Starting phenix.real_space_refine on Thu Mar 21 04:02:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msh_9220/03_2024/6msh_9220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msh_9220/03_2024/6msh_9220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msh_9220/03_2024/6msh_9220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msh_9220/03_2024/6msh_9220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msh_9220/03_2024/6msh_9220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msh_9220/03_2024/6msh_9220_updated.pdb" } resolution = 3.6 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= 0.001 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 11 5.49 5 S 601 5.16 5 C 65498 2.51 5 N 17836 2.21 5 O 19782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 140": "NH1" <-> "NH2" Residue "U ARG 159": "NH1" <-> "NH2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "U ARG 616": "NH1" <-> "NH2" Residue "V ARG 236": "NH1" <-> "NH2" Residue "V ARG 306": "NH1" <-> "NH2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 355": "NH1" <-> "NH2" Residue "V ARG 397": "NH1" <-> "NH2" Residue "W ARG 8": "NH1" <-> "NH2" Residue "W ARG 12": "NH1" <-> "NH2" Residue "W ARG 55": "NH1" <-> "NH2" Residue "W ARG 182": "NH1" <-> "NH2" Residue "W GLU 237": "OE1" <-> "OE2" Residue "W ARG 329": "NH1" <-> "NH2" Residue "W ARG 357": "NH1" <-> "NH2" Residue "W ARG 364": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 137": "NH1" <-> "NH2" Residue "Y ARG 176": "NH1" <-> "NH2" Residue "Y ARG 177": "NH1" <-> "NH2" Residue "Y ARG 267": "NH1" <-> "NH2" Residue "Y ARG 297": "NH1" <-> "NH2" Residue "Y ARG 300": "NH1" <-> "NH2" Residue "Y ARG 312": "NH1" <-> "NH2" Residue "Y ARG 342": "NH1" <-> "NH2" Residue "Y ARG 358": "NH1" <-> "NH2" Residue "Y ARG 379": "NH1" <-> "NH2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z ARG 209": "NH1" <-> "NH2" Residue "Z ARG 267": "NH1" <-> "NH2" Residue "a ARG 196": "NH1" <-> "NH2" Residue "a ARG 226": "NH1" <-> "NH2" Residue "a ARG 270": "NH1" <-> "NH2" Residue "a ARG 284": "NH1" <-> "NH2" Residue "a ARG 289": "NH1" <-> "NH2" Residue "b ARG 70": "NH1" <-> "NH2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 104": "NH1" <-> "NH2" Residue "c TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 175": "NH1" <-> "NH2" Residue "d PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 52": "NH1" <-> "NH2" Residue "d ARG 65": "NH1" <-> "NH2" Residue "d ARG 111": "NH1" <-> "NH2" Residue "f ARG 456": "NH1" <-> "NH2" Residue "f ARG 687": "NH1" <-> "NH2" Residue "f ARG 740": "NH1" <-> "NH2" Residue "f ARG 807": "NH1" <-> "NH2" Residue "f ARG 828": "NH1" <-> "NH2" Residue "f ARG 879": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "F ARG 269": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 344": "NH1" <-> "NH2" Residue "F ARG 347": "NH1" <-> "NH2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L ARG 239": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "P PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "h ARG 4": "NH1" <-> "NH2" Residue "i ARG 249": "NH1" <-> "NH2" Residue "j PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 157": "NH1" <-> "NH2" Residue "l ARG 239": "NH1" <-> "NH2" Residue "m ARG 19": "NH1" <-> "NH2" Residue "m ARG 187": "NH1" <-> "NH2" Residue "m ARG 232": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "p PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 103729 Number of models: 1 Model: "" Number of chains: 52 Chain: "U" Number of atoms: 6398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6398 Classifications: {'peptide': 820} Link IDs: {'CIS': 2, 'PTRANS': 30, 'TRANS': 787} Chain breaks: 2 Chain: "V" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3852 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 22, 'TRANS': 457} Chain: "W" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3703 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 445} Chain: "X" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3009 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 368} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 275} Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "e" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain breaks: 1 Chain: "f" Number of atoms: 6840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 6840 Classifications: {'peptide': 886} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 848} Chain: "A" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2767 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2706 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3105 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 379} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3040 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 361} Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3097 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 19, 'TRANS': 369} Chain: "F" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "v" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1826 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "K" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} 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: "Q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1826 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "h" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "i" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "j" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "k" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "l" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "m" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "n" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "o" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "p" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} 