22 247.040 133.423 73.011 1.00114.66 S ATOM A09YM SG CYS z 36 247.367 135.088 76.068 1.00121.32 S Time building chain proxies: 42.05, per 1000 atoms: 0.37 Number of scatterers: 113129 At special positions: 0 Unit cell: (294.68, 244.86, 272.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 16 29.99 Fe 4 26.01 S 638 16.00 P 142 15.00 Mg 1 11.99 O 21268 8.00 N 19733 7.00 C 71327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 3 255 " - pdb=" SG CYS 3 257 " distance=2.04 Simple disulfide: pdb=" SG CYS B 945 " - pdb=" SG CYS B 986 " distance=2.07 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: 34.00 Conformation dependent library (CDL) restraints added in 14.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 71000 " pdb="FE4 SF4 71000 " - pdb=" SG CYS 7 190 " pdb="FE2 SF4 71000 " - pdb=" SG CYS 7 155 " pdb="FE1 SF4 71000 " - pdb=" SG CYS 7 116 " pdb="FE3 SF4 71000 " - pdb=" SG CYS 7 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 0 400 " pdb="ZN ZN 0 400 " - pdb=" SG CYS 0 6 " pdb="ZN ZN 0 400 " - pdb=" SG CYS 0 9 " pdb="ZN ZN 0 400 " - pdb=" SG CYS 0 31 " pdb="ZN ZN 0 400 " - pdb=" SG CYS 0 34 " pdb=" ZN 0 401 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 46 " pdb=" ZN 2 401 " pdb="ZN ZN 2 401 " - pdb=" SG CYS 2 345 " pdb="ZN ZN 2 401 " - pdb=" SG CYS 2 371 " pdb="ZN ZN 2 401 " - pdb=" SG CYS 2 368 " pdb="ZN ZN 2 401 " - pdb=" SG CYS 2 348 " pdb=" ZN 2 402 " pdb="ZN ZN 2 402 " - pdb=" SG CYS 2 363 " pdb="ZN ZN 2 402 " - pdb=" SG CYS 2 385 " pdb="ZN ZN 2 402 " - pdb=" SG CYS 2 382 " pdb="ZN ZN 2 402 " - pdb=" SG CYS 2 360 " pdb=" ZN 2 403 " pdb="ZN ZN 2 403 " - pdb=" SG CYS 2 291 " pdb="ZN ZN 2 403 " - pdb=" SG CYS 2 308 " pdb="ZN ZN 2 403 " - pdb=" SG CYS 2 305 " pdb="ZN ZN 2 403 " - pdb=" SG CYS 2 294 " pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 271 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 285 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 268 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 282 " pdb=" ZN R 401 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 34 " pdb="ZN ZN R 401 " - pdb=" NE2 HIS R 18 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 37 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 15 " pdb=" ZN U 501 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 132 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 157 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 129 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 154 " pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" NE2 HIS o 84 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 154 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 111 " pdb=" ZN p1201 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1122 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1119 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1137 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1140 " pdb=" ZN q 301 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 94 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 97 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " Number of angles added : 63 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26382 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: 509 helices and 113 sheets defined 50.2% alpha, 12.2% beta 41 base pairs and 114 stacking pairs defined. Time for finding SS restraints: 76.10 Creating SS restraints... Processing helix chain '0' and resid 31 through 42 removed outlier: 3.814A pdb=" N ARG 0 41 " --> pdb=" O LEU 0 37 " (cutoff:3.500A) Processing helix chain '0' and resid 65 through 83 removed outlier: 4.547A pdb=" N ILE 0 81 " --> pdb=" O LYS 0 77 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR 0 82 " --> pdb=" O VAL 0 78 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASN 0 83 " --> pdb=" O LEU 0 79 " (cutoff:3.500A) Processing helix chain '0' and resid 85 through 90 removed outlier: 3.604A pdb=" N PHE 0 89 " --> pdb=" O ARG 0 85 " (cutoff:3.500A) Proline residue: 0 90 - end of helix No H-bonds generated for 'chain '0' and resid 85 through 90' Processing helix chain '0' and resid 91 through 112 removed outlier: 3.732A pdb=" N TYR 0 95 " --> pdb=" O SER 0 91 " (cutoff:3.500A) Processing helix chain '0' and resid 113 through 132 removed outlier: 4.198A pdb=" N ASN 0 117 " --> pdb=" O VAL 0 113 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR 0 118 " --> pdb=" O ASP 0 114 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP 0 131 " --> pdb=" O LYS 0 127 " (cutoff:3.500A) Processing helix chain '0' and resid 133 through 171 Processing helix chain '0' and resid 267 through 276 removed outlier: 3.794A pdb=" N TYR 0 271 " --> pdb=" O GLY 0 267 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU 0 272 " --> pdb=" O ARG 0 268 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN 0 273 " --> pdb=" O LEU 0 269 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS 0 274 " --> pdb=" O GLY 0 270 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL 0 275 " --> pdb=" O TYR 0 271 " (cutoff:3.500A) Processing helix chain '0' and resid 279 through 286 removed outlier: 4.690A pdb=" N ALA 0 284 " --> pdb=" O PRO 0 280 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY 0 285 " --> pdb=" O GLN 0 281 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY 0 286 " --> pdb=" O ASP 0 282 " (cutoff:3.500A) Processing helix chain '0' and resid 288 through 302 removed outlier: 4.426A pdb=" N ALA 0 292 " --> pdb=" O THR 0 288 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS 0 293 " --> pdb=" O SER 0 289 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER 0 302 " --> pdb=" O GLN 0 298 " (cutoff:3.500A) Processing helix chain '0' and resid 12 through 17 Proline residue: 0 17 - end of helix No H-bonds generated for 'chain '0' and resid 12 through 17' Processing helix chain '1' and resid 107 through 121 removed outlier: 4.212A pdb=" N GLU 1 112 " --> pdb=" O ASN 1 108 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU 1 113 " --> pdb=" O LYS 1 109 " (cutoff:3.500A) Processing helix chain '1' and resid 122 through 132 removed outlier: 3.535A pdb=" N GLN 1 126 " --> pdb=" O PRO 1 122 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU 1 127 " --> pdb=" O VAL 1 123 " (cutoff:3.500A) Processing helix chain '1' and resid 138 through 147 removed outlier: 3.728A pdb=" N ARG 1 146 " --> pdb=" O PHE 1 142 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU 1 147 " --> pdb=" O TRP 1 143 " (cutoff:3.500A) Processing helix chain '1' and resid 152 through 157 removed outlier: 6.254A pdb=" N SER 1 156 " --> pdb=" O THR 1 152 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR 1 157 " --> pdb=" O ASP 1 153 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 152 through 157' Processing helix chain '1' and resid 164 through 169 removed outlier: 6.221A pdb=" N ALA 1 168 " --> pdb=" O VAL 1 164 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA 1 169 " --> pdb=" O GLY 1 165 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 164 through 169' Processing helix chain '1' and resid 190 through 200 Processing helix chain '1' and resid 201 through 211 removed outlier: 3.578A pdb=" N VAL 1 211 " --> pdb=" O TYR 1 207 " (cutoff:3.500A) Processing helix chain '1' and resid 216 through 226 removed outlier: 4.474A pdb=" N GLN 1 226 " --> pdb=" O THR 1 222 " (cutoff:3.500A) Processing helix chain '1' and resid 239 through 256 removed outlier: 4.753A pdb=" N PHE 1 243 " --> pdb=" O SER 1 239 " (cutoff:3.500A) Processing helix chain '1' and resid 268 through 276 Proline residue: 1 276 - end of helix Processing helix chain '1' and resid 295 through 318 Processing helix chain '1' and resid 346 through 366 removed outlier: 4.054A pdb=" N LYS 1 350 " --> pdb=" O GLN 1 346 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG 1 351 " --> pdb=" O PRO 1 347 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU 1 359 " --> pdb=" O GLN 1 355 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR 1 360 " --> pdb=" O GLU 1 356 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLU 1 361 " --> pdb=" O SER 1 357 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP 1 362 " --> pdb=" O ILE 1 358 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU 1 363 " --> pdb=" O GLU 1 359 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN 1 366 " --> pdb=" O ASP 1 362 " (cutoff:3.500A) Processing helix chain '1' and resid 378 through 385 removed outlier: 4.457A pdb=" N TYR 1 382 " --> pdb=" O LYS 1 378 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY 1 385 " --> pdb=" O ARG 1 381 " (cutoff:3.500A) Processing helix chain '1' and resid 396 through 413 removed outlier: 4.204A pdb=" N ILE 1 400 " --> pdb=" O THR 1 396 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE 1 401 " --> pdb=" O SER 1 397 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU 1 412 " --> pdb=" O ARG 1 408 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA 1 413 " --> pdb=" O GLN 1 409 " (cutoff:3.500A) Processing helix chain '1' and resid 420 through 436 removed outlier: 4.515A pdb=" N THR 1 432 " --> pdb=" O SER 1 428 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA 1 433 " --> pdb=" O SER 1 429 " (cutoff:3.500A) Proline residue: 1 436 - end of helix Processing helix chain '1' and resid 455 through 480 Proline residue: 1 480 - end of helix Processing helix chain '1' and resid 485 through 516 removed outlier: 3.517A pdb=" N LYS 1 489 " --> pdb=" O PHE 1 485 " (cutoff:3.500A) Proline residue: 1 507 - end of helix removed outlier: 3.820A pdb=" N GLN 1 515 " --> pdb=" O LYS 1 511 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR 1 516 " --> pdb=" O ILE 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 522 through 547 removed outlier: 3.754A pdb=" N GLU 1 526 " --> pdb=" O VAL 1 522 " (cutoff:3.500A) Processing helix chain '1' and resid 227 through 232 removed outlier: 5.866A pdb=" N ARG 1 232 " --> pdb=" O SER 1 227 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 227 through 232' Processing helix chain '2' and resid 68 through 74 removed outlier: 4.610A pdb=" N GLU 2 72 " --> pdb=" O SER 2 68 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP 2 73 " --> pdb=" O ARG 2 69 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN 2 74 " --> pdb=" O THR 2 70 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 68 through 74' Processing helix chain '2' and resid 79 through 99 Processing helix chain '2' and resid 123 through 138 removed outlier: 4.141A pdb=" N HIS 2 127 " --> pdb=" O ASN 2 123 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP 2 136 " --> pdb=" O LYS 2 132 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET 2 137 " --> pdb=" O LYS 2 133 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR 2 138 " --> pdb=" O ALA 2 134 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 157 removed outlier: 4.703A pdb=" N SER 2 148 " --> pdb=" O SER 2 144 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU 2 149 " --> pdb=" O LEU 2 145 " (cutoff:3.500A) Processing helix chain '2' and resid 181 through 193 removed outlier: 5.048A pdb=" N LYS 2 193 " --> pdb=" O LEU 2 189 " (cutoff:3.500A) Processing helix chain '2' and resid 205 through 215 Processing helix chain '2' and resid 224 through 237 removed outlier: 3.596A pdb=" N TYR 2 228 " --> pdb=" O ASP 2 224 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER 2 237 " --> pdb=" O THR 2 233 " (cutoff:3.500A) Processing helix chain '2' and resid 314 through 327 removed outlier: 4.169A pdb=" N LEU 2 318 " --> pdb=" O SER 2 314 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA 2 319 " --> pdb=" O ALA 2 315 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER 2 321 " --> pdb=" O HIS 2 317 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR 2 322 " --> pdb=" O LEU 2 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N HIS 2 323 " --> pdb=" O ALA 2 319 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS 2 324 " --> pdb=" O ARG 2 320 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU 2 325 " --> pdb=" O SER 2 321 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE 2 326 " --> pdb=" O TYR 2 322 " (cutoff:3.500A) Proline residue: 2 327 - end of helix Processing helix chain '2' and resid 368 through 377 Processing helix chain '2' and resid 382 through 387 removed outlier: 3.730A pdb=" N ILE 2 386 " --> pdb=" O CYS 2 382 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS 2 387 " --> pdb=" O PRO 2 383 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 382 through 387' Processing helix chain '3' and resid 18 through 29 removed outlier: 3.787A pdb=" N GLU 3 29 " --> pdb=" O GLN 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 33 through 53 removed outlier: 4.095A pdb=" N ASN 3 52 " --> pdb=" O HIS 3 48 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG 3 53 " --> pdb=" O LEU 3 49 " (cutoff:3.500A) Processing helix chain '3' and resid 101 through 120 removed outlier: 4.006A pdb=" N ALA 3 107 " --> pdb=" O LEU 3 103 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR 3 120 " --> pdb=" O LYS 3 116 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 152 removed outlier: 5.793A pdb=" N SER 3 136 " --> pdb=" O LEU 3 132 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL 3 151 " --> pdb=" O MET 3 147 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS 3 152 " --> pdb=" O ASN 3 148 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 188 removed outlier: 4.240A pdb=" N ASN 3 179 " --> pdb=" O MET 3 175 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 3 180 " --> pdb=" O ASN 3 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN 3 188 " --> pdb=" O ALA 3 184 " (cutoff:3.500A) Processing helix chain '3' and resid 200 through 211 removed outlier: 3.992A pdb=" N GLY 3 211 " --> pdb=" O CYS 3 207 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 230 removed outlier: 4.480A pdb=" N TYR 3 226 " --> pdb=" O SER 3 222 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU 3 227 " --> pdb=" O LEU 3 223 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 241 removed outlier: 4.179A pdb=" N SER 3 239 " --> pdb=" O GLN 3 235 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLN 3 240 " --> pdb=" O ASP 3 236 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 26 removed outlier: 4.689A pdb=" N LEU 4 23 " --> pdb=" O LEU 4 19 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLY 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU 4 26 " --> pdb=" O PHE 4 22 " (cutoff:3.500A) Processing helix chain '4' and resid 27 through 37 removed outlier: 3.609A pdb=" N ASP 4 32 " --> pdb=" O PRO 4 28 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR 4 35 " --> pdb=" O LEU 4 31 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY 4 36 " --> pdb=" O ASP 4 32 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N HIS 4 37 " --> pdb=" O ARG 4 33 " (cutoff:3.500A) Processing helix chain '4' and resid 38 through 48 removed outlier: 3.774A pdb=" N GLU 4 47 " --> pdb=" O ALA 4 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU 4 48 " --> pdb=" O VAL 4 44 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 61 removed outlier: 5.254A pdb=" N PHE 4 61 " --> pdb=" O MET 4 57 " (cutoff:3.500A) Processing helix chain '4' and resid 67 through 75 removed outlier: 3.795A pdb=" N VAL 4 71 " --> pdb=" O PRO 4 67 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL 4 75 " --> pdb=" O VAL 4 71 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 94 removed outlier: 3.586A pdb=" N GLU 4 84 " --> pdb=" O SER 4 80 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU 4 85 " --> pdb=" O LYS 4 81 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N SER 4 86 " --> pdb=" O ALA 4 82 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG 4 94 " --> pdb=" O LEU 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 123 Processing helix chain '4' and resid 144 through 165 Processing helix chain '4' and resid 172 through 183 removed outlier: 5.861A pdb=" N ALA 4 176 " --> pdb=" O SER 4 172 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN 4 177 " --> pdb=" O GLN 4 173 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY 4 183 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 197 through 207 removed outlier: 4.120A pdb=" N LEU 4 206 " --> pdb=" O GLN 4 202 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP 4 207 " --> pdb=" O PHE 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 208 through 224 removed outlier: 4.040A pdb=" N THR 4 222 " --> pdb=" O GLN 4 218 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA 4 223 " --> pdb=" O TYR 4 219 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN 4 224 " --> pdb=" O LEU 4 220 " (cutoff:3.500A) Processing helix chain '4' and resid 229 through 243 removed outlier: 3.534A pdb=" N ILE 4 233 " --> pdb=" O ASP 4 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE 4 242 " --> pdb=" O PHE 4 238 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER 4 243 " --> pdb=" O GLN 4 239 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 269 Processing helix chain '4' and resid 284 through 290 removed outlier: 3.667A pdb=" N ASN 4 289 " --> pdb=" O ARG 4 285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 4 290 " --> pdb=" O LEU 4 286 " (cutoff:3.500A) Processing helix chain '4' and resid 321 through 332 Processing helix chain '4' and resid 347 through 358 Processing helix chain '4' and resid 360 through 372 removed outlier: 4.387A pdb=" N ILE 4 364 " --> pdb=" O THR 4 360 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE 4 365 " --> pdb=" O ALA 4 361 " (cutoff:3.500A) Processing helix chain '4' and resid 385 through 400 removed outlier: 4.195A pdb=" N ASP 4 389 " --> pdb=" O PRO 4 385 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG 4 398 " --> pdb=" O TRP 4 394 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 429 removed outlier: 3.541A pdb=" N PHE 4 418 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU 4 419 " --> pdb=" O GLN 4 415 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU 4 420 " --> pdb=" O VAL 4 416 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU 4 421 " --> pdb=" O ASP 4 417 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA 4 423 " --> pdb=" O GLU 4 419 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS 4 424 " --> pdb=" O LEU 4 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA 4 425 " --> pdb=" O LEU 4 421 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 4 428 " --> pdb=" O HIS 4 424 " (cutoff:3.500A) Processing helix chain '4' and resid 444 through 462 removed outlier: 3.555A pdb=" N HIS 4 448 " --> pdb=" O THR 4 444 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER 4 449 " --> pdb=" O PRO 4 445 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP 4 450 " --> pdb=" O ALA 4 446 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG 4 453 " --> pdb=" O SER 4 449 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 27 removed outlier: 4.646A pdb=" N GLN 5 18 " --> pdb=" O PRO 5 14 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE 5 19 " --> pdb=" O ALA 5 15 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU 5 20 " --> pdb=" O MET 5 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU 5 21 " --> pdb=" O LYS 5 17 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU 5 23 " --> pdb=" O PHE 5 19 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 60 removed outlier: 4.005A pdb=" N GLU 5 55 " --> pdb=" O ASN 5 51 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY 5 58 " --> pdb=" O GLN 5 54 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU 5 59 " --> pdb=" O GLU 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 104 Processing helix chain '6' and resid 119 through 130 removed outlier: 3.654A pdb=" N GLY 6 130 " --> pdb=" O ALA 6 126 " (cutoff:3.500A) Processing helix chain '6' and resid 132 through 144 Processing helix chain '6' and resid 149 through 160 removed outlier: 3.678A pdb=" N MET 6 153 " --> pdb=" O PRO 6 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS 6 159 " --> pdb=" O PHE 6 155 " (cutoff:3.500A) Processing helix chain '6' and resid 182 through 191 removed outlier: 3.906A pdb=" N ASP 6 191 " --> pdb=" O HIS 6 187 " (cutoff:3.500A) Processing helix chain '6' and resid 192 through 198 Processing helix chain '6' and resid 276 through 288 Processing helix chain '6' and resid 296 through 301 removed outlier: 4.421A pdb=" N SER 6 301 " --> pdb=" O PHE 6 297 " (cutoff:3.500A) Processing helix chain '6' and resid 317 through 329 Processing helix chain '6' and resid 345 through 358 removed outlier: 3.640A pdb=" N GLY 6 350 " --> pdb=" O LYS 6 346 " (cutoff:3.500A) Processing helix chain '6' and resid 367 through 379 removed outlier: 4.315A pdb=" N VAL 6 371 " --> pdb=" O SER 6 367 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU 6 372 " --> pdb=" O ALA 6 368 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN 6 377 " --> pdb=" O GLN 6 373 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE 6 378 " --> pdb=" O TRP 6 374 " (cutoff:3.500A) Processing helix chain '6' and resid 383 through 388 removed outlier: 3.726A pdb=" N SER 6 387 " --> pdb=" O THR 6 383 " (cutoff:3.500A) Processing helix chain '6' and resid 421 through 434 removed outlier: 4.120A pdb=" N MET 6 427 " --> pdb=" O ALA 6 423 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU 6 428 " --> pdb=" O GLU 6 424 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP 6 429 " --> pdb=" O ARG 6 425 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU 6 430 " --> pdb=" O VAL 6 426 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS 6 431 " --> pdb=" O MET 6 427 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR 6 432 " --> pdb=" O GLU 6 428 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN 6 433 " --> pdb=" O TRP 6 429 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 447 removed outlier: 4.332A pdb=" N ILE 6 446 " --> pdb=" O GLU 6 442 " (cutoff:3.500A) Proline residue: 6 447 - end of helix No H-bonds generated for 'chain '6' and resid 442 through 447' Processing helix chain '6' and resid 449 through 458 removed outlier: 4.345A pdb=" N ARG 6 453 " --> pdb=" O LYS 6 449 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU 6 455 " --> pdb=" O PHE 6 451 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 6 458 " --> pdb=" O VAL 6 454 " (cutoff:3.500A) Processing helix chain '6' and resid 480 through 485 Processing helix chain '6' and resid 492 through 500 removed outlier: 3.872A pdb=" N ASN 6 499 " --> pdb=" O GLU 6 495 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY 6 500 " --> pdb=" O LEU 6 496 " (cutoff:3.500A) Processing helix chain '6' and resid 515 through 526 removed outlier: 3.609A pdb=" N ARG 6 520 " --> pdb=" O PRO 6 516 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU 6 521 " --> pdb=" O GLU 6 517 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR 6 522 " --> pdb=" O PHE 6 518 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL 6 523 " --> pdb=" O TYR 6 519 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA 6 524 " --> pdb=" O ARG 6 520 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE 6 525 " --> pdb=" O GLU 6 521 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LYS 6 526 " --> pdb=" O TYR 6 522 " (cutoff:3.500A) Processing helix chain '6' and resid 527 through 537 removed outlier: 4.716A pdb=" N ILE 6 531 " --> pdb=" O THR 6 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET 6 536 " --> pdb=" O LEU 6 532 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASN 6 537 " --> pdb=" O LEU 6 533 " (cutoff:3.500A) Processing helix chain '6' and resid 538 through 555 removed outlier: 3.565A pdb=" N ALA 6 543 " --> pdb=" O ASN 6 539 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG 6 553 " --> pdb=" O LYS 6 549 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG 6 554 " --> pdb=" O PHE 6 550 " (cutoff:3.500A) Processing helix chain '6' and resid 566 through 576 removed outlier: 3.941A pdb=" N GLU 6 570 " --> pdb=" O PHE 6 566 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR 6 571 " --> pdb=" O ALA 6 567 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA 6 572 " --> pdb=" O LEU 6 568 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU 6 575 " --> pdb=" O TYR 6 571 " (cutoff:3.500A) Processing helix chain '6' and resid 585 through 598 removed outlier: 4.022A pdb=" N GLN 6 591 " --> pdb=" O GLY 6 587 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN 6 594 " --> pdb=" O MET 6 590 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE 6 596 " --> pdb=" O ILE 6 592 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS 6 597 " --> pdb=" O LEU 6 593 " (cutoff:3.500A) Processing helix chain '6' and resid 633 through 643 removed outlier: 6.617A pdb=" N ALA 6 637 " --> pdb=" O ARG 6 633 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLN 6 638 " --> pdb=" O ARG 6 634 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY 6 641 " --> pdb=" O ALA 6 637 " (cutoff:3.500A) Processing helix chain '6' and resid 669 through 684 removed outlier: 4.362A pdb=" N LYS 6 675 " --> pdb=" O ALA 6 671 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN 6 677 " --> pdb=" O SER 6 673 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG 6 678 " --> pdb=" O THR 6 674 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE 6 679 " --> pdb=" O LYS 6 675 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP 6 682 " --> pdb=" O ARG 6 678 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY 6 684 " --> pdb=" O LEU 6 680 " (cutoff:3.500A) Processing helix chain '6' and resid 705 through 720 removed outlier: 4.094A pdb=" N GLN 6 709 " --> pdb=" O THR 6 705 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN 6 710 " --> pdb=" O LYS 6 706 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU 6 712 " --> pdb=" O GLU 6 708 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU 6 713 " --> pdb=" O GLN 6 709 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN 6 714 " --> pdb=" O GLN 6 710 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS 6 715 " --> pdb=" O GLN 6 711 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA 6 718 " --> pdb=" O GLN 6 714 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR 6 720 " --> pdb=" O VAL 6 716 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 33 removed outlier: 4.463A pdb=" N PHE 7 22 " --> pdb=" O TYR 7 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG 7 26 " --> pdb=" O PHE 7 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG 7 30 " --> pdb=" O ARG 7 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR 7 31 " --> pdb=" O GLU 7 27 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 63 removed outlier: 3.991A pdb=" N LEU 7 55 " --> pdb=" O SER 7 51 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE 7 56 " --> pdb=" O LEU 7 52 " (cutoff:3.500A) Processing helix chain '7' and resid 76 through 99 removed outlier: 3.556A pdb=" N GLY 7 99 " --> pdb=" O GLU 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 116 removed outlier: 3.792A pdb=" N CYS 7 116 " --> pdb=" O ARG 7 112 " (cutoff:3.500A) Processing helix chain '7' and resid 118 through 124 Proline residue: 7 123 - end of helix Processing helix chain '7' and resid 126 through 138 Processing helix chain '7' and resid 139 through 149 removed outlier: 4.162A pdb=" N ARG 7 143 " --> pdb=" O ALA 7 139 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA 7 144 " --> pdb=" O SER 7 140 " (cutoff:3.500A) Processing helix chain '7' and resid 155 through 164 removed outlier: 6.494A pdb=" N GLU 7 159 " --> pdb=" O CYS 7 155 " (cutoff:3.500A) Processing helix chain '7' and resid 176 through 188 removed outlier: 3.534A pdb=" N GLN 7 187 " --> pdb=" O LEU 7 183 " (cutoff:3.500A) Processing helix chain '7' and resid 190 through 199 Processing helix chain '7' and resid 208 through 214 removed outlier: 3.760A pdb=" N LEU 7 212 " --> pdb=" O SER 7 208 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP 7 214 " --> pdb=" O HIS 7 210 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 229 removed outlier: 4.423A pdb=" N LYS 7 228 " --> pdb=" O GLU 7 224 " (cutoff:3.500A) Processing helix chain '7' and resid 238 through 248 Processing helix chain '7' and resid 252 through 277 Processing helix chain '7' and resid 278 through 290 Processing helix chain '7' and resid 325 through 346 removed outlier: 4.378A pdb=" N VAL 7 346 " --> pdb=" O TRP 7 342 " (cutoff:3.500A) Processing helix chain '7' and resid 353 through 364 Processing helix chain '7' and resid 368 through 387 removed outlier: 3.694A pdb=" N LEU 7 372 " --> pdb=" O GLN 7 368 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS 7 375 " --> pdb=" O PRO 7 371 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA 7 376 " --> pdb=" O LEU 7 372 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU 7 377 " --> pdb=" O ARG 7 373 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU 7 387 " --> pdb=" O LEU 7 383 " (cutoff:3.500A) Processing helix chain '7' and resid 390 through 410 removed outlier: 4.217A pdb=" N PHE 7 394 " --> pdb=" O ASP 7 390 " (cutoff:3.500A) Proline residue: 7 396 - end of helix Processing helix chain '7' and resid 439 through 451 removed outlier: 4.882A pdb=" N ALA 7 443 " --> pdb=" O ASP 7 439 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE 7 444 " --> pdb=" O ALA 7 440 " (cutoff:3.500A) Proline residue: 7 446 - end of helix Processing helix chain '7' and resid 464 through 472 Proline residue: 7 468 - end of helix Processing helix chain '7' and resid 513 through 531 Processing helix chain '7' and resid 541 through 556 removed outlier: 3.760A pdb=" N TYR 7 553 " --> pdb=" O VAL 7 549 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN 7 555 " --> pdb=" O SER 7 551 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY 7 556 " --> pdb=" O TRP 7 552 " (cutoff:3.500A) Processing helix chain '7' and resid 557 through 565 Processing helix chain '7' and resid 573 through 591 removed outlier: 3.609A pdb=" N THR 7 577 " --> pdb=" O ASP 7 573 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER 7 578 " --> pdb=" O GLY 7 574 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS 7 588 " --> pdb=" O TYR 7 584 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU 7 589 " --> pdb=" O GLN 7 585 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 608 removed outlier: 3.938A pdb=" N GLU 7 606 " --> pdb=" O GLY 7 602 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY 7 607 " --> pdb=" O LYS 7 603 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE 7 608 " --> pdb=" O VAL 7 604 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 602 through 608' Processing helix chain '7' and resid 630 through 643 removed outlier: 5.537A pdb=" N LYS 7 634 " --> pdb=" O SER 7 630 " (cutoff:3.500A) Processing helix chain '7' and resid 647 through 665 removed outlier: 3.643A pdb=" N THR 7 653 " --> pdb=" O ASN 7 649 " (cutoff:3.500A) Processing helix chain '7' and resid 682 through 687 removed outlier: 4.398A pdb=" N ARG 7 686 " --> pdb=" O LYS 7 682 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLY 7 687 " --> pdb=" O ARG 7 683 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 682 through 687' Processing helix chain '7' and resid 688 through 694 removed outlier: 3.810A pdb=" N LEU 7 693 " --> pdb=" O LYS 7 689 " (cutoff:3.500A) Proline residue: 7 694 - end of helix Processing helix chain '7' and resid 695 through 702 removed outlier: 4.982A pdb=" N HIS 7 700 " --> pdb=" O TRP 7 696 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N THR 7 702 " --> pdb=" O GLN 7 698 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 726 removed outlier: 4.815A pdb=" N GLN 7 726 " --> pdb=" O ARG 7 722 " (cutoff:3.500A) Processing helix chain '7' and resid 729 through 734 removed outlier: 4.172A pdb=" N GLN 7 733 " --> pdb=" O HIS 7 729 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 7 734 " --> pdb=" O ARG 7 730 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 729 through 734' Processing helix chain '8' and resid 56 through 70 removed outlier: 3.871A pdb=" N LEU 8 69 " --> pdb=" O LEU 8 65 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER 8 70 " --> pdb=" O LEU 8 66 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 103 Processing helix chain '8' and resid 110 through 132 removed outlier: 3.516A pdb=" N HIS 8 131 " --> pdb=" O TYR 8 127 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP 8 132 " --> pdb=" O LEU 8 128 " (cutoff:3.500A) Processing helix chain '8' and resid 180 through 186 removed outlier: 3.717A pdb=" N LEU 8 184 " --> pdb=" O ALA 8 180 " (cutoff:3.500A) Processing helix chain '8' and resid 192 through 209 removed outlier: 3.952A pdb=" N MET 8 196 " --> pdb=" O VAL 8 192 " (cutoff:3.500A) Processing helix chain '8' and resid 218 through 229 removed outlier: 5.921A pdb=" N LEU 8 222 " --> pdb=" O ASP 8 218 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR 8 223 " --> pdb=" O LEU 8 219 " (cutoff:3.500A) Processing helix chain '8' and resid 233 through 238 Proline residue: 8 238 - end of helix Processing helix chain '8' and resid 256 through 262 removed outlier: 4.003A pdb=" N PHE 8 261 " --> pdb=" O LEU 8 257 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER 8 262 " --> pdb=" O HIS 8 258 " (cutoff:3.500A) Processing helix chain '8' and resid 265 through 277 removed outlier: 4.073A pdb=" N LEU 8 269 " --> pdb=" O GLY 8 265 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU 8 277 " --> pdb=" O GLN 8 273 " (cutoff:3.500A) Processing helix chain '8' and resid 279 through 284 removed outlier: 6.794A pdb=" N ILE 8 284 " --> pdb=" O PRO 8 280 " (cutoff:3.500A) Processing helix chain '8' and resid 285 through 293 removed outlier: 3.638A pdb=" N ALA 8 289 " --> pdb=" O THR 8 285 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N MET 8 292 " --> pdb=" O GLN 8 288 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS 8 293 " --> pdb=" O ALA 8 289 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 12 removed outlier: 3.769A pdb=" N TRP 9 11 " --> pdb=" O GLN 9 7 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR 9 12 " --> pdb=" O LYS 9 8 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 7 through 12' Processing helix chain '9' and resid 15 through 38 removed outlier: 4.317A pdb=" N LEU 9 19 " --> pdb=" O SER 9 15 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA 9 20 " --> pdb=" O GLU 9 16 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY 9 38 " --> pdb=" O ALA 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 49 through 71 removed outlier: 4.587A pdb=" N MET 9 54 " --> pdb=" O PRO 9 50 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL 9 70 " --> pdb=" O GLU 9 66 " (cutoff:3.500A) Processing helix chain '9' and resid 76 through 94 removed outlier: 3.911A pdb=" N VAL 9 80 " --> pdb=" O PRO 9 76 " (cutoff:3.500A) Processing helix chain '9' and resid 95 through 100 removed outlier: 3.916A pdb=" N TYR 9 99 " --> pdb=" O SER 9 95 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS 9 100 " --> pdb=" O VAL 9 96 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 95 through 100' Processing helix chain '9' and resid 101 through 116 Processing helix chain '9' and resid 121 through 129 removed outlier: 4.389A pdb=" N LEU 9 129 " --> pdb=" O PHE 9 125 " (cutoff:3.500A) Processing helix chain '9' and resid 133 through 154 Processing helix chain '9' and resid 163 through 178 removed outlier: 3.864A pdb=" N THR 9 176 " --> pdb=" O ILE 9 172 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG 9 177 " --> pdb=" O ASP 9 173 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR 9 178 " --> pdb=" O LEU 9 174 " (cutoff:3.500A) Processing helix chain '9' and resid 186 through 202 removed outlier: 3.685A pdb=" N THR 9 190 " --> pdb=" O ILE 9 186 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP 9 193 " --> pdb=" O LYS 9 189 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG 9 197 " --> pdb=" O ASP 9 193 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU 9 200 " --> pdb=" O ASN 9 196 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR 9 201 " --> pdb=" O ARG 9 197 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASP 9 202 " --> pdb=" O ILE 9 198 " (cutoff:3.500A) Processing helix chain '9' and resid 208 through 225 removed outlier: 3.841A pdb=" N ALA 9 224 " --> pdb=" O SER 9 220 " (cutoff:3.500A) Processing helix chain '9' and resid 228 through 237 removed outlier: 3.501A pdb=" N LEU 9 232 " --> pdb=" O MET 9 228 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET 9 237 " --> pdb=" O SER 9 233 " (cutoff:3.500A) Processing helix chain '9' and resid 240 through 262 removed outlier: 4.112A pdb=" N TYR 9 262 " --> pdb=" O LEU 9 258 " (cutoff:3.500A) Processing helix chain '9' and resid 267 through 284 removed outlier: 4.442A pdb=" N ALA 9 271 " --> pdb=" O SER 9 267 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA 9 283 " --> pdb=" O ARG 9 279 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU 9 284 " --> pdb=" O CYS 9 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 398 through 404 removed outlier: 4.071A pdb=" N PHE A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N MET A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 404' Processing helix chain 'A' and resid 409 through 415 removed outlier: 5.559A pdb=" N ILE A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.571A pdb=" N VAL A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.872A pdb=" N ASN A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 484 " --> pdb=" O TRP A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 484' Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.636A pdb=" N TYR A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.633A pdb=" N PHE A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 658 removed outlier: 4.835A pdb=" N ILE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.115A pdb=" N LEU A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 667 through 672' Processing helix chain 'A' and resid 796 through 819 removed outlier: 5.895A pdb=" N LYS A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 removed outlier: 3.977A pdb=" N ILE A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Proline residue: A 835 - end of helix Processing helix chain 'A' and resid 838 through 850 removed outlier: 3.624A pdb=" N ILE A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N CYS A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 902 removed outlier: 3.855A pdb=" N VAL A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Proline residue: A 882 - end of helix removed outlier: 3.771A pdb=" N GLY A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 931 Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 932 through 944 Processing helix chain 'A' and resid 1055 through 1079 Processing helix chain 'A' and resid 1187 through 1205 removed outlier: 3.508A pdb=" N PHE A1205 " --> pdb=" O LYS A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 Proline residue: A 604 - end of helix No H-bonds generated for 'chain 'A' and resid 599 through 604' Processing helix chain 'B' and resid 88 through 93 removed outlier: 4.932A pdb=" N GLU B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 93' Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.736A pdb=" N PHE B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 removed outlier: 4.731A pdb=" N LYS B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 185 through 190 removed outlier: 4.787A pdb=" N TRP B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 296 removed outlier: 3.718A pdb=" N SER B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 356 Proline residue: B 340 - end of helix Processing helix chain 'B' and resid 366 through 386 removed outlier: 4.084A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 409 removed outlier: 4.014A pdb=" N LEU B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 removed outlier: 3.847A pdb=" N LEU B 441 " --> pdb=" O HIS B 437 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 437 through 442' Processing helix chain 'B' and resid 443 through 465 removed outlier: 3.789A pdb=" N SER B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 486 removed outlier: 3.977A pdb=" N SER B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN B 486 " --> pdb=" O THR B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 498 removed outlier: 6.244A pdb=" N TRP B 493 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N MET B 496 " --> pdb=" O MET B 492 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 498' Processing helix chain 'B' and resid 499 through 511 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 595 through 601 removed outlier: 3.818A pdb=" N ASN B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 600 " --> pdb=" O SER B 596 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS B 601 " --> pdb=" O ARG B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 601' Processing helix chain 'B' and resid 645 through 655 Processing helix chain 'B' and resid 658 through 673 removed outlier: 3.803A pdb=" N GLU B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LYS B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Proline residue: B 673 - end of helix Processing helix chain 'B' and resid 674 through 688 removed outlier: 3.510A pdb=" N GLN B 687 " --> pdb=" O ASP B 683 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 710 removed outlier: 3.547A pdb=" N ARG B 695 " --> pdb=" O PHE B 691 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 743 through 760 removed outlier: 5.883A pdb=" N TYR B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) Proline residue: B 754 - end of helix removed outlier: 4.181A pdb=" N LEU B 759 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 782 removed outlier: 3.533A pdb=" N THR B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 782 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 806 removed outlier: 3.507A pdb=" N SER B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 843 removed outlier: 4.203A pdb=" N LEU B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 829 " --> pdb=" O ASP B 825 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 865 removed outlier: 4.500A pdb=" N GLY B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 879 removed outlier: 4.189A pdb=" N GLU B 879 " --> pdb=" O LYS B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 902 removed outlier: 3.573A pdb=" N ARG B 902 " --> pdb=" O THR B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 917 removed outlier: 3.525A pdb=" N LEU B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 917 " --> pdb=" O MET B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 934 Proline residue: B 934 - end of helix Processing helix chain 'B' and resid 946 through 959 removed outlier: 3.559A pdb=" N VAL B 950 " --> pdb=" O ASN B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 979 removed outlier: 6.181A pdb=" N ARG B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N CYS B 969 " --> pdb=" O TRP B 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 889 removed outlier: 4.075A pdb=" N LEU D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN D 879 " --> pdb=" O GLN D 875 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 888 " --> pdb=" O GLU D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 932 removed outlier: 5.780A pdb=" N TYR D 901 " --> pdb=" O ASP D 897 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN D 912 " --> pdb=" O GLN D 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 916 " --> pdb=" O ASN D 912 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR D 920 " --> pdb=" O LYS D 916 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN D 923 " --> pdb=" O GLU D 919 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 924 " --> pdb=" O THR D 920 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN D 925 " --> pdb=" O ALA D 921 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 926 " --> pdb=" O GLN D 922 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER D 927 " --> pdb=" O GLN D 923 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR D 928 " --> pdb=" O LYS D 924 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS D 929 " --> pdb=" O ASN D 925 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP D 930 " --> pdb=" O PHE D 926 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP D 931 " --> pdb=" O SER D 927 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP D 932 " --> pdb=" O TYR D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 965 removed outlier: 4.657A pdb=" N GLN D 943 " --> pdb=" O ASP D 939 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 944 " --> pdb=" O VAL D 940 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 958 " --> pdb=" O GLU D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 1009 removed outlier: 3.671A pdb=" N GLN D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU D 995 " --> pdb=" O MET D 991 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1071 removed outlier: 3.623A pdb=" N LEU D1063 " --> pdb=" O ASN D1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS D1066 " --> pdb=" O ASP D1062 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN D1069 " --> pdb=" O PHE D1065 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU D1070 " --> pdb=" O CYS D1066 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG D1071 " --> pdb=" O LEU D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1085 removed outlier: 4.426A pdb=" N LEU D1084 " --> pdb=" O TYR D1080 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D1085 " --> pdb=" O LYS D1081 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 228 removed outlier: 3.997A pdb=" N TYR E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLU E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 255 removed outlier: 3.810A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU E 235 " --> pdb=" O CYS E 231 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) Proline residue: E 242 - end of helix Processing helix chain 'E' and resid 256 through 268 removed outlier: 3.752A pdb=" N SER E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 286 removed outlier: 3.658A pdb=" N ARG E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 282 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER E 284 " --> pdb=" O ARG E 280 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 3.802A pdb=" N MET E 291 " --> pdb=" O LYS E 287 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN E 294 " --> pdb=" O HIS E 290 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 303 removed outlier: 3.708A pdb=" N THR E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 322 removed outlier: 4.310A pdb=" N LEU E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 removed outlier: 5.453A pdb=" N TRP E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN E 331 " --> pdb=" O ASN E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 356 removed outlier: 3.906A pdb=" N ALA E 354 " --> pdb=" O GLN E 350 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET E 355 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 3.835A pdb=" N ASN E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 removed outlier: 4.691A pdb=" N ILE E 427 " --> pdb=" O PRO E 423 " (cutoff:3.500A) Proline residue: E 428 - end of helix No H-bonds generated for 'chain 'E' and resid 423 through 428' Processing helix chain 'E' and resid 433 through 451 removed outlier: 3.553A pdb=" N LYS E 437 " --> pdb=" O LYS E 433 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 446 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL E 451 " --> pdb=" O THR E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 517 removed outlier: 5.246A pdb=" N LEU E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP E 517 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 529 removed outlier: 3.521A pdb=" N MET E 528 " --> pdb=" O LEU E 524 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASP E 529 " --> pdb=" O GLU E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 745 removed outlier: 4.760A pdb=" N PHE E 744 " --> pdb=" O ALA E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 769 Processing helix chain 'F' and resid 15 through 27 removed outlier: 3.750A pdb=" N MET F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 62 removed outlier: 3.556A pdb=" N LEU F 39 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR F 40 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 79 Processing helix chain 'F' and resid 113 through 121 Proline residue: F 121 - end of helix Processing helix chain 'F' and resid 217 through 233 removed outlier: 4.865A pdb=" N GLY F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 249 Processing helix chain 'F' and resid 255 through 274 removed outlier: 4.048A pdb=" N VAL F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN F 273 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 292 removed outlier: 4.038A pdb=" N ASN F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 314 removed outlier: 5.373A pdb=" N HIS F 302 " --> pdb=" O GLU F 298 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Proline residue: F 306 - end of helix Processing helix chain 'F' and resid 319 through 345 removed outlier: 4.294A pdb=" N VAL F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN F 325 " --> pdb=" O PRO F 321 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N HIS F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER F 345 " --> pdb=" O CYS F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 Processing helix chain 'F' and resid 369 through 383 removed outlier: 4.189A pdb=" N LEU F 383 " --> pdb=" O GLY F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 391 removed outlier: 4.250A pdb=" N ILE F 388 " --> pdb=" O GLY F 384 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 389 " --> pdb=" O HIS F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 409 removed outlier: 5.108A pdb=" N GLY F 409 " --> pdb=" O SER F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 438 Proline residue: F 433 - end of helix Processing helix chain 'F' and resid 446 through 452 removed outlier: 4.506A pdb=" N ALA F 450 " --> pdb=" O ASP F 446 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU F 451 " --> pdb=" O ALA F 447 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE F 452 " --> pdb=" O TYR F 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 446 through 452' Processing helix chain 'F' and resid 456 through 473 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 36 through 44 removed outlier: 4.785A pdb=" N LYS G 40 " --> pdb=" O HIS G 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 removed outlier: 3.537A pdb=" N ILE G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 127 through 132' Processing helix chain 'G' and resid 161 through 177 removed outlier: 3.507A pdb=" N THR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL G 177 " --> pdb=" O ASP G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 Processing helix chain 'H' and resid 28 through 49 removed outlier: 4.759A pdb=" N ARG H 33 " --> pdb=" O TYR H 29 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL H 39 " --> pdb=" O ARG H 35 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR H 46 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY H 49 " --> pdb=" O LEU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 84 removed outlier: 3.517A pdb=" N LYS H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 101 removed outlier: 3.885A pdb=" N ILE H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL H 98 " --> pdb=" O VAL H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 removed outlier: 4.636A pdb=" N LEU H 107 " --> pdb=" O ASN H 103 " (cutoff:3.500A) Proline residue: H 108 - end of helix removed outlier: 3.569A pdb=" N ARG H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 160 removed outlier: 4.334A pdb=" N TYR H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 198 removed outlier: 3.854A pdb=" N GLY H 198 " --> pdb=" O MET H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 227 removed outlier: 4.265A pdb=" N THR H 225 " --> pdb=" O ILE H 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 27 removed outlier: 3.579A pdb=" N MET I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 62 Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.538A pdb=" N VAL I 71 " --> pdb=" O ASP I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 101 removed outlier: 3.676A pdb=" N ASP I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN I 101 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 122 removed outlier: 4.766A pdb=" N LEU I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.015A pdb=" N GLN J 122 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLU J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 143 removed outlier: 3.690A pdb=" N TYR J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA J 142 " --> pdb=" O TYR J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 176 removed outlier: 3.628A pdb=" N ILE J 152 " --> pdb=" O ASP J 148 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN J 172 " --> pdb=" O ASN J 168 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS J 173 " --> pdb=" O ASP J 169 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET J 176 " --> pdb=" O GLN J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 208 Proline residue: J 202 - end of helix removed outlier: 3.936A pdb=" N GLU J 206 " --> pdb=" O PRO J 202 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR J 207 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 71 removed outlier: 5.667A pdb=" N GLN L 64 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP L 71 " --> pdb=" O VAL L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 107 removed outlier: 3.533A pdb=" N GLN L 86 " --> pdb=" O GLU L 82 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 123 removed outlier: 6.103A pdb=" N GLN L 117 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS L 119 " --> pdb=" O ASP L 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 Processing helix chain 'O' and resid 30 through 51 removed outlier: 5.581A pdb=" N LEU O 34 " --> pdb=" O PRO O 30 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA O 49 " --> pdb=" O ASN O 45 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN O 50 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG O 51 " --> pdb=" O ALA O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 8 removed outlier: 4.242A pdb=" N TYR O 6 " --> pdb=" O TYR O 3 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG O 7 " --> pdb=" O GLN O 4 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN O 8 " --> pdb=" O LEU O 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 3 through 8' Processing helix chain 'P' and resid 179 through 187 removed outlier: 3.519A pdb=" N ILE P 183 " --> pdb=" O ASP P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 245 removed outlier: 3.629A pdb=" N LEU P 244 " --> pdb=" O VAL P 240 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY P 245 " --> pdb=" O VAL P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.575A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 336 removed outlier: 3.749A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'Q' and resid 9 through 33 removed outlier: 3.774A pdb=" N LEU Q 13 " --> pdb=" O THR Q 9 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASP Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE Q 28 " --> pdb=" O ASP Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 54 removed outlier: 3.765A pdb=" N LEU Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU Q 50 " --> pdb=" O TRP Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 63 Processing helix chain 'Q' and resid 313 through 318 removed outlier: 4.900A pdb=" N GLU Q 317 " --> pdb=" O PRO Q 313 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP Q 318 " --> pdb=" O LEU Q 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 313 through 318' Processing helix chain 'Q' and resid 323 through 329 removed outlier: 4.481A pdb=" N GLU Q 327 " --> pdb=" O GLU Q 323 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU Q 328 " --> pdb=" O GLU Q 324 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE Q 329 " --> pdb=" O GLY Q 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 323 through 329' Processing helix chain 'R' and resid 111 through 129 removed outlier: 4.207A pdb=" N ILE R 128 " --> pdb=" O MET R 124 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN R 129 " --> pdb=" O ALA R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 149 removed outlier: 3.506A pdb=" N VAL R 135 " --> pdb=" O PRO R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 172 Processing helix chain 'R' and resid 176 through 184 removed outlier: 3.515A pdb=" N VAL R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 203 Processing helix chain 'R' and resid 210 through 223 removed outlier: 4.569A pdb=" N PHE R 214 " --> pdb=" O THR R 210 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER R 216 " --> pdb=" O GLY R 212 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG R 217 " --> pdb=" O ASP R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 243 Processing helix chain 'R' and resid 249 through 266 removed outlier: 3.514A pdb=" N VAL R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA R 266 " --> pdb=" O SER R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 279 Processing helix chain 'R' and resid 281 through 294 Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 295 through 300 removed outlier: 3.887A pdb=" N PHE R 300 " --> pdb=" O ALA R 296 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 10 Processing helix chain 'S' and resid 38 through 43 removed outlier: 4.050A pdb=" N TRP S 42 " --> pdb=" O ASN S 38 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN S 43 " --> pdb=" O PHE S 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 38 through 43' Processing helix chain 'T' and resid 9 through 15 Processing helix chain 'T' and resid 24 through 34 removed outlier: 3.759A pdb=" N LYS T 33 " --> pdb=" O GLN T 29 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA T 34 " --> pdb=" O GLN T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 64 removed outlier: 3.650A pdb=" N ASN T 64 " --> pdb=" O GLU T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 136 removed outlier: 3.916A pdb=" N SER T 136 " --> pdb=" O ILE T 132 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 171 removed outlier: 3.567A pdb=" N GLU T 166 " --> pdb=" O ASN T 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG T 167 " --> pdb=" O ILE T 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 195 removed outlier: 3.643A pdb=" N ASP T 185 " --> pdb=" O GLN T 181 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA T 190 " --> pdb=" O MET T 186 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE T 191 " --> pdb=" O LEU T 187 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS T 193 " --> pdb=" O SER T 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS T 194 " --> pdb=" O ALA T 190 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN T 195 " --> pdb=" O PHE T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 198 through 207 removed outlier: 4.444A pdb=" N LYS T 207 " --> pdb=" O VAL T 203 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 221 Processing helix chain 'U' and resid 11 through 25 Processing helix chain 'U' and resid 28 through 39 removed outlier: 3.775A pdb=" N ALA U 33 " --> pdb=" O GLU U 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE U 36 " --> pdb=" O LEU U 32 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 53 Processing helix chain 'U' and resid 55 through 70 Processing helix chain 'U' and resid 101 through 117 Processing helix chain 'U' and resid 137 through 145 removed outlier: 3.565A pdb=" N LEU U 144 " --> pdb=" O GLU U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 196 Proline residue: U 186 - end of helix Processing helix chain 'V' and resid 76 through 92 removed outlier: 4.340A pdb=" N ASN V 83 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN V 90 " --> pdb=" O LYS V 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY V 92 " --> pdb=" O ARG V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 107 Processing helix chain 'V' and resid 112 through 128 removed outlier: 4.465A pdb=" N LEU V 124 " --> pdb=" O MET V 120 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL V 125 " --> pdb=" O THR V 121 " (cutoff:3.500A) Proline residue: V 128 - end of helix Processing helix chain 'V' and resid 151 through 156 Processing helix chain 'V' and resid 166 through 171 removed outlier: 4.664A pdb=" N ILE V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 176 through 188 removed outlier: 3.997A pdb=" N LYS V 180 " --> pdb=" O PRO V 176 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL V 182 " --> pdb=" O SER V 178 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS V 183 " --> pdb=" O GLN V 179 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN V 188 " --> pdb=" O ALA V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 222 removed outlier: 3.653A pdb=" N ARG V 221 " --> pdb=" O GLN V 217 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER V 222 " --> pdb=" O LYS V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 229 through 239 Processing helix chain 'c' and resid 1 through 22 removed outlier: 3.550A pdb=" N ALA c 20 " --> pdb=" O GLN c 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU c 21 " --> pdb=" O ILE c 17 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY c 22 " --> pdb=" O CYS c 18 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 57 removed outlier: 3.562A pdb=" N HIS c 32 " --> pdb=" O LEU c 28 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP c 36 " --> pdb=" O HIS c 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN c 43 " --> pdb=" O GLN c 39 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER c 53 " --> pdb=" O CYS c 49 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR c 56 " --> pdb=" O TYR c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 74 removed outlier: 3.935A pdb=" N GLN c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 86 removed outlier: 3.608A pdb=" N GLU c 81 " --> pdb=" O LEU c 77 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP c 82 " --> pdb=" O HIS c 78 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 843 through 860 removed outlier: 3.584A pdb=" N GLU d 847 " --> pdb=" O VAL d 843 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU d 848 " --> pdb=" O ASN d 844 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER d 849 " --> pdb=" O LEU d 845 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA d 850 " --> pdb=" O SER d 846 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG d 851 " --> pdb=" O GLU d 847 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE d 852 " --> pdb=" O GLU d 848 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU d 853 " --> pdb=" O SER d 849 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR d 855 " --> pdb=" O ARG d 851 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN d 856 " --> pdb=" O ILE d 852 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER d 857 " --> pdb=" O LEU d 853 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU d 858 " --> pdb=" O ALA d 854 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU d 859 " --> pdb=" O THR d 855 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL d 860 " --> pdb=" O ASN d 856 " (cutoff:3.500A) Processing helix chain 'd' and resid 874 through 890 removed outlier: 3.673A pdb=" N ARG d 880 " --> pdb=" O ALA d 876 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU d 883 " --> pdb=" O GLN d 879 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LYS d 888 " --> pdb=" O GLU d 884 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N HIS d 889 " --> pdb=" O ILE d 885 " (cutoff:3.500A) Processing helix chain 'd' and resid 895 through 932 removed outlier: 4.559A pdb=" N VAL d 899 " --> pdb=" O HIS d 895 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER d 900 " --> pdb=" O PRO d 896 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS d 904 " --> pdb=" O SER d 900 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN d 907 " --> pdb=" O SER d 903 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU d 913 " --> pdb=" O ARG d 909 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU d 919 " --> pdb=" O GLU d 915 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR d 920 " --> pdb=" O LYS d 916 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN d 923 " --> pdb=" O GLU d 919 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS d 924 " --> pdb=" O THR d 920 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN d 925 " --> pdb=" O ALA d 921 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE d 926 " --> pdb=" O GLN d 922 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER d 927 " --> pdb=" O GLN d 923 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N TYR d 928 " --> pdb=" O LYS d 924 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N LYS d 929 " --> pdb=" O ASN d 925 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ASP d 930 " --> pdb=" O PHE d 926 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP d 931 " --> pdb=" O SER d 927 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP d 932 " --> pdb=" O TYR d 928 " (cutoff:3.500A) Processing helix chain 'd' and resid 939 through 968 removed outlier: 4.071A pdb=" N GLN d 943 " --> pdb=" O ASP d 939 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE d 946 " --> pdb=" O ALA d 942 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS d 955 " --> pdb=" O ASP d 951 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS d 958 " --> pdb=" O GLU d 954 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU d 962 " --> pdb=" O LYS d 958 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET d 967 " --> pdb=" O ARG d 963 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG d 968 " --> pdb=" O GLU d 964 " (cutoff:3.500A) Processing helix chain 'd' and resid 1059 through 1071 removed outlier: 3.754A pdb=" N LEU d1063 " --> pdb=" O ASN d1059 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS d1066 " --> pdb=" O ASP d1062 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN d1069 " --> pdb=" O PHE d1065 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU d1070 " --> pdb=" O CYS d1066 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ARG d1071 " --> pdb=" O LEU d1067 " (cutoff:3.500A) Processing helix chain 'd' and resid 1076 through 1085 removed outlier: 3.688A pdb=" N TYR d1080 " --> pdb=" O SER d1076 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU d1084 " --> pdb=" O TYR d1080 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS d1085 " --> pdb=" O LYS d1081 " (cutoff:3.500A) Processing helix chain 'e' and resid 210 through 228 removed outlier: 4.468A pdb=" N TYR e 214 " --> pdb=" O ASP e 210 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU e 215 " --> pdb=" O PRO e 211 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU e 216 " --> pdb=" O THR e 212 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR e 217 " --> pdb=" O MET e 213 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR e 218 " --> pdb=" O TYR e 214 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER e 219 " --> pdb=" O GLU e 215 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS e 223 " --> pdb=" O SER e 219 " (cutoff:3.500A) Processing helix chain 'e' and resid 229 through 255 removed outlier: 4.815A pdb=" N ALA e 234 " --> pdb=" O ASP e 230 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU e 235 " --> pdb=" O CYS e 231 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN e 238 " --> pdb=" O ALA e 234 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU e 239 " --> pdb=" O GLU e 235 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE e 240 " --> pdb=" O LEU e 236 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR e 241 " --> pdb=" O SER e 237 " (cutoff:3.500A) Proline residue: e 242 - end of helix removed outlier: 3.937A pdb=" N HIS e 246 " --> pdb=" O PRO e 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU e 249 " --> pdb=" O VAL e 245 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR e 253 " --> pdb=" O LEU e 249 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASN e 254 " --> pdb=" O GLU e 250 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN e 255 " --> pdb=" O LEU e 251 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 267 removed outlier: 6.025A pdb=" N ALA e 260 " --> pdb=" O HIS e 256 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER e 262 " --> pdb=" O ASN e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 275 through 286 removed outlier: 4.169A pdb=" N VAL e 281 " --> pdb=" O ASP e 277 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU e 282 " --> pdb=" O ASP e 278 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER e 283 " --> pdb=" O LEU e 279 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER e 284 " --> pdb=" O ARG e 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU e 285 " --> pdb=" O VAL e 281 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N THR e 286 " --> pdb=" O LEU e 282 " (cutoff:3.500A) Processing helix chain 'e' and resid 287 through 294 removed outlier: 3.905A pdb=" N MET e 291 " --> pdb=" O LYS e 287 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY e 293 " --> pdb=" O GLU e 289 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN e 294 " --> pdb=" O HIS e 290 " (cutoff:3.500A) Processing helix chain 'e' and resid 310 through 323 removed outlier: 3.604A pdb=" N GLN e 315 " --> pdb=" O ARG e 311 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU e 317 " --> pdb=" O SER e 313 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN e 322 " --> pdb=" O LYS e 318 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU e 323 " --> pdb=" O ARG e 319 " (cutoff:3.500A) Processing helix chain 'e' and resid 327 through 335 removed outlier: 3.841A pdb=" N ASN e 331 " --> pdb=" O ASN e 327 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL e 333 " --> pdb=" O ILE e 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN e 334 " --> pdb=" O TRP e 330 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU e 335 " --> pdb=" O ASN e 331 " (cutoff:3.500A) Processing helix chain 'e' and resid 423 through 428 removed outlier: 4.671A pdb=" N ILE e 427 " --> pdb=" O PRO e 423 " (cutoff:3.500A) Proline residue: e 428 - end of helix No H-bonds generated for 'chain 'e' and resid 423 through 428' Processing helix chain 'e' and resid 433 through 450 removed outlier: 3.791A pdb=" N ASP e 439 " --> pdb=" O SER e 435 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE e 441 " --> pdb=" O LYS e 437 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU e 446 " --> pdb=" O MET e 442 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR e 447 " --> pdb=" O ASN e 443 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS e 449 " --> pdb=" O LYS e 445 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG e 450 " --> pdb=" O GLU e 446 " (cutoff:3.500A) Processing helix chain 'e' and resid 511 through 517 removed outlier: 3.724A pdb=" N LEU e 515 " --> pdb=" O SER e 511 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE e 516 " --> pdb=" O ASP e 512 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP e 517 " --> pdb=" O LEU e 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 511 through 517' Processing helix chain 'e' and resid 522 through 528 removed outlier: 3.504A pdb=" N ARG e 526 " --> pdb=" O ASP e 522 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N MET e 528 " --> pdb=" O LEU e 524 " (cutoff:3.500A) Processing helix chain 'e' and resid 739 through 745 removed outlier: 3.886A pdb=" N ALA e 743 " --> pdb=" O ASP e 739 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE e 744 " --> pdb=" O ALA e 740 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU e 745 " --> pdb=" O ILE e 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 739 through 745' Processing helix chain 'e' and resid 764 through 769 removed outlier: 4.118A pdb=" N LEU e 769 " --> pdb=" O SER e 765 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 27 removed outlier: 3.950A pdb=" N MET f 19 " --> pdb=" O PRO f 15 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS f 20 " --> pdb=" O SER f 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL f 21 " --> pdb=" O GLU f 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL f 22 " --> pdb=" O SER f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 32 through 62 removed outlier: 3.535A pdb=" N ASP f 41 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU f 42 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS f 48 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP f 53 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS f 56 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE f 57 " --> pdb=" O ASP f 53 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS f 62 " --> pdb=" O MET f 58 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 79 removed outlier: 4.019A pdb=" N ILE f 71 " --> pdb=" O THR f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 113 through 120 removed outlier: 3.817A pdb=" N ILE f 117 " --> pdb=" O ASP f 113 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR f 120 " --> pdb=" O ASP f 116 " (cutoff:3.500A) Processing helix chain 'f' and resid 217 through 233 removed outlier: 3.539A pdb=" N CYS f 231 " --> pdb=" O ILE f 227 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL f 232 " --> pdb=" O THR f 228 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY f 233 " --> pdb=" O GLU f 229 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 249 removed outlier: 3.631A pdb=" N ARG f 239 " --> pdb=" O CYS f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 252 through 273 Proline residue: f 257 - end of helix removed outlier: 3.528A pdb=" N ASN f 270 " --> pdb=" O GLY f 266 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL f 271 " --> pdb=" O VAL f 267 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL f 272 " --> pdb=" O ARG f 268 " (cutoff:3.500A) Processing helix chain 'f' and resid 275 through 292 removed outlier: 3.526A pdb=" N LEU f 279 " --> pdb=" O ASN f 275 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP f 291 " --> pdb=" O LYS f 287 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN f 292 " --> pdb=" O ALA f 288 " (cutoff:3.500A) Processing helix chain 'f' and resid 300 through 313 removed outlier: 4.050A pdb=" N LEU f 304 " --> pdb=" O TYR f 300 " (cutoff:3.500A) Proline residue: f 306 - end of helix removed outlier: 3.550A pdb=" N CYS f 311 " --> pdb=" O ALA f 307 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE f 312 " --> pdb=" O VAL f 308 " (cutoff:3.500A) Processing helix chain 'f' and resid 325 through 344 removed outlier: 4.119A pdb=" N LEU f 329 " --> pdb=" O ASN f 325 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE f 344 " --> pdb=" O ILE f 340 " (cutoff:3.500A) Processing helix chain 'f' and resid 350 through 365 removed outlier: 3.838A pdb=" N ASP f 365 " --> pdb=" O LYS f 361 " (cutoff:3.500A) Processing helix chain 'f' and resid 369 through 384 removed outlier: 4.055A pdb=" N GLY f 384 " --> pdb=" O LEU f 380 " (cutoff:3.500A) Processing helix chain 'f' and resid 385 through 396 removed outlier: 4.239A pdb=" N LEU f 393 " --> pdb=" O LYS f 389 " (cutoff:3.500A) Proline residue: f 394 - end of helix Processing helix chain 'f' and resid 397 through 407 removed outlier: 3.690A pdb=" N GLU f 401 " --> pdb=" O GLN f 397 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER f 405 " --> pdb=" O GLU f 401 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL f 406 " --> pdb=" O ARG f 402 " (cutoff:3.500A) Processing helix chain 'f' and resid 415 through 439 removed outlier: 3.609A pdb=" N GLY f 419 " --> pdb=" O ILE f 415 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA f 420 " --> pdb=" O ASP f 416 " (cutoff:3.500A) Proline residue: f 433 - end of helix removed outlier: 3.726A pdb=" N ARG f 439 " --> pdb=" O LEU f 435 " (cutoff:3.500A) Processing helix chain 'f' and resid 445 through 451 removed outlier: 4.371A pdb=" N GLU f 451 " --> pdb=" O ALA f 447 " (cutoff:3.500A) Processing helix chain 'f' and resid 453 through 473 Proline residue: f 457 - end of helix Processing helix chain 'i' and resid 13 through 27 removed outlier: 3.502A pdb=" N ALA i 20 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN i 21 " --> pdb=" O GLN i 17 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY i 27 " --> pdb=" O LEU i 23 " (cutoff:3.500A) Processing helix chain 'i' and resid 32 through 62 removed outlier: 4.569A pdb=" N ILE i 36 " --> pdb=" O GLU i 32 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN i 37 " --> pdb=" O PRO i 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU i 41 " --> pdb=" O ASN i 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA i 43 " --> pdb=" O MET i 39 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP i 52 " --> pdb=" O THR i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 80 removed outlier: 3.512A pdb=" N VAL i 71 " --> pdb=" O ASP i 67 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG i 78 " --> pdb=" O ALA i 74 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA i 79 " --> pdb=" O ILE i 75 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP i 80 " --> pdb=" O GLN i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 102 removed outlier: 3.967A pdb=" N ASP i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN i 98 " --> pdb=" O ASP i 94 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN i 101 " --> pdb=" O ARG i 97 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR i 102 " --> pdb=" O GLN i 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 117 through 122 removed outlier: 5.679A pdb=" N