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: "q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ALA X 359 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.50 residue: pdb=" N GLN X 380 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.50 residue: pdb=" N GLY Z 30 " occ=0.38 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.38 residue: pdb=" N ILE b 90 " occ=0.46 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.46 residue: pdb=" N SER b 115 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.70 residue: pdb=" N ILE b 140 " occ=0.39 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.39 residue: pdb=" N VAL b 173 " occ=0.89 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.89 residue: pdb=" N GLY b 191 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.50 residue: pdb=" N ILE d 63 " occ=0.78 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.78 residue: pdb=" N SER d 70 " occ=0.95 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.95 residue: pdb=" N MET d 95 " occ=0.66 ... (6 atoms not shown) pdb=" CE MET d 95 " occ=0.66 residue: pdb=" N MET d 144 " occ=0.52 ... (6 atoms not shown) pdb=" CE MET d 144 " occ=0.52 Time building chain proxies: 39.97, per 1000 atoms: 0.39 Number of scatterers: 103729 At special positions: 0 Unit cell: (335.65, 204.13, 226.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 601 16.00 P 11 15.00 O 19782 8.00 N 17836 7.00 C 65498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.02 Simple disulfide: pdb=" SG CYS m 41 " - pdb=" SG CYS m 186 " distance=2.02 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: 31.08 Conformation dependent library (CDL) restraints added in 14.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24908 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: 480 helices and 80 sheets defined 55.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 49.30 Creating SS restraints... Processing helix chain 'U' and resid 7 through 15 removed outlier: 4.015A pdb=" N LEU U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP U 15 " --> pdb=" O LEU U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 35 removed outlier: 3.533A pdb=" N PHE U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASN U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TRP U 35 " --> pdb=" O VAL U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 removed outlier: 5.411A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP U 43 " --> pdb=" O SER U 39 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU U 50 " --> pdb=" O GLU U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 removed outlier: 3.628A pdb=" N PHE U 68 " --> pdb=" O ALA U 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR U 69 " --> pdb=" O SER U 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS U 70 " --> pdb=" O LYS U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 4.259A pdb=" N GLY U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 91 removed outlier: 4.926A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 119 removed outlier: 3.644A pdb=" N GLU U 98 " --> pdb=" O SER U 94 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR U 99 " --> pdb=" O GLU U 95 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE U 100 " --> pdb=" O TYR U 96 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU U 118 " --> pdb=" O GLU U 114 " (cutoff:3.500A) Proline residue: U 119 - end of helix Processing helix chain 'U' and resid 127 through 145 removed outlier: 3.857A pdb=" N GLU U 131 " --> pdb=" O ASP U 127 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS U 136 " --> pdb=" O GLY U 132 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS U 145 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 3.798A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 4.257A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU U 168 " --> pdb=" O GLU U 164 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU U 169 " --> pdb=" O LYS U 165 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 187 removed outlier: 3.887A pdb=" N TYR U 179 " --> pdb=" O GLY U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 208 removed outlier: 4.498A pdb=" N ASN U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE U 204 " --> pdb=" O VAL U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 213 through 224 removed outlier: 3.821A pdb=" N CYS U 217 " --> pdb=" O PHE U 213 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP U 224 " --> pdb=" O LEU U 220 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 4.130A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER U 230 " --> pdb=" O PRO U 226 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE U 232 " --> pdb=" O ALA U 228 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS U 235 " --> pdb=" O ASP U 231 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP U 240 " --> pdb=" O LEU U 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 242 through 256 removed outlier: 3.525A pdb=" N TYR U 246 " --> pdb=" O LEU U 242 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE U 250 " --> pdb=" O TYR U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 270 removed outlier: 3.788A pdb=" N LEU U 261 " --> pdb=" O SER U 257 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG U 269 " --> pdb=" O ILE U 265 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR U 270 " --> pdb=" O GLN U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 removed outlier