LEU i 122 " --> pdb=" O ASP i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 114 through 125 removed outlier: 3.699A pdb=" N ASP j 118 " --> pdb=" O THR j 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU j 120 " --> pdb=" O LEU j 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET j 121 " --> pdb=" O VAL j 117 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN j 122 " --> pdb=" O ASP j 118 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU j 124 " --> pdb=" O LEU j 120 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP j 125 " --> pdb=" O MET j 121 " (cutoff:3.500A) Processing helix chain 'j' and resid 131 through 143 removed outlier: 3.747A pdb=" N ASN j 140 " --> pdb=" O GLY j 136 " (cutoff:3.500A) Processing helix chain 'j' and resid 148 through 178 removed outlier: 3.886A pdb=" N ILE j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG j 153 " --> pdb=" O PRO j 149 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU j 157 " --> pdb=" O ARG j 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE j 162 " --> pdb=" O ALA j 158 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE j 163 " --> pdb=" O ALA j 159 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN j 168 " --> pdb=" O SER j 164 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU j 171 " --> pdb=" O ALA j 167 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS j 177 " --> pdb=" O HIS j 173 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLY j 178 " --> pdb=" O CYS j 174 " (cutoff:3.500A) Processing helix chain 'j' and resid 196 through 208 Proline residue: j 202 - end of helix removed outlier: 3.573A pdb=" N SER j 205 " --> pdb=" O THR j 201 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU j 206 " --> pdb=" O PRO j 202 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR j 207 " --> pdb=" O ALA j 203 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY j 208 " --> pdb=" O LEU j 204 " (cutoff:3.500A) Processing helix chain 'k' and resid 114 through 127 removed outlier: 3.993A pdb=" N LEU k 118 " --> pdb=" O SER k 114 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN k 119 " --> pdb=" O GLU k 115 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG k 125 " --> pdb=" O TYR k 121 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER k 127 " --> pdb=" O MET k 123 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 143 removed outlier: 4.100A pdb=" N ARG k 136 " --> pdb=" O ALA k 132 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE k 141 " --> pdb=" O LEU k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 177 removed outlier: 3.606A pdb=" N ALA k 153 " --> pdb=" O ASN k 149 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER k 158 " --> pdb=" O MET k 154 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS k 159 " --> pdb=" O SER k 155 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU k 167 " --> pdb=" O GLY k 163 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU k 168 " --> pdb=" O GLU k 164 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP k 171 " --> pdb=" O GLU k 167 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY k 177 " --> pdb=" O CYS k 173 " (cutoff:3.500A) Processing helix chain 'k' and resid 183 through 198 removed outlier: 3.678A pdb=" N MET k 187 " --> pdb=" O GLN k 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS k 197 " --> pdb=" O ARG k 193 " (cutoff:3.500A) Processing helix chain 'l' and resid 59 through 71 removed outlier: 6.019A pdb=" N LEU l 63 " --> pdb=" O THR l 59 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN l 64 " --> pdb=" O LYS l 60 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL l 70 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 107 removed outlier: 3.597A pdb=" N MET l 83 " --> pdb=" O ASP l 79 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN l 86 " --> pdb=" O GLU l 82 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA l 88 " --> pdb=" O LEU l 84 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP l 89 " --> pdb=" O LEU l 85 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS l 107 " --> pdb=" O ALA l 103 " (cutoff:3.500A) Processing helix chain 'l' and resid 112 through 123 removed outlier: 4.175A pdb=" N VAL l 116 " --> pdb=" O GLU l 112 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU l 118 " --> pdb=" O LYS l 114 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS l 119 " --> pdb=" O ASP l 115 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 145 through 161 removed outlier: 3.794A pdb=" N ALA l 153 " --> pdb=" O LYS l 149 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU l 154 " --> pdb=" O GLN l 150 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE l 155 " --> pdb=" O ARG l 151 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG l 156 " --> pdb=" O MET l 152 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS l 157 " --> pdb=" O ALA l 153 " (cutoff:3.500A) Processing helix chain 'm' and resid 33 through 44 removed outlier: 3.862A pdb=" N ARG m 37 " --> pdb=" O SER m 33 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 76 removed outlier: 3.602A pdb=" N ILE m 56 " --> pdb=" O GLU m 52 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP m 59 " --> pdb=" O ASP m 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA m 72 " --> pdb=" O MET m 68 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER m 74 " --> pdb=" O HIS m 70 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE m 75 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY m 76 " --> pdb=" O ALA m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 81 through 93 removed outlier: 4.109A pdb=" N ASP m 85 " --> pdb=" O VAL m 81 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE m 86 " --> pdb=" O GLN m 82 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL m 87 " --> pdb=" O VAL m 83 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE m 88 " --> pdb=" O GLU m 84 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU m 89 " --> pdb=" O ASP m 85 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE m 90 " --> pdb=" O ILE m 86 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG m 91 " --> pdb=" O VAL m 87 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS m 92 " --> pdb=" O PHE m 88 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 81 through 93' Processing helix chain 'm' and resid 94 through 114 removed outlier: 3.517A pdb=" N VAL m 100 " --> pdb=" O LYS m 96 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP m 102 " --> pdb=" O ALA m 98 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU m 103 " --> pdb=" O ARG m 99 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN m 107 " --> pdb=" O LEU m 103 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU m 108 " --> pdb=" O LEU m 104 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA m 113 " --> pdb=" O GLU m 109 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG m 114 " --> pdb=" O LEU m 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 35 Processing helix chain 'o' and resid 99 through 111 removed outlier: 4.964A pdb=" N CYS o 111 " --> pdb=" O LEU o 107 " (cutoff:3.500A) Processing helix chain 'o' and resid 123 through 133 removed outlier: 3.747A pdb=" N LYS o 127 " --> pdb=" O ASN o 123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS o 132 " --> pdb=" O ASP o 128 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER o 133 " --> pdb=" O ILE o 129 " (cutoff:3.500A) Processing helix chain 'o' and resid 136 through 152 removed outlier: 3.850A pdb=" N LEU o 147 " --> pdb=" O HIS o 143 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS o 149 " --> pdb=" O TYR o 145 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS o 151 " --> pdb=" O LEU o 147 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASN o 152 " --> pdb=" O CYS o 148 " (cutoff:3.500A) Processing helix chain 'o' and resid 217 through 228 removed outlier: 3.930A pdb=" N ARG o 227 " --> pdb=" O GLU o 223 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE o 228 " --> pdb=" O ILE o 224 " (cutoff:3.500A) Processing helix chain 'o' and resid 229 through 237 removed outlier: 3.601A pdb=" N CYS o 233 " --> pdb=" O SER o 229 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE o 234 " --> pdb=" O ASP o 230 " (cutoff:3.500A) Processing helix chain 'o' and resid 244 through 249 removed outlier: 3.992A pdb=" N MET o 248 " --> pdb=" O ARG o 244 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE o 249 " --> pdb=" O PRO o 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 244 through 249' Processing helix chain 'o' and resid 257 through 262 removed outlier: 3.530A pdb=" N ARG o 261 " --> pdb=" O PRO o 257 " (cutoff:3.500A) Proline residue: o 262 - end of helix No H-bonds generated for 'chain 'o' and resid 257 through 262' Processing helix chain 'o' and resid 274 through 297 removed outlier: 3.829A pdb=" N HIS o 278 " --> pdb=" O ASP o 274 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS o 279 " --> pdb=" O ASP o 275 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG o 292 " --> pdb=" O ASN o 288 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY o 297 " --> pdb=" O ASN o 293 " (cutoff:3.500A) Processing helix chain 'o' and resid 299 through 319 removed outlier: 6.540A pdb=" N ILE o 303 " --> pdb=" O ALA o 299 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ALA o 304 " --> pdb=" O ALA o 300 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU o 305 " --> pdb=" O HIS o 301 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU o 309 " --> pdb=" O GLU o 305 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL o 318 " --> pdb=" O VAL o 314 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP o 319 " --> pdb=" O ALA o 315 " (cutoff:3.500A) Processing helix chain 'o' and resid 338 through 344 removed outlier: 3.638A pdb=" N LEU o 343 " --> pdb=" O LEU o 339 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS o 344 " --> pdb=" O LYS o 340 " (cutoff:3.500A) Processing helix chain 'o' and resid 381 through 389 removed outlier: 4.011A pdb=" N ASN o 387 " --> pdb=" O SER o 383 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR o 389 " --> pdb=" O ALA o 385 " (cutoff:3.500A) Processing helix chain 'o' and resid 398 through 409 removed outlier: 3.744A pdb=" N ARG o 408 " --> pdb=" O GLU o 404 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY o 409 " --> pdb=" O LEU o 405 " (cutoff:3.500A) Processing helix chain 'o' and resid 428 through 433 removed outlier: 3.521A pdb=" N HIS o 432 " --> pdb=" O ASP o 428 " (cutoff:3.500A) Proline residue: o 433 - end of helix No H-bonds generated for 'chain 'o' and resid 428 through 433' Processing helix chain 'o' and resid 465 through 470 removed outlier: 4.696A pdb=" N MET o 469 " --> pdb=" O HIS o 465 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N MET o 470 " --> pdb=" O LYS o 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 465 through 470' Processing helix chain 'o' and resid 485 through 493 removed outlier: 4.502A pdb=" N THR o 489 " --> pdb=" O ASN o 485 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR o 490 " --> pdb=" O LEU o 486 " (cutoff:3.500A) Proline residue: o 491 - end of helix No H-bonds generated for 'chain 'o' and resid 485 through 493' Processing helix chain 'o' and resid 508 through 518 removed outlier: 4.091A pdb=" N ARG o 512 " --> pdb=" O SER o 508 " (cutoff:3.500A) Processing helix chain 'o' and resid 520 through 525 removed outlier: 3.733A pdb=" N MET o 524 " --> pdb=" O MET o 520 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE o 525 " --> pdb=" O VAL o 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 520 through 525' Processing helix chain 'o' and resid 539 through 550 removed outlier: 4.209A pdb=" N THR o 543 " --> pdb=" O GLN o 539 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA o 544 " --> pdb=" O ASP o 540 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS o 550 " --> pdb=" O ARG o 546 " (cutoff:3.500A) Processing helix chain 'o' and resid 556 through 567 removed outlier: 3.530A pdb=" N VAL o 560 " --> pdb=" O GLU o 556 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU o 567 " --> pdb=" O LEU o 563 " (cutoff:3.500A) Processing helix chain 'o' and resid 587 through 597 removed outlier: 4.325A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE o 596 " --> pdb=" O PHE o 592 " (cutoff:3.500A) Proline residue: o 597 - end of helix Processing helix chain 'o' and resid 612 through 617 removed outlier: 4.390A pdb=" N GLY o 616 " --> pdb=" O ASP o 612 " (cutoff:3.500A) Proline residue: o 617 - end of helix No H-bonds generated for 'chain 'o' and resid 612 through 617' Processing helix chain 'o' and resid 651 through 660 Processing helix chain 'o' and resid 661 through 684 removed outlier: 4.121A pdb=" N THR o 665 " --> pdb=" O GLY o 661 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG o 666 " --> pdb=" O HIS o 662 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU o 667 " --> pdb=" O ASP o 663 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE o 682 " --> pdb=" O ASN o 678 " (cutoff:3.500A) Processing helix chain 'o' and resid 688 through 694 removed outlier: 4.509A pdb=" N SER o 692 " --> pdb=" O GLY o 688 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE o 693 " --> pdb=" O ILE o 689 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA o 694 " --> pdb=" O GLY o 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 688 through 694' Processing helix chain 'o' and resid 695 through 723 removed outlier: 3.814A pdb=" N TYR o 699 " --> pdb=" O ASP o 695 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN o 700 " --> pdb=" O SER o 696 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE o 714 " --> pdb=" O LYS o 710 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN o 722 " --> pdb=" O GLU o 718 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN o 723 " --> pdb=" O LYS o 719 " (cutoff:3.500A) Processing helix chain 'o' and resid 732 through 760 removed outlier: 3.624A pdb=" N SER o 759 " --> pdb=" O SER o 755 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU o 760 " --> pdb=" O ALA o 756 " (cutoff:3.500A) Processing helix chain 'o' and resid 764 through 773 removed outlier: 3.509A pdb=" N SER o 768 " --> pdb=" O ASN o 764 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET o 769 " --> pdb=" O ASN o 765 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER o 772 " --> pdb=" O SER o 768 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY o 773 " --> pdb=" O MET o 769 " (cutoff:3.500A) Processing helix chain 'o' and resid 777 through 786 removed outlier: 3.906A pdb=" N ILE o 781 " --> pdb=" O SER o 777 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER o 782 " --> pdb=" O LYS o 778 " (cutoff:3.500A) Processing helix chain 'o' and resid 816 through 821 removed outlier: 3.873A pdb=" N ARG o 820 " --> pdb=" O GLY o 816 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY o 821 " --> pdb=" O PRO o 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 816 through 821' Processing helix chain 'o' and resid 832 through 869 removed outlier: 4.223A pdb=" N THR o 850 " --> pdb=" O GLY o 846 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA o 851 " --> pdb=" O LEU o 847 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR o 854 " --> pdb=" O THR o 850 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU o 869 " --> pdb=" O ILE o 865 " (cutoff:3.500A) Processing helix chain 'o' and resid 912 through 921 removed outlier: 3.757A pdb=" N GLU o 917 " --> pdb=" O ASN o 913 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG o 921 " --> pdb=" O GLU o 917 " (cutoff:3.500A) Processing helix chain 'o' and resid 926 through 934 removed outlier: 5.818A pdb=" N LEU o 930 " --> pdb=" O ASN o 926 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG o 931 " --> pdb=" O GLU o 927 " (cutoff:3.500A) Processing helix chain 'o' and resid 935 through 945 removed outlier: 3.678A pdb=" N LYS o 940 " --> pdb=" O GLU o 936 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP o 941 " --> pdb=" O ASP o 937 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU o 943 " --> pdb=" O VAL o 939 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER o 944 " --> pdb=" O LYS o 940 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN o 945 " --> pdb=" O ASP o 941 " (cutoff:3.500A) Processing helix chain 'o' and resid 946 through 971 removed outlier: 3.754A pdb=" N GLU o 955 " --> pdb=" O GLU o 951 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE o 956 " --> pdb=" O LEU o 952 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU o 957 " --> pdb=" O GLU o 953 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP o 962 " --> pdb=" O ARG o 958 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL o 968 " --> pdb=" O GLU o 964 " (cutoff:3.500A) Proline residue: o 971 - end of helix Processing helix chain 'o' and resid 982 through 995 removed outlier: 3.962A pdb=" N MET o 986 " --> pdb=" O ASN o 982 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS o 992 " --> pdb=" O TRP o 988 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE o 994 " --> pdb=" O ALA o 990 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS o 995 " --> pdb=" O GLN o 991 " (cutoff:3.500A) Processing helix chain 'o' and resid 1005 through 1020 removed outlier: 3.515A pdb=" N LYS o1019 " --> pdb=" O GLU o1015 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU o1020 " --> pdb=" O LEU o1016 " (cutoff:3.500A) Processing helix chain 'o' and resid 1027 through 1039 removed outlier: 6.078A pdb=" N GLN o1032 " --> pdb=" O PRO o1028 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA o1033 " --> pdb=" O LEU o1029 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN o1034 " --> pdb=" O SER o1030 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU o1035 " --> pdb=" O ARG o1031 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU o1039 " --> pdb=" O GLU o1035 " (cutoff:3.500A) Processing helix chain 'o' and resid 1040 through 1050 removed outlier: 3.747A pdb=" N CYS o1050 " --> pdb=" O ARG o1046 " (cutoff:3.500A) Processing helix chain 'o' and resid 1051 through 1057 Processing helix chain 'o' and resid 1061 through 1080 removed outlier: 3.537A pdb=" N PHE o1065 " --> pdb=" O SER o1061 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP o1066 " --> pdb=" O GLY o1062 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP o1067 " --> pdb=" O GLU o1063 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU o1068 " --> pdb=" O ALA o1064 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU o1073 " --> pdb=" O LEU o1069 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER o1074 " --> pdb=" O GLY o1070 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN o1078 " --> pdb=" O SER o1074 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA o1079 " --> pdb=" O LYS o1075 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE o1080 " --> pdb=" O PHE o1076 " (cutoff:3.500A) Processing helix chain 'o' and resid 1086 through 1103 removed outlier: 3.513A pdb=" N SER o1094 " --> pdb=" O LEU o1090 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU o1095 " --> pdb=" O ALA o1091 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY o1096 " --> pdb=" O ALA o1092 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU o1097 " --> pdb=" O GLN o1093 " (cutoff:3.500A) Proline residue: o1098 - end of helix removed outlier: 3.740A pdb=" N GLN o1101 " --> pdb=" O GLU o1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET o1102 " --> pdb=" O PRO o1098 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N THR o1103 " --> pdb=" O ALA o1099 " (cutoff:3.500A) Processing helix chain 'o' and resid 1120 through 1130 removed outlier: 4.503A pdb=" N ILE o1130 " --> pdb=" O GLU o1126 " (cutoff:3.500A) Processing helix chain 'o' and resid 1145 through 1151 removed outlier: 4.199A pdb=" N ARG o1149 " --> pdb=" O GLY o1145 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA o1151 " --> pdb=" O SER o1147 " (cutoff:3.500A) Processing helix chain 'o' and resid 1152 through 1163 removed outlier: 5.666A pdb=" N HIS o1163 " --> pdb=" O CYS o1159 " (cutoff:3.500A) Processing helix chain 'o' and resid 1165 through 1171 removed outlier: 4.273A pdb=" N VAL o1169 " --> pdb=" O THR o1165 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA o1171 " --> pdb=" O ARG o1167 " (cutoff:3.500A) Processing helix chain 'o' and resid 1189 through 1200 removed outlier: 4.160A pdb=" N MET o1199 " --> pdb=" O VAL o1195 " (cutoff:3.500A) Proline residue: o1200 - end of helix Processing helix chain 'o' and resid 1217 through 1225 removed outlier: 4.176A pdb=" N ARG o1224 " --> pdb=" O HIS o1220 " (cutoff:3.500A) Processing helix chain 'o' and resid 1227 through 1239 removed outlier: 3.943A pdb=" N ILE o1231 " --> pdb=" O THR o1227 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY o1238 " --> pdb=" O LYS o1234 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE o1239 " --> pdb=" O ILE o1235 " (cutoff:3.500A) Processing helix chain 'o' and resid 1280 through 1296 removed outlier: 3.727A pdb=" N LEU o1293 " --> pdb=" O GLU o1289 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR o1294 " --> pdb=" O SER o1290 " (cutoff:3.500A) Processing helix chain 'o' and resid 1342 through 1349 removed outlier: 3.565A pdb=" N VAL o1346 " --> pdb=" O SER o1342 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER o1348 " --> pdb=" O MET o1344 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU o1349 " --> pdb=" O ARG o1345 " (cutoff:3.500A) Processing helix chain 'o' and resid 1361 through 1369 removed outlier: 3.646A pdb=" N ILE o1365 " --> pdb=" O ASP o1361 " (cutoff:3.500A) Processing helix chain 'o' and resid 1370 through 1388 removed outlier: 4.528A pdb=" N VAL o1374 " --> pdb=" O GLY o1370 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE o1388 " --> pdb=" O HIS o1384 " (cutoff:3.500A) Processing helix chain 'o' and resid 1394 through 1407 removed outlier: 4.193A pdb=" N LEU o1398 " --> pdb=" O ASN o1394 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR o1406 " --> pdb=" O CYS o1402 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS o1407 " --> pdb=" O ASP o1403 " (cutoff:3.500A) Processing helix chain 'o' and resid 1415 through 1422 removed outlier: 4.886A pdb=" N GLN o1422 " --> pdb=" O GLY o1418 " (cutoff:3.500A) Processing helix chain 'o' and resid 1425 through 1433 removed outlier: 3.998A pdb=" N LYS o1429 " --> pdb=" O GLY o1425 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER o1431 " --> pdb=" O LEU o1427 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE o1432 " --> pdb=" O MET o1428 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU o1433 " --> pdb=" O LYS o1429 " (cutoff:3.500A) Processing helix chain 'o' and resid 1434 through 1446 removed outlier: 3.589A pdb=" N VAL o1438 " --> pdb=" O GLU o1434 " (cutoff:3.500A) Processing helix chain 'o' and resid 1453 through 1461 removed outlier: 4.102A pdb=" N ASN o1457 " --> pdb=" O GLY o1453 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU o1460 " --> pdb=" O GLU o1456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY o1461 " --> pdb=" O ASN o1457 " (cutoff:3.500A) Processing helix chain 'o' and resid 1476 through 1484 removed outlier: 3.643A pdb=" N CYS o1480 " --> pdb=" O ASP o1476 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR o1482 " --> pdb=" O GLU o1478 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY o1483 " --> pdb=" O LYS o1479 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N MET o1484 " --> pdb=" O CYS o1480 " (cutoff:3.500A) Processing helix chain 'o' and resid 434 through 439 removed outlier: 3.731A pdb=" N ASP o 437 " --> pdb=" O LYS o 434 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS o 439 " --> pdb=" O SER o 436 " (cutoff:3.500A) Processing helix chain 'o' and resid 348 through 353 removed outlier: 5.567A pdb=" N ASN o 353 " --> pdb=" O GLY o 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 348 through 353' Processing helix chain 'p' and resid 21 through 37 removed outlier: 3.760A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) Processing helix chain 'p' and resid 40 through 61 removed outlier: 4.081A pdb=" N SER p 46 " --> pdb=" O GLN p 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE p 47 " --> pdb=" O GLN p 43 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP p 48 " --> pdb=" O LEU p 44 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER p 54 " --> pdb=" O PHE p 50 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL p 55 " --> pdb=" O ILE p 51 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLN p 56 " --> pdb=" O GLN p 52 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE p 58 " --> pdb=" O SER p 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL p 59 " --> pdb=" O VAL p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 109 through 117 removed outlier: 3.567A pdb=" N ARG p 114 " --> pdb=" O PRO p 110 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN p 117 " --> pdb=" O ALA p 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 175 removed outlier: 3.761A pdb=" N GLU p 173 " --> pdb=" O ARG p 169 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN p 175 " --> pdb=" O LEU p 171 " (cutoff:3.500A) Processing helix chain 'p' and resid 246 through 253 removed outlier: 3.576A pdb=" N SER p 250 " --> pdb=" O GLY p 246 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA p 251 " --> pdb=" O ALA p 247 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE p 252 " --> pdb=" O LYS p 248 " (cutoff:3.500A) Processing helix chain 'p' and resid 268 through 277 removed outlier: 3.546A pdb=" N VAL p 272 " --> pdb=" O PRO p 268 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU p 276 " --> pdb=" O VAL p 272 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY p 277 " --> pdb=" O PHE p 273 " (cutoff:3.500A) Processing helix chain 'p' and resid 280 through 289 removed outlier: 3.818A pdb=" N LEU p 285 " --> pdb=" O ASP p 281 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU p 286 " --> pdb=" O ARG p 282 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS p 287 " --> pdb=" O ASP p 283 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE p 288 " --> pdb=" O ILE p 284 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE p 289 " --> pdb=" O LEU p 285 " (cutoff:3.500A) Processing helix chain 'p' and resid 295 through 309 removed outlier: 3.802A pdb=" N MET p 300 " --> pdb=" O GLU p 296 " (cutoff:3.500A) Proline residue: p 303 - end of helix removed outlier: 3.777A pdb=" N ASP p 306 " --> pdb=" O LYS p 302 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU p 307 " --> pdb=" O PRO p 303 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA p 308 " --> pdb=" O SER p 304 " (cutoff:3.500A) Processing helix chain 'p' and resid 313 through 325 removed outlier: 4.262A pdb=" N ARG p 324 " --> pdb=" O PHE p 320 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY p 325 " --> pdb=" O ILE p 321 " (cutoff:3.500A) Processing helix chain 'p' and resid 331 through 345 removed outlier: 4.242A pdb=" N ARG p 335 " --> pdb=" O THR p 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS p 340 " --> pdb=" O ILE p 336 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU p 341 " --> pdb=" O LYS p 337 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL p 342 " --> pdb=" O TYR p 338 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU p 343 " --> pdb=" O ALA p 339 " (cutoff:3.500A) Processing helix chain 'p' and resid 357 through 378 removed outlier: 4.411A pdb=" N LYS p 361 " --> pdb=" O CYS p 357 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA p 362 " --> pdb=" O GLU p 358 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU p 374 " --> pdb=" O HIS p 370 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA p 375 " --> pdb=" O ARG p 371 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA p 376 " --> pdb=" O LEU p 372 " (cutoff:3.500A) Processing helix chain 'p' and resid 387 through 392 removed outlier: 4.491A pdb=" N LYS p 391 " --> pdb=" O HIS p 387 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG p 392 " --> pdb=" O TYR p 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 387 through 392' Processing helix chain 'p' and resid 397 through 424 removed outlier: 4.121A pdb=" N PHE p 402 " --> pdb=" O PRO p 398 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY p 406 " --> pdb=" O PHE p 402 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET p 407 " --> pdb=" O LEU p 403 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN p 410 " --> pdb=" O GLY p 406 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU p 411 " --> pdb=" O MET p 407 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU p 414 " --> pdb=" O ASN p 410 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL p 415 " --> pdb=" O LEU p 411 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG p 416 " --> pdb=" O LEU p 412 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE p 417 " --> pdb=" O LYS p 413 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR p 418 " --> pdb=" O GLU p 414 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS p 421 " --> pdb=" O ILE p 417 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE p 422 " --> pdb=" O TYR p 418 " (cutoff:3.500A) Processing helix chain 'p' and resid 430 through 435 removed outlier: 4.078A pdb=" N ALA p 434 " --> pdb=" O ASN p 430 " (cutoff:3.500A) Processing helix chain 'p' and resid 437 through 451 removed outlier: 3.790A pdb=" N SER p 441 " --> pdb=" O THR p 437 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP p 442 " --> pdb=" O ARG p 438 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER p 447 " --> pdb=" O GLY p 443 " (cutoff:3.500A) Processing helix chain 'p' and resid 474 through 484 removed outlier: 3.513A pdb=" N LEU p 479 " --> pdb=" O PHE p 475 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER p 480 " --> pdb=" O ALA p 476 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS p 481 " --> pdb=" O SER p 477 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG p 483 " --> pdb=" O LEU p 479 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG p 484 " --> pdb=" O SER p 480 " (cutoff:3.500A) Processing helix chain 'p' and resid 495 through 500 removed outlier: 4.554A pdb=" N ARG p 499 " --> pdb=" O LEU p 495 " (cutoff:3.500A) Processing helix chain 'p' and resid 538 through 549 removed outlier: 3.540A pdb=" N PHE p 544 " --> pdb=" O PRO p 540 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU p 547 " --> pdb=" O GLU p 543 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER p 549 " --> pdb=" O LEU p 545 " (cutoff:3.500A) Processing helix chain 'p' and resid 557 through 562 removed outlier: 4.441A pdb=" N ILE p 561 " --> pdb=" O SER p 557 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA p 562 " --> pdb=" O PRO p 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 557 through 562' Processing helix chain 'p' and resid 579 through 594 removed outlier: 3.582A pdb=" N LEU p 583 " --> pdb=" O ASP p 579 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN p 585 " --> pdb=" O GLU p 581 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS p 589 " --> pdb=" O ASN p 585 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN p 593 " --> pdb=" O LYS p 589 " (cutoff:3.500A) Processing helix chain 'p' and resid 636 through 646 removed outlier: 3.985A pdb=" N ILE p 640 " --> pdb=" O LYS p 636 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN p 642 " --> pdb=" O ARG p 638 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU p 645 " --> pdb=" O ASP p 641 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG p 646 " --> pdb=" O GLN p 642 " (cutoff:3.500A) Processing helix chain 'p' and resid 652 through 660 removed outlier: 3.946A pdb=" N SER p 659 " --> pdb=" O ASP p 655 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY p 660 " --> pdb=" O LEU p 656 " (cutoff:3.500A) Processing helix chain 'p' and resid 666 through 674 removed outlier: 3.913A pdb=" N GLU p 671 " --> pdb=" O THR p 667 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR p 672 " --> pdb=" O LEU p 668 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL p 673 " --> pdb=" O GLU p 669 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET p 674 " --> pdb=" O GLU p 670 " (cutoff:3.500A) Processing helix chain 'p' and resid 705 through 711 removed outlier: 3.989A pdb=" N SER p 709 " --> pdb=" O GLY p 705 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE p 710 " --> pdb=" O VAL p 706 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE p 711 " --> pdb=" O CYS p 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 705 through 711' Processing helix chain 'p' and resid 718 through 732 removed outlier: 3.801A pdb=" N ASN p 722 " --> pdb=" O GLN p 718 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR p 723 " --> pdb=" O SER p 719 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER p 726 " --> pdb=" O ASN p 722 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS p 730 " --> pdb=" O SER p 726 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA p 732 " --> pdb=" O MET p 728 " (cutoff:3.500A) Processing helix chain 'p' and resid 739 through 744 removed outlier: 3.742A pdb=" N ARG p 743 " --> pdb=" O ASN p 739 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N MET p 744 " --> pdb=" O PHE p 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 739 through 744' Processing helix chain 'p' and resid 763 through 768 removed outlier: 4.865A pdb=" N LEU p 767 " --> pdb=" O SER p 763 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG p 768 " --> pdb=" O MET p 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 763 through 768' Processing helix chain 'p' and resid 797 through 804 removed outlier: 3.541A pdb=" N VAL p 801 " --> pdb=" O ASN p 797 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG p 803 " --> pdb=" O SER p 799 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY p 804 " --> pdb=" O ALA p 800 " (cutoff:3.500A) Processing helix chain 'p' and resid 950 through 955 Proline residue: p 955 - end of helix Processing helix chain 'p' and resid 968 through 976 removed outlier: 4.894A pdb=" N ILE p 972 " --> pdb=" O ASN p 968 " (cutoff:3.500A) Proline residue: p 973 - end of helix Processing helix chain 'p' and resid 977 through 994 removed outlier: 4.094A pdb=" N LEU p 981 " --> pdb=" O THR p 977 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU p 983 " --> pdb=" O GLY p 979 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS p 984 " --> pdb=" O HIS p 980 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU p 985 " --> pdb=" O LEU p 981 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS p 988 " --> pdb=" O CYS p 984 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL p 989 " --> pdb=" O LEU p 985 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN p 992 " --> pdb=" O LYS p 988 " (cutoff:3.500A) Processing helix chain 'p' and resid 1007 through 1019 removed outlier: 3.911A pdb=" N ILE p1011 " --> pdb=" O ASN p1007 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU p1014 " --> pdb=" O LYS p1010 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR p1018 " --> pdb=" O LEU p1014 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY p1019 " --> pdb=" O LEU p1015 " (cutoff:3.500A) Processing helix chain 'p' and resid 1054 through 1059 removed outlier: 4.301A pdb=" N LYS p1058 " --> pdb=" O MET p1054 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE p1059 " --> pdb=" O VAL p1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 1054 through 1059' Processing helix chain 'p' and resid 1087 through 1098 removed outlier: 3.530A pdb=" N ASP p1092 " --> pdb=" O GLU p1088 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN p1094 " --> pdb=" O GLU p1090 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE p1095 " --> pdb=" O ARG p1091 " (cutoff:3.500A) Processing helix chain 'p' and resid 1099 through 1108 removed outlier: 3.627A pdb=" N LEU p1103 " --> pdb=" O ALA p1099 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU p1107 " --> pdb=" O LEU p1103 " (cutoff:3.500A) Processing helix chain 'p' and resid 1152 through 1166 removed outlier: 3.532A pdb=" N LYS p1156 " --> pdb=" O PRO p1152 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU p1158 " --> pdb=" O ALA p1154 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET p1165 " --> pdb=" O GLU p1161 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER p1166 " --> pdb=" O LEU p1162 " (cutoff:3.500A) Processing helix chain 'p' and resid 699 through 704 removed outlier: 4.053A pdb=" N ILE p 703 " --> pdb=" O PRO p 700 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU p 704 " --> pdb=" O SER p 701 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 40 removed outlier: 3.954A pdb=" N ARG q 35 " --> pdb=" O ALA q 31 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL q 37 " --> pdb=" O SER q 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE q 38 " --> pdb=" O ILE q 34 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE q 39 " --> pdb=" O ARG q 35 " (cutoff:3.500A) Processing helix chain 'q' and resid 60 through 71 removed outlier: 3.508A pdb=" N ILE q 64 " --> pdb=" O HIS q 60 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS q 66 " --> pdb=" O GLU q 62 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY q 69 " --> pdb=" O ALA q 65 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU q 70 " --> pdb=" O HIS q 66 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE q 71 " --> pdb=" O ARG q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 83 removed outlier: 3.790A pdb=" N LEU q 82 " --> pdb=" O ILE q 78 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLN q 83 " --> pdb=" O VAL q 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 78 through 83' Processing helix chain 'q' and resid 240 through 271 removed outlier: 4.255A pdb=" N VAL q 245 " --> pdb=" O PRO q 241 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU q 246 " --> pdb=" O GLU q 242 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS q 254 " --> pdb=" O SER q 250 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP q 258 " --> pdb=" O LYS q 254 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR q 261 " --> pdb=" O SER q 257 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER q 269 " --> pdb=" O HIS q 265 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL q 271 " --> pdb=" O ILE q 267 " (cutoff:3.500A) Processing helix chain 'r' and resid 33 through 52 removed outlier: 3.505A pdb=" N LEU r 40 " --> pdb=" O GLU r 36 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU r 42 " --> pdb=" O HIS r 38 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS r 43 " --> pdb=" O MET r 39 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER r 50 " --> pdb=" O GLN r 46 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA r 51 " --> pdb=" O GLN r 47 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU r 52 " --> pdb=" O ASN r 48 " (cutoff:3.500A) Processing helix chain 'r' and resid 58 through 72 removed outlier: 4.863A pdb=" N MET r 62 " --> pdb=" O SER r 58 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG r 70 " --> pdb=" O ASN r 66 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE r 71 " --> pdb=" O TYR r 67 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER r 72 " --> pdb=" O THR r 68 " (cutoff:3.500A) Processing helix chain 'r' and resid 76 through 89 removed outlier: 3.792A pdb=" N SER r 85 " --> pdb=" O ALA r 81 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN r 89 " --> pdb=" O SER r 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 93 through 104 removed outlier: 3.774A pdb=" N LEU r 97 " --> pdb=" O HIS r 93 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA r 98 " --> pdb=" O LYS r 94 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU r 100 " --> pdb=" O GLU r 96 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN r 102 " --> pdb=" O ALA r 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU r 103 " --> pdb=" O CYS r 99 " (cutoff:3.500A) Processing helix chain 'r' and resid 107 through 116 Proline residue: r 116 - end of helix Processing helix chain 'r' and resid 123 through 139 removed outlier: 4.054A pdb=" N LEU r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER r 139 " --> pdb=" O GLN r 135 " (cutoff:3.500A) Processing helix chain 'r' and resid 23 through 28 removed outlier: 4.031A pdb=" N GLU r 27 " --> pdb=" O LYS r 24 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR r 28 " --> pdb=" O GLU r 25 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 25 removed outlier: 4.790A pdb=" N GLU s 6 " --> pdb=" O ASP s 2 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP s 11 " --> pdb=" O THR s 7 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN s 19 " --> pdb=" O LYS s 15 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS s 22 " --> pdb=" O MET s 18 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY s 25 " --> pdb=" O CYS s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 29 through 35 removed outlier: 3.899A pdb=" N LEU s 33 " --> pdb=" O THR s 29 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP s 34 " --> pdb=" O GLN s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 36 through 45 Processing helix chain 's' and resid 54 through 59 removed outlier: 7.375A pdb=" N LEU s 58 " --> pdb=" O ARG s 54 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR s 59 " --> pdb=" O ARG s 55 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 54 through 59' Processing helix chain 's' and resid 83 through 98 removed outlier: 4.510A pdb=" N ILE s 87 " --> pdb=" O GLY s 83 " (cutoff:3.500A) Processing helix chain 's' and resid 111 through 122 removed outlier: 3.519A pdb=" N LEU s 118 " --> pdb=" O ALA s 114 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL s 119 " --> pdb=" O LYS s 115 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP s 120 " --> pdb=" O GLN s 116 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N MET s 121 " --> pdb=" O SER s 117 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA s 122 " --> pdb=" O LEU s 118 " (cutoff:3.500A) Processing helix chain 's' and resid 131 through 137 removed outlier: 3.729A pdb=" N LEU s 135 " --> pdb=" O LEU s 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU s 136 " --> pdb=" O GLN s 132 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE s 137 " --> pdb=" O GLN s 133 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 131 through 137' Processing helix chain 's' and resid 138 through 143 removed outlier: 4.222A pdb=" N HIS s 142 " --> pdb=" O ASN s 138 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLU s 143 " --> pdb=" O ILE s 139 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 138 through 143' Processing helix chain 's' and resid 152 through 164 removed outlier: 4.064A pdb=" N THR s 157 " --> pdb=" O LYS s 153 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU s 158 " --> pdb=" O GLU s 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU s 160 " --> pdb=" O VAL s 156 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA s 161 " --> pdb=" O THR s 157 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS s 164 " --> pdb=" O LEU s 160 " (cutoff:3.500A) Processing helix chain 's' and resid 177 through 184 removed outlier: 3.579A pdb=" N GLY s 184 " --> pdb=" O ALA s 180 " (cutoff:3.500A) Processing helix chain 't' and resid 58 through 76 removed outlier: 3.682A pdb=" N ALA t 63 " --> pdb=" O LYS t 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY t 67 " --> pdb=" O ALA t 63 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 100 removed outlier: 3.891A pdb=" N ALA t 93 " --> pdb=" O PRO t 89 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET t 94 " --> pdb=" O LEU t 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS t 95 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU t 96 " --> pdb=" O ILE t 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU t 97 " --> pdb=" O ALA t 93 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA t 99 " --> pdb=" O LYS t 95 " (cutoff:3.500A) Processing helix chain 't' and resid 119 through 124 removed outlier: 3.587A pdb=" N LEU t 123 " --> pdb=" O GLY t 119 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE t 124 " --> pdb=" O VAL t 120 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 119 through 124' Processing helix chain 'u' and resid 21 through 37 removed outlier: 3.661A pdb=" N THR u 25 " --> pdb=" O ASN u 21 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS u 27 " --> pdb=" O LEU u 23 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR u 32 " --> pdb=" O GLN u 28 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU u 33 " --> pdb=" O LYS u 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL u 34 " --> pdb=" O LEU u 30 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY u 36 " --> pdb=" O THR u 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR u 37 " --> pdb=" O GLU u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 109 through 114 removed outlier: 3.528A pdb=" N ILE u 113 " --> pdb=" O SER u 109 " (cutoff:3.500A) Proline residue: u 114 - end of helix No H-bonds generated for 'chain 'u' and resid 109 through 114' Processing helix chain 'v' and resid 128 through 133 removed outlier: 3.852A pdb=" N LEU v 132 " --> pdb=" O ASP v 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS v 133 " --> pdb=" O ALA v 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 128 through 133' Processing helix chain 'w' and resid 63 through 68 removed outlier: 4.725A pdb=" N GLN w 67 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing helix chain 'w' and resid 69 through 75 removed outlier: 3.716A pdb=" N VAL w 72 " --> pdb=" O ILE w 69 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER w 73 " --> pdb=" O ALA w 70 " (cutoff:3.500A) Processing helix chain 'x' and resid 17 through 28 removed outlier: 3.815A pdb=" N ALA x 27 " --> pdb=" O GLY x 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU x 28 " --> pdb=" O LEU x 24 " (cutoff:3.500A) Processing helix chain 'x' and resid 30 through 39 removed outlier: 3.800A pdb=" N ASP x 36 " --> pdb=" O GLY x 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY x 39 " --> pdb=" O LEU x 35 " (cutoff:3.500A) Processing helix chain 'x' and resid 42 through 51 removed outlier: 3.641A pdb=" N ARG x 47 " --> pdb=" O TYR x 43 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 54 through 62 removed outlier: 4.911A pdb=" N LYS x 58 " --> pdb=" O ASP x 54 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU x 59 " --> pdb=" O LEU x 55 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU x 60 " --> pdb=" O ILE x 56 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN x 61 " --> pdb=" O GLU x 57 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR x 62 " --> pdb=" O LYS x 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 54 through 62' Processing helix chain 'y' and resid 39 through 54 removed outlier: 4.113A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE y 46 " --> pdb=" O LEU y 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS y 47 " --> pdb=" O GLY y 43 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN y 49 " --> pdb=" O ILE y 45 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS y 52 " --> pdb=" O SER y 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP y 53 " --> pdb=" O GLN y 49 " (cutoff:3.500A) Proline residue: y 54 - end of helix Processing helix chain 'y' and resid 82 through 113 removed outlier: 3.559A pdb=" N ASP y 93 " --> pdb=" O ASN y 89 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU y 100 " --> pdb=" O SER y 96 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS y 110 " --> pdb=" O ARG y 106 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS y 112 " --> pdb=" O ALA y 108 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN y 113 " --> pdb=" O ILE y 109 " (cutoff:3.500A) Processing helix chain 'y' and resid 5 through 10 removed outlier: 3.500A pdb=" N SER y 9 " --> pdb=" O ALA y 6 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 20 through 23 Processing sheet with id= 2, first strand: chain '2' and resid 102 through 109 removed outlier: 3.589A pdb=" N GLN 2 103 " --> pdb=" O ARG 2 59 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS 2 60 " --> pdb=" O SER 2 164 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '2' and resid 255 through 259 removed outlier: 6.118A pdb=" N GLN 2 256 " --> pdb=" O PHE 2 290 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE 2 290 " --> pdb=" O GLN 2 256 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '2' and resid 331 through 335 Processing sheet with id= 5, first strand: chain '3' and resid 54 through 62 removed outlier: 4.552A pdb=" N ASN 3 9 " --> pdb=" O SER 3 54 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 3 11 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA 3 166 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '3' and resid 265 through 269 removed outlier: 4.262A pdb=" N SER 3 273 " --> pdb=" O CYS 3 268 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '4' and resid 96 through 100 Processing sheet with id= 8, first strand: chain '4' and resid 306 through 310 removed outlier: 7.154A pdb=" N PHE 4 306 " --> pdb=" O TYR 4 318 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR 4 313 " --> pdb=" O VAL 4 346 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '4' and resid 433 through 436 removed outlier: 4.496A pdb=" N PHE 4 433 " --> pdb=" O VAL 4 442 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '5' and resid 8 through 12 removed outlier: 3.865A pdb=" N VAL 5 8 " --> pdb=" O VAL 5 45 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL 5 45 " --> pdb=" O VAL 5 8 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR 5 41 " --> pdb=" O CYS 5 12 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS 5 42 " --> pdb=" O ILE 5 38 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN 5 36 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '6' and resid 75 through 79 removed outlier: 5.714A pdb=" N GLY 6 82 " --> pdb=" O LEU 6 118 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '6' and resid 267 through 272 removed outlier: 7.273A pdb=" N CYS 6 180 " --> pdb=" O LYS 6 165 " (cutoff:3.500A) removed outlier: 12.328A pdb=" N LYS 6 165 " --> pdb=" O CYS 6 180 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 6 292 " --> pdb=" O VAL 6 166 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 6 168 " --> pdb=" O LEU 6 292 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '6' and resid 335 through 340 removed outlier: 5.655A pdb=" N GLY 6 336 " --> pdb=" O CYS 6 462 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE 6 338 " --> pdb=" O LEU 6 464 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU 6 340 " --> pdb=" O LEU 6 466 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '6' and resid 361 through 365 Processing sheet with id= 15, first strand: chain '6' and resid 557 through 562 removed outlier: 3.610A pdb=" N VAL 6 622 " --> pdb=" O LYS 6 557 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE 6 559 " --> pdb=" O VAL 6 622 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE 6 561 " --> pdb=" O ILE 6 624 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE 6 658 " --> pdb=" O ASN 6 621 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU 6 623 " --> pdb=" O PHE 6 658 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR 6 660 " --> pdb=" O LEU 6 623 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN 6 625 " --> pdb=" O TYR 6 660 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN 6 506 " --> pdb=" O ALA 6 657 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER 6 686 " --> pdb=" O VAL 6 505 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP 6 511 " --> pdb=" O ILE 6 690 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '7' and resid 1 through 4 removed outlier: 3.726A pdb=" N MET 7 1 " --> pdb=" O PHE 7 12 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '7' and resid 172 through 175 removed outlier: 3.897A pdb=" N VAL 7 204 " --> pdb=" O LEU 7 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU 7 109 " --> pdb=" O VAL 7 206 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL 7 231 " --> pdb=" O SER 7 453 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '7' and resid 348 through 352 removed outlier: 7.350A pdb=" N HIS 7 348 " --> pdb=" O PRO 7 420 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '7' and resid 489 through 496 removed outlier: 3.601A pdb=" N CYS 7 491 " --> pdb=" O GLY 7 675 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET 7 677 " --> pdb=" O CYS 7 491 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET 7 493 " --> pdb=" O MET 7 677 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE 7 679 " --> pdb=" O MET 7 493 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP 7 681 " --> pdb=" O ILE 7 495 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG 7 616 " --> pdb=" O TYR 7 674 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA 7 617 " --> pdb=" O GLY 7 534 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 7 597 " --> pdb=" O PHE 7 568 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL 7 599 " --> pdb=" O GLU 7 570 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '8' and resid 15 through 18 removed outlier: 4.915A pdb=" N LYS 8 28 " --> pdb=" O ASP 8 16 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL 8 26 " --> pdb=" O LEU 8 18 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE 8 23 " --> pdb=" O LYS 8 44 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '8' and resid 79 through 82 removed outlier: 3.791A pdb=" N ASP 8 79 " --> pdb=" O VAL 8 90 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '8' and resid 133 through 136 removed outlier: 3.559A pdb=" N LEU 8 134 " --> pdb=" O LYS 8 160 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG 8 136 " --> pdb=" O LEU 8 158 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU 8 158 " --> pdb=" O ARG 8 136 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '8' and resid 142 through 146 removed outlier: 8.150A pdb=" N ASN 8 142 " --> pdb=" O ALA 8 154 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL 8 150 " --> pdb=" O ASP 8 146 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'A' and resid 679 through 684 Processing sheet with id= 25, first strand: chain 'A' and resid 720 through 725 removed outlier: 3.519A pdb=" N CYS A 725 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG A 706 " --> pdb=" O CYS A 725 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 705 " --> pdb=" O GLN A 738 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 738 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 762 through 767 removed outlier: 3.816A pdb=" N GLY A 770 " --> pdb=" O THR A 767 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'A' and resid 851 through 854 removed outlier: 3.731A pdb=" N TRP A 861 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'A' and resid 1164 through 1173 removed outlier: 4.095A pdb=" N LYS A1177 " --> pdb=" O ASP A1173 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.901A pdb=" N THR B 52 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS B 30 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N HIS B 235 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.353A pdb=" N ASN B 61 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B 130 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 83 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 70 through 73 removed outlier: 6.851A pdb=" N ASN B 149 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 74 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 159 through 163 removed outlier: 6.065A pdb=" N LEU B 249 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 254 through 259 removed outlier: 6.037A pdb=" N VAL B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 270 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N SER B 321 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 305 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 322 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLU B 315 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 573 through 580 Processing sheet with id= 35, first strand: chain 'B' and resid 586 through 592 removed outlier: 5.112A pdb=" N LEU B 586 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 542 " --> pdb=" O CYS B 592 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS B 530 " --> pdb=" O ASP B 551 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE B 535 " --> pdb=" O GLU B 643 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 603 through 606 removed outlier: 5.641A pdb=" N GLU B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 37 through 40 removed outlier: 4.751A pdb=" N ASN B 37 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 46 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 44 through 54 Processing sheet with id= 39, first strand: chain 'B' and resid 222 through 226 removed outlier: 3.702A pdb=" N GLU B 222 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS B 231 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'E' and resid 305 through 309 removed outlier: 4.227A pdb=" N LEU E 307 " --> pdb=" O TYR E 338 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP E 340 " --> pdb=" O LEU E 307 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'E' and resid 460 through 467 removed outlier: 3.876A pdb=" N GLY E 795 " --> pdb=" O TYR E 464 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'E' and resid 475 through 479 removed outlier: 6.019A pdb=" N LEU E 484 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR E 493 " --> pdb=" O PHE E 489 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 548 through 552 removed outlier: 6.323A pdb=" N TYR E 557 " --> pdb=" O SER E 552 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN E 556 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU E 572 " --> pdb=" O ASN E 556 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU E 569 " --> pdb=" O LEU E 578 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR E 576 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'E' and resid 590 through 594 removed outlier: 6.228A pdb=" N TYR E 599 " --> pdb=" O SER E 594 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 632 through 636 removed outlier: 5.781A pdb=" N TYR E 641 " --> pdb=" O HIS E 636 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ASN E 640 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR E 650 " --> pdb=" O SER E 646 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU E 653 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN E 660 " --> pdb=" O ASP E 655 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'E' and resid 674 through 678 removed outlier: 5.472A pdb=" N PHE E 683 " --> pdb=" O SER E 678 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ARG E 682 " --> pdb=" O ILE E 698 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'E' and resid 716 through 720 removed outlier: 6.202A pdb=" N ILE E 725 " --> pdb=" O SER E 720 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN E 733 " --> pdb=" O THR E 775 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR E 773 " --> pdb=" O VAL E 735 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY E 771 " --> pdb=" O LEU E 737 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'E' and resid 566 through 569 removed outlier: 3.649A pdb=" N VAL E 579 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'E' and resid 650 through 653 removed outlier: 3.616A pdb=" N ARG E 663 " --> pdb=" O LEU E 653 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.578A pdb=" N ARG G 19 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N HIS G 53 " --> pdb=" O HIS G 48 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'G' and resid 85 through 88 removed outlier: 6.602A pdb=" N SER G 76 " --> pdb=" O THR G 88 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA G 89 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'O' and resid 64 through 67 removed outlier: 4.196A pdb=" N THR O 64 " --> pdb=" O VAL O 75 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'O' and resid 78 through 83 Processing sheet with id= 54, first strand: chain 'P' and resid 163 through 166 removed outlier: 6.496A pdb=" N VAL P 259 " --> pdb=" O GLN P 166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE P 300 " --> pdb=" O MET P 295 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU P 302 " --> pdb=" O TYR P 293 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE P 280 " --> pdb=" O ARG P 294 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'P' and resid 189 through 192 removed outlier: 5.588A pdb=" N ASN P 189 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS P 218 " --> pdb=" O PHE P 214 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL P 169 " --> pdb=" O GLN P 256 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Q' and resid 333 through 337 removed outlier: 4.396A pdb=" N VAL Q 334 " --> pdb=" O ASN Q 359 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN Q 359 " --> pdb=" O VAL Q 334 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Q' and resid 341 through 344 Processing sheet with id= 58, first strand: chain 'R' and resid 23 through 26 removed outlier: 3.639A pdb=" N ASP R 31 " --> pdb=" O ASP R 26 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET R 32 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU R 39 " --> pdb=" O CYS R 34 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'S' and resid 15 through 18 removed outlier: 4.307A pdb=" N ALA S 134 " --> pdb=" O CYS S 130 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR S 124 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'S' and resid 27 through 31 removed outlier: 3.701A pdb=" N ALA S 30 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TRP S 143 " --> pdb=" O LYS S 115 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'T' and resid 41 through 47 removed outlier: 11.284A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS T 81 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN T 112 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'T' and resid 95 through 99 removed outlier: 6.779A pdb=" N VAL T 95 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'T' and resid 222 through 225 Processing sheet with id= 64, first strand: chain 'U' and resid 71 through 77 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'U' and resid 127 through 130 removed outlier: 3.557A pdb=" N SER U 134 " --> pdb=" O CYS U 129 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 190 through 193 Processing sheet with id= 67, first strand: chain 'e' and resid 460 through 467 removed outlier: 3.824A pdb=" N ALA e 793 " --> pdb=" O CYS e 462 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR e 464 " --> pdb=" O ALA e 793 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE e 466 " --> pdb=" O GLY e 795 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA e 794 " --> pdb=" O HIS e 782 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS e 782 " --> pdb=" O ALA e 794 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'e' and resid 474 through 479 removed outlier: 6.592A pdb=" N LEU e 484 " --> pdb=" O THR e 479 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR e 493 " --> pdb=" O PHE e 489 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 548 through 552 removed outlier: 6.254A pdb=" N TYR e 557 " --> pdb=" O SER e 552 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN e 556 " --> pdb=" O LEU e 572 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU e 572 " --> pdb=" O ASN e 556 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU e 569 " --> pdb=" O LEU e 578 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR e 576 " --> pdb=" O SER e 571 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 590 through 594 removed outlier: 6.222A pdb=" N TYR e 599 " --> pdb=" O SER e 594 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'e' and resid 632 through 636 removed outlier: 5.759A pdb=" N TYR e 641 " --> pdb=" O HIS e 636 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN e 640 " --> pdb=" O VAL e 656 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG e 652 " --> pdb=" O THR e 644 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG e 663 " --> pdb=" O LEU e 653 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'e' and resid 674 through 678 removed outlier: 5.271A pdb=" N PHE e 683 " --> pdb=" O SER e 678 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ARG e 682 " --> pdb=" O ILE e 698 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'e' and resid 716 through 720 removed outlier: 6.674A pdb=" N ILE e 725 " --> pdb=" O SER e 720 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASN e 733 " --> pdb=" O THR e 775 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR e 773 " --> pdb=" O VAL e 735 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU e 737 " --> pdb=" O GLY e 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY e 771 " --> pdb=" O LEU e 737 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'e' and resid 566 through 569 removed outlier: 3.835A pdb=" N VAL e 579 " --> pdb=" O LEU e 569 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'f' and resid 94 through 98 removed outlier: 3.506A pdb=" N LEU f 104 " --> pdb=" O ALA f 97 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'o' and resid 85 through 89 Processing sheet with id= 77, first strand: chain 'o' and resid 189 through 193 removed outlier: 3.772A pdb=" N GLU o 201 " --> pdb=" O ARG o 190 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU o 198 " --> pdb=" O LEU o 216 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'o' and resid 376 through 379 removed outlier: 6.875A pdb=" N ASP o 376 " --> pdb=" O GLY o 471 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL o 456 " --> pdb=" O HIS o 472 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP o 454 " --> pdb=" O VAL o 474 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR o 365 " --> pdb=" O MET o 501 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE o 361 " --> pdb=" O LEU o 505 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU o 484 " --> pdb=" O THR o 368 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'o' and resid 390 through 394 removed outlier: 4.775A pdb=" N TYR o 444 " --> pdb=" O VAL o 394 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'o' and resid 602 through 605 No H-bonds generated for sheet with id= 80 Processing sheet with id= 81, first strand: chain 'o' and resid 901 through 906 removed outlier: 3.570A pdb=" N LEU o 906 " --> pdb=" O SER o 975 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N SER o 975 " --> pdb=" O LEU o 906 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'o' and resid 1172 through 1177 removed outlier: 3.682A pdb=" N ASN o1172 " --> pdb=" O GLU o1215 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU o1211 " --> pdb=" O TYR o1176 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N TRP o1210 " --> pdb=" O ILE o1261 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE o1261 " --> pdb=" O TRP o1210 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'o' and resid 1306 through 1309 removed outlier: 4.403A pdb=" N LYS o1306 " --> pdb=" O ASP o1339 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU o1337 " --> pdb=" O TYR o1308 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER o1138 " --> pdb=" O ASN o1360 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'o' and resid 1318 through 1323 removed outlier: 4.491A pdb=" N GLU o1327 " --> pdb=" O THR o1323 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'p' and resid 64 through 68 removed outlier: 3.657A pdb=" N ILE p 65 " --> pdb=" O LEU p 86 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU p 86 " --> pdb=" O ILE p 65 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP p 127 " --> pdb=" O GLU p 89 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE p 91 " --> pdb=" O TYR p 125 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR p 125 " --> pdb=" O ILE p 91 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU p 140 " --> pdb=" O VAL p 132 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'p' and resid 97 through 100 removed outlier: 4.599A pdb=" N ALA p 104 " --> pdb=" O GLU p 100 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'p' and resid 184 through 187 Processing sheet with id= 88, first strand: chain 'p' and resid 203 through 209 removed outlier: 4.852A pdb=" N THR p 204 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG p 222 " --> pdb=" O THR p 204 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR p 217 " --> pdb=" O MET p 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS p 221 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE p 235 " --> pdb=" O CYS p 221 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU p 240 " --> pdb=" O ARG p 255 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG p 255 " --> pdb=" O LEU p 240 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'p' and resid 530 through 533 removed outlier: 5.130A pdb=" N ARG p 620 " --> pdb=" O SER p 533 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG p 623 " --> pdb=" O ILE p 665 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'p' and resid 601 through 605 removed outlier: 3.623A pdb=" N SER p 602 " --> pdb=" O TYR p 615 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'p' and resid 746 through 752 removed outlier: 5.972A pdb=" N THR p 746 " --> pdb=" O SER p 813 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER p 813 " --> pdb=" O THR p 746 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL p 750 " --> pdb=" O VAL p 809 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ARG p 807 " --> pdb=" O TYR p 752 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG p 922 " --> pdb=" O ASP p 905 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL p 926 " --> pdb=" O THR p 901 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N THR p 901 " --> pdb=" O VAL p 926 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU p 900 " --> pdb=" O GLY p 862 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY p 862 " --> pdb=" O GLU p 900 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL p 858 " --> pdb=" O VAL p 904 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'p' and resid 758 through 761 removed outlier: 3.516A pdb=" N THR p 760 " --> pdb=" O GLY p 997 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'p' and resid 776 through 782 removed outlier: 4.461A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'p' and resid 827 through 830 removed outlier: 4.653A pdb=" N GLY p 868 " --> pdb=" O GLU p 830 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE p 867 " --> pdb=" O THR p 894 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR p 888 " --> pdb=" O LEU p 873 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'p' and resid 933 through 936 removed outlier: 5.384A pdb=" N ASP p 933 " --> pdb=" O CYS p 945 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'p' and resid 1114 through 1119 Processing sheet with id= 97, first strand: chain 'p' and resid 1126 through 1130 Processing sheet with id= 98, first strand: chain 'p' and resid 121 through 125 No H-bonds generated for sheet with id= 98 Processing sheet with id= 99, first strand: chain 'p' and resid 906 through 911 removed outlier: 3.748A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'q' and resid 8 through 12 removed outlier: 6.522A pdb=" N LYS q 20 " --> pdb=" O THR q 12 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE q 21 " --> pdb=" O TYR q 231 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU q 234 " --> pdb=" O GLY q 181 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY q 181 " --> pdb=" O GLU q 234 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'q' and resid 48 through 53 removed outlier: 3.574A pdb=" N TRP q 49 " --> pdb=" O TYR q 164 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG q 160 " --> pdb=" O ASP q 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU q 158 " --> pdb=" O SER q 56 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA q 54 " --> pdb=" O ARG q 160 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'q' and resid 98 through 107 removed outlier: 3.530A pdb=" N VAL q 99 " --> pdb=" O ALA q 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA q 163 " --> pdb=" O PHE q 101 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN q 157 " --> pdb=" O CYS q 107 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 's' and resid 60 through 63 removed outlier: 3.751A pdb=" N VAL s 60 " --> pdb=" O VAL s 74 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG s 101 " --> pdb=" O GLN s 71 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 's' and resid 146 through 150 removed outlier: 3.805A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN s 189 " --> pdb=" O VAL s 209 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER s 197 " --> pdb=" O GLY s 201 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 't' and resid 106 through 109 Processing sheet with id=106, first strand: chain 'u' and resid 55 through 59 removed outlier: 5.278A pdb=" N ALA u 56 " --> pdb=" O PRO u 69 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'u' and resid 84 through 88 Processing sheet with id=108, first strand: chain 'u' and resid 97 through 100 Processing sheet with id=109, first strand: chain 'v' and resid 5 through 12 removed outlier: 3.501A pdb=" N PHE v 56 " --> pdb=" O PHE v 10 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP v 54 " --> pdb=" O VAL v 12 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER v 139 " --> pdb=" O VAL v 96 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'v' and resid 26 through 33 removed outlier: 5.107A pdb=" N MET v 37 " --> pdb=" O SER v 32 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY v 127 " --> pdb=" O LEU v 112 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER v 113 " --> pdb=" O GLU v 100 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG v 98 " --> pdb=" O TYR v 115 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'w' and resid 25 through 28 Processing sheet with id=112, first strand: chain 'y' and resid 18 through 24 removed outlier: 5.763A pdb=" N LYS y 18 " --> pdb=" O ASN y 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR y 20 " --> pdb=" O THR y 34 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA y 30 " --> pdb=" O ASP y 24 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASN y 29 " --> pdb=" O THR y 77 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'z' and resid 23 through 27 removed outlier: 5.089A pdb=" N THR z 24 " --> pdb=" O CYS z 19 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS z 19 " --> pdb=" O THR z 24 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE z 43 " --> pdb=" O GLY z 20 " (cutoff:3.500A) 4565 hydrogen bonds defined for protein. 13539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 114 stacking parallelities Total time for adding SS restraints: 49.12 Time building geometry restraints manager: 37.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 46617 1.40 - 1.62: 68067 1.62 - 1.84: 1002 1.84 - 2.06: 1 2.06 - 2.28: 12 Bond restraints: 115699 Sorted by residual: bond pdb=" C GLN U 183 " pdb=" O GLN U 183 " ideal model delta sigma weight residual 1.236 1.332 -0.095 1.15e-02 7.56e+03 6.85e+01 bond pdb=" C THR 6 432 " pdb=" N GLN 6 433 " ideal model delta sigma weight residual 1.332 1.427 -0.094 1.29e-02 6.01e+03 5.33e+01 bond pdb=" C GLU P 326 " pdb=" O GLU P 326 " ideal model delta sigma weight residual 1.236 1.316 -0.080 1.15e-02 7.56e+03 4.80e+01 bond pdb=" C ARG U 124 " pdb=" N ALA U 125 " ideal model delta sigma weight residual 1.334 1.420 -0.086 1.25e-02 6.40e+03 4.71e+01 bond pdb=" C GLU P 323 " pdb=" O GLU P 323 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.19e-02 7.06e+03 4.46e+01 ... (remaining 115694 not shown) Histogram of bond angle deviations from ideal: 73.01 - 86.11: 12 86.11 - 99.20: 38 99.20 - 112.29: 59332 112.29 - 125.39: 95552 125.39 - 138.48: 2179 Bond angle restraints: 157113 Sorted by residual: angle pdb=" CA PRO U 186 " pdb=" N PRO U 186 " pdb=" CD PRO U 186 " ideal model delta sigma weight residual 112.00 93.52 18.48 1.40e+00 5.10e-01 1.74e+02 angle pdb=" N VAL 1 421 " pdb=" CA VAL 1 421 " pdb=" C VAL 1 421 " ideal model delta sigma weight residual 110.82 98.89 11.93 9.70e-01 1.06e+00 1.51e+02 angle pdb=" C GLU F 81 " pdb=" N PRO F 82 " pdb=" CA PRO F 82 " ideal model delta sigma weight residual 119.05 130.60 -11.55 1.11e+00 8.12e-01 1.08e+02 angle pdb=" N HIS B 491 " pdb=" CA HIS B 491 " pdb=" C HIS B 491 " ideal model delta sigma weight residual 111.28 100.62 10.66 1.09e+00 8.42e-01 9.57e+01 angle pdb=" O3' DC Y 36 " pdb=" C3' DC Y 36 " pdb=" C2' DC Y 36 " ideal model delta sigma weight residual 111.50 96.98 14.52 1.50e+00 4.44e-01 9.36e+01 ... (remaining 157108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.36: 63733 20.36 - 40.73: 4996 40.73 - 61.09: 1242 61.09 - 81.46: 145 81.46 - 101.82: 35 Dihedral angle restraints: 70151 sinusoidal: 29491 harmonic: 40660 Sorted by residual: dihedral pdb=" C LYS 1 353 " pdb=" N LYS 1 353 " pdb=" CA LYS 1 353 " pdb=" CB LYS 1 353 " ideal model delta harmonic sigma weight residual -122.60 -146.78 24.18 0 2.50e+00 1.60e-01 9.36e+01 dihedral pdb=" N LYS o 581 " pdb=" C LYS o 581 " pdb=" CA LYS o 581 " pdb=" CB LYS o 581 " ideal model delta harmonic sigma weight residual 122.80 144.49 -21.69 0 2.50e+00 1.60e-01 7.53e+01 dihedral pdb=" C LYS o 581 " pdb=" N LYS o 581 " pdb=" CA LYS o 581 " pdb=" CB LYS o 581 " ideal model delta harmonic sigma weight residual -122.60 -143.70 21.10 0 2.50e+00 1.60e-01 7.12e+01 ... (remaining 70148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 17028 0.185 - 0.370: 513 0.370 - 0.556: 40 0.556 - 0.741: 2 0.741 - 0.926: 4 Chirality restraints: 17587 Sorted by residual: chirality pdb=" CA LYS o 581 " pdb=" N LYS o 581 " pdb=" C LYS o 581 " pdb=" CB LYS o 581 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CA LYS 1 353 " pdb=" N LYS 1 353 " pdb=" C LYS 1 353 " pdb=" CB LYS 1 353 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" CA CYS t 76 " pdb=" N CYS t 76 " pdb=" C CYS t 76 " pdb=" CB CYS t 76 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 17584 not shown) Planarity restraints: 19780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU U 185 " 0.110 5.00e-02 4.00e+02 1.51e-01 3.62e+01 pdb=" N PRO U 186 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO U 186 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO U 186 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 969 " 0.028 2.00e-02 2.50e+03 5.74e-02 3.30e+01 pdb=" C PRO A 969 " -0.099 2.00e-02 2.50e+03 pdb=" O PRO A 969 " 0.038 2.00e-02 2.50e+03 pdb=" N ASN A 970 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG 6 645 " -0.028 2.00e-02 2.50e+03 5.67e-02 3.22e+01 pdb=" C ARG 6 645 " 0.098 2.00e-02 2.50e+03 pdb=" O ARG 6 645 " -0.038 2.00e-02 2.50e+03 pdb=" N ALA 6 646 " -0.032 2.00e-02 2.50e+03 ... (remaining 19777 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 170 2.10 - 2.80: 30725 2.80 - 3.50: 148331 3.50 - 4.20: 264152 4.20 - 4.90: 453287 Nonbonded interactions: 896665 Sorted by model distance: nonbonded pdb=" N MET A 491 " pdb=" CE MET A 491 " model vdw 1.402 3.540 nonbonded pdb=" O ARG F 404 " pdb=" OD1 ASP F 408 " model vdw 1.405 3.040 nonbonded pdb=" OD2 ASP U 69 " pdb=" CG2 VAL U 100 " model vdw 1.459 3.460 nonbonded pdb=" OE1 GLU 6 619 " pdb=" CA LYS 6 648 " model vdw 1.492 3.470 nonbonded pdb=" CB GLU 0 264 " pdb=" CD2 LEU 0 269 " model vdw 1.497 3.860 ... (remaining 896660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 209 through 343 or resid 363 through 798)) selection = (chain 'e' and (resid 209 through 378 or resid 417 through 747 or resid 754 thro \ ugh 798)) } ncs_group { reference = (chain 'F' and (resid 10 through 150 or resid 210 or resid 214 through 473)) selection = (chain 'f' and (resid 10 through 106 or (resid 107 through 108 and (name N or na \ me CA or name C or name O or name CB )) or resid 109 through 123 or (resid 124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 125 through 473 \ )) } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 13 through 132) } ncs_group { reference = chain 'J' selection = (chain 'j' and (resid 114 through 177 or resid 192 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.060 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: 28.300 Check model and map are aligned: 1.130 Set scattering table: 0.750 Process input model: 321.530 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.500 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: 0.030 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 363.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1023 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 115699 Z= 0.529 Angle : 1.134 18.482 157113 Z= 0.751 Chirality : 0.077 0.926 17587 Planarity : 0.007 0.151 19780 Dihedral : 15.516 101.821 43763 Min Nonbonded Distance : 1.402 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.31 % Favored : 91.90 % Rotamer: Outliers : 3.39 % Allowed : 6.94 % Favored : 89.68 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.06), residues: 13701 helix: -2.28 (0.06), residues: 5612 sheet: -1.61 (0.12), residues: 1617 loop : -2.64 (0.07), residues: 6472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP T 19 HIS 0.021 0.002 HIS 4 161 PHE 0.034 0.002 PHE 4 215 TYR 0.069 0.002 TYR 2 228 ARG 0.063 0.001 ARG p1078 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1690 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 405 poor density : 1285 time to evaluate : 9.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0 97 ASP cc_start: 0.6685 (m-30) cc_final: 0.6471 (m-30) REVERT: 1 222 THR cc_start: 0.7861 (m) cc_final: 0.7524 (p) REVERT: 1 362 ASP cc_start: -0.3233 (OUTLIER) cc_final: -0.3607 (m-30) REVERT: 2 71 MET cc_start: -0.2875 (mmp) cc_final: -0.3192 (tpt) REVERT: 2 137 MET cc_start: -0.2692 (ptm) cc_final: -0.3082 (ptt) REVERT: 2 252 MET cc_start: -0.1852 (tpp) cc_final: -0.2052 (ttt) REVERT: 3 42 MET cc_start: -0.3558 (mtm) cc_final: -0.4872 (mmt) REVERT: 3 51 MET cc_start: -0.2787 (mtp) cc_final: -0.3297 (tpt) REVERT: 3 119 MET cc_start: -0.2653 (mmm) cc_final: -0.4950 (mtt) REVERT: 4 215 PHE cc_start: -0.2108 (OUTLIER) cc_final: -0.2430 (t80) REVERT: 4 216 MET cc_start: 0.3238 (mmp) cc_final: 0.2503 (mmt) REVERT: 6 303 ASN cc_start: -0.5326 (OUTLIER) cc_final: -0.6681 (t0) REVERT: 6 357 VAL cc_start: -0.2011 (OUTLIER) cc_final: -0.3694 (p) REVERT: 6 415 HIS cc_start: -0.1003 (OUTLIER) cc_final: -0.1298 (m170) REVERT: 6 528 LYS cc_start: -0.2117 (OUTLIER) cc_final: -0.2886 (mttt) REVERT: 6 575 LEU cc_start: -0.2327 (OUTLIER) cc_final: -0.3912 (pp) REVERT: 6 616 ASP cc_start: -0.1356 (OUTLIER) cc_final: -0.1734 (p0) REVERT: 7 42 MET cc_start: -0.3380 (tpp) cc_final: -0.3998 (ttt) REVERT: 7 247 MET cc_start: -0.4922 (ttm) cc_final: -0.6082 (mtm) REVERT: 7 657 MET cc_start: -0.2595 (mmp) cc_final: -0.3141 (tpp) REVERT: A 416 TRP cc_start: -0.1758 (OUTLIER) cc_final: -0.2440 (m100) REVERT: A 661 GLU cc_start: -0.2238 (OUTLIER) cc_final: -0.3697 (tt0) REVERT: A 711 ASP cc_start: 0.0727 (OUTLIER) cc_final: 0.0000 (t70) REVERT: A 942 MET cc_start: -0.1692 (mmm) cc_final: -0.2013 (mmt) REVERT: B 322 MET cc_start: -0.2670 (ttt) cc_final: -0.2908 (ttt) REVERT: B 614 MET cc_start: -0.3559 (mtt) cc_final: -0.4103 (mtt) REVERT: E 746 ASP cc_start: 0.1674 (OUTLIER) cc_final: 0.1470 (p0) REVERT: E 747 LEU cc_start: -0.3233 (OUTLIER) cc_final: -0.4230 (mt) REVERT: F 26 MET cc_start: -0.4058 (ttm) cc_final: -0.4662 (ttt) REVERT: F 62 LYS cc_start: -0.3786 (OUTLIER) cc_final: -0.5892 (tttm) REVERT: F 271 VAL cc_start: -0.5025 (OUTLIER) cc_final: -0.5271 (t) REVERT: F 290 MET cc_start: 0.0260 (mtm) cc_final: -0.1127 (mmt) REVERT: F 295 LEU cc_start: -0.5225 (OUTLIER) cc_final: -0.5642 (mp) REVERT: F 309 MET cc_start: -0.4117 (mmt) cc_final: -0.4517 (mmt) REVERT: G 131 ILE cc_start: 0.1441 (OUTLIER) cc_final: 0.0364 (tp) REVERT: H 100 MET cc_start: -0.3130 (mtt) cc_final: -0.3437 (mtp) REVERT: H 132 LYS cc_start: -0.4209 (OUTLIER) cc_final: -0.6044 (mttt) REVERT: H 161 LYS cc_start: 0.1890 (OUTLIER) cc_final: 0.1593 (mmtt) REVERT: I 19 MET cc_start: -0.3920 (tpp) cc_final: -0.4660 (ttm) REVERT: I 32 GLU cc_start: -0.2033 (OUTLIER) cc_final: -0.2574 (mt-10) REVERT: I 60 HIS cc_start: -0.2448 (OUTLIER) cc_final: -0.4356 (m-70) REVERT: J 176 MET cc_start: 0.2187 (mtt) cc_final: 0.1580 (ptt) REVERT: J 192 LYS cc_start: 0.2759 (OUTLIER) cc_final: 0.2068 (pttp) REVERT: J 197 MET cc_start: -0.2649 (mmm) cc_final: -0.4799 (mtt) REVERT: P 169 VAL cc_start: -0.1893 (OUTLIER) cc_final: -0.2347 (m) REVERT: P 252 ASP cc_start: -0.6156 (OUTLIER) cc_final: -0.6594 (t70) REVERT: T 85 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.4828 (mp) REVERT: T 215 GLU cc_start: -0.1618 (OUTLIER) cc_final: -0.4368 (mm-30) REVERT: U 174 ARG cc_start: -0.3994 (OUTLIER) cc_final: -0.6568 (mtm180) REVERT: V 191 PHE cc_start: 0.2580 (OUTLIER) cc_final: 0.2281 (p90) REVERT: d 857 SER cc_start: -0.1383 (m) cc_final: -0.1584 (m) REVERT: e 528 MET cc_start: 0.1054 (mmt) cc_final: -0.0517 (mmt) REVERT: e 731 MET cc_start: 0.2198 (mmm) cc_final: 0.1314 (mpp) REVERT: f 19 MET cc_start: -0.3254 (mmt) cc_final: -0.5476 (mmt) REVERT: f 290 MET cc_start: -0.1115 (mtt) cc_final: -0.1653 (mmt) REVERT: i 26 MET cc_start: -0.0859 (mmp) cc_final: -0.1438 (tpt) REVERT: i 39 MET cc_start: -0.1983 (mmp) cc_final: -0.3171 (mmt) REVERT: j 176 MET cc_start: -0.3310 (mtm) cc_final: -0.3787 (ptt) REVERT: l 152 MET cc_start: -0.3089 (tpp) cc_final: -0.4225 (mtt) REVERT: m 39 MET cc_start: -0.3127 (mtp) cc_final: -0.4726 (mtt) REVERT: m 40 MET cc_start: -0.3043 (mtp) cc_final: -0.3245 (mtt) REVERT: o 104 MET cc_start: 0.5227 (ppp) cc_final: 0.4041 (ttt) REVERT: o 514 GLU cc_start: 0.2640 (pt0) cc_final: 0.2403 (pt0) REVERT: o 554 PHE cc_start: 0.7494 (m-80) cc_final: 0.7133 (m-80) REVERT: o 660 MET cc_start: 0.7993 (mmm) cc_final: 0.7665 (mmp) REVERT: o 693 ILE cc_start: 0.5614 (tt) cc_final: 0.5398 (mt) REVERT: o 744 ILE cc_start: 0.6726 (mt) cc_final: 0.5860 (mt) REVERT: o 1031 ARG cc_start: 0.3247 (ttp80) cc_final: 0.3004 (mtm110) REVERT: o 1257 LEU cc_start: 0.9114 (pp) cc_final: 0.8806 (pp) REVERT: o 1292 MET cc_start: 0.7578 (mmp) cc_final: 0.6611 (mmt) REVERT: o 1301 ILE cc_start: 0.6107 (mp) cc_final: 0.5862 (mm) REVERT: o 1342 SER cc_start: 0.7438 (t) cc_final: 0.7140 (p) REVERT: o 1410 HIS cc_start: 0.6544 (p-80) cc_final: 0.6287 (p-80) REVERT: o 1427 LEU cc_start: 0.7857 (mt) cc_final: 0.7553 (mt) REVERT: p 22 TRP cc_start: 0.3583 (t-100) cc_final: 0.3119 (t60) REVERT: p 108 MET cc_start: -0.1420 (ptm) cc_final: -0.2030 (tpt) REVERT: p 529 MET cc_start: -0.1415 (mtp) cc_final: -0.1662 (mmm) REVERT: p 790 GLN cc_start: 0.0923 (mt0) cc_final: 0.0071 (mm-40) REVERT: p 833 THR cc_start: 0.6344 (m) cc_final: 0.5945 (t) REVERT: p 908 MET cc_start: -0.2968 (ttp) cc_final: -0.4197 (ttp) REVERT: p 1084 LEU cc_start: 0.2983 (mt) cc_final: 0.2074 (mm) REVERT: s 127 LEU cc_start: 0.7092 (mp) cc_final: 0.6808 (tp) REVERT: t 92 ILE cc_start: 0.6117 (mt) cc_final: 0.5908 (mt) REVERT: u 16 ARG cc_start: 0.6057 (ptt-90) cc_final: 0.5637 (ttm170) REVERT: u 117 MET cc_start: -0.2308 (mtm) cc_final: -0.3563 (ttm) REVERT: u 144 ARG cc_start: 0.1110 (OUTLIER) cc_final: -0.0655 (ttm-80) REVERT: w 43 ASP cc_start: 0.7788 (m-30) cc_final: 0.7537 (t0) REVERT: y 51 LEU cc_start: 0.6211 (mp) cc_final: 0.5972 (mt) outliers start: 405 outliers final: 90 residues processed: 1670 average time/residue: 1.0051 time to fit residues: 2849.2155 Evaluate side-chains 908 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 789 time to evaluate : 10.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 363 LEU Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 2 residue 313 VAL Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 188 THR Chi-restraints excluded: chain 4 residue 215 PHE Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 6 residue 157 LYS Chi-restraints excluded: chain 6 residue 302 VAL Chi-restraints excluded: chain 6 residue 303 ASN Chi-restraints excluded: chain 6 residue 310 LEU Chi-restraints excluded: chain 6 residue 357 VAL Chi-restraints excluded: chain 6 residue 404 SER Chi-restraints excluded: chain 6 residue 413 LEU Chi-restraints excluded: chain 6 residue 415 HIS Chi-restraints excluded: chain 6 residue 434 GLU Chi-restraints excluded: chain 6 residue 528 LYS Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 575 LEU Chi-restraints excluded: chain 6 residue 597 LYS Chi-restraints excluded: chain 6 residue 616 ASP Chi-restraints excluded: chain 6 residue 633 ARG Chi-restraints excluded: chain 6 residue 648 LYS Chi-restraints excluded: chain 6 residue 650 MET Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 48 LYS Chi-restraints excluded: chain 7 residue 98 GLU Chi-restraints excluded: chain 7 residue 425 THR Chi-restraints excluded: chain 7 residue 464 LEU Chi-restraints excluded: chain 9 residue 243 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 486 TRP Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 450 ARG Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 745 GLU Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 335 ARG Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 182 GLU Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 159 TYR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 60 HIS Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 68 CYS Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 252 ASP Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 120 GLU Chi-restraints excluded: chain R residue 127 ARG Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 166 GLU Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain T residue 215 GLU Chi-restraints excluded: chain T residue 228 ILE Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 114 ILE Chi-restraints excluded: chain U residue 174 ARG Chi-restraints excluded: chain U residue 185 GLU Chi-restraints excluded: chain U residue 186 PRO Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 191 PHE Chi-restraints excluded: chain V residue 194 ARG Chi-restraints excluded: chain V residue 225 VAL Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain u residue 144 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 1161 optimal weight: 0.2980 chunk 1042 optimal weight: 0.0870 chunk 578 optimal weight: 5.9990 chunk 356 optimal weight: 4.9990 chunk 703 optimal weight: 0.0970 chunk 557 optimal weight: 5.9990 chunk 1078 optimal weight: 0.1980 chunk 417 optimal weight: 50.0000 chunk 655 optimal weight: 50.0000 chunk 802 optimal weight: 6.9990 chunk 1249 optimal weight: 0.0870 overall best weight: 0.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 210 ASN 1 213 HIS 1 384 HIS 2 147 ASN 2 235 HIS 2 256 GLN 2 257 HIS 2 317 HIS 2 324 HIS 2 340 ASN ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 108 ASN 3 179 ASN 3 187 GLN 3 248 HIS ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 161 HIS 4 181 GLN 4 312 ASN ** 4 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 390 GLN 4 415 GLN 4 458 GLN 4 460 HIS ** 6 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 112 HIS 6 172 HIS 6 181 HIS ** 6 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 444 HIS 6 497 GLN 6 551 HIS ** 6 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 591 GLN 6 595 ASN ** 6 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 683 GLN ** 7 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 384 HIS 7 434 HIS 7 452 GLN 7 555 GLN 7 562 GLN 7 585 GLN 7 729 HIS 7 733 GLN 8 73 ASN 8 279 ASN ** 9 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 100 HIS ** 9 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 247 GLN A 401 ASN A 508 ASN A 569 ASN A 860 ASN A 896 GLN A1073 GLN B 30 HIS B 137 HIS B 235 HIS B 348 GLN B 415 HIS B 509 ASN B 521 GLN B 750 GLN B 813 ASN B 908 GLN B 916 ASN ** D 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 ASN D 992 GLN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1075 HIS E 254 ASN E 255 GLN E 351 GLN E 616 HIS E 636 HIS E 640 ASN F 59 HIS F 119 ASN F 270 ASN F 273 GLN F 275 ASN F 316 GLN H 145 HIS I 21 GLN I 38 GLN I 76 GLN I 81 GLN I 98 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 GLN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 GLN O 27 GLN O 54 ASN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 352 HIS Q 361 ASN R 229 GLN ** R 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 195 GLN ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 ASN U 123 ASN V 117 GLN V 204 ASN c 104 ASN d 912 ASN d1069 ASN e 294 ASN e 336 HIS e 673 HIS f 325 ASN f 326 HIS f 422 HIS k 139 GLN o 123 ASN o 296 ASN o 301 HIS o 311 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 485 ASN o 493 ASN o 721 HIS o 723 ASN o 731 ASN o 739 ASN ** o 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 861 GLN o 913 ASN o 950 ASN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1101 GLN ** o1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1230 GLN o1244 ASN o1248 ASN o1332 GLN o1360 ASN ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 111 ASN ** p 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS p 319 ASN p 370 HIS p 503 ASN p 570 ASN ** p 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1094 GLN ** p1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1120 ASN ** q 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 ASN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 131 ASN w 56 ASN w 74 GLN x 26 GLN y 2 ASN y 29 ASN Total number of N/Q/H flips: 137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1133 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 115699 Z= 0.218 Angle : 0.728 17.286 157113 Z= 0.377 Chirality : 0.045 0.348 17587 Planarity : 0.005 0.113 19780 Dihedral : 12.677 117.367 16941 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.27 % Favored : 94.49 % Rotamer: Outliers : 2.71 % Allowed : 11.86 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.35 (0.07), residues: 13701 helix: -0.90 (0.06), residues: 5717 sheet: -1.14 (0.12), residues: 1649 loop : -2.28 (0.07), residues: 6335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 612 HIS 0.019 0.001 HIS L 105 PHE 0.043 0.002 PHE 4 79 TYR 0.040 0.002 TYR 6 410 ARG 0.015 0.001 ARG 6 472 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 879 time to evaluate : 9.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 120 LYS cc_start: 0.1142 (OUTLIER) cc_final: -0.0452 (pttp) REVERT: 1 362 ASP cc_start: -0.3338 (OUTLIER) cc_final: -0.3900 (m-30) REVERT: 2 137 MET cc_start: -0.2200 (ptm) cc_final: -0.2997 (ptt) REVERT: 2 153 MET cc_start: 0.1269 (tpt) cc_final: 0.0901 (mmp) REVERT: 2 252 MET cc_start: -0.1642 (tpp) cc_final: -0.2030 (ttt) REVERT: 3 42 MET cc_start: -0.3665 (mtm) cc_final: -0.4912 (mmt) REVERT: 3 51 MET cc_start: -0.2847 (mtp) cc_final: -0.3299 (tpt) REVERT: 4 163 MET cc_start: -0.2829 (mmm) cc_final: -0.3189 (mmp) REVERT: 4 216 MET cc_start: 0.3336 (mmp) cc_final: 0.2971 (mmt) REVERT: 4 376 MET cc_start: -0.3869 (mtt) cc_final: -0.4638 (mtt) REVERT: 6 303 ASN cc_start: -0.5052 (OUTLIER) cc_final: -0.6457 (t0) REVERT: 6 438 MET cc_start: -0.1358 (OUTLIER) cc_final: -0.2000 (mtm) REVERT: 6 450 MET cc_start: -0.1179 (mmm) cc_final: -0.1811 (mmp) REVERT: 6 597 LYS cc_start: -0.0434 (OUTLIER) cc_final: -0.1909 (mptt) REVERT: 6 696 MET cc_start: -0.2959 (ttt) cc_final: -0.4277 (tpt) REVERT: 7 42 MET cc_start: -0.3697 (tpp) cc_final: -0.4437 (ttm) REVERT: 7 247 MET cc_start: -0.4955 (ttm) cc_final: -0.5762 (mtm) REVERT: 7 657 MET cc_start: -0.2988 (mmp) cc_final: -0.3582 (mpp) REVERT: A 352 MET cc_start: 0.0175 (mtt) cc_final: -0.0158 (ptp) REVERT: A 661 GLU cc_start: -0.2381 (OUTLIER) cc_final: -0.3790 (tt0) REVERT: A 691 MET cc_start: 0.3536 (mmt) cc_final: 0.3316 (mmm) REVERT: A 809 VAL cc_start: -0.1695 (OUTLIER) cc_final: -0.2084 (p) REVERT: A 1203 GLU cc_start: -0.1834 (OUTLIER) cc_final: -0.2208 (pm20) REVERT: B 237 MET cc_start: 0.3050 (tpt) cc_final: 0.2736 (tpp) REVERT: B 322 MET cc_start: -0.2231 (ttt) cc_final: -0.2504 (ttt) REVERT: B 614 MET cc_start: -0.3083 (mtt) cc_final: -0.3742 (mtt) REVERT: E 355 MET cc_start: -0.1803 (tpp) cc_final: -0.2022 (tpt) REVERT: E 432 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4051 (tt) REVERT: E 747 LEU cc_start: -0.3104 (OUTLIER) cc_final: -0.3416 (mm) REVERT: F 26 MET cc_start: -0.3910 (ttm) cc_final: -0.4328 (mtp) REVERT: F 60 MET cc_start: -0.2995 (tpp) cc_final: -0.3264 (mmt) REVERT: F 290 MET cc_start: 0.0634 (mtm) cc_final: -0.0668 (mmt) REVERT: F 295 LEU cc_start: -0.5258 (OUTLIER) cc_final: -0.5825 (mp) REVERT: F 309 MET cc_start: -0.4180 (mmt) cc_final: -0.4689 (mmt) REVERT: G 147 ARG cc_start: 0.0166 (OUTLIER) cc_final: -0.0557 (ttt180) REVERT: H 132 LYS cc_start: -0.4178 (OUTLIER) cc_final: -0.6082 (pttt) REVERT: H 161 LYS cc_start: 0.1470 (OUTLIER) cc_final: 0.0631 (mmtt) REVERT: I 19 MET cc_start: -0.4367 (tpp) cc_final: -0.5021 (ttm) REVERT: J 176 MET cc_start: 0.2035 (mtt) cc_final: 0.1680 (ptt) REVERT: J 192 LYS cc_start: 0.2405 (OUTLIER) cc_final: 0.1529 (pttp) REVERT: J 197 MET cc_start: -0.4310 (mmm) cc_final: -0.5465 (mtt) REVERT: L 83 MET cc_start: -0.1664 (mtp) cc_final: -0.2170 (mtt) REVERT: O 59 ARG cc_start: 0.3205 (OUTLIER) cc_final: 0.0658 (ptt-90) REVERT: R 46 ILE cc_start: 0.0830 (OUTLIER) cc_final: 0.0555 (tp) REVERT: R 120 GLU cc_start: 0.3303 (OUTLIER) cc_final: 0.2785 (mp0) REVERT: R 128 ILE cc_start: -0.4106 (OUTLIER) cc_final: -0.4342 (pt) REVERT: T 149 VAL cc_start: 0.1338 (OUTLIER) cc_final: 0.0973 (t) REVERT: T 215 GLU cc_start: -0.0524 (OUTLIER) cc_final: -0.2606 (mm-30) REVERT: U 116 THR cc_start: 0.0914 (OUTLIER) cc_final: 0.0652 (p) REVERT: U 174 ARG cc_start: -0.4080 (OUTLIER) cc_final: -0.6614 (mtm180) REVERT: U 184 ILE cc_start: -0.1206 (OUTLIER) cc_final: -0.1805 (tt) REVERT: d 857 SER cc_start: -0.1427 (m) cc_final: -0.1636 (m) REVERT: e 247 MET cc_start: -0.2168 (mtp) cc_final: -0.3021 (ptp) REVERT: e 291 MET cc_start: -0.4488 (mtm) cc_final: -0.4731 (mtt) REVERT: e 442 MET cc_start: -0.1245 (ppp) cc_final: -0.1829 (ppp) REVERT: e 528 MET cc_start: 0.0732 (mmt) cc_final: -0.0893 (mmt) REVERT: e 612 TRP cc_start: -0.0407 (OUTLIER) cc_final: -0.0640 (m100) REVERT: e 731 MET cc_start: 0.1986 (mmm) cc_final: 0.1417 (mpp) REVERT: f 19 MET cc_start: -0.3614 (mmt) cc_final: -0.4485 (mmt) REVERT: f 60 MET cc_start: -0.3477 (mmt) cc_final: -0.3915 (mpp) REVERT: f 290 MET cc_start: -0.0555 (mtt) cc_final: -0.1480 (mmp) REVERT: i 26 MET cc_start: -0.0443 (mmp) cc_final: -0.3332 (mmt) REVERT: i 39 MET cc_start: -0.2282 (mmp) cc_final: -0.3457 (mmt) REVERT: j 121 MET cc_start: 0.5845 (ppp) cc_final: 0.5492 (pmm) REVERT: j 176 MET cc_start: -0.3372 (mtm) cc_final: -0.3941 (ptt) REVERT: l 83 MET cc_start: -0.4050 (ttt) cc_final: -0.4309 (ttt) REVERT: l 152 MET cc_start: -0.3208 (tpp) cc_final: -0.4621 (mtt) REVERT: m 39 MET cc_start: -0.3050 (mtp) cc_final: -0.3839 (mtp) REVERT: m 40 MET cc_start: -0.3173 (mtp) cc_final: -0.3410 (mtt) REVERT: o 104 MET cc_start: 0.5099 (ppp) cc_final: 0.4181 (ttt) REVERT: o 317 MET cc_start: -0.2196 (tpt) cc_final: -0.2581 (mmt) REVERT: o 355 MET cc_start: 0.4384 (mpp) cc_final: 0.4168 (mpp) REVERT: o 565 MET cc_start: 0.4807 (tpt) cc_final: 0.3151 (mtt) REVERT: o 626 THR cc_start: 0.4742 (OUTLIER) cc_final: 0.4473 (p) REVERT: o 744 ILE cc_start: 0.6235 (mt) cc_final: 0.5969 (mt) REVERT: o 769 MET cc_start: 0.4262 (tpp) cc_final: 0.3612 (tpp) REVERT: o 872 MET cc_start: 0.6762 (ppp) cc_final: 0.6327 (ppp) REVERT: o 899 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6564 (pm20) REVERT: o 1031 ARG cc_start: 0.2680 (ttp80) cc_final: 0.2129 (ppt170) REVERT: o 1068 LEU cc_start: 0.6435 (tp) cc_final: 0.6140 (tp) REVERT: o 1199 MET cc_start: 0.6938 (ppp) cc_final: 0.5696 (pmm) REVERT: o 1228 MET cc_start: 0.6251 (tpp) cc_final: 0.5328 (tpp) REVERT: o 1249 ASP cc_start: 0.6857 (p0) cc_final: 0.6476 (p0) REVERT: o 1257 LEU cc_start: 0.9082 (pp) cc_final: 0.8671 (pt) REVERT: o 1292 MET cc_start: 0.7438 (mmp) cc_final: 0.6617 (mmt) REVERT: o 1451 MET cc_start: 0.4899 (mmt) cc_final: 0.4656 (mmt) REVERT: p 112 GLU cc_start: 0.4230 (OUTLIER) cc_final: 0.3784 (tt0) REVERT: p 214 LYS cc_start: 0.7229 (pttm) cc_final: 0.6799 (tptt) REVERT: p 266 GLU cc_start: 0.6831 (mp0) cc_final: 0.6296 (mt-10) REVERT: p 320 PHE cc_start: 0.7731 (t80) cc_final: 0.7530 (t80) REVERT: p 728 MET cc_start: 0.1810 (ppp) cc_final: 0.0630 (tpp) REVERT: p 796 MET cc_start: -0.0510 (tpp) cc_final: -0.1139 (pmm) REVERT: p 908 MET cc_start: -0.2951 (ttp) cc_final: -0.4544 (ttp) REVERT: p 976 MET cc_start: 0.5569 (mpp) cc_final: 0.2964 (ppp) REVERT: p 1170 ARG cc_start: 0.3227 (mtp-110) cc_final: 0.1885 (mtm-85) REVERT: s 127 LEU cc_start: 0.7155 (mp) cc_final: 0.6697 (tp) REVERT: t 102 ILE cc_start: 0.3495 (pt) cc_final: 0.3288 (tt) REVERT: u 16 ARG cc_start: 0.6449 (ptt-90) cc_final: 0.6139 (mtt180) REVERT: u 117 MET cc_start: -0.2699 (mtm) cc_final: -0.4309 (ttm) REVERT: w 43 ASP cc_start: 0.7810 (m-30) cc_final: 0.7458 (t0) REVERT: y 51 LEU cc_start: 0.6097 (mp) cc_final: 0.5716 (mt) outliers start: 324 outliers final: 137 residues processed: 1159 average time/residue: 0.9395 time to fit residues: 1903.6213 Evaluate side-chains 891 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 726 time to evaluate : 9.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 120 LYS Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 412 GLU Chi-restraints excluded: chain 2 residue 177 CYS Chi-restraints excluded: chain 2 residue 182 ILE Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 2 residue 313 VAL Chi-restraints excluded: chain 3 residue 283 THR Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 188 THR Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 5 residue 9 LEU Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 302 VAL Chi-restraints excluded: chain 6 residue 303 ASN Chi-restraints excluded: chain 6 residue 310 LEU Chi-restraints excluded: chain 6 residue 419 ARG Chi-restraints excluded: chain 6 residue 438 MET Chi-restraints excluded: chain 6 residue 439 ILE Chi-restraints excluded: chain 6 residue 458 VAL Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 597 LYS Chi-restraints excluded: chain 6 residue 650 MET Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 425 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 709 THR Chi-restraints excluded: chain 9 residue 84 CYS Chi-restraints excluded: chain 9 residue 207 TYR Chi-restraints excluded: chain 9 residue 211 GLN Chi-restraints excluded: chain 9 residue 218 LEU Chi-restraints excluded: chain 9 residue 243 THR Chi-restraints excluded: chain 9 residue 245 LEU Chi-restraints excluded: chain 9 residue 273 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 68 CYS Chi-restraints excluded: chain P residue 221 CYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain P residue 306 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 120 GLU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 GLU Chi-restraints excluded: chain T residue 228 ILE Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain U residue 174 ARG Chi-restraints excluded: chain U residue 184 ILE Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 194 ARG Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain V residue 225 VAL Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain k residue 185 LYS Chi-restraints excluded: chain k residue 186 HIS Chi-restraints excluded: chain l residue 64 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 456 VAL Chi-restraints excluded: chain o residue 458 PHE Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 626 THR Chi-restraints excluded: chain o residue 635 LEU Chi-restraints excluded: chain o residue 715 GLU Chi-restraints excluded: chain o residue 737 PHE Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 899 GLU Chi-restraints excluded: chain o residue 900 SER Chi-restraints excluded: chain o residue 966 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1212 LEU Chi-restraints excluded: chain o residue 1435 THR Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain p residue 131 THR Chi-restraints excluded: chain p residue 382 LEU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 583 LEU Chi-restraints excluded: chain p residue 733 MET Chi-restraints excluded: chain p residue 788 TYR Chi-restraints excluded: chain p residue 858 VAL Chi-restraints excluded: chain p residue 888 THR Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1095 ILE Chi-restraints excluded: chain p residue 1158 LEU Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 106 ILE Chi-restraints excluded: chain u residue 21 ASN Chi-restraints excluded: chain u residue 94 LYS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain v residue 42 ASP Chi-restraints excluded: chain v residue 56 PHE Chi-restraints excluded: chain w residue 56 ASN Chi-restraints excluded: chain y residue 69 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 694 optimal weight: 10.0000 chunk 387 optimal weight: 7.9990 chunk 1039 optimal weight: 2.9990 chunk 850 optimal weight: 50.0000 chunk 344 optimal weight: 1.9990 chunk 1251 optimal weight: 0.3980 chunk 1352 optimal weight: 0.3980 chunk 1114 optimal weight: 0.8980 chunk 1241 optimal weight: 0.9990 chunk 426 optimal weight: 50.0000 chunk 1004 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 300 ASN ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 379 GLN 6 83 HIS ** 6 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 187 HIS ** 6 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 328 HIS 7 519 ASN 7 564 ASN ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 259 HIS 8 279 ASN 9 136 GLN ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 450 GLN B 813 ASN B 882 HIS B 933 ASN D 875 GLN ** D 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 352 HIS ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 254 ASN e 616 HIS ** f 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 98 GLN k 205 HIS ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 148 HIS ** o 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 311 GLN o 372 ASN o 485 ASN o 678 ASN o 757 GLN o 765 ASN o 780 ASN ** o 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1005 HIS ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 319 ASN p 639 HIS ** p 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 173 HIS ** q 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 56 ASN x 52 HIS y 2 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1434 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 115699 Z= 0.232 Angle : 0.682 13.658 157113 Z= 0.353 Chirality : 0.044 0.279 17587 Planarity : 0.005 0.170 19780 Dihedral : 12.150 119.005 16777 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.47 % Favored : 94.32 % Rotamer: Outliers : 2.76 % Allowed : 13.53 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.67 (0.07), residues: 13701 helix: -0.17 (0.07), residues: 5762 sheet: -0.86 (0.13), residues: 1564 loop : -2.06 (0.07), residues: 6375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP o 479 HIS 0.017 0.001 HIS 4 373 PHE 0.044 0.002 PHE O 81 TYR 0.033 0.002 TYR p1047 ARG 0.037 0.001 ARG O 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 808 time to evaluate : 9.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0 120 LYS cc_start: 0.1377 (OUTLIER) cc_final: 0.0350 (pttp) REVERT: 1 226 GLN cc_start: 0.1101 (pm20) cc_final: 0.0328 (pm20) REVERT: 1 362 ASP cc_start: -0.3140 (OUTLIER) cc_final: -0.3916 (m-30) REVERT: 1 411 MET cc_start: -0.4231 (tpt) cc_final: -0.4699 (tpt) REVERT: 2 137 MET cc_start: -0.2270 (ptm) cc_final: -0.3126 (ptt) REVERT: 2 159 MET cc_start: -0.2958 (ttm) cc_final: -0.3526 (ptm) REVERT: 2 252 MET cc_start: -0.1994 (tpp) cc_final: -0.2450 (ttt) REVERT: 3 42 MET cc_start: -0.3826 (mtm) cc_final: -0.5002 (mmt) REVERT: 3 51 MET cc_start: -0.2684 (mtp) cc_final: -0.3720 (tpt) REVERT: 4 163 MET cc_start: -0.2931 (mmm) cc_final: -0.3182 (mmp) REVERT: 4 216 MET cc_start: 0.3197 (mmp) cc_final: 0.2184 (mmt) REVERT: 4 334 MET cc_start: -0.1519 (tmm) cc_final: -0.1931 (tmm) REVERT: 4 376 MET cc_start: -0.3755 (mtt) cc_final: -0.4819 (mtt) REVERT: 6 438 MET cc_start: -0.1300 (mtp) cc_final: -0.1880 (mtm) REVERT: 6 450 MET cc_start: -0.1173 (mmm) cc_final: -0.1792 (mmp) REVERT: 6 514 MET cc_start: 0.2484 (mmm) cc_final: 0.1961 (mtt) REVERT: 6 597 LYS cc_start: -0.0033 (OUTLIER) cc_final: -0.1807 (mptt) REVERT: 6 624 ILE cc_start: 0.2252 (OUTLIER) cc_final: 0.1697 (mm) REVERT: 6 696 MET cc_start: -0.3457 (ttt) cc_final: -0.4388 (tpp) REVERT: 7 42 MET cc_start: -0.3605 (tpp) cc_final: -0.4626 (ttt) REVERT: 7 247 MET cc_start: -0.4725 (ttm) cc_final: -0.5330 (mtm) REVERT: 7 438 MET cc_start: 0.1782 (mpp) cc_final: 0.0188 (mmm) REVERT: 7 483 MET cc_start: 0.4270 (mmm) cc_final: 0.3452 (mmm) REVERT: 7 657 MET cc_start: -0.2814 (mmp) cc_final: -0.3807 (mpp) REVERT: A 661 GLU cc_start: -0.2285 (OUTLIER) cc_final: -0.3901 (tt0) REVERT: A 691 MET cc_start: 0.3486 (mmt) cc_final: 0.2965 (mmm) REVERT: A 966 VAL cc_start: 0.5509 (OUTLIER) cc_final: 0.5276 (m) REVERT: A 1203 GLU cc_start: -0.2211 (OUTLIER) cc_final: -0.2540 (pm20) REVERT: B 170 MET cc_start: -0.0974 (ttp) cc_final: -0.1259 (ppp) REVERT: B 237 MET cc_start: 0.3313 (tpt) cc_final: 0.3078 (tpt) REVERT: B 614 MET cc_start: -0.2786 (mtt) cc_final: -0.3429 (mtt) REVERT: B 634 MET cc_start: -0.3829 (OUTLIER) cc_final: -0.4758 (tpt) REVERT: B 709 MET cc_start: -0.3225 (ptt) cc_final: -0.3567 (ptt) REVERT: B 987 LEU cc_start: -0.2907 (OUTLIER) cc_final: -0.3119 (mp) REVERT: E 291 MET cc_start: 0.1282 (ptm) cc_final: 0.0811 (mtp) REVERT: E 355 MET cc_start: -0.2039 (tpp) cc_final: -0.2654 (tpt) REVERT: E 432 LEU cc_start: 0.5017 (OUTLIER) cc_final: 0.3980 (tt) REVERT: F 26 MET cc_start: -0.3877 (ttm) cc_final: -0.4252 (mtp) REVERT: F 60 MET cc_start: -0.2976 (tpp) cc_final: -0.3227 (mmt) REVERT: F 290 MET cc_start: 0.0397 (mtm) cc_final: 0.0016 (mtt) REVERT: F 295 LEU cc_start: -0.4904 (OUTLIER) cc_final: -0.5321 (mp) REVERT: F 309 MET cc_start: -0.4254 (mmt) cc_final: -0.4747 (mmt) REVERT: G 74 MET cc_start: 0.4012 (mmm) cc_final: 0.3637 (mmm) REVERT: G 147 ARG cc_start: 0.0313 (OUTLIER) cc_final: -0.0363 (ttt180) REVERT: G 148 PHE cc_start: 0.2307 (OUTLIER) cc_final: 0.1793 (m-10) REVERT: H 50 PHE cc_start: -0.0670 (OUTLIER) cc_final: -0.1097 (m-80) REVERT: H 132 LYS cc_start: -0.4153 (OUTLIER) cc_final: -0.6089 (pttt) REVERT: H 161 LYS cc_start: 0.1447 (OUTLIER) cc_final: 0.0944 (mmtt) REVERT: I 19 MET cc_start: -0.4470 (tpp) cc_final: -0.5098 (ttm) REVERT: J 176 MET cc_start: 0.2620 (mtt) cc_final: 0.1927 (ptt) REVERT: J 192 LYS cc_start: 0.2253 (OUTLIER) cc_final: 0.1395 (ptmm) REVERT: J 197 MET cc_start: -0.4199 (mmm) cc_final: -0.5435 (mtt) REVERT: L 56 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.5715 (tm-30) REVERT: L 61 LYS cc_start: 0.3863 (OUTLIER) cc_final: 0.3570 (pttm) REVERT: L 83 MET cc_start: -0.1631 (mtp) cc_final: -0.2137 (mtt) REVERT: L 126 MET cc_start: 0.0101 (ttt) cc_final: -0.0787 (ppp) REVERT: O 68 CYS cc_start: 0.2154 (OUTLIER) cc_final: 0.1928 (m) REVERT: P 219 MET cc_start: 0.0631 (ttt) cc_final: 0.0203 (ttt) REVERT: P 258 MET cc_start: -0.0500 (mtt) cc_final: -0.0738 (mmt) REVERT: Q 37 GLN cc_start: 0.2736 (OUTLIER) cc_final: 0.2530 (pp30) REVERT: R 128 ILE cc_start: -0.3221 (OUTLIER) cc_final: -0.3552 (pt) REVERT: R 173 VAL cc_start: -0.1824 (OUTLIER) cc_final: -0.3059 (t) REVERT: T 215 GLU cc_start: -0.0517 (OUTLIER) cc_final: -0.2824 (mm-30) REVERT: U 174 ARG cc_start: -0.4003 (OUTLIER) cc_final: -0.6516 (mtt180) REVERT: V 173 GLU cc_start: -0.3350 (OUTLIER) cc_final: -0.5751 (tm-30) REVERT: V 191 PHE cc_start: 0.2644 (OUTLIER) cc_final: 0.2379 (p90) REVERT: c 116 ASP cc_start: -0.1378 (OUTLIER) cc_final: -0.3138 (p0) REVERT: d 857 SER cc_start: -0.1919 (m) cc_final: -0.2154 (m) REVERT: e 213 MET cc_start: 0.0190 (mmp) cc_final: -0.0401 (tpp) REVERT: e 247 MET cc_start: -0.2347 (mtp) cc_final: -0.3160 (ptp) REVERT: e 528 MET cc_start: 0.1006 (mmt) cc_final: -0.1040 (mmt) REVERT: e 731 MET cc_start: 0.1976 (mmm) cc_final: 0.1574 (mpp) REVERT: f 19 MET cc_start: -0.3266 (mmt) cc_final: -0.4264 (mmt) REVERT: f 60 MET cc_start: -0.3454 (mmt) cc_final: -0.4285 (mpp) REVERT: f 290 MET cc_start: -0.0594 (mtt) cc_final: -0.1259 (mmt) REVERT: i 12 MET cc_start: 0.1709 (tpt) cc_final: 0.1385 (tpt) REVERT: i 19 MET cc_start: -0.3000 (tpt) cc_final: -0.4566 (tpt) REVERT: i 26 MET cc_start: -0.1058 (mmp) cc_final: -0.3676 (tpt) REVERT: j 176 MET cc_start: -0.3477 (mtm) cc_final: -0.3954 (ptt) REVERT: l 83 MET cc_start: -0.3889 (ttt) cc_final: -0.4237 (ttt) REVERT: l 152 MET cc_start: -0.3265 (tpp) cc_final: -0.4627 (mtt) REVERT: m 39 MET cc_start: -0.2729 (mtp) cc_final: -0.4846 (mtm) REVERT: o 104 MET cc_start: 0.5459 (ppp) cc_final: 0.4597 (ttt) REVERT: o 266 MET cc_start: 0.1108 (ptp) cc_final: 0.0251 (ttp) REVERT: o 317 MET cc_start: -0.1257 (tpt) cc_final: -0.1519 (mmt) REVERT: o 355 MET cc_start: 0.5099 (mpp) cc_final: 0.4814 (mpp) REVERT: o 524 MET cc_start: 0.7395 (mmm) cc_final: 0.6666 (mtp) REVERT: o 556 GLU cc_start: 0.6987 (pm20) cc_final: 0.6459 (tt0) REVERT: o 611 ASP cc_start: 0.5427 (p0) cc_final: 0.5165 (p0) REVERT: o 626 THR cc_start: 0.5874 (OUTLIER) cc_final: 0.5536 (p) REVERT: o 687 ILE cc_start: 0.2806 (tp) cc_final: 0.2349 (tp) REVERT: o 744 ILE cc_start: 0.6613 (mt) cc_final: 0.6303 (mt) REVERT: o 872 MET cc_start: 0.7574 (ppp) cc_final: 0.7297 (ppp) REVERT: o 899 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6372 (pm20) REVERT: o 1249 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6685 (p0) REVERT: o 1292 MET cc_start: 0.7533 (mmp) cc_final: 0.6760 (mmt) REVERT: o 1303 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8503 (tm-30) REVERT: o 1309 MET cc_start: 0.6079 (ppp) cc_final: 0.5857 (ppp) REVERT: o 1403 ASP cc_start: 0.8087 (m-30) cc_final: 0.7823 (m-30) REVERT: p 108 MET cc_start: -0.0140 (ptm) cc_final: -0.1254 (mmt) REVERT: p 239 MET cc_start: 0.6519 (ptm) cc_final: 0.6297 (ptp) REVERT: p 391 LYS cc_start: 0.4108 (mmtp) cc_final: 0.2424 (tptp) REVERT: p 497 LYS cc_start: 0.6565 (pptt) cc_final: 0.5072 (mttp) REVERT: p 1090 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7287 (mm-30) REVERT: s 54 ARG cc_start: 0.8340 (mmm160) cc_final: 0.7873 (mmp80) REVERT: s 127 LEU cc_start: 0.6876 (mp) cc_final: 0.6434 (tp) REVERT: t 57 MET cc_start: 0.4373 (tmm) cc_final: 0.4127 (tmm) REVERT: u 116 GLU cc_start: 0.0527 (OUTLIER) cc_final: -0.0177 (pp20) REVERT: u 117 MET cc_start: -0.2506 (mtm) cc_final: -0.3995 (ttm) REVERT: w 43 ASP cc_start: 0.7900 (m-30) cc_final: 0.7560 (t0) REVERT: y 24 ASP cc_start: 0.6199 (t0) cc_final: 0.5653 (t70) REVERT: y 44 ASN cc_start: 0.5247 (t0) cc_final: 0.4938 (t0) outliers start: 330 outliers final: 163 residues processed: 1079 average time/residue: 0.9274 time to fit residues: 1753.7843 Evaluate side-chains 896 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 701 time to evaluate : 9.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 120 LYS Chi-restraints excluded: chain 0 residue 295 ARG Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 2 residue 58 MET Chi-restraints excluded: chain 2 residue 177 CYS Chi-restraints excluded: chain 2 residue 182 ILE Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 2 residue 313 VAL Chi-restraints excluded: chain 2 residue 322 TYR Chi-restraints excluded: chain 3 residue 230 VAL Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 188 THR Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 4 residue 432 VAL Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 303 ASN Chi-restraints excluded: chain 6 residue 310 LEU Chi-restraints excluded: chain 6 residue 417 THR Chi-restraints excluded: chain 6 residue 458 VAL Chi-restraints excluded: chain 6 residue 494 MET Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 534 TYR Chi-restraints excluded: chain 6 residue 597 LYS Chi-restraints excluded: chain 6 residue 624 ILE Chi-restraints excluded: chain 6 residue 650 MET Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 423 ASP Chi-restraints excluded: chain 7 residue 427 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 626 VAL Chi-restraints excluded: chain 7 residue 709 THR Chi-restraints excluded: chain 7 residue 714 VAL Chi-restraints excluded: chain 9 residue 52 GLU Chi-restraints excluded: chain 9 residue 84 CYS Chi-restraints excluded: chain 9 residue 207 TYR Chi-restraints excluded: chain 9 residue 211 GLN Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain D residue 940 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 68 CYS Chi-restraints excluded: chain P residue 221 CYS Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain Q residue 37 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 303 ASP Chi-restraints excluded: chain T residue 191 PHE Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 GLU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 108 ASP Chi-restraints excluded: chain U residue 148 MET Chi-restraints excluded: chain U residue 174 ARG Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 173 GLU Chi-restraints excluded: chain V residue 191 PHE Chi-restraints excluded: chain V residue 225 VAL Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 116 ASP Chi-restraints excluded: chain e residue 451 VAL Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain k residue 185 LYS Chi-restraints excluded: chain k residue 186 HIS Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 187 TYR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 372 ASN Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 593 SER Chi-restraints excluded: chain o residue 626 THR Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 715 GLU Chi-restraints excluded: chain o residue 755 SER Chi-restraints excluded: chain o residue 879 VAL Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 899 GLU Chi-restraints excluded: chain o residue 900 SER Chi-restraints excluded: chain o residue 966 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1198 GLU Chi-restraints excluded: chain o residue 1249 ASP Chi-restraints excluded: chain o residue 1315 ASP Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain p residue 119 THR Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 550 MET Chi-restraints excluded: chain p residue 583 LEU Chi-restraints excluded: chain p residue 674 MET Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 733 MET Chi-restraints excluded: chain p residue 735 VAL Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 833 THR Chi-restraints excluded: chain p residue 858 VAL Chi-restraints excluded: chain p residue 888 THR Chi-restraints excluded: chain p residue 964 ASP Chi-restraints excluded: chain p residue 983 GLU Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1059 ILE Chi-restraints excluded: chain p residue 1158 LEU Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 194 HIS Chi-restraints excluded: chain q residue 196 VAL Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 177 ASP Chi-restraints excluded: chain s residue 179 VAL Chi-restraints excluded: chain t residue 106 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 110 ARG Chi-restraints excluded: chain u residue 116 GLU Chi-restraints excluded: chain u residue 120 ASP Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 58 LEU Chi-restraints excluded: chain v residue 71 ASP Chi-restraints excluded: chain y residue 34 THR Chi-restraints excluded: chain y residue 69 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 1236 optimal weight: 0.9990 chunk 941 optimal weight: 20.0000 chunk 649 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 chunk 597 optimal weight: 50.0000 chunk 840 optimal weight: 5.9990 chunk 1256 optimal weight: 2.9990 chunk 1330 optimal weight: 1.9990 chunk 656 optimal weight: 0.0060 chunk 1190 optimal weight: 2.9990 chunk 358 optimal weight: 4.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 365 ASN ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 238 ASN ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 247 GLN B 576 ASN D 895 HIS ** D 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 GLN T 231 ASN U 109 HIS c 43 GLN d 936 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 220 GLN i 37 ASN j 173 HIS ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 485 ASN ** o 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 861 GLN ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1457 ASN ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 42 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 197 GLN ** p 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 741 HIS ** p 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 906 GLN ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1053 HIS q 5 ASN q 32 ASN ** q 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 135 GLN u 21 ASN v 130 ASN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 22 ASN y 69 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1697 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 115699 Z= 0.256 Angle : 0.694 23.363 157113 Z= 0.355 Chirality : 0.044 0.423 17587 Planarity : 0.005 0.224 19780 Dihedral : 11.940 120.723 16742 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.39 % Favored : 94.42 % Rotamer: Outliers : 2.99 % Allowed : 14.50 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.30 (0.07), residues: 13701 helix: 0.26 (0.07), residues: 5736 sheet: -0.66 (0.13), residues: 1605 loop : -1.99 (0.07), residues: 6360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP f 135 HIS 0.019 0.001 HIS q 173 PHE 0.033 0.002 PHE B 727 TYR 0.048 0.002 TYR p1047 ARG 0.027 0.001 ARG B 725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 768 time to evaluate : 9.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1 230 PHE cc_start: -0.3559 (t80) cc_final: -0.5364 (m-80) REVERT: 1 232 ARG cc_start: -0.3473 (mpt180) cc_final: -0.6347 (mmt180) REVERT: 1 362 ASP cc_start: -0.3251 (OUTLIER) cc_final: -0.3871 (m-30) REVERT: 2 137 MET cc_start: -0.1927 (ptm) cc_final: -0.2916 (ptt) REVERT: 2 252 MET cc_start: -0.2005 (tpp) cc_final: -0.2285 (ttt) REVERT: 3 42 MET cc_start: -0.3778 (mtm) cc_final: -0.4897 (mmt) REVERT: 3 51 MET cc_start: -0.2479 (mtp) cc_final: -0.3315 (tpt) REVERT: 3 146 ARG cc_start: -0.1566 (OUTLIER) cc_final: -0.2697 (ptt90) REVERT: 4 140 LYS cc_start: -0.2344 (OUTLIER) cc_final: -0.2579 (pptt) REVERT: 4 163 MET cc_start: -0.2920 (mmm) cc_final: -0.3238 (mmp) REVERT: 4 216 MET cc_start: 0.3242 (mmp) cc_final: 0.2213 (mmt) REVERT: 4 254 MET cc_start: -0.2496 (ttt) cc_final: -0.3222 (tpt) REVERT: 4 376 MET cc_start: -0.3705 (mtt) cc_final: -0.4424 (mtt) REVERT: 6 438 MET cc_start: -0.1515 (OUTLIER) cc_final: -0.2457 (mtm) REVERT: 6 450 MET cc_start: -0.1156 (mmm) cc_final: -0.1768 (mmp) REVERT: 6 536 MET cc_start: -0.1546 (ppp) cc_final: -0.1869 (ppp) REVERT: 6 624 ILE cc_start: 0.2428 (OUTLIER) cc_final: 0.1866 (mm) REVERT: 6 696 MET cc_start: -0.3673 (ttt) cc_final: -0.4193 (tpt) REVERT: 7 30 ARG cc_start: 0.3715 (OUTLIER) cc_final: 0.3479 (mtm-85) REVERT: 7 42 MET cc_start: -0.3600 (tpp) cc_final: -0.4569 (ttt) REVERT: 7 438 MET cc_start: 0.1784 (mpp) cc_final: 0.0271 (mmm) REVERT: 7 483 MET cc_start: 0.4676 (mmm) cc_final: 0.4060 (mmm) REVERT: 7 657 MET cc_start: -0.2978 (mmp) cc_final: -0.3922 (mpp) REVERT: 8 240 MET cc_start: -0.1242 (tpt) cc_final: -0.2047 (tpp) REVERT: 9 85 MET cc_start: 0.3727 (mmm) cc_final: 0.3509 (mmp) REVERT: 9 245 LEU cc_start: 0.3470 (pp) cc_final: 0.3035 (tt) REVERT: A 649 MET cc_start: 0.4383 (ppp) cc_final: 0.4063 (ppp) REVERT: A 661 GLU cc_start: -0.1669 (OUTLIER) cc_final: -0.3471 (tt0) REVERT: A 696 MET cc_start: -0.2842 (ppp) cc_final: -0.4139 (ptt) REVERT: B 170 MET cc_start: 0.0191 (ttp) cc_final: -0.0255 (ppp) REVERT: B 237 MET cc_start: 0.3195 (tpt) cc_final: 0.2956 (tpt) REVERT: B 322 MET cc_start: -0.2383 (ttt) cc_final: -0.2928 (mtp) REVERT: B 334 MET cc_start: -0.4372 (OUTLIER) cc_final: -0.5067 (tpt) REVERT: B 614 MET cc_start: -0.2376 (mtt) cc_final: -0.3213 (mtt) REVERT: B 634 MET cc_start: -0.4048 (OUTLIER) cc_final: -0.5263 (tpt) REVERT: B 709 MET cc_start: -0.3193 (ptt) cc_final: -0.3413 (ptt) REVERT: E 432 LEU cc_start: 0.4970 (OUTLIER) cc_final: 0.3928 (tt) REVERT: E 703 MET cc_start: -0.0279 (tpt) cc_final: -0.1043 (tpt) REVERT: F 19 MET cc_start: -0.4655 (tpt) cc_final: -0.4963 (tpt) REVERT: F 26 MET cc_start: -0.3434 (ttm) cc_final: -0.3973 (mtp) REVERT: F 60 MET cc_start: -0.2884 (tpp) cc_final: -0.3091 (mmt) REVERT: F 290 MET cc_start: 0.0026 (mtm) cc_final: -0.0281 (mtt) REVERT: F 295 LEU cc_start: -0.4976 (OUTLIER) cc_final: -0.5211 (mp) REVERT: G 74 MET cc_start: 0.3833 (mmm) cc_final: 0.3631 (mmm) REVERT: G 147 ARG cc_start: 0.0248 (OUTLIER) cc_final: -0.0443 (ttt180) REVERT: G 148 PHE cc_start: 0.2466 (OUTLIER) cc_final: 0.1942 (m-10) REVERT: H 132 LYS cc_start: -0.4081 (OUTLIER) cc_final: -0.6005 (pttt) REVERT: H 161 LYS cc_start: 0.1175 (OUTLIER) cc_final: 0.0683 (mmtt) REVERT: I 19 MET cc_start: -0.4765 (tpp) cc_final: -0.5408 (ttm) REVERT: J 176 MET cc_start: 0.2402 (mtt) cc_final: 0.1776 (ptt) REVERT: J 192 LYS cc_start: 0.2289 (OUTLIER) cc_final: 0.1314 (ptmm) REVERT: J 197 MET cc_start: -0.4038 (mmm) cc_final: -0.5452 (mtt) REVERT: L 56 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6314 (tm-30) REVERT: L 61 LYS cc_start: 0.4023 (OUTLIER) cc_final: 0.3654 (pttm) REVERT: L 126 MET cc_start: -0.0287 (ttt) cc_final: -0.1545 (ttp) REVERT: P 219 MET cc_start: 0.0772 (OUTLIER) cc_final: 0.0109 (ttt) REVERT: P 242 GLN cc_start: -0.4972 (OUTLIER) cc_final: -0.5798 (tp40) REVERT: P 258 MET cc_start: 0.0399 (mtt) cc_final: -0.0014 (mmt) REVERT: Q 37 GLN cc_start: 0.3272 (OUTLIER) cc_final: 0.2986 (pp30) REVERT: R 128 ILE cc_start: -0.2699 (OUTLIER) cc_final: -0.3097 (pt) REVERT: T 215 GLU cc_start: -0.0558 (OUTLIER) cc_final: -0.2593 (mm-30) REVERT: U 174 ARG cc_start: -0.3603 (OUTLIER) cc_final: -0.6514 (mtt90) REVERT: V 194 ARG cc_start: 0.0626 (OUTLIER) cc_final: -0.0877 (tmm-80) REVERT: d 857 SER cc_start: -0.1975 (m) cc_final: -0.2221 (m) REVERT: e 213 MET cc_start: -0.0027 (mmp) cc_final: -0.0550 (tpp) REVERT: e 247 MET cc_start: -0.2111 (mtp) cc_final: -0.3091 (ptp) REVERT: e 442 MET cc_start: -0.2039 (ppp) cc_final: -0.2379 (ppp) REVERT: e 528 MET cc_start: 0.0351 (mmt) cc_final: -0.1588 (mmt) REVERT: e 612 TRP cc_start: -0.0170 (OUTLIER) cc_final: -0.0562 (m100) REVERT: e 696 TRP cc_start: -0.1992 (OUTLIER) cc_final: -0.3078 (m-10) REVERT: e 703 MET cc_start: 0.0875 (mpp) cc_final: -0.0443 (mmt) REVERT: f 19 MET cc_start: -0.3357 (mmt) cc_final: -0.4286 (mmt) REVERT: f 60 MET cc_start: -0.3755 (mmt) cc_final: -0.4455 (mpp) REVERT: f 290 MET cc_start: -0.0584 (mtt) cc_final: -0.1336 (mmt) REVERT: i 12 MET cc_start: 0.1942 (tpt) cc_final: 0.1442 (tpt) REVERT: i 19 MET cc_start: -0.3026 (tpt) cc_final: -0.4159 (tpt) REVERT: i 26 MET cc_start: -0.0952 (mmp) cc_final: -0.3501 (mmt) REVERT: j 176 MET cc_start: -0.3308 (mtm) cc_final: -0.3856 (ptt) REVERT: k 187 MET cc_start: 0.2584 (OUTLIER) cc_final: 0.2224 (ppp) REVERT: l 83 MET cc_start: -0.3694 (ttt) cc_final: -0.4141 (ttt) REVERT: l 152 MET cc_start: -0.3142 (tpp) cc_final: -0.4702 (mtt) REVERT: m 39 MET cc_start: -0.2579 (mtp) cc_final: -0.3508 (mtp) REVERT: m 91 ARG cc_start: 0.0179 (ptt-90) cc_final: -0.0173 (tmt170) REVERT: o 104 MET cc_start: 0.5827 (ppp) cc_final: 0.4938 (ttt) REVERT: o 266 MET cc_start: 0.1258 (ptp) cc_final: 0.0212 (ttp) REVERT: o 355 MET cc_start: 0.5404 (mpp) cc_final: 0.4900 (mpp) REVERT: o 501 MET cc_start: 0.7877 (ttm) cc_final: 0.7659 (tpp) REVERT: o 520 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7422 (mmt) REVERT: o 524 MET cc_start: 0.7536 (mmm) cc_final: 0.7236 (mtp) REVERT: o 565 MET cc_start: 0.8711 (tpt) cc_final: 0.8442 (tpp) REVERT: o 744 ILE cc_start: 0.6699 (mt) cc_final: 0.6177 (mt) REVERT: o 899 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: o 1086 MET cc_start: 0.8603 (mmm) cc_final: 0.7975 (mmp) REVERT: o 1199 MET cc_start: 0.7234 (ppp) cc_final: 0.6654 (ppp) REVERT: o 1228 MET cc_start: 0.6541 (mmm) cc_final: 0.6220 (mmm) REVERT: o 1279 MET cc_start: 0.3946 (tpp) cc_final: 0.3713 (tpp) REVERT: o 1292 MET cc_start: 0.7497 (mmp) cc_final: 0.6991 (mmt) REVERT: o 1303 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8597 (tp-100) REVERT: o 1381 GLU cc_start: 0.7926 (tp30) cc_final: 0.7719 (tp30) REVERT: o 1386 ILE cc_start: 0.7421 (tp) cc_final: 0.7211 (tp) REVERT: o 1389 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6325 (p0) REVERT: p 109 MET cc_start: -0.0007 (ttp) cc_final: -0.0612 (ttp) REVERT: p 594 MET cc_start: -0.1430 (mpp) cc_final: -0.1761 (mpp) REVERT: p 617 ASP cc_start: 0.3912 (OUTLIER) cc_final: 0.3158 (p0) REVERT: p 938 ARG cc_start: 0.4856 (OUTLIER) cc_final: 0.2990 (mtm180) REVERT: p 1021 HIS cc_start: 0.0144 (t70) cc_final: -0.0361 (t-170) REVERT: p 1023 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.5499 (mmm160) REVERT: q 66 HIS cc_start: -0.0211 (OUTLIER) cc_final: -0.0731 (t-90) REVERT: q 82 LEU cc_start: 0.4053 (OUTLIER) cc_final: 0.3675 (mt) REVERT: s 54 ARG cc_start: 0.8377 (mmm160) cc_final: 0.8022 (mmp80) REVERT: s 99 ILE cc_start: -0.2326 (OUTLIER) cc_final: -0.2621 (tt) REVERT: s 128 GLU cc_start: 0.8278 (mp0) cc_final: 0.7997 (mp0) REVERT: s 151 MET cc_start: 0.3753 (tmm) cc_final: 0.3415 (ppp) REVERT: t 57 MET cc_start: 0.5765 (tmm) cc_final: 0.5333 (tmm) REVERT: t 96 GLU cc_start: 0.7778 (tp30) cc_final: 0.7464 (tp30) REVERT: u 16 ARG cc_start: 0.3910 (mtt180) cc_final: 0.3028 (mtt-85) REVERT: u 117 MET cc_start: -0.2557 (mtm) cc_final: -0.4218 (ttm) REVERT: w 108 MET cc_start: 0.4207 (mmp) cc_final: 0.3888 (mmp) REVERT: y 24 ASP cc_start: 0.6650 (t0) cc_final: 0.6185 (t0) outliers start: 357 outliers final: 170 residues processed: 1071 average time/residue: 0.9169 time to fit residues: 1723.1721 Evaluate side-chains 896 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 689 time to evaluate : 9.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 2 residue 58 MET Chi-restraints excluded: chain 2 residue 177 CYS Chi-restraints excluded: chain 2 residue 182 ILE Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 255 CYS Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 140 LYS Chi-restraints excluded: chain 4 residue 158 VAL Chi-restraints excluded: chain 4 residue 197 THR Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 4 residue 432 VAL Chi-restraints excluded: chain 4 residue 449 SER Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 303 ASN Chi-restraints excluded: chain 6 residue 438 MET Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 597 LYS Chi-restraints excluded: chain 6 residue 604 THR Chi-restraints excluded: chain 6 residue 624 ILE Chi-restraints excluded: chain 7 residue 6 ASP Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 30 ARG Chi-restraints excluded: chain 7 residue 388 ILE Chi-restraints excluded: chain 7 residue 423 ASP Chi-restraints excluded: chain 7 residue 427 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 626 VAL Chi-restraints excluded: chain 7 residue 714 VAL Chi-restraints excluded: chain 8 residue 195 ASP Chi-restraints excluded: chain 8 residue 255 ILE Chi-restraints excluded: chain 9 residue 70 VAL Chi-restraints excluded: chain 9 residue 84 CYS Chi-restraints excluded: chain 9 residue 165 ARG Chi-restraints excluded: chain 9 residue 247 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain D residue 895 HIS Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 242 GLN Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain P residue 306 VAL Chi-restraints excluded: chain Q residue 37 GLN Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 303 ASP Chi-restraints excluded: chain T residue 191 PHE Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 GLU Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 146 ASP Chi-restraints excluded: chain U residue 174 ARG Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 194 ARG Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain k residue 187 MET Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 226 LYS Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 429 LEU Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 520 MET Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 567 LEU Chi-restraints excluded: chain o residue 593 SER Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 665 THR Chi-restraints excluded: chain o residue 715 GLU Chi-restraints excluded: chain o residue 850 THR Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 899 GLU Chi-restraints excluded: chain o residue 900 SER Chi-restraints excluded: chain o residue 966 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1163 HIS Chi-restraints excluded: chain o residue 1198 GLU Chi-restraints excluded: chain o residue 1212 LEU Chi-restraints excluded: chain o residue 1315 ASP Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain o residue 1435 THR Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 131 THR Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 567 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 617 ASP Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 678 THR Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 733 MET Chi-restraints excluded: chain p residue 735 VAL Chi-restraints excluded: chain p residue 740 PHE Chi-restraints excluded: chain p residue 796 MET Chi-restraints excluded: chain p residue 860 VAL Chi-restraints excluded: chain p residue 865 VAL Chi-restraints excluded: chain p residue 888 THR Chi-restraints excluded: chain p residue 938 ARG Chi-restraints excluded: chain p residue 954 MET Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 983 GLU Chi-restraints excluded: chain p residue 1006 VAL Chi-restraints excluded: chain p residue 1023 ARG Chi-restraints excluded: chain p residue 1043 ILE Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1057 ASP Chi-restraints excluded: chain p residue 1150 ARG Chi-restraints excluded: chain p residue 1158 LEU Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 131 THR Chi-restraints excluded: chain q residue 169 PHE Chi-restraints excluded: chain q residue 184 PHE Chi-restraints excluded: chain q residue 194 HIS Chi-restraints excluded: chain q residue 195 THR Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 99 ILE Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 177 ASP Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 106 ILE Chi-restraints excluded: chain u residue 110 ARG Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 58 LEU Chi-restraints excluded: chain x residue 18 TRP Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain z residue 26 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 1107 optimal weight: 0.6980 chunk 755 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 990 optimal weight: 20.0000 chunk 548 optimal weight: 40.0000 chunk 1134 optimal weight: 0.9980 chunk 919 optimal weight: 0.9980 chunk 1 optimal weight: 0.0030 chunk 679 optimal weight: 6.9990 chunk 1193 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 161 HIS ** 4 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 625 GLN ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 247 GLN ** D 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN D1053 GLN ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 GLN O 24 GLN O 27 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 368 ASN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 410 ASN o 449 HIS o 662 HIS o 757 GLN ** o 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1332 GLN ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1462 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 503 ASN ** p 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1021 HIS ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 217 GLN ** s 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1893 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 115699 Z= 0.276 Angle : 0.698 15.049 157113 Z= 0.359 Chirality : 0.045 0.370 17587 Planarity : 0.005 0.121 19780 Dihedral : 11.852 120.537 16727 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.93 % Favored : 93.86 % Rotamer: Outliers : 3.00 % Allowed : 15.58 % Favored : 81.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.07), residues: 13701 helix: 0.45 (0.07), residues: 5769 sheet: -0.73 (0.13), residues: 1632 loop : -1.93 (0.07), residues: 6300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP o 479 HIS 0.067 0.001 HIS D 895 PHE 0.035 0.002 PHE p 806 TYR 0.035 0.002 TYR p1048 ARG 0.015 0.001 ARG o 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 773 time to evaluate : 9.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1 230 PHE cc_start: -0.3729 (t80) cc_final: -0.5525 (m-80) REVERT: 1 232 ARG cc_start: -0.3592 (mpt180) cc_final: -0.6236 (mmt180) REVERT: 1 362 ASP cc_start: -0.3260 (OUTLIER) cc_final: -0.3969 (m-30) REVERT: 2 137 MET cc_start: -0.1750 (ptm) cc_final: -0.2801 (ptt) REVERT: 3 42 MET cc_start: -0.3846 (mtm) cc_final: -0.4951 (mmt) REVERT: 3 51 MET cc_start: -0.2621 (mtp) cc_final: -0.3731 (tpt) REVERT: 4 140 LYS cc_start: -0.2264 (OUTLIER) cc_final: -0.2531 (pptt) REVERT: 4 163 MET cc_start: -0.3176 (mmm) cc_final: -0.3473 (mmp) REVERT: 4 216 MET cc_start: 0.2988 (mmp) cc_final: 0.2006 (mmt) REVERT: 4 334 MET cc_start: -0.1553 (tmm) cc_final: -0.1795 (tmm) REVERT: 4 376 MET cc_start: -0.3737 (mtt) cc_final: -0.4742 (mtt) REVERT: 5 16 MET cc_start: 0.0934 (mmp) cc_final: 0.0721 (mmp) REVERT: 6 438 MET cc_start: -0.1576 (mtp) cc_final: -0.2350 (mtm) REVERT: 6 450 MET cc_start: -0.1020 (mmm) cc_final: -0.1785 (mmp) REVERT: 6 624 ILE cc_start: 0.2703 (OUTLIER) cc_final: 0.2142 (mm) REVERT: 6 696 MET cc_start: -0.3575 (ttt) cc_final: -0.4409 (tpp) REVERT: 7 42 MET cc_start: -0.3715 (tpp) cc_final: -0.4560 (ttt) REVERT: 7 438 MET cc_start: 0.1732 (mpp) cc_final: 0.0342 (mmm) REVERT: 7 483 MET cc_start: 0.5047 (mmm) cc_final: 0.4420 (mmm) REVERT: 7 657 MET cc_start: -0.3193 (mmp) cc_final: -0.3778 (mpp) REVERT: 9 85 MET cc_start: 0.3506 (mmm) cc_final: 0.3286 (mmp) REVERT: 9 245 LEU cc_start: 0.3693 (pp) cc_final: 0.3403 (pp) REVERT: A 352 MET cc_start: 0.0044 (ptp) cc_final: -0.1813 (ppp) REVERT: A 607 MET cc_start: -0.4130 (mtp) cc_final: -0.4532 (mtt) REVERT: A 649 MET cc_start: 0.4582 (ppp) cc_final: 0.4337 (ppp) REVERT: A 661 GLU cc_start: -0.1711 (OUTLIER) cc_final: -0.2480 (tp30) REVERT: A 696 MET cc_start: -0.2769 (ppp) cc_final: -0.3913 (ptt) REVERT: B 237 MET cc_start: 0.3265 (tpt) cc_final: 0.2953 (tpt) REVERT: B 334 MET cc_start: -0.4293 (OUTLIER) cc_final: -0.4863 (tpt) REVERT: B 614 MET cc_start: -0.2375 (mtt) cc_final: -0.3148 (mtt) REVERT: B 634 MET cc_start: -0.3996 (OUTLIER) cc_final: -0.5082 (tpt) REVERT: B 709 MET cc_start: -0.3496 (ptt) cc_final: -0.3845 (ptt) REVERT: E 432 LEU cc_start: 0.4696 (OUTLIER) cc_final: 0.3717 (tt) REVERT: E 612 TRP cc_start: -0.0641 (OUTLIER) cc_final: -0.1310 (m100) REVERT: E 703 MET cc_start: 0.0008 (tpt) cc_final: -0.0883 (tpt) REVERT: F 19 MET cc_start: -0.4707 (tpt) cc_final: -0.5024 (tpt) REVERT: F 26 MET cc_start: -0.3785 (ttm) cc_final: -0.4288 (mtp) REVERT: F 285 MET cc_start: -0.3793 (tpp) cc_final: -0.4178 (tpt) REVERT: F 290 MET cc_start: -0.0270 (mtm) cc_final: -0.0533 (mmt) REVERT: G 147 ARG cc_start: 0.0234 (OUTLIER) cc_final: -0.0537 (ttt180) REVERT: G 148 PHE cc_start: 0.2294 (OUTLIER) cc_final: 0.1904 (m-10) REVERT: H 132 LYS cc_start: -0.3989 (OUTLIER) cc_final: -0.5995 (pttt) REVERT: H 161 LYS cc_start: 0.0923 (OUTLIER) cc_final: 0.0367 (mmtt) REVERT: I 19 MET cc_start: -0.5094 (tpp) cc_final: -0.5751 (ttm) REVERT: I 26 MET cc_start: -0.2529 (mmt) cc_final: -0.3895 (mtt) REVERT: J 176 MET cc_start: 0.2316 (mtt) cc_final: 0.1894 (ptt) REVERT: J 192 LYS cc_start: 0.2318 (OUTLIER) cc_final: 0.1251 (ptmm) REVERT: J 197 MET cc_start: -0.4250 (mmm) cc_final: -0.5284 (mtt) REVERT: L 56 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6301 (tm-30) REVERT: L 61 LYS cc_start: 0.3950 (OUTLIER) cc_final: 0.3660 (pttm) REVERT: L 83 MET cc_start: -0.1312 (mtp) cc_final: -0.1637 (mtp) REVERT: L 126 MET cc_start: 0.0246 (ttt) cc_final: -0.1056 (ttp) REVERT: P 219 MET cc_start: 0.0720 (OUTLIER) cc_final: 0.0159 (ttt) REVERT: P 258 MET cc_start: 0.0353 (mtt) cc_final: -0.1169 (mmm) REVERT: Q 358 MET cc_start: -0.0036 (mmp) cc_final: -0.0277 (mmp) REVERT: R 46 ILE cc_start: 0.2703 (OUTLIER) cc_final: 0.2394 (tp) REVERT: R 128 ILE cc_start: -0.1692 (OUTLIER) cc_final: -0.2092 (pt) REVERT: T 215 GLU cc_start: 0.0072 (OUTLIER) cc_final: -0.2139 (mm-30) REVERT: U 174 ARG cc_start: -0.3760 (OUTLIER) cc_final: -0.6457 (mtm180) REVERT: c 73 MET cc_start: -0.1960 (mmt) cc_final: -0.2172 (mmt) REVERT: c 116 ASP cc_start: -0.1406 (OUTLIER) cc_final: -0.3265 (p0) REVERT: d 857 SER cc_start: -0.2487 (m) cc_final: -0.2714 (m) REVERT: e 213 MET cc_start: -0.0029 (mmp) cc_final: -0.0560 (tpp) REVERT: e 247 MET cc_start: -0.2099 (mtp) cc_final: -0.3295 (ptp) REVERT: e 442 MET cc_start: -0.1838 (ppp) cc_final: -0.2252 (ppp) REVERT: e 528 MET cc_start: 0.0400 (mmt) cc_final: -0.1730 (mmt) REVERT: e 612 TRP cc_start: -0.0003 (OUTLIER) cc_final: -0.0273 (m100) REVERT: e 696 TRP cc_start: -0.2136 (OUTLIER) cc_final: -0.2928 (m-10) REVERT: e 703 MET cc_start: 0.1067 (mpp) cc_final: -0.0574 (mmt) REVERT: f 19 MET cc_start: -0.3233 (mmt) cc_final: -0.4232 (mmt) REVERT: f 26 MET cc_start: -0.4093 (OUTLIER) cc_final: -0.4843 (ttt) REVERT: f 60 MET cc_start: -0.3569 (mmt) cc_final: -0.4425 (mpp) REVERT: f 290 MET cc_start: -0.0612 (mtt) cc_final: -0.1327 (mmt) REVERT: i 12 MET cc_start: 0.1818 (tpt) cc_final: 0.1520 (tpt) REVERT: i 18 MET cc_start: -0.2733 (OUTLIER) cc_final: -0.3063 (tmt) REVERT: i 19 MET cc_start: -0.3329 (tpt) cc_final: -0.4421 (tpt) REVERT: i 26 MET cc_start: -0.1065 (mmp) cc_final: -0.3349 (tpt) REVERT: i 39 MET cc_start: -0.3353 (tpt) cc_final: -0.3791 (mmt) REVERT: j 176 MET cc_start: -0.3361 (mtm) cc_final: -0.3961 (ptt) REVERT: l 83 MET cc_start: -0.3777 (ttt) cc_final: -0.4244 (ttt) REVERT: l 152 MET cc_start: -0.3298 (tpp) cc_final: -0.4757 (mtt) REVERT: o 104 MET cc_start: 0.6052 (ppp) cc_final: 0.5196 (mtt) REVERT: o 266 MET cc_start: 0.1201 (ptp) cc_final: 0.0240 (ttp) REVERT: o 520 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7786 (mmt) REVERT: o 626 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7378 (p) REVERT: o 769 MET cc_start: 0.8018 (mtt) cc_final: 0.7810 (mtt) REVERT: o 827 TYR cc_start: 0.4865 (m-80) cc_final: 0.1756 (m-80) REVERT: o 849 ASP cc_start: 0.6472 (p0) cc_final: 0.6204 (t0) REVERT: o 1004 LEU cc_start: 0.5266 (OUTLIER) cc_final: 0.5034 (mp) REVERT: o 1215 GLU cc_start: 0.5271 (OUTLIER) cc_final: 0.4917 (tp30) REVERT: o 1228 MET cc_start: 0.7076 (mmm) cc_final: 0.6822 (mmm) REVERT: o 1249 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6994 (p0) REVERT: o 1279 MET cc_start: 0.3895 (tpp) cc_final: 0.3566 (tpp) REVERT: o 1292 MET cc_start: 0.7588 (mmp) cc_final: 0.7063 (mmt) REVERT: o 1389 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.6710 (p0) REVERT: o 1395 TYR cc_start: 0.8891 (t80) cc_final: 0.8608 (t80) REVERT: o 1456 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: o 1476 ASP cc_start: 0.0783 (OUTLIER) cc_final: -0.0696 (t0) REVERT: o 1484 MET cc_start: 0.4268 (tmm) cc_final: 0.4064 (tmm) REVERT: p 109 MET cc_start: 0.0201 (ttp) cc_final: -0.0102 (ttp) REVERT: p 176 GLU cc_start: 0.4607 (OUTLIER) cc_final: 0.3546 (mt-10) REVERT: p 230 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5524 (mmp80) REVERT: p 288 ILE cc_start: 0.5164 (OUTLIER) cc_final: 0.4737 (tp) REVERT: p 478 THR cc_start: 0.3196 (OUTLIER) cc_final: 0.2435 (t) REVERT: p 597 ILE cc_start: -0.0374 (OUTLIER) cc_final: -0.0808 (mt) REVERT: p 617 ASP cc_start: 0.4260 (OUTLIER) cc_final: 0.3610 (p0) REVERT: p 917 LYS cc_start: 0.5263 (OUTLIER) cc_final: 0.4092 (tmtt) REVERT: p 938 ARG cc_start: 0.4851 (OUTLIER) cc_final: 0.1963 (mtm180) REVERT: p 964 ASP cc_start: -0.0174 (OUTLIER) cc_final: -0.0567 (m-30) REVERT: p 1023 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5589 (mmp80) REVERT: p 1108 PHE cc_start: 0.4063 (t80) cc_final: 0.3773 (t80) REVERT: p 1114 TYR cc_start: 0.6987 (t80) cc_final: 0.6753 (t80) REVERT: r 36 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6989 (tp30) REVERT: s 54 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8274 (mmp80) REVERT: s 151 MET cc_start: 0.3578 (tmm) cc_final: 0.3090 (mmm) REVERT: t 96 GLU cc_start: 0.7629 (tp30) cc_final: 0.7151 (tp30) REVERT: u 16 ARG cc_start: 0.4044 (mtt180) cc_final: 0.3536 (mtt-85) REVERT: u 59 ILE cc_start: 0.2764 (OUTLIER) cc_final: 0.2479 (mt) REVERT: u 117 MET cc_start: -0.2497 (mtm) cc_final: -0.3945 (ttm) REVERT: w 108 MET cc_start: 0.5609 (mmp) cc_final: 0.5387 (mmp) REVERT: x 16 ASN cc_start: 0.5094 (OUTLIER) cc_final: 0.2731 (t0) REVERT: x 53 VAL cc_start: -0.2241 (OUTLIER) cc_final: -0.3040 (t) REVERT: y 24 ASP cc_start: 0.7353 (t0) cc_final: 0.6994 (t70) REVERT: y 71 ILE cc_start: 0.8559 (tt) cc_final: 0.8056 (pt) outliers start: 358 outliers final: 194 residues processed: 1068 average time/residue: 0.9163 time to fit residues: 1720.2083 Evaluate side-chains 928 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 687 time to evaluate : 9.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 363 LEU Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 2 residue 58 MET Chi-restraints excluded: chain 2 residue 177 CYS Chi-restraints excluded: chain 2 residue 182 ILE Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 180 VAL Chi-restraints excluded: chain 3 residue 230 VAL Chi-restraints excluded: chain 3 residue 255 CYS Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 140 LYS Chi-restraints excluded: chain 4 residue 158 VAL Chi-restraints excluded: chain 4 residue 197 THR Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 303 ASN Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 494 MET Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 534 TYR Chi-restraints excluded: chain 6 residue 624 ILE Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 427 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 493 MET Chi-restraints excluded: chain 7 residue 510 THR Chi-restraints excluded: chain 7 residue 709 THR Chi-restraints excluded: chain 7 residue 714 VAL Chi-restraints excluded: chain 8 residue 255 ILE Chi-restraints excluded: chain 9 residue 70 VAL Chi-restraints excluded: chain 9 residue 84 CYS Chi-restraints excluded: chain 9 residue 165 ARG Chi-restraints excluded: chain 9 residue 211 GLN Chi-restraints excluded: chain 9 residue 218 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain D residue 940 VAL Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain E residue 612 TRP Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 306 VAL Chi-restraints excluded: chain Q residue 37 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 303 ASP Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 191 PHE Chi-restraints excluded: chain T residue 215 GLU Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 108 ASP Chi-restraints excluded: chain U residue 146 ASP Chi-restraints excluded: chain U residue 148 MET Chi-restraints excluded: chain U residue 174 ARG Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 192 VAL Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 116 ASP Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain k residue 185 LYS Chi-restraints excluded: chain l residue 56 GLN Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 226 LYS Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 520 MET Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 542 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 593 SER Chi-restraints excluded: chain o residue 626 THR Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 715 GLU Chi-restraints excluded: chain o residue 770 VAL Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 850 THR Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 900 SER Chi-restraints excluded: chain o residue 906 LEU Chi-restraints excluded: chain o residue 908 THR Chi-restraints excluded: chain o residue 966 LEU Chi-restraints excluded: chain o residue 1004 LEU Chi-restraints excluded: chain o residue 1065 PHE Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1139 LEU Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1163 HIS Chi-restraints excluded: chain o residue 1198 GLU Chi-restraints excluded: chain o residue 1215 GLU Chi-restraints excluded: chain o residue 1249 ASP Chi-restraints excluded: chain o residue 1315 ASP Chi-restraints excluded: chain o residue 1358 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain o residue 1435 THR Chi-restraints excluded: chain o residue 1456 GLU Chi-restraints excluded: chain o residue 1476 ASP Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 119 THR Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 230 ARG Chi-restraints excluded: chain p residue 262 TYR Chi-restraints excluded: chain p residue 288 ILE Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 509 VAL Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 617 ASP Chi-restraints excluded: chain p residue 657 VAL Chi-restraints excluded: chain p residue 667 THR Chi-restraints excluded: chain p residue 674 MET Chi-restraints excluded: chain p residue 694 THR Chi-restraints excluded: chain p residue 733 MET Chi-restraints excluded: chain p residue 735 VAL Chi-restraints excluded: chain p residue 738 THR Chi-restraints excluded: chain p residue 740 PHE Chi-restraints excluded: chain p residue 802 ASP Chi-restraints excluded: chain p residue 833 THR Chi-restraints excluded: chain p residue 845 TYR Chi-restraints excluded: chain p residue 860 VAL Chi-restraints excluded: chain p residue 865 VAL Chi-restraints excluded: chain p residue 888 THR Chi-restraints excluded: chain p residue 911 LEU Chi-restraints excluded: chain p residue 917 LYS Chi-restraints excluded: chain p residue 938 ARG Chi-restraints excluded: chain p residue 959 GLU Chi-restraints excluded: chain p residue 964 ASP Chi-restraints excluded: chain p residue 983 GLU Chi-restraints excluded: chain p residue 1006 VAL Chi-restraints excluded: chain p residue 1023 ARG Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1054 MET Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 169 PHE Chi-restraints excluded: chain q residue 173 HIS Chi-restraints excluded: chain q residue 184 PHE Chi-restraints excluded: chain q residue 185 GLU Chi-restraints excluded: chain q residue 189 ASP Chi-restraints excluded: chain q residue 194 HIS Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain q residue 267 ILE Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 177 ASP Chi-restraints excluded: chain s residue 179 VAL Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 106 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 59 ILE Chi-restraints excluded: chain u residue 94 LYS Chi-restraints excluded: chain u residue 110 ARG Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 58 LEU Chi-restraints excluded: chain v residue 71 ASP Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 111 TYR Chi-restraints excluded: chain x residue 1 MET Chi-restraints excluded: chain x residue 16 ASN Chi-restraints excluded: chain x residue 18 TRP Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain x residue 59 LEU Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain z residue 26 ASN Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 447 optimal weight: 7.9990 chunk 1197 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 780 optimal weight: 40.0000 chunk 328 optimal weight: 6.9990 chunk 1331 optimal weight: 0.0370 chunk 1105 optimal weight: 4.9990 chunk 616 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 440 optimal weight: 20.0000 chunk 698 optimal weight: 4.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 228 HIS ** 2 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 376 HIS ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 352 GLN ** 4 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 275 GLN A 702 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS B 331 HIS B 908 GLN ** D 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 ASN T 91 GLN e 254 ASN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 81 GLN ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 410 ASN p 468 GLN p 481 HIS p 725 GLN ** p 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 66 HIS q 83 GLN ** q 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 262 GLN q 265 HIS s 35 GLN u 28 GLN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 84 HIS ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2152 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.218 115699 Z= 0.394 Angle : 0.826 21.510 157113 Z= 0.427 Chirality : 0.049 0.608 17587 Planarity : 0.007 0.229 19780 Dihedral : 12.039 120.452 16714 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 3.24 % Allowed : 16.25 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.10 % 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: -1.20 (0.07), residues: 13701 helix: 0.47 (0.07), residues: 5721 sheet: -0.83 (0.13), residues: 1587 loop : -2.00 (0.07), residues: 6393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP S 143 HIS 0.022 0.001 HIS q 173 PHE 0.108 0.002 PHE p 806 TYR 0.056 0.002 TYR p 736 ARG 0.019 0.001 ARG p 803 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 782 time to evaluate : 9.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1 230 PHE cc_start: -0.3485 (t80) cc_final: -0.4888 (m-80) REVERT: 1 232 ARG cc_start: -0.3433 (mpt180) cc_final: -0.6223 (mmt180) REVERT: 1 362 ASP cc_start: -0.3413 (OUTLIER) cc_final: -0.3978 (m-30) REVERT: 2 137 MET cc_start: -0.2230 (ptm) cc_final: -0.3343 (ptt) REVERT: 2 252 MET cc_start: -0.2834 (ttt) cc_final: -0.3260 (tmm) REVERT: 3 42 MET cc_start: -0.3933 (mtm) cc_final: -0.4999 (mmt) REVERT: 3 51 MET cc_start: -0.2883 (mtp) cc_final: -0.3667 (tpt) REVERT: 3 146 ARG cc_start: -0.1295 (OUTLIER) cc_final: -0.2080 (ptt-90) REVERT: 4 140 LYS cc_start: -0.1929 (OUTLIER) cc_final: -0.2317 (pptt) REVERT: 4 216 MET cc_start: 0.3074 (mmp) cc_final: 0.2076 (mmt) REVERT: 4 254 MET cc_start: -0.2354 (ttt) cc_final: -0.3027 (tpt) REVERT: 4 334 MET cc_start: -0.1289 (tmm) cc_final: -0.1567 (tmm) REVERT: 4 376 MET cc_start: -0.3812 (mtt) cc_final: -0.4438 (mtt) REVERT: 6 438 MET cc_start: -0.1439 (OUTLIER) cc_final: -0.2357 (mtm) REVERT: 6 450 MET cc_start: -0.0789 (mmm) cc_final: -0.1580 (mmp) REVERT: 6 624 ILE cc_start: 0.2976 (OUTLIER) cc_final: 0.2554 (mm) REVERT: 6 696 MET cc_start: -0.3836 (ttt) cc_final: -0.4626 (tpp) REVERT: 7 30 ARG cc_start: 0.4129 (OUTLIER) cc_final: 0.3786 (mtm-85) REVERT: 7 42 MET cc_start: -0.3737 (tpp) cc_final: -0.4664 (ttt) REVERT: 7 438 MET cc_start: 0.1879 (mpp) cc_final: 0.0603 (mmm) REVERT: 7 483 MET cc_start: 0.4945 (mmm) cc_final: 0.4278 (mmm) REVERT: 7 545 MET cc_start: 0.2593 (mmm) cc_final: 0.2250 (mmm) REVERT: 7 657 MET cc_start: -0.3484 (mmp) cc_final: -0.4116 (mpp) REVERT: 9 245 LEU cc_start: 0.3822 (pp) cc_final: 0.3604 (pp) REVERT: A 607 MET cc_start: -0.3889 (mtp) cc_final: -0.4347 (mtt) REVERT: A 649 MET cc_start: 0.4709 (ppp) cc_final: 0.4441 (ppp) REVERT: A 661 GLU cc_start: -0.1914 (OUTLIER) cc_final: -0.2485 (tp30) REVERT: A 696 MET cc_start: -0.2675 (ppp) cc_final: -0.3669 (ptt) REVERT: A 879 MET cc_start: 0.2643 (ppp) cc_final: 0.2302 (ppp) REVERT: B 170 MET cc_start: 0.0312 (OUTLIER) cc_final: -0.0136 (tmm) REVERT: B 237 MET cc_start: 0.3389 (tpt) cc_final: 0.3066 (tpt) REVERT: B 262 MET cc_start: -0.3552 (ptt) cc_final: -0.3762 (ptt) REVERT: B 334 MET cc_start: -0.3759 (OUTLIER) cc_final: -0.4461 (tpt) REVERT: B 614 MET cc_start: -0.2434 (mtt) cc_final: -0.3269 (mtt) REVERT: B 634 MET cc_start: -0.4023 (OUTLIER) cc_final: -0.5118 (tpt) REVERT: B 709 MET cc_start: -0.3202 (ptt) cc_final: -0.3528 (ptt) REVERT: B 726 MET cc_start: 0.0822 (OUTLIER) cc_final: 0.0597 (ptt) REVERT: E 612 TRP cc_start: -0.0836 (OUTLIER) cc_final: -0.1446 (m100) REVERT: E 703 MET cc_start: -0.0107 (tpt) cc_final: -0.0819 (tpt) REVERT: F 19 MET cc_start: -0.4595 (tpt) cc_final: -0.4966 (tpt) REVERT: F 26 MET cc_start: -0.3629 (ttm) cc_final: -0.4184 (mtt) REVERT: F 290 MET cc_start: -0.0245 (mtm) cc_final: -0.0496 (mmt) REVERT: G 147 ARG cc_start: 0.0081 (OUTLIER) cc_final: -0.0733 (ttt180) REVERT: G 148 PHE cc_start: 0.2075 (OUTLIER) cc_final: 0.1640 (m-10) REVERT: H 132 LYS cc_start: -0.3999 (OUTLIER) cc_final: -0.5959 (pttt) REVERT: H 161 LYS cc_start: 0.1089 (OUTLIER) cc_final: 0.0409 (mmtt) REVERT: I 19 MET cc_start: -0.5003 (tpp) cc_final: -0.5593 (ttm) REVERT: I 26 MET cc_start: -0.2305 (mmt) cc_final: -0.4280 (mtt) REVERT: J 192 LYS cc_start: 0.2196 (OUTLIER) cc_final: 0.1091 (ptmm) REVERT: J 197 MET cc_start: -0.4208 (mmm) cc_final: -0.5106 (mtt) REVERT: L 61 LYS cc_start: 0.4325 (OUTLIER) cc_final: 0.4050 (pttm) REVERT: L 126 MET cc_start: 0.0219 (ttt) cc_final: -0.1135 (ttp) REVERT: P 202 MET cc_start: -0.1769 (mtt) cc_final: -0.2490 (tpp) REVERT: P 219 MET cc_start: 0.0692 (OUTLIER) cc_final: -0.0635 (ttt) REVERT: Q 358 MET cc_start: -0.0738 (mmp) cc_final: -0.1076 (mmp) REVERT: c 73 MET cc_start: -0.1761 (mmt) cc_final: -0.1987 (mmt) REVERT: d 857 SER cc_start: -0.2451 (m) cc_final: -0.2675 (m) REVERT: e 213 MET cc_start: -0.0114 (mmp) cc_final: -0.0573 (tpp) REVERT: e 442 MET cc_start: -0.1832 (ppp) cc_final: -0.2404 (ppp) REVERT: e 528 MET cc_start: 0.0222 (mmt) cc_final: -0.2030 (mmt) REVERT: e 612 TRP cc_start: -0.0173 (OUTLIER) cc_final: -0.0433 (m100) REVERT: e 696 TRP cc_start: -0.2069 (OUTLIER) cc_final: -0.2905 (m-10) REVERT: e 703 MET cc_start: 0.1202 (mpp) cc_final: -0.0318 (mmt) REVERT: f 19 MET cc_start: -0.3367 (mmt) cc_final: -0.5501 (mmt) REVERT: f 26 MET cc_start: -0.4019 (OUTLIER) cc_final: -0.4929 (ttt) REVERT: f 60 MET cc_start: -0.3272 (mmt) cc_final: -0.4381 (mpp) REVERT: f 283 MET cc_start: -0.2312 (mmt) cc_final: -0.2555 (mmt) REVERT: f 290 MET cc_start: -0.0669 (mtt) cc_final: -0.1528 (mmt) REVERT: i 12 MET cc_start: 0.1961 (tpt) cc_final: 0.1687 (tpt) REVERT: i 19 MET cc_start: -0.2880 (tpt) cc_final: -0.4053 (tpt) REVERT: i 26 MET cc_start: -0.1337 (mmp) cc_final: -0.3248 (tpt) REVERT: i 39 MET cc_start: -0.3370 (tpt) cc_final: -0.3954 (mmt) REVERT: j 176 MET cc_start: -0.3204 (mtm) cc_final: -0.4170 (ptt) REVERT: k 179 MET cc_start: 0.2187 (pmm) cc_final: 0.1935 (pmm) REVERT: l 83 MET cc_start: -0.3805 (ttt) cc_final: -0.4301 (ttt) REVERT: l 152 MET cc_start: -0.3217 (tpp) cc_final: -0.4855 (mtt) REVERT: o 458 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: o 683 GLU cc_start: 0.7835 (tp30) cc_final: 0.7605 (tp30) REVERT: o 794 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6837 (tp30) REVERT: o 831 LEU cc_start: 0.3602 (OUTLIER) cc_final: 0.3384 (mp) REVERT: o 1063 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: o 1199 MET cc_start: 0.6941 (ppp) cc_final: 0.6515 (ppp) REVERT: o 1215 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5968 (tp30) REVERT: o 1292 MET cc_start: 0.7977 (mmp) cc_final: 0.7569 (mmt) REVERT: o 1303 GLN cc_start: 0.8671 (tp40) cc_final: 0.8307 (tm-30) REVERT: o 1389 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7182 (p0) REVERT: o 1456 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: o 1459 MET cc_start: 0.8132 (ptp) cc_final: 0.7864 (ptm) REVERT: o 1476 ASP cc_start: 0.2287 (OUTLIER) cc_final: 0.0650 (t0) REVERT: p 109 MET cc_start: 0.0572 (ttp) cc_final: 0.0370 (ttp) REVERT: p 176 GLU cc_start: 0.5284 (OUTLIER) cc_final: 0.4664 (mt-10) REVERT: p 217 TYR cc_start: 0.8096 (m-10) cc_final: 0.7809 (m-10) REVERT: p 230 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.6003 (mmp80) REVERT: p 388 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.4410 (t80) REVERT: p 529 MET cc_start: 0.3470 (ppp) cc_final: 0.3061 (mmt) REVERT: p 550 MET cc_start: 0.1330 (OUTLIER) cc_final: 0.0829 (ppp) REVERT: p 597 ILE cc_start: 0.1280 (OUTLIER) cc_final: 0.0678 (mt) REVERT: p 617 ASP cc_start: 0.4653 (OUTLIER) cc_final: 0.4046 (p0) REVERT: p 733 MET cc_start: 0.2413 (OUTLIER) cc_final: 0.0485 (mpp) REVERT: p 784 SER cc_start: 0.8796 (m) cc_final: 0.8386 (p) REVERT: p 917 LYS cc_start: 0.5453 (OUTLIER) cc_final: 0.4467 (tptp) REVERT: p 963 PRO cc_start: 0.7411 (Cg_endo) cc_final: 0.7145 (Cg_exo) REVERT: p 1075 MET cc_start: 0.6311 (ppp) cc_final: 0.5987 (pmm) REVERT: p 1095 ILE cc_start: 0.8341 (tp) cc_final: 0.8065 (pt) REVERT: p 1172 MET cc_start: 0.8301 (pmm) cc_final: 0.7827 (pmm) REVERT: q 24 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7331 (mm-30) REVERT: q 123 ASN cc_start: -0.2676 (OUTLIER) cc_final: -0.3160 (p0) REVERT: r 36 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6990 (tp30) REVERT: s 174 GLN cc_start: 0.6907 (pm20) cc_final: 0.5649 (pm20) REVERT: s 208 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7718 (tt) REVERT: u 16 ARG cc_start: 0.4332 (mtt180) cc_final: 0.3916 (mtt180) REVERT: u 68 TYR cc_start: 0.3504 (m-80) cc_final: 0.1609 (m-80) REVERT: u 117 MET cc_start: -0.2494 (mtm) cc_final: -0.3898 (ttm) REVERT: w 43 ASP cc_start: 0.8351 (m-30) cc_final: 0.7987 (t0) REVERT: w 69 ILE cc_start: -0.1541 (OUTLIER) cc_final: -0.2009 (mt) REVERT: x 16 ASN cc_start: 0.5208 (OUTLIER) cc_final: 0.2981 (t0) REVERT: x 53 VAL cc_start: -0.1359 (OUTLIER) cc_final: -0.2144 (p) outliers start: 387 outliers final: 245 residues processed: 1098 average time/residue: 0.9616 time to fit residues: 1847.5861 Evaluate side-chains 997 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 709 time to evaluate : 9.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 123 GLU Chi-restraints excluded: chain 1 residue 228 HIS Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 1 residue 375 ASN Chi-restraints excluded: chain 2 residue 58 MET Chi-restraints excluded: chain 2 residue 70 THR Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 2 residue 301 LEU Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 255 CYS Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 140 LYS Chi-restraints excluded: chain 4 residue 158 VAL Chi-restraints excluded: chain 4 residue 197 THR Chi-restraints excluded: chain 4 residue 251 VAL Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 4 residue 432 VAL Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 438 MET Chi-restraints excluded: chain 6 residue 458 VAL Chi-restraints excluded: chain 6 residue 494 MET Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 575 LEU Chi-restraints excluded: chain 6 residue 624 ILE Chi-restraints excluded: chain 6 residue 667 THR Chi-restraints excluded: chain 7 residue 24 TYR Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 30 ARG Chi-restraints excluded: chain 7 residue 388 ILE Chi-restraints excluded: chain 7 residue 427 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 493 MET Chi-restraints excluded: chain 7 residue 709 THR Chi-restraints excluded: chain 7 residue 714 VAL Chi-restraints excluded: chain 9 residue 70 VAL Chi-restraints excluded: chain 9 residue 84 CYS Chi-restraints excluded: chain 9 residue 165 ARG Chi-restraints excluded: chain 9 residue 207 TYR Chi-restraints excluded: chain 9 residue 218 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain E residue 612 TRP Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 303 ASP Chi-restraints excluded: chain S residue 124 TYR Chi-restraints excluded: chain T residue 147 LYS Chi-restraints excluded: chain T residue 210 VAL Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 76 MET Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 108 ASP Chi-restraints excluded: chain U residue 146 ASP Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 192 VAL Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 451 VAL Chi-restraints excluded: chain e residue 536 LEU Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain i residue 52 ASP Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 200 LEU Chi-restraints excluded: chain m residue 45 ASP Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 202 TRP Chi-restraints excluded: chain o residue 226 LYS Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 399 ILE Chi-restraints excluded: chain o residue 452 ASP Chi-restraints excluded: chain o residue 458 PHE Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 542 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 567 LEU Chi-restraints excluded: chain o residue 574 VAL Chi-restraints excluded: chain o residue 593 SER Chi-restraints excluded: chain o residue 637 MET Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 717 ILE Chi-restraints excluded: chain o residue 770 VAL Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 806 THR Chi-restraints excluded: chain o residue 831 LEU Chi-restraints excluded: chain o residue 850 THR Chi-restraints excluded: chain o residue 875 TYR Chi-restraints excluded: chain o residue 876 ASP Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 900 SER Chi-restraints excluded: chain o residue 908 THR Chi-restraints excluded: chain o residue 1019 LYS Chi-restraints excluded: chain o residue 1029 LEU Chi-restraints excluded: chain o residue 1063 GLU Chi-restraints excluded: chain o residue 1065 PHE Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1139 LEU Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1163 HIS Chi-restraints excluded: chain o residue 1196 TYR Chi-restraints excluded: chain o residue 1198 GLU Chi-restraints excluded: chain o residue 1215 GLU Chi-restraints excluded: chain o residue 1248 ASN Chi-restraints excluded: chain o residue 1289 GLU Chi-restraints excluded: chain o residue 1294 THR Chi-restraints excluded: chain o residue 1315 ASP Chi-restraints excluded: chain o residue 1342 SER Chi-restraints excluded: chain o residue 1358 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1406 THR Chi-restraints excluded: chain o residue 1435 THR Chi-restraints excluded: chain o residue 1456 GLU Chi-restraints excluded: chain o residue 1460 LEU Chi-restraints excluded: chain o residue 1474 LEU Chi-restraints excluded: chain o residue 1476 ASP Chi-restraints excluded: chain o residue 1480 CYS Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 119 THR Chi-restraints excluded: chain p residue 126 VAL Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 131 THR Chi-restraints excluded: chain p residue 170 ASP Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 230 ARG Chi-restraints excluded: chain p residue 331 THR Chi-restraints excluded: chain p residue 382 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain p residue 452 ASN Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 509 VAL Chi-restraints excluded: chain p residue 550 MET Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 617 ASP Chi-restraints excluded: chain p residue 639 HIS Chi-restraints excluded: chain p residue 646 ARG Chi-restraints excluded: chain p residue 657 VAL Chi-restraints excluded: chain p residue 666 ASP Chi-restraints excluded: chain p residue 667 THR Chi-restraints excluded: chain p residue 694 THR Chi-restraints excluded: chain p residue 725 GLN Chi-restraints excluded: chain p residue 733 MET Chi-restraints excluded: chain p residue 735 VAL Chi-restraints excluded: chain p residue 738 THR Chi-restraints excluded: chain p residue 740 PHE Chi-restraints excluded: chain p residue 760 THR Chi-restraints excluded: chain p residue 766 TYR Chi-restraints excluded: chain p residue 845 TYR Chi-restraints excluded: chain p residue 860 VAL Chi-restraints excluded: chain p residue 865 VAL Chi-restraints excluded: chain p residue 911 LEU Chi-restraints excluded: chain p residue 917 LYS Chi-restraints excluded: chain p residue 938 ARG Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 964 ASP Chi-restraints excluded: chain p residue 983 GLU Chi-restraints excluded: chain p residue 1006 VAL Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1057 ASP Chi-restraints excluded: chain q residue 38 PHE Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 60 HIS Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 123 ASN Chi-restraints excluded: chain q residue 128 ILE Chi-restraints excluded: chain q residue 131 THR Chi-restraints excluded: chain q residue 169 PHE Chi-restraints excluded: chain q residue 173 HIS Chi-restraints excluded: chain q residue 184 PHE Chi-restraints excluded: chain q residue 185 GLU Chi-restraints excluded: chain q residue 194 HIS Chi-restraints excluded: chain q residue 195 THR Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain q residue 228 ARG Chi-restraints excluded: chain q residue 249 LEU Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 93 HIS Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain s residue 208 LEU Chi-restraints excluded: chain s residue 209 VAL Chi-restraints excluded: chain t residue 57 MET Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 79 VAL Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 104 ILE Chi-restraints excluded: chain t residue 115 TYR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 110 ARG Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 58 LEU Chi-restraints excluded: chain v residue 66 GLU Chi-restraints excluded: chain v residue 71 ASP Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 111 TYR Chi-restraints excluded: chain x residue 1 MET Chi-restraints excluded: chain x residue 6 ARG Chi-restraints excluded: chain x residue 8 PHE Chi-restraints excluded: chain x residue 16 ASN Chi-restraints excluded: chain x residue 18 TRP Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain x residue 59 LEU Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 73 ILE Chi-restraints excluded: chain z residue 26 ASN Chi-restraints excluded: chain z residue 34 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 1283 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 758 optimal weight: 9.9990 chunk 972 optimal weight: 40.0000 chunk 753 optimal weight: 0.0060 chunk 1120 optimal weight: 2.9990 chunk 743 optimal weight: 7.9990 chunk 1326 optimal weight: 6.9990 chunk 829 optimal weight: 20.0000 chunk 808 optimal weight: 7.9990 chunk 612 optimal weight: 0.0980 overall best weight: 2.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 228 HIS ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 683 GLN ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN B 331 HIS B 652 GLN ** D 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** Q 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 GLN ** U 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 181 ASN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 21 GLN ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 749 HIS ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 980 HIS q 66 HIS ** q 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 4 HIS u 60 GLN ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 69 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2180 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 115699 Z= 0.294 Angle : 0.711 18.359 157113 Z= 0.364 Chirality : 0.045 0.356 17587 Planarity : 0.005 0.086 19780 Dihedral : 11.836 122.207 16699 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 2.84 % Allowed : 17.35 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: -1.02 (0.07), residues: 13701 helix: 0.62 (0.07), residues: 5766 sheet: -0.77 (0.13), residues: 1600 loop : -1.91 (0.07), residues: 6335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP p 506 HIS 0.032 0.001 HIS p 98 PHE 0.058 0.002 PHE p1002 TYR 0.044 0.001 TYR p 736 ARG 0.018 0.001 ARG s 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 766 time to evaluate : 9.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1 230 PHE cc_start: -0.3448 (t80) cc_final: -0.4783 (m-80) REVERT: 1 232 ARG cc_start: -0.3293 (mpt180) cc_final: -0.5829 (tpt170) REVERT: 1 362 ASP cc_start: -0.3330 (OUTLIER) cc_final: -0.3955 (m-30) REVERT: 2 137 MET cc_start: -0.2200 (ptm) cc_final: -0.3354 (ptt) REVERT: 2 252 MET cc_start: -0.2185 (ttt) cc_final: -0.2979 (ttt) REVERT: 3 42 MET cc_start: -0.3785 (mtm) cc_final: -0.4928 (mmt) REVERT: 3 51 MET cc_start: -0.2890 (mtp) cc_final: -0.3696 (tpt) REVERT: 3 146 ARG cc_start: -0.1094 (OUTLIER) cc_final: -0.2449 (ptt90) REVERT: 4 140 LYS cc_start: -0.2136 (OUTLIER) cc_final: -0.2531 (pptt) REVERT: 4 216 MET cc_start: 0.3109 (mmp) cc_final: 0.2077 (mmt) REVERT: 4 334 MET cc_start: -0.1455 (tmm) cc_final: -0.1690 (tmm) REVERT: 4 376 MET cc_start: -0.3531 (mtt) cc_final: -0.4790 (mtt) REVERT: 6 438 MET cc_start: -0.1451 (OUTLIER) cc_final: -0.2351 (mtm) REVERT: 6 450 MET cc_start: -0.0715 (mmm) cc_final: -0.1466 (mmt) REVERT: 6 624 ILE cc_start: 0.3337 (OUTLIER) cc_final: 0.2895 (mm) REVERT: 6 696 MET cc_start: -0.3760 (ttt) cc_final: -0.4540 (tpp) REVERT: 7 30 ARG cc_start: 0.3990 (OUTLIER) cc_final: 0.3782 (mtm-85) REVERT: 7 42 MET cc_start: -0.3755 (tpp) cc_final: -0.4416 (ttt) REVERT: 7 438 MET cc_start: 0.1682 (mpp) cc_final: 0.0440 (mmm) REVERT: 7 483 MET cc_start: 0.4928 (mmm) cc_final: 0.3980 (mmp) REVERT: 7 657 MET cc_start: -0.3500 (mmp) cc_final: -0.3854 (mpp) REVERT: 9 245 LEU cc_start: 0.3703 (pp) cc_final: 0.3475 (pp) REVERT: A 352 MET cc_start: -0.0323 (ptp) cc_final: -0.1856 (ppp) REVERT: A 607 MET cc_start: -0.4015 (mtp) cc_final: -0.4561 (mtt) REVERT: A 649 MET cc_start: 0.4684 (ppp) cc_final: 0.4356 (ppp) REVERT: A 661 GLU cc_start: -0.1863 (OUTLIER) cc_final: -0.2575 (tp30) REVERT: A 696 MET cc_start: -0.2693 (ppp) cc_final: -0.3610 (ptt) REVERT: B 237 MET cc_start: 0.3446 (tpt) cc_final: 0.3086 (tpt) REVERT: B 334 MET cc_start: -0.3695 (OUTLIER) cc_final: -0.4392 (tpt) REVERT: B 614 MET cc_start: -0.2218 (mtt) cc_final: -0.3092 (mtt) REVERT: B 634 MET cc_start: -0.4035 (OUTLIER) cc_final: -0.5126 (tpt) REVERT: B 709 MET cc_start: -0.3475 (ptt) cc_final: -0.3716 (ptt) REVERT: E 612 TRP cc_start: -0.0847 (OUTLIER) cc_final: -0.1452 (m100) REVERT: E 703 MET cc_start: 0.0204 (tpt) cc_final: -0.0618 (tpt) REVERT: F 19 MET cc_start: -0.4765 (tpt) cc_final: -0.5065 (tpt) REVERT: F 26 MET cc_start: -0.3598 (ttm) cc_final: -0.4117 (mtt) REVERT: F 255 MET cc_start: -0.5075 (tpt) cc_final: -0.5325 (tpt) REVERT: F 285 MET cc_start: -0.4145 (tpp) cc_final: -0.4429 (tpt) REVERT: G 147 ARG cc_start: 0.0142 (OUTLIER) cc_final: -0.0478 (ttt180) REVERT: G 148 PHE cc_start: 0.2173 (OUTLIER) cc_final: 0.1703 (m-10) REVERT: H 132 LYS cc_start: -0.3963 (OUTLIER) cc_final: -0.5934 (pttt) REVERT: H 161 LYS cc_start: 0.1211 (OUTLIER) cc_final: 0.0460 (mmtt) REVERT: I 19 MET cc_start: -0.4903 (tpp) cc_final: -0.5531 (ttm) REVERT: I 26 MET cc_start: -0.2496 (mmt) cc_final: -0.4254 (mtt) REVERT: J 192 LYS cc_start: 0.1944 (OUTLIER) cc_final: 0.0934 (ptmm) REVERT: J 197 MET cc_start: -0.4329 (mmm) cc_final: -0.5029 (mtt) REVERT: L 61 LYS cc_start: 0.4046 (OUTLIER) cc_final: 0.3723 (pttm) REVERT: L 83 MET cc_start: -0.1065 (mtp) cc_final: -0.1764 (mtp) REVERT: L 126 MET cc_start: 0.0081 (ttt) cc_final: -0.0890 (ttp) REVERT: P 219 MET cc_start: 0.1070 (OUTLIER) cc_final: 0.0120 (ttt) REVERT: R 313 LEU cc_start: -0.1263 (OUTLIER) cc_final: -0.1543 (mt) REVERT: U 110 MET cc_start: 0.3608 (mmm) cc_final: 0.3120 (mmm) REVERT: c 73 MET cc_start: -0.1757 (mmt) cc_final: -0.2017 (mmt) REVERT: d 857 SER cc_start: -0.2463 (m) cc_final: -0.2704 (m) REVERT: e 213 MET cc_start: -0.0075 (mmp) cc_final: -0.0520 (tpp) REVERT: e 442 MET cc_start: -0.1798 (ppp) cc_final: -0.2323 (ppp) REVERT: e 528 MET cc_start: 0.0068 (mmt) cc_final: -0.2380 (mmt) REVERT: e 612 TRP cc_start: -0.0348 (OUTLIER) cc_final: -0.0606 (m100) REVERT: e 696 TRP cc_start: -0.2105 (OUTLIER) cc_final: -0.2947 (m-10) REVERT: e 703 MET cc_start: 0.0960 (mpp) cc_final: -0.0576 (mmt) REVERT: f 19 MET cc_start: -0.3369 (mmt) cc_final: -0.5564 (mmt) REVERT: f 26 MET cc_start: -0.4181 (OUTLIER) cc_final: -0.5081 (ttt) REVERT: f 60 MET cc_start: -0.3328 (mmt) cc_final: -0.4441 (mpp) REVERT: f 283 MET cc_start: -0.2193 (mmt) cc_final: -0.2446 (mmt) REVERT: f 290 MET cc_start: -0.0844 (mtt) cc_final: -0.1687 (mmt) REVERT: i 12 MET cc_start: 0.2068 (tpt) cc_final: 0.1754 (tpt) REVERT: i 18 MET cc_start: -0.3165 (tmt) cc_final: -0.4115 (tmt) REVERT: i 19 MET cc_start: -0.2963 (tpt) cc_final: -0.4110 (tpt) REVERT: i 26 MET cc_start: -0.1169 (mmp) cc_final: -0.3286 (tpt) REVERT: i 39 MET cc_start: -0.3392 (tpt) cc_final: -0.3923 (mmt) REVERT: j 176 MET cc_start: -0.3215 (mtm) cc_final: -0.4224 (ptt) REVERT: k 179 MET cc_start: 0.2558 (pmm) cc_final: 0.2340 (pmm) REVERT: l 83 MET cc_start: -0.3763 (ttt) cc_final: -0.4308 (ttt) REVERT: l 152 MET cc_start: -0.3323 (tpp) cc_final: -0.5076 (mtt) REVERT: o 19 LYS cc_start: 0.8133 (tptm) cc_final: 0.7749 (tptp) REVERT: o 266 MET cc_start: 0.1628 (ptp) cc_final: 0.0410 (ttp) REVERT: o 517 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8170 (tm-30) REVERT: o 794 GLU cc_start: 0.7654 (mm-30) cc_final: 0.6713 (tp30) REVERT: o 845 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7705 (pp20) REVERT: o 862 ARG cc_start: 0.7272 (mmm160) cc_final: 0.6973 (mmm160) REVERT: o 1004 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6486 (mp) REVERT: o 1199 MET cc_start: 0.7320 (ppp) cc_final: 0.6076 (pmm) REVERT: o 1215 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6035 (tp30) REVERT: o 1228 MET cc_start: 0.6938 (mmm) cc_final: 0.6729 (mmm) REVERT: o 1249 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7141 (p0) REVERT: o 1292 MET cc_start: 0.7906 (mmp) cc_final: 0.7619 (mmt) REVERT: o 1303 GLN cc_start: 0.8687 (tp40) cc_final: 0.8198 (mp10) REVERT: o 1343 LEU cc_start: 0.9475 (mt) cc_final: 0.9154 (tt) REVERT: o 1395 TYR cc_start: 0.9018 (t80) cc_final: 0.8701 (t80) REVERT: o 1405 MET cc_start: 0.8588 (tpp) cc_final: 0.8388 (tpp) REVERT: o 1456 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: o 1476 ASP cc_start: 0.2113 (OUTLIER) cc_final: 0.0644 (t0) REVERT: p 176 GLU cc_start: 0.4862 (OUTLIER) cc_final: 0.4370 (mt-10) REVERT: p 200 MET cc_start: 0.8609 (mmt) cc_final: 0.8270 (mmt) REVERT: p 217 TYR cc_start: 0.8174 (m-10) cc_final: 0.7947 (m-10) REVERT: p 230 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6497 (mmp80) REVERT: p 239 MET cc_start: 0.8213 (ttp) cc_final: 0.7916 (ttp) REVERT: p 298 MET cc_start: 0.5005 (mmp) cc_final: 0.3016 (ttp) REVERT: p 448 LEU cc_start: 0.8803 (mt) cc_final: 0.8568 (tp) REVERT: p 550 MET cc_start: 0.1370 (OUTLIER) cc_final: 0.1014 (ppp) REVERT: p 597 ILE cc_start: 0.0942 (OUTLIER) cc_final: 0.0476 (mt) REVERT: p 617 ASP cc_start: 0.4957 (OUTLIER) cc_final: 0.4379 (p0) REVERT: p 753 TYR cc_start: 0.5565 (m-80) cc_final: 0.4476 (m-80) REVERT: p 784 SER cc_start: 0.8865 (m) cc_final: 0.8331 (p) REVERT: p 917 LYS cc_start: 0.5495 (OUTLIER) cc_final: 0.4320 (tmtt) REVERT: p 927 ARG cc_start: 0.1869 (mmm160) cc_final: 0.1427 (mmp-170) REVERT: p 1020 TYR cc_start: 0.4117 (OUTLIER) cc_final: 0.2679 (t80) REVERT: p 1064 ARG cc_start: 0.7502 (mmm-85) cc_final: 0.7183 (mtp-110) REVERT: q 22 ILE cc_start: 0.6027 (mt) cc_final: 0.5658 (mt) REVERT: q 24 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7437 (mm-30) REVERT: q 250 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.7885 (p) REVERT: r 36 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6754 (tp30) REVERT: s 174 GLN cc_start: 0.6512 (pm20) cc_final: 0.6074 (pm20) REVERT: s 208 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7565 (tt) REVERT: u 60 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: u 68 TYR cc_start: 0.3114 (m-80) cc_final: 0.1432 (m-80) REVERT: u 104 MET cc_start: -0.1399 (ttp) cc_final: -0.2197 (tpp) REVERT: u 117 MET cc_start: -0.2518 (mtm) cc_final: -0.3857 (ttm) REVERT: w 43 ASP cc_start: 0.8391 (m-30) cc_final: 0.7866 (t0) REVERT: w 69 ILE cc_start: -0.1435 (OUTLIER) cc_final: -0.1927 (mt) REVERT: x 53 VAL cc_start: -0.1451 (OUTLIER) cc_final: -0.2197 (t) outliers start: 339 outliers final: 201 residues processed: 1044 average time/residue: 0.9263 time to fit residues: 1697.6920 Evaluate side-chains 964 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 723 time to evaluate : 9.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 1 residue 375 ASN Chi-restraints excluded: chain 2 residue 58 MET Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 175 MET Chi-restraints excluded: chain 3 residue 230 VAL Chi-restraints excluded: chain 3 residue 255 CYS Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 140 LYS Chi-restraints excluded: chain 4 residue 158 VAL Chi-restraints excluded: chain 4 residue 197 THR Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 4 residue 432 VAL Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 6 residue 119 THR Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 272 VAL Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 438 MET Chi-restraints excluded: chain 6 residue 494 MET Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 575 LEU Chi-restraints excluded: chain 6 residue 624 ILE Chi-restraints excluded: chain 6 residue 667 THR Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 30 ARG Chi-restraints excluded: chain 7 residue 427 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 493 MET Chi-restraints excluded: chain 7 residue 709 THR Chi-restraints excluded: chain 7 residue 714 VAL Chi-restraints excluded: chain 8 residue 237 TRP Chi-restraints excluded: chain 8 residue 255 ILE Chi-restraints excluded: chain 9 residue 70 VAL Chi-restraints excluded: chain 9 residue 84 CYS Chi-restraints excluded: chain 9 residue 165 ARG Chi-restraints excluded: chain 9 residue 207 TYR Chi-restraints excluded: chain 9 residue 218 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain E residue 528 MET Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain E residue 612 TRP Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 189 ASN Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 303 ASP Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain T residue 210 VAL Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 129 CYS Chi-restraints excluded: chain U residue 146 ASP Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 536 LEU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 200 LEU Chi-restraints excluded: chain m residue 45 ASP Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 226 LYS Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 446 VAL Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 542 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 567 LEU Chi-restraints excluded: chain o residue 574 VAL Chi-restraints excluded: chain o residue 593 SER Chi-restraints excluded: chain o residue 614 ASP Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 665 THR Chi-restraints excluded: chain o residue 682 ILE Chi-restraints excluded: chain o residue 717 ILE Chi-restraints excluded: chain o residue 770 VAL Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 850 THR Chi-restraints excluded: chain o residue 876 ASP Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 906 LEU Chi-restraints excluded: chain o residue 1004 LEU Chi-restraints excluded: chain o residue 1005 HIS Chi-restraints excluded: chain o residue 1019 LYS Chi-restraints excluded: chain o residue 1029 LEU Chi-restraints excluded: chain o residue 1065 PHE Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1163 HIS Chi-restraints excluded: chain o residue 1198 GLU Chi-restraints excluded: chain o residue 1215 GLU Chi-restraints excluded: chain o residue 1249 ASP Chi-restraints excluded: chain o residue 1358 THR Chi-restraints excluded: chain o residue 1371 ILE Chi-restraints excluded: chain o residue 1435 THR Chi-restraints excluded: chain o residue 1456 GLU Chi-restraints excluded: chain o residue 1474 LEU Chi-restraints excluded: chain o residue 1476 ASP Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 27 TRP Chi-restraints excluded: chain p residue 92 TYR Chi-restraints excluded: chain p residue 126 VAL Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain p residue 230 ARG Chi-restraints excluded: chain p residue 331 THR Chi-restraints excluded: chain p residue 393 LEU Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain p residue 452 ASN Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 550 MET Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 607 ILE Chi-restraints excluded: chain p residue 617 ASP Chi-restraints excluded: chain p residue 643 LEU Chi-restraints excluded: chain p residue 667 THR Chi-restraints excluded: chain p residue 694 THR Chi-restraints excluded: chain p residue 733 MET Chi-restraints excluded: chain p residue 740 PHE Chi-restraints excluded: chain p residue 766 TYR Chi-restraints excluded: chain p residue 845 TYR Chi-restraints excluded: chain p residue 860 VAL Chi-restraints excluded: chain p residue 865 VAL Chi-restraints excluded: chain p residue 917 LYS Chi-restraints excluded: chain p residue 938 ARG Chi-restraints excluded: chain p residue 983 GLU Chi-restraints excluded: chain p residue 1006 VAL Chi-restraints excluded: chain p residue 1020 TYR Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain p residue 1150 ARG Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 38 PHE Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 173 HIS Chi-restraints excluded: chain q residue 185 GLU Chi-restraints excluded: chain q residue 195 THR Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain q residue 250 SER Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 93 HIS Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 130 PHE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain s residue 208 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 60 GLN Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 58 LEU Chi-restraints excluded: chain v residue 71 ASP Chi-restraints excluded: chain v residue 72 ASP Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain v residue 125 LEU Chi-restraints excluded: chain v residue 146 LYS Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 111 TYR Chi-restraints excluded: chain x residue 1 MET Chi-restraints excluded: chain x residue 16 ASN Chi-restraints excluded: chain x residue 18 TRP Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain x residue 59 LEU Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain z residue 26 ASN Chi-restraints excluded: chain z residue 34 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 820 optimal weight: 20.0000 chunk 529 optimal weight: 50.0000 chunk 792 optimal weight: 0.0030 chunk 399 optimal weight: 1.9990 chunk 260 optimal weight: 0.0570 chunk 256 optimal weight: 50.0000 chunk 843 optimal weight: 8.9990 chunk 903 optimal weight: 0.0870 chunk 655 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 1042 optimal weight: 0.9980 overall best weight: 0.6288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 157 HIS A 702 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 48 ASN ** Q 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 109 HIS ** d 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 685 HIS ** o 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 765 ASN o1077 ASN ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 390 ASN ** p 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 503 ASN ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2115 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 115699 Z= 0.177 Angle : 0.639 15.973 157113 Z= 0.322 Chirality : 0.043 0.338 17587 Planarity : 0.004 0.080 19780 Dihedral : 11.673 123.214 16697 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.30 % Favored : 94.51 % Rotamer: Outliers : 2.25 % Allowed : 18.13 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.01 % 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: -0.76 (0.07), residues: 13701 helix: 0.81 (0.07), residues: 5757 sheet: -0.53 (0.13), residues: 1554 loop : -1.77 (0.07), residues: 6390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP p 22 HIS 0.016 0.001 HIS p 98 PHE 0.034 0.001 PHE p1002 TYR 0.032 0.001 TYR p 736 ARG 0.011 0.000 ARG 1 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 773 time to evaluate : 8.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1 230 PHE cc_start: -0.3833 (t80) cc_final: -0.5550 (m-80) REVERT: 1 232 ARG cc_start: -0.3319 (mpt180) cc_final: -0.5869 (tpt170) REVERT: 1 362 ASP cc_start: -0.3371 (OUTLIER) cc_final: -0.4052 (m-30) REVERT: 2 137 MET cc_start: -0.2241 (ptm) cc_final: -0.3330 (ptt) REVERT: 2 252 MET cc_start: -0.2275 (ttt) cc_final: -0.3179 (tmm) REVERT: 3 42 MET cc_start: -0.3830 (mtm) cc_final: -0.4937 (mmt) REVERT: 3 51 MET cc_start: -0.2893 (mtp) cc_final: -0.3695 (tpt) REVERT: 3 146 ARG cc_start: -0.1345 (OUTLIER) cc_final: -0.1567 (ptt180) REVERT: 4 140 LYS cc_start: -0.2260 (OUTLIER) cc_final: -0.2569 (pptt) REVERT: 4 216 MET cc_start: 0.3128 (mmp) cc_final: 0.2105 (mmt) REVERT: 4 254 MET cc_start: -0.1514 (ttt) cc_final: -0.2340 (tpt) REVERT: 4 334 MET cc_start: -0.1390 (tmm) cc_final: -0.1619 (tmm) REVERT: 4 376 MET cc_start: -0.3587 (mtt) cc_final: -0.4929 (mtt) REVERT: 6 438 MET cc_start: -0.1466 (OUTLIER) cc_final: -0.2819 (mtt) REVERT: 6 450 MET cc_start: -0.0745 (mmm) cc_final: -0.1467 (mmt) REVERT: 6 624 ILE cc_start: 0.3415 (OUTLIER) cc_final: 0.3008 (mm) REVERT: 6 696 MET cc_start: -0.4105 (ttt) cc_final: -0.4620 (tpp) REVERT: 7 40 LEU cc_start: -0.5018 (OUTLIER) cc_final: -0.5256 (mt) REVERT: 7 42 MET cc_start: -0.4207 (tpp) cc_final: -0.4973 (ttt) REVERT: 7 323 ILE cc_start: -0.6530 (OUTLIER) cc_final: -0.6733 (mt) REVERT: 7 438 MET cc_start: 0.1638 (mpp) cc_final: 0.0416 (mmm) REVERT: 7 483 MET cc_start: 0.4951 (mmm) cc_final: 0.4404 (mmm) REVERT: 7 657 MET cc_start: -0.3529 (mmp) cc_final: -0.3927 (mpp) REVERT: A 352 MET cc_start: -0.0556 (ptp) cc_final: -0.1944 (ppp) REVERT: A 607 MET cc_start: -0.3729 (mtp) cc_final: -0.4385 (mtt) REVERT: A 649 MET cc_start: 0.4671 (ppp) cc_final: 0.4363 (ppp) REVERT: A 661 GLU cc_start: -0.1379 (OUTLIER) cc_final: -0.2674 (tp30) REVERT: A 879 MET cc_start: 0.2994 (ppp) cc_final: 0.2481 (ppp) REVERT: B 170 MET cc_start: -0.0074 (OUTLIER) cc_final: -0.0298 (tmm) REVERT: B 237 MET cc_start: 0.3438 (tpt) cc_final: 0.3080 (tpt) REVERT: B 334 MET cc_start: -0.3614 (OUTLIER) cc_final: -0.4302 (tpt) REVERT: B 614 MET cc_start: -0.2216 (mtt) cc_final: -0.3053 (mtt) REVERT: B 634 MET cc_start: -0.4060 (OUTLIER) cc_final: -0.5118 (tpt) REVERT: B 709 MET cc_start: -0.3340 (ptt) cc_final: -0.3621 (ptt) REVERT: E 612 TRP cc_start: -0.0869 (OUTLIER) cc_final: -0.1460 (m100) REVERT: E 703 MET cc_start: -0.0063 (tpt) cc_final: -0.0789 (tpt) REVERT: F 19 MET cc_start: -0.4718 (tpt) cc_final: -0.5031 (tpt) REVERT: F 26 MET cc_start: -0.3661 (ttm) cc_final: -0.4185 (mtt) REVERT: F 285 MET cc_start: -0.3973 (tpp) cc_final: -0.4318 (tpt) REVERT: G 147 ARG cc_start: 0.0195 (OUTLIER) cc_final: -0.0802 (ttt180) REVERT: G 148 PHE cc_start: 0.2222 (OUTLIER) cc_final: 0.1696 (m-10) REVERT: H 132 LYS cc_start: -0.4079 (OUTLIER) cc_final: -0.5979 (pttt) REVERT: H 161 LYS cc_start: 0.0872 (OUTLIER) cc_final: 0.0245 (mmtt) REVERT: I 19 MET cc_start: -0.4753 (tpp) cc_final: -0.5394 (ttm) REVERT: I 26 MET cc_start: -0.2427 (mmt) cc_final: -0.4285 (mtt) REVERT: J 192 LYS cc_start: 0.1902 (OUTLIER) cc_final: 0.0921 (ptmt) REVERT: J 197 MET cc_start: -0.4437 (mmm) cc_final: -0.4978 (mtt) REVERT: L 61 LYS cc_start: 0.4222 (OUTLIER) cc_final: 0.3998 (pttm) REVERT: L 83 MET cc_start: -0.1764 (mtp) cc_final: -0.2435 (mtt) REVERT: L 126 MET cc_start: 0.0001 (ttt) cc_final: -0.0868 (ttp) REVERT: P 219 MET cc_start: 0.1012 (OUTLIER) cc_final: 0.0673 (ttt) REVERT: P 221 CYS cc_start: -0.1541 (OUTLIER) cc_final: -0.1816 (m) REVERT: P 258 MET cc_start: 0.0288 (mtt) cc_final: -0.0240 (mmt) REVERT: R 107 MET cc_start: -0.0829 (tpt) cc_final: -0.1655 (pmm) REVERT: c 73 MET cc_start: -0.1746 (mmt) cc_final: -0.1997 (mmt) REVERT: d 857 SER cc_start: -0.2461 (m) cc_final: -0.2697 (m) REVERT: e 213 MET cc_start: 0.0158 (mmp) cc_final: -0.0279 (tpp) REVERT: e 442 MET cc_start: -0.1706 (ppp) cc_final: -0.2202 (ppp) REVERT: e 528 MET cc_start: -0.0141 (mmt) cc_final: -0.2371 (mmt) REVERT: e 612 TRP cc_start: -0.0316 (OUTLIER) cc_final: -0.0581 (m100) REVERT: e 696 TRP cc_start: -0.2100 (OUTLIER) cc_final: -0.2928 (m-10) REVERT: e 703 MET cc_start: 0.1070 (mpp) cc_final: -0.0645 (mmt) REVERT: f 19 MET cc_start: -0.3381 (mmt) cc_final: -0.5589 (mmt) REVERT: f 26 MET cc_start: -0.4040 (OUTLIER) cc_final: -0.5149 (ttt) REVERT: f 60 MET cc_start: -0.3350 (mmt) cc_final: -0.4552 (mpp) REVERT: f 283 MET cc_start: -0.2177 (mmt) cc_final: -0.2434 (mmt) REVERT: f 290 MET cc_start: -0.0859 (mtt) cc_final: -0.1720 (mmt) REVERT: i 12 MET cc_start: 0.2138 (tpt) cc_final: 0.1884 (tpt) REVERT: i 18 MET cc_start: -0.3298 (tmt) cc_final: -0.4112 (tmt) REVERT: i 19 MET cc_start: -0.2923 (tpt) cc_final: -0.4106 (tpt) REVERT: i 26 MET cc_start: -0.1300 (mmp) cc_final: -0.3285 (tpt) REVERT: i 39 MET cc_start: -0.3355 (tpt) cc_final: -0.3865 (mmt) REVERT: j 176 MET cc_start: -0.3241 (mtm) cc_final: -0.4211 (ptt) REVERT: l 83 MET cc_start: -0.3789 (ttt) cc_final: -0.4341 (ttt) REVERT: l 152 MET cc_start: -0.3366 (tpp) cc_final: -0.4928 (mtt) REVERT: o 19 LYS cc_start: 0.8082 (tptm) cc_final: 0.7638 (tptp) REVERT: o 266 MET cc_start: 0.1631 (ptp) cc_final: 0.0520 (ttp) REVERT: o 794 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6594 (tp30) REVERT: o 849 ASP cc_start: 0.7551 (m-30) cc_final: 0.7152 (m-30) REVERT: o 1071 GLU cc_start: 0.8329 (pt0) cc_final: 0.8116 (pt0) REVERT: o 1199 MET cc_start: 0.7265 (ppp) cc_final: 0.6625 (pmm) REVERT: o 1215 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5952 (tp30) REVERT: o 1249 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7047 (p0) REVERT: o 1292 MET cc_start: 0.7914 (mmp) cc_final: 0.7674 (mmt) REVERT: o 1303 GLN cc_start: 0.8740 (tp40) cc_final: 0.8349 (mp10) REVERT: o 1343 LEU cc_start: 0.9435 (mt) cc_final: 0.9140 (tt) REVERT: o 1345 ARG cc_start: 0.8971 (ptp-110) cc_final: 0.8723 (ptp90) REVERT: o 1395 TYR cc_start: 0.9016 (t80) cc_final: 0.8429 (t80) REVERT: o 1456 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: p 37 LYS cc_start: 0.2089 (OUTLIER) cc_final: 0.1267 (mmtp) REVERT: p 200 MET cc_start: 0.8460 (mmt) cc_final: 0.8045 (mmt) REVERT: p 230 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6596 (mmp80) REVERT: p 298 MET cc_start: 0.4752 (mmp) cc_final: 0.2801 (ttp) REVERT: p 478 THR cc_start: 0.2580 (OUTLIER) cc_final: 0.2300 (m) REVERT: p 513 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7122 (tm-30) REVERT: p 529 MET cc_start: 0.2387 (ppp) cc_final: 0.1740 (mmt) REVERT: p 550 MET cc_start: 0.1241 (OUTLIER) cc_final: 0.0692 (ppp) REVERT: p 597 ILE cc_start: 0.0500 (OUTLIER) cc_final: -0.0033 (mt) REVERT: p 728 MET cc_start: 0.2297 (ppp) cc_final: 0.0397 (ppp) REVERT: p 917 LYS cc_start: 0.4877 (OUTLIER) cc_final: 0.3812 (tmtt) REVERT: q 22 ILE cc_start: 0.6099 (mt) cc_final: 0.5630 (tt) REVERT: q 78 ILE cc_start: 0.2171 (tt) cc_final: 0.1822 (mt) REVERT: q 239 LEU cc_start: 0.4164 (mt) cc_final: 0.3907 (mt) REVERT: s 54 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8045 (mmp80) REVERT: s 127 LEU cc_start: 0.7372 (pt) cc_final: 0.7051 (pp) REVERT: s 208 LEU cc_start: 0.8248 (mt) cc_final: 0.7876 (tt) REVERT: u 68 TYR cc_start: 0.2447 (m-80) cc_final: 0.0258 (m-80) REVERT: u 104 MET cc_start: -0.1340 (ttp) cc_final: -0.2085 (tpp) REVERT: u 117 MET cc_start: -0.2471 (mtm) cc_final: -0.3726 (ttm) REVERT: w 43 ASP cc_start: 0.8317 (m-30) cc_final: 0.7770 (t0) REVERT: w 69 ILE cc_start: -0.1667 (OUTLIER) cc_final: -0.2604 (mp) REVERT: w 108 MET cc_start: 0.6297 (mmp) cc_final: 0.5867 (mmp) REVERT: w 110 LEU cc_start: 0.0870 (OUTLIER) cc_final: 0.0358 (mt) REVERT: x 59 LEU cc_start: 0.3130 (OUTLIER) cc_final: 0.2394 (mm) outliers start: 269 outliers final: 172 residues processed: 984 average time/residue: 0.9727 time to fit residues: 1692.6436 Evaluate side-chains 938 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 730 time to evaluate : 9.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 2 residue 58 MET Chi-restraints excluded: chain 2 residue 70 THR Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 175 MET Chi-restraints excluded: chain 3 residue 230 VAL Chi-restraints excluded: chain 3 residue 255 CYS Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 140 LYS Chi-restraints excluded: chain 4 residue 158 VAL Chi-restraints excluded: chain 4 residue 197 THR Chi-restraints excluded: chain 4 residue 251 VAL Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 4 residue 432 VAL Chi-restraints excluded: chain 6 residue 119 THR Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 272 VAL Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 330 ASN Chi-restraints excluded: chain 6 residue 405 VAL Chi-restraints excluded: chain 6 residue 438 MET Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 534 TYR Chi-restraints excluded: chain 6 residue 575 LEU Chi-restraints excluded: chain 6 residue 624 ILE Chi-restraints excluded: chain 6 residue 667 THR Chi-restraints excluded: chain 7 residue 5 VAL Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 323 ILE Chi-restraints excluded: chain 7 residue 427 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 493 MET Chi-restraints excluded: chain 7 residue 510 THR Chi-restraints excluded: chain 7 residue 709 THR Chi-restraints excluded: chain 7 residue 714 VAL Chi-restraints excluded: chain 8 residue 237 TRP Chi-restraints excluded: chain 8 residue 255 ILE Chi-restraints excluded: chain 9 residue 70 VAL Chi-restraints excluded: chain 9 residue 84 CYS Chi-restraints excluded: chain 9 residue 165 ARG Chi-restraints excluded: chain 9 residue 218 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain D residue 940 VAL Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain E residue 528 MET Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain E residue 612 TRP Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 221 CYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain Q residue 352 HIS Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain T residue 210 VAL Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 146 ASP Chi-restraints excluded: chain U residue 148 MET Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 192 VAL Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 938 SER Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 451 VAL Chi-restraints excluded: chain e residue 536 LEU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 200 LEU Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 458 PHE Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 542 LEU Chi-restraints excluded: chain o residue 593 SER Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 665 THR Chi-restraints excluded: chain o residue 850 THR Chi-restraints excluded: chain o residue 906 LEU Chi-restraints excluded: chain o residue 1004 LEU Chi-restraints excluded: chain o residue 1065 PHE Chi-restraints excluded: chain o residue 1139 LEU Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1163 HIS Chi-restraints excluded: chain o residue 1198 GLU Chi-restraints excluded: chain o residue 1215 GLU Chi-restraints excluded: chain o residue 1249 ASP Chi-restraints excluded: chain o residue 1315 ASP Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1435 THR Chi-restraints excluded: chain o residue 1456 GLU Chi-restraints excluded: chain o residue 1474 LEU Chi-restraints excluded: chain o residue 1480 CYS Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 37 LYS Chi-restraints excluded: chain p residue 131 THR Chi-restraints excluded: chain p residue 230 ARG Chi-restraints excluded: chain p residue 259 THR Chi-restraints excluded: chain p residue 331 THR Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 390 ASN Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 550 MET Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 639 HIS Chi-restraints excluded: chain p residue 643 LEU Chi-restraints excluded: chain p residue 646 ARG Chi-restraints excluded: chain p residue 667 THR Chi-restraints excluded: chain p residue 740 PHE Chi-restraints excluded: chain p residue 766 TYR Chi-restraints excluded: chain p residue 802 ASP Chi-restraints excluded: chain p residue 845 TYR Chi-restraints excluded: chain p residue 865 VAL Chi-restraints excluded: chain p residue 917 LYS Chi-restraints excluded: chain p residue 938 ARG Chi-restraints excluded: chain p residue 1006 VAL Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1150 ARG Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 173 HIS Chi-restraints excluded: chain q residue 195 THR Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 93 HIS Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 54 ARG Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 104 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 71 ASP Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain v residue 125 LEU Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain x residue 59 LEU Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 73 ILE Chi-restraints excluded: chain z residue 26 ASN Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 1206 optimal weight: 0.3980 chunk 1270 optimal weight: 0.9980 chunk 1159 optimal weight: 0.0030 chunk 1235 optimal weight: 0.0030 chunk 743 optimal weight: 5.9990 chunk 538 optimal weight: 7.9990 chunk 970 optimal weight: 5.9990 chunk 379 optimal weight: 20.0000 chunk 1116 optimal weight: 3.9990 chunk 1168 optimal weight: 0.6980 chunk 1231 optimal weight: 4.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN 1 228 HIS 1 355 GLN ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 108 ASN 3 185 GLN ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 379 GLN 6 97 GLN 6 539 ASN ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 555 GLN ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN ** Q 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 181 GLN ** d 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 735 GLN ** o 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1077 ASN ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1384 HIS p 42 GLN p 188 ASN ** p 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 570 ASN ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2101 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 115699 Z= 0.167 Angle : 0.630 16.005 157113 Z= 0.316 Chirality : 0.043 0.361 17587 Planarity : 0.004 0.140 19780 Dihedral : 11.560 122.953 16695 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.20 % Favored : 94.61 % Rotamer: Outliers : 1.93 % Allowed : 18.55 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.01 % 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: -0.61 (0.07), residues: 13701 helix: 0.93 (0.07), residues: 5756 sheet: -0.42 (0.13), residues: 1564 loop : -1.68 (0.07), residues: 6381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP p 573 HIS 0.040 0.001 HIS Q 352 PHE 0.030 0.001 PHE p1002 TYR 0.030 0.001 TYR p1048 ARG 0.014 0.000 ARG e 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 750 time to evaluate : 9.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 230 PHE cc_start: -0.3760 (t80) cc_final: -0.5536 (m-80) REVERT: 1 232 ARG cc_start: -0.3300 (mpt180) cc_final: -0.5793 (tpt170) REVERT: 1 362 ASP cc_start: -0.2989 (OUTLIER) cc_final: -0.3721 (m-30) REVERT: 1 408 ARG cc_start: 0.1121 (mmp-170) cc_final: 0.0893 (mmp-170) REVERT: 2 137 MET cc_start: -0.2032 (ptm) cc_final: -0.3201 (ptt) REVERT: 2 252 MET cc_start: -0.2168 (ttt) cc_final: -0.2941 (ttt) REVERT: 3 42 MET cc_start: -0.3833 (mtm) cc_final: -0.4952 (mmt) REVERT: 3 51 MET cc_start: -0.2990 (mtp) cc_final: -0.3828 (tpt) REVERT: 3 146 ARG cc_start: -0.1071 (OUTLIER) cc_final: -0.2233 (ptt-90) REVERT: 4 140 LYS cc_start: -0.2275 (OUTLIER) cc_final: -0.2585 (pptt) REVERT: 4 216 MET cc_start: 0.3133 (mmp) cc_final: 0.2104 (mmt) REVERT: 4 334 MET cc_start: -0.1402 (tmm) cc_final: -0.1602 (tmm) REVERT: 4 376 MET cc_start: -0.3672 (mtt) cc_final: -0.4965 (mtt) REVERT: 6 438 MET cc_start: -0.1517 (OUTLIER) cc_final: -0.2863 (mtt) REVERT: 6 450 MET cc_start: -0.0846 (mmm) cc_final: -0.1530 (mmp) REVERT: 6 536 MET cc_start: -0.1368 (ppp) cc_final: -0.1865 (ppp) REVERT: 6 696 MET cc_start: -0.4014 (ttt) cc_final: -0.4538 (tpp) REVERT: 7 40 LEU cc_start: -0.4999 (OUTLIER) cc_final: -0.5238 (mt) REVERT: 7 42 MET cc_start: -0.4216 (tpp) cc_final: -0.4926 (ttt) REVERT: 7 323 ILE cc_start: -0.6495 (OUTLIER) cc_final: -0.6699 (mt) REVERT: 7 438 MET cc_start: 0.1797 (mpp) cc_final: 0.0585 (mmm) REVERT: 7 483 MET cc_start: 0.5032 (mmm) cc_final: 0.4528 (mmm) REVERT: 7 657 MET cc_start: -0.3659 (mmp) cc_final: -0.4032 (mpp) REVERT: A 607 MET cc_start: -0.3616 (mtp) cc_final: -0.4219 (mtt) REVERT: A 649 MET cc_start: 0.4655 (ppp) cc_final: 0.4360 (ppp) REVERT: A 661 GLU cc_start: -0.1421 (OUTLIER) cc_final: -0.2655 (tp30) REVERT: A 696 MET cc_start: -0.2821 (ppp) cc_final: -0.4128 (ptt) REVERT: A 879 MET cc_start: 0.3041 (ppp) cc_final: 0.2472 (ppp) REVERT: B 170 MET cc_start: 0.0386 (OUTLIER) cc_final: -0.0012 (tmm) REVERT: B 237 MET cc_start: 0.3432 (tpt) cc_final: 0.3075 (tpt) REVERT: B 334 MET cc_start: -0.3551 (OUTLIER) cc_final: -0.4295 (tpt) REVERT: B 607 MET cc_start: 0.1367 (mpp) cc_final: 0.0917 (mpp) REVERT: B 614 MET cc_start: -0.2354 (mtt) cc_final: -0.3176 (mtt) REVERT: B 634 MET cc_start: -0.4078 (OUTLIER) cc_final: -0.5111 (tpt) REVERT: B 709 MET cc_start: -0.3408 (ptt) cc_final: -0.3663 (ptt) REVERT: E 612 TRP cc_start: -0.0917 (OUTLIER) cc_final: -0.1478 (m100) REVERT: E 703 MET cc_start: 0.0214 (tpt) cc_final: -0.0311 (tpt) REVERT: E 747 LEU cc_start: -0.2544 (OUTLIER) cc_final: -0.2803 (mt) REVERT: F 19 MET cc_start: -0.4700 (tpt) cc_final: -0.5007 (tpt) REVERT: F 26 MET cc_start: -0.3613 (ttm) cc_final: -0.4197 (mtt) REVERT: F 285 MET cc_start: -0.4046 (tpp) cc_final: -0.4421 (tpt) REVERT: G 147 ARG cc_start: 0.0168 (OUTLIER) cc_final: -0.0730 (ttt180) REVERT: G 148 PHE cc_start: 0.2041 (OUTLIER) cc_final: 0.1577 (m-10) REVERT: H 132 LYS cc_start: -0.4017 (OUTLIER) cc_final: -0.5956 (pttt) REVERT: H 161 LYS cc_start: 0.0729 (OUTLIER) cc_final: 0.0145 (mmtt) REVERT: H 194 MET cc_start: 0.1351 (pmm) cc_final: 0.0099 (ppp) REVERT: I 19 MET cc_start: -0.4737 (tpp) cc_final: -0.5461 (ttm) REVERT: I 26 MET cc_start: -0.2559 (mmt) cc_final: -0.4407 (mtt) REVERT: J 192 LYS cc_start: 0.1798 (OUTLIER) cc_final: 0.0868 (ptmt) REVERT: J 197 MET cc_start: -0.4540 (mmm) cc_final: -0.5044 (mtt) REVERT: L 61 LYS cc_start: 0.4555 (OUTLIER) cc_final: 0.4331 (pttm) REVERT: L 126 MET cc_start: -0.0205 (ttt) cc_final: -0.1133 (ttp) REVERT: O 35 GLN cc_start: 0.5789 (mm110) cc_final: 0.5254 (pp30) REVERT: P 219 MET cc_start: 0.0874 (OUTLIER) cc_final: 0.0608 (ttt) REVERT: P 221 CYS cc_start: -0.1636 (OUTLIER) cc_final: -0.1854 (m) REVERT: P 258 MET cc_start: 0.0303 (mtt) cc_final: -0.0236 (mmt) REVERT: U 110 MET cc_start: 0.3616 (mmm) cc_final: 0.3094 (mmm) REVERT: c 73 MET cc_start: -0.1756 (mmt) cc_final: -0.1991 (mmt) REVERT: d 857 SER cc_start: -0.2521 (m) cc_final: -0.2740 (m) REVERT: e 213 MET cc_start: 0.0189 (mmp) cc_final: -0.0197 (tpp) REVERT: e 247 MET cc_start: -0.2954 (ptp) cc_final: -0.3783 (ptt) REVERT: e 442 MET cc_start: -0.1687 (ppp) cc_final: -0.2184 (ppp) REVERT: e 528 MET cc_start: -0.0294 (mmt) cc_final: -0.2533 (mmt) REVERT: e 696 TRP cc_start: -0.2206 (OUTLIER) cc_final: -0.3000 (m-10) REVERT: e 703 MET cc_start: 0.1046 (mpp) cc_final: -0.0638 (mmt) REVERT: f 19 MET cc_start: -0.3375 (mmt) cc_final: -0.5620 (mmt) REVERT: f 26 MET cc_start: -0.3935 (OUTLIER) cc_final: -0.4925 (ttt) REVERT: f 60 MET cc_start: -0.3444 (mmt) cc_final: -0.4727 (mpp) REVERT: f 283 MET cc_start: -0.2256 (mmt) cc_final: -0.2531 (mmt) REVERT: f 285 MET cc_start: -0.5801 (ttt) cc_final: -0.6023 (ttt) REVERT: f 290 MET cc_start: -0.1176 (mtt) cc_final: -0.1936 (mmt) REVERT: i 12 MET cc_start: 0.2128 (tpt) cc_final: 0.1788 (tpt) REVERT: i 18 MET cc_start: -0.3294 (tmt) cc_final: -0.4112 (tmt) REVERT: i 19 MET cc_start: -0.2940 (tpt) cc_final: -0.4095 (tpt) REVERT: i 26 MET cc_start: -0.1241 (mmp) cc_final: -0.3174 (tpt) REVERT: i 39 MET cc_start: -0.3333 (tpt) cc_final: -0.3976 (mmt) REVERT: j 176 MET cc_start: -0.3092 (mtm) cc_final: -0.4126 (ptt) REVERT: l 83 MET cc_start: -0.3672 (ttt) cc_final: -0.4263 (ttt) REVERT: l 152 MET cc_start: -0.3214 (tpp) cc_final: -0.4887 (mtt) REVERT: o 19 LYS cc_start: 0.8061 (tptm) cc_final: 0.7742 (tptp) REVERT: o 266 MET cc_start: 0.1539 (ptp) cc_final: 0.0260 (ttt) REVERT: o 461 GLN cc_start: 0.6867 (tp40) cc_final: 0.6442 (tp40) REVERT: o 561 MET cc_start: 0.8350 (mtt) cc_final: 0.8013 (mtp) REVERT: o 794 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6600 (tp30) REVERT: o 849 ASP cc_start: 0.7550 (m-30) cc_final: 0.7178 (m-30) REVERT: o 1093 GLN cc_start: 0.8622 (pt0) cc_final: 0.8339 (pt0) REVERT: o 1199 MET cc_start: 0.7426 (ppp) cc_final: 0.6771 (pmm) REVERT: o 1215 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5876 (tp30) REVERT: o 1249 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6960 (p0) REVERT: o 1259 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8219 (tp) REVERT: o 1292 MET cc_start: 0.7906 (mmp) cc_final: 0.7633 (mmt) REVERT: o 1303 GLN cc_start: 0.8688 (tp40) cc_final: 0.8339 (mp10) REVERT: o 1343 LEU cc_start: 0.9421 (mt) cc_final: 0.9198 (tt) REVERT: o 1345 ARG cc_start: 0.8984 (ptp-110) cc_final: 0.8633 (ptm-80) REVERT: o 1456 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: p 37 LYS cc_start: 0.1714 (OUTLIER) cc_final: 0.1259 (mmtp) REVERT: p 200 MET cc_start: 0.8455 (mmt) cc_final: 0.8124 (mmt) REVERT: p 230 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6753 (mmp80) REVERT: p 298 MET cc_start: 0.4748 (mmp) cc_final: 0.2835 (ttp) REVERT: p 478 THR cc_start: 0.2778 (OUTLIER) cc_final: 0.2493 (m) REVERT: p 508 MET cc_start: 0.6475 (tpp) cc_final: 0.6213 (tpp) REVERT: p 513 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7017 (tm-30) REVERT: p 529 MET cc_start: 0.2027 (ppp) cc_final: 0.1595 (mmt) REVERT: p 550 MET cc_start: 0.1581 (OUTLIER) cc_final: 0.1227 (ppp) REVERT: p 597 ILE cc_start: 0.0316 (OUTLIER) cc_final: -0.0001 (mt) REVERT: p 677 MET cc_start: 0.1719 (mpp) cc_final: 0.1515 (mmt) REVERT: p 728 MET cc_start: 0.1914 (ppp) cc_final: -0.0603 (ttp) REVERT: p 917 LYS cc_start: 0.4661 (OUTLIER) cc_final: 0.3972 (tmtt) REVERT: p 1020 TYR cc_start: 0.4228 (OUTLIER) cc_final: 0.3078 (t80) REVERT: q 22 ILE cc_start: 0.6149 (mt) cc_final: 0.5638 (tt) REVERT: q 78 ILE cc_start: 0.2174 (OUTLIER) cc_final: 0.1793 (mt) REVERT: s 127 LEU cc_start: 0.7446 (pt) cc_final: 0.7143 (pp) REVERT: s 208 LEU cc_start: 0.8135 (mt) cc_final: 0.7788 (tt) REVERT: u 59 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5334 (mt) REVERT: u 117 MET cc_start: -0.2184 (mtm) cc_final: -0.3742 (ttm) REVERT: w 43 ASP cc_start: 0.8213 (m-30) cc_final: 0.7671 (t0) REVERT: w 69 ILE cc_start: -0.1250 (OUTLIER) cc_final: -0.1822 (mp) REVERT: w 110 LEU cc_start: 0.0865 (OUTLIER) cc_final: 0.0269 (mt) REVERT: x 56 ILE cc_start: -0.0715 (tp) cc_final: -0.0966 (tp) REVERT: x 59 LEU cc_start: 0.3057 (OUTLIER) cc_final: 0.2286 (mm) REVERT: x 60 LEU cc_start: 0.3742 (mt) cc_final: 0.3438 (mt) outliers start: 231 outliers final: 156 residues processed: 929 average time/residue: 0.9553 time to fit residues: 1567.3128 Evaluate side-chains 925 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 731 time to evaluate : 9.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 1 residue 355 GLN Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 2 residue 58 MET Chi-restraints excluded: chain 2 residue 70 THR Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 175 MET Chi-restraints excluded: chain 3 residue 230 VAL Chi-restraints excluded: chain 3 residue 255 CYS Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 140 LYS Chi-restraints excluded: chain 4 residue 158 VAL Chi-restraints excluded: chain 4 residue 197 THR Chi-restraints excluded: chain 4 residue 251 VAL Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 4 residue 432 VAL Chi-restraints excluded: chain 6 residue 119 THR Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 272 VAL Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 438 MET Chi-restraints excluded: chain 6 residue 530 ARG Chi-restraints excluded: chain 6 residue 534 TYR Chi-restraints excluded: chain 6 residue 575 LEU Chi-restraints excluded: chain 6 residue 667 THR Chi-restraints excluded: chain 7 residue 5 VAL Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 323 ILE Chi-restraints excluded: chain 7 residue 427 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 493 MET Chi-restraints excluded: chain 7 residue 510 THR Chi-restraints excluded: chain 7 residue 709 THR Chi-restraints excluded: chain 7 residue 714 VAL Chi-restraints excluded: chain 8 residue 237 TRP Chi-restraints excluded: chain 9 residue 70 VAL Chi-restraints excluded: chain 9 residue 84 CYS Chi-restraints excluded: chain 9 residue 165 ARG Chi-restraints excluded: chain 9 residue 218 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain D residue 940 VAL Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain E residue 528 MET Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain E residue 612 TRP Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 221 CYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain T residue 210 VAL Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 146 ASP Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 192 VAL Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 451 VAL Chi-restraints excluded: chain e residue 536 LEU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 672 ILE Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 200 LEU Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 458 PHE Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 593 SER Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 665 THR Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 850 THR Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 906 LEU Chi-restraints excluded: chain o residue 1004 LEU Chi-restraints excluded: chain o residue 1065 PHE Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1163 HIS Chi-restraints excluded: chain o residue 1198 GLU Chi-restraints excluded: chain o residue 1215 GLU Chi-restraints excluded: chain o residue 1248 ASN Chi-restraints excluded: chain o residue 1249 ASP Chi-restraints excluded: chain o residue 1259 ILE Chi-restraints excluded: chain o residue 1315 ASP Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1435 THR Chi-restraints excluded: chain o residue 1456 GLU Chi-restraints excluded: chain o residue 1474 LEU Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 37 LYS Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 215 TYR Chi-restraints excluded: chain p residue 230 ARG Chi-restraints excluded: chain p residue 259 THR Chi-restraints excluded: chain p residue 331 THR Chi-restraints excluded: chain p residue 347 MET Chi-restraints excluded: chain p residue 393 LEU Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 550 MET Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 639 HIS Chi-restraints excluded: chain p residue 643 LEU Chi-restraints excluded: chain p residue 646 ARG Chi-restraints excluded: chain p residue 667 THR Chi-restraints excluded: chain p residue 740 PHE Chi-restraints excluded: chain p residue 796 MET Chi-restraints excluded: chain p residue 845 TYR Chi-restraints excluded: chain p residue 865 VAL Chi-restraints excluded: chain p residue 917 LYS Chi-restraints excluded: chain p residue 938 ARG Chi-restraints excluded: chain p residue 1020 TYR Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1150 ARG Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 173 HIS Chi-restraints excluded: chain q residue 195 THR Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 93 HIS Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 104 ILE Chi-restraints excluded: chain u residue 59 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 71 ASP Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain x residue 1 MET Chi-restraints excluded: chain x residue 59 LEU Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain z residue 26 ASN Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 811 optimal weight: 5.9990 chunk 1306 optimal weight: 0.7980 chunk 797 optimal weight: 0.9990 chunk 619 optimal weight: 50.0000 chunk 908 optimal weight: 40.0000 chunk 1370 optimal weight: 0.9990 chunk 1261 optimal weight: 0.6980 chunk 1091 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 843 optimal weight: 30.0000 chunk 669 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 355 GLN ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 700 HIS ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1077 ASN ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 452 ASN ** p 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 951 GLN ** q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 177 ASN ** r 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2142 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 115699 Z= 0.183 Angle : 0.637 15.834 157113 Z= 0.319 Chirality : 0.043 0.385 17587 Planarity : 0.004 0.122 19780 Dihedral : 11.525 122.225 16695 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.33 % Favored : 94.48 % Rotamer: Outliers : 1.81 % Allowed : 18.81 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.07), residues: 13701 helix: 0.98 (0.07), residues: 5774 sheet: -0.41 (0.13), residues: 1572 loop : -1.67 (0.08), residues: 6355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP e 612 HIS 0.016 0.001 HIS p 98 PHE 0.035 0.001 PHE p1002 TYR 0.044 0.001 TYR p1047 ARG 0.018 0.000 ARG R 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27402 Ramachandran restraints generated. 13701 Oldfield, 0 Emsley, 13701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 752 time to evaluate : 9.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 3 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1 230 PHE cc_start: -0.3856 (t80) cc_final: -0.5550 (m-80) REVERT: 1 232 ARG cc_start: -0.2884 (mpt180) cc_final: -0.5603 (tpt170) REVERT: 1 362 ASP cc_start: -0.2796 (OUTLIER) cc_final: -0.3606 (m-30) REVERT: 2 137 MET cc_start: -0.1914 (ptm) cc_final: -0.2990 (ptt) REVERT: 2 252 MET cc_start: -0.2255 (ttt) cc_final: -0.3036 (ttt) REVERT: 3 42 MET cc_start: -0.3758 (mtm) cc_final: -0.4914 (mmt) REVERT: 3 51 MET cc_start: -0.2949 (mtp) cc_final: -0.3838 (tpt) REVERT: 3 146 ARG cc_start: -0.0927 (OUTLIER) cc_final: -0.2185 (ptt-90) REVERT: 4 140 LYS cc_start: -0.2349 (OUTLIER) cc_final: -0.2647 (pptt) REVERT: 4 216 MET cc_start: 0.3105 (mmp) cc_final: 0.2099 (mmt) REVERT: 4 376 MET cc_start: -0.3843 (mtt) cc_final: -0.4823 (mtt) REVERT: 6 438 MET cc_start: -0.1506 (OUTLIER) cc_final: -0.2789 (mtt) REVERT: 6 450 MET cc_start: -0.0910 (mmm) cc_final: -0.1699 (mmp) REVERT: 6 536 MET cc_start: -0.1591 (ppp) cc_final: -0.2005 (ppp) REVERT: 6 696 MET cc_start: -0.3942 (ttt) cc_final: -0.4557 (tpp) REVERT: 7 40 LEU cc_start: -0.4417 (OUTLIER) cc_final: -0.4710 (mt) REVERT: 7 42 MET cc_start: -0.4184 (tpp) cc_final: -0.5129 (ttt) REVERT: 7 438 MET cc_start: 0.2021 (mpp) cc_final: 0.0789 (mmm) REVERT: 7 483 MET cc_start: 0.4891 (mmm) cc_final: 0.4681 (mmm) REVERT: 7 657 MET cc_start: -0.3785 (mmp) cc_final: -0.4154 (mpp) REVERT: A 352 MET cc_start: -0.0490 (ptp) cc_final: -0.2102 (ppp) REVERT: A 491 MET cc_start: 0.0284 (mmm) cc_final: -0.0645 (tpt) REVERT: A 607 MET cc_start: -0.3784 (mtp) cc_final: -0.4297 (mtt) REVERT: A 649 MET cc_start: 0.4476 (ppp) cc_final: 0.4210 (ppp) REVERT: A 661 GLU cc_start: -0.1224 (OUTLIER) cc_final: -0.2548 (tp30) REVERT: A 665 MET cc_start: -0.4086 (mtp) cc_final: -0.5063 (ttm) REVERT: A 696 MET cc_start: -0.2824 (ppp) cc_final: -0.4030 (ptt) REVERT: A 879 MET cc_start: 0.3417 (ppp) cc_final: 0.2903 (ppp) REVERT: B 237 MET cc_start: 0.3432 (tpt) cc_final: 0.3065 (tpt) REVERT: B 334 MET cc_start: -0.3515 (OUTLIER) cc_final: -0.4234 (tpt) REVERT: B 607 MET cc_start: 0.0995 (mpp) cc_final: 0.0522 (mpp) REVERT: B 614 MET cc_start: -0.2337 (mtt) cc_final: -0.3148 (mtt) REVERT: B 634 MET cc_start: -0.3996 (OUTLIER) cc_final: -0.5043 (tpt) REVERT: B 709 MET cc_start: -0.3331 (ptt) cc_final: -0.3633 (ptt) REVERT: E 612 TRP cc_start: -0.1172 (OUTLIER) cc_final: -0.1687 (m100) REVERT: E 703 MET cc_start: 0.0052 (tpt) cc_final: -0.0398 (tpt) REVERT: E 747 LEU cc_start: -0.2793 (OUTLIER) cc_final: -0.3029 (mt) REVERT: F 19 MET cc_start: -0.4682 (tpt) cc_final: -0.5002 (tpt) REVERT: F 26 MET cc_start: -0.3650 (ttm) cc_final: -0.4221 (mtt) REVERT: F 285 MET cc_start: -0.4103 (tpp) cc_final: -0.4489 (tpt) REVERT: G 147 ARG cc_start: 0.0146 (OUTLIER) cc_final: -0.0748 (ttt180) REVERT: G 148 PHE cc_start: 0.2093 (OUTLIER) cc_final: 0.1582 (m-10) REVERT: H 132 LYS cc_start: -0.3672 (OUTLIER) cc_final: -0.5705 (pttt) REVERT: H 161 LYS cc_start: 0.0699 (OUTLIER) cc_final: 0.0045 (mmtt) REVERT: H 194 MET cc_start: 0.1290 (pmm) cc_final: -0.0002 (ppp) REVERT: I 19 MET cc_start: -0.4831 (tpp) cc_final: -0.5534 (ttm) REVERT: I 26 MET cc_start: -0.2606 (mmt) cc_final: -0.4408 (mtt) REVERT: J 192 LYS cc_start: 0.2109 (OUTLIER) cc_final: 0.1050 (ptmt) REVERT: J 197 MET cc_start: -0.4480 (mmm) cc_final: -0.5005 (mtt) REVERT: L 83 MET cc_start: -0.1790 (mtp) cc_final: -0.2444 (mtt) REVERT: L 126 MET cc_start: -0.0262 (ttt) cc_final: -0.1151 (ttp) REVERT: O 35 GLN cc_start: 0.5739 (mm110) cc_final: 0.5265 (pp30) REVERT: P 219 MET cc_start: 0.0933 (OUTLIER) cc_final: 0.0716 (ttt) REVERT: P 221 CYS cc_start: -0.1600 (OUTLIER) cc_final: -0.1803 (m) REVERT: P 258 MET cc_start: 0.0166 (mtt) cc_final: -0.0284 (mmt) REVERT: Q 47 GLU cc_start: 0.5787 (tp30) cc_final: 0.5569 (tp30) REVERT: R 107 MET cc_start: -0.0658 (tpt) cc_final: -0.1107 (pmm) REVERT: U 110 MET cc_start: 0.3577 (mmm) cc_final: 0.3036 (mmm) REVERT: c 73 MET cc_start: -0.1834 (mmt) cc_final: -0.2060 (mmt) REVERT: d 857 SER cc_start: -0.2491 (m) cc_final: -0.2712 (m) REVERT: e 213 MET cc_start: -0.0114 (mmp) cc_final: -0.0437 (tpp) REVERT: e 442 MET cc_start: -0.1681 (ppp) cc_final: -0.2195 (ppp) REVERT: e 528 MET cc_start: -0.0434 (mmt) cc_final: -0.2403 (mmt) REVERT: e 696 TRP cc_start: -0.2441 (OUTLIER) cc_final: -0.3144 (m-10) REVERT: e 703 MET cc_start: 0.1036 (mpp) cc_final: -0.0697 (mmt) REVERT: f 19 MET cc_start: -0.3405 (mmt) cc_final: -0.5674 (mmt) REVERT: f 26 MET cc_start: -0.3562 (OUTLIER) cc_final: -0.4402 (ttt) REVERT: f 60 MET cc_start: -0.3423 (mmt) cc_final: -0.4688 (mpp) REVERT: f 283 MET cc_start: -0.2234 (mmt) cc_final: -0.2506 (mmt) REVERT: f 290 MET cc_start: -0.1229 (mtt) cc_final: -0.2115 (mmt) REVERT: i 12 MET cc_start: 0.2017 (tpt) cc_final: 0.1679 (tpt) REVERT: i 18 MET cc_start: -0.3185 (tmt) cc_final: -0.4095 (tmt) REVERT: i 19 MET cc_start: -0.2860 (tpt) cc_final: -0.4022 (tpt) REVERT: i 26 MET cc_start: -0.1313 (mmp) cc_final: -0.3134 (tpt) REVERT: i 39 MET cc_start: -0.3392 (tpt) cc_final: -0.4020 (mmt) REVERT: j 176 MET cc_start: -0.3128 (mtm) cc_final: -0.4174 (ptt) REVERT: l 83 MET cc_start: -0.3704 (ttt) cc_final: -0.4300 (ttt) REVERT: l 152 MET cc_start: -0.3307 (tpp) cc_final: -0.4701 (mtt) REVERT: o 19 LYS cc_start: 0.8107 (tptm) cc_final: 0.7652 (tptp) REVERT: o 238 MET cc_start: 0.1092 (ptm) cc_final: 0.0007 (ptm) REVERT: o 266 MET cc_start: 0.1407 (ptp) cc_final: 0.0029 (ttt) REVERT: o 461 GLN cc_start: 0.6908 (tp40) cc_final: 0.6542 (tp40) REVERT: o 561 MET cc_start: 0.8424 (mtt) cc_final: 0.8064 (mtp) REVERT: o 794 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6565 (tp30) REVERT: o 849 ASP cc_start: 0.7558 (m-30) cc_final: 0.7152 (m-30) REVERT: o 1093 GLN cc_start: 0.8607 (pt0) cc_final: 0.8357 (pt0) REVERT: o 1160 ARG cc_start: 0.7225 (ttp-170) cc_final: 0.6819 (mtp180) REVERT: o 1199 MET cc_start: 0.7438 (ppp) cc_final: 0.6767 (pmm) REVERT: o 1215 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6044 (tp30) REVERT: o 1249 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6906 (p0) REVERT: o 1292 MET cc_start: 0.7968 (mmp) cc_final: 0.7739 (mmt) REVERT: o 1303 GLN cc_start: 0.8686 (tp40) cc_final: 0.8392 (mp10) REVERT: o 1343 LEU cc_start: 0.9441 (mt) cc_final: 0.9205 (tt) REVERT: o 1456 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: o 1459 MET cc_start: 0.8139 (mtp) cc_final: 0.7780 (mtt) REVERT: p 116 ARG cc_start: 0.6090 (mtp180) cc_final: 0.5427 (ptt180) REVERT: p 200 MET cc_start: 0.8500 (mmt) cc_final: 0.8233 (mmt) REVERT: p 230 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6861 (mmp80) REVERT: p 274 ARG cc_start: 0.6770 (mtt180) cc_final: 0.6477 (tpp80) REVERT: p 298 MET cc_start: 0.4771 (mmp) cc_final: 0.2979 (ttp) REVERT: p 478 THR cc_start: 0.3004 (OUTLIER) cc_final: 0.2790 (m) REVERT: p 529 MET cc_start: 0.2401 (ppp) cc_final: 0.1890 (mmt) REVERT: p 597 ILE cc_start: 0.0610 (OUTLIER) cc_final: 0.0150 (mt) REVERT: p 917 LYS cc_start: 0.4639 (OUTLIER) cc_final: 0.3819 (tmtt) REVERT: p 1020 TYR cc_start: 0.4343 (OUTLIER) cc_final: 0.3117 (t80) REVERT: s 127 LEU cc_start: 0.7406 (pt) cc_final: 0.6914 (pp) REVERT: s 208 LEU cc_start: 0.8187 (mt) cc_final: 0.7813 (tt) REVERT: u 59 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.5613 (mt) REVERT: u 117 MET cc_start: -0.2246 (mtm) cc_final: -0.3798 (ttm) REVERT: w 43 ASP cc_start: 0.8228 (m-30) cc_final: 0.7689 (t0) REVERT: w 69 ILE cc_start: -0.1281 (OUTLIER) cc_final: -0.1887 (mp) REVERT: x 56 ILE cc_start: -0.0701 (tp) cc_final: -0.0912 (tp) REVERT: x 59 LEU cc_start: 0.2904 (OUTLIER) cc_final: 0.2040 (mm) REVERT: x 60 LEU cc_start: 0.3690 (mt) cc_final: 0.3394 (mt) REVERT: y 73 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.7937 (tt) outliers start: 216 outliers final: 163 residues processed: 921 average time/residue: 0.9196 time to fit residues: 1492.3989 Evaluate side-chains 920 residues out of total 12326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 726 time to evaluate : 9.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 152 GLU Chi-restraints excluded: chain 1 residue 355 GLN Chi-restraints excluded: chain 1 residue 362 ASP Chi-restraints excluded: chain 1 residue 372 ILE Chi-restraints excluded: chain 2 residue 58 MET Chi-restraints excluded: chain 2 residue 70 THR Chi-restraints excluded: chain 2 residue 185 LEU Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 175 MET Chi-restraints excluded: chain 3 residue 230 VAL Chi-restraints excluded: chain 3 residue 255 CYS Chi-restraints excluded: chain 4 residue 23 LEU Chi-restraints excluded: chain 4 residue 140 LYS Chi-restraints excluded: chain 4 residue 197 THR Chi-restraints excluded: chain 4 residue 251 VAL Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 400 ARG Chi-restraints excluded: chain 4 residue 432 VAL Chi-restraints excluded: chain 6 residue 119 THR Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 272 VAL Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 405 VAL Chi-restraints excluded: chain 6 residue 438 MET Chi-restraints excluded: chain 6 residue 458 VAL Chi-restraints excluded: chain 6 residue 534 TYR Chi-restraints excluded: chain 6 residue 575 LEU Chi-restraints excluded: chain 6 residue 667 THR Chi-restraints excluded: chain 7 residue 5 VAL Chi-restraints excluded: chain 7 residue 29 LYS Chi-restraints excluded: chain 7 residue 40 LEU Chi-restraints excluded: chain 7 residue 427 THR Chi-restraints excluded: chain 7 residue 460 THR Chi-restraints excluded: chain 7 residue 493 MET Chi-restraints excluded: chain 7 residue 510 THR Chi-restraints excluded: chain 7 residue 709 THR Chi-restraints excluded: chain 7 residue 714 VAL Chi-restraints excluded: chain 8 residue 237 TRP Chi-restraints excluded: chain 8 residue 255 ILE Chi-restraints excluded: chain 9 residue 70 VAL Chi-restraints excluded: chain 9 residue 165 ARG Chi-restraints excluded: chain 9 residue 218 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain D residue 940 VAL Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain E residue 528 MET Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain E residue 612 TRP Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 221 CYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain T residue 210 VAL Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 146 ASP Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 159 ASP Chi-restraints excluded: chain V residue 192 VAL Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 451 VAL Chi-restraints excluded: chain e residue 536 LEU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 672 ILE Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 297 LEU Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 200 LEU Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain o residue 101 VAL Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 422 ASP Chi-restraints excluded: chain o residue 458 PHE Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 521 VAL Chi-restraints excluded: chain o residue 593 SER Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 665 THR Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 850 THR Chi-restraints excluded: chain o residue 883 ILE Chi-restraints excluded: chain o residue 906 LEU Chi-restraints excluded: chain o residue 1016 LEU Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1163 HIS Chi-restraints excluded: chain o residue 1198 GLU Chi-restraints excluded: chain o residue 1215 GLU Chi-restraints excluded: chain o residue 1248 ASN Chi-restraints excluded: chain o residue 1249 ASP Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1456 GLU Chi-restraints excluded: chain o residue 1474 LEU Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 131 THR Chi-restraints excluded: chain p residue 230 ARG Chi-restraints excluded: chain p residue 331 THR Chi-restraints excluded: chain p residue 393 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 452 ASN Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 639 HIS Chi-restraints excluded: chain p residue 643 LEU Chi-restraints excluded: chain p residue 667 THR Chi-restraints excluded: chain p residue 740 PHE Chi-restraints excluded: chain p residue 796 MET Chi-restraints excluded: chain p residue 845 TYR Chi-restraints excluded: chain p residue 865 VAL Chi-restraints excluded: chain p residue 917 LYS Chi-restraints excluded: chain p residue 1020 TYR Chi-restraints excluded: chain p residue 1048 TYR Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain p residue 1150 ARG Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 159 LEU Chi-restraints excluded: chain q residue 173 HIS Chi-restraints excluded: chain q residue 177 ASN Chi-restraints excluded: chain q residue 195 THR Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain r residue 15 GLU Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 104 ILE Chi-restraints excluded: chain u residue 59 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 71 ASP Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 110 LEU Chi-restraints excluded: chain w residue 111 TYR Chi-restraints excluded: chain x residue 1 MET Chi-restraints excluded: chain x residue 59 LEU Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 73 ILE Chi-restraints excluded: chain z residue 26 ASN Chi-restraints excluded: chain z residue 34 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1376 random chunks: chunk 867 optimal weight: 0.9990 chunk 1162 optimal weight: 0.2980 chunk 334 optimal weight: 0.7980 chunk 1006 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 303 optimal weight: 7.9990 chunk 1093 optimal weight: 0.9980 chunk 457 optimal weight: 30.0000 chunk 1122 optimal weight: 2.9990 chunk 138 optimal weight: 40.0000 chunk 201 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 239 GLN ** 4 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 ASN ** R 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 HIS ** f 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 188 ASN ** p 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 503 ASN ** p 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 650 ASN ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 948 GLN ** q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5177 r_free = 0.5177 target = 0.233507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.228898 restraints weight = 371983.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.229341 restraints weight = 537516.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.229356 restraints weight = 372505.773| |-----------------------------------------------------------------------------| r_work (final): 0.5125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2935 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 115699 Z= 0.210 Angle : 0.657 17.873 157113 Z= 0.331 Chirality : 0.044 0.432 17587 Planarity : 0.004 0.084 19780 Dihedral : 11.520 121.585 16691 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.59 % Favored : 94.22 % Rotamer: Outliers : 1.86 % Allowed : 18.82 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.01 % 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 (0.07), residues: 13701 helix: 1.04 (0.07), residues: 5790 sheet: -0.41 (0.13), residues: 1600 loop : -1.66 (0.08), residues: 6311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP e 612 HIS 0.018 0.001 HIS p 98 PHE 0.037 0.001 PHE p1002 TYR 0.053 0.001 TYR p1047 ARG 0.018 0.000 ARG p 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27508.44 seconds wall clock time: 481 minutes 34.65 seconds (28894.65 seconds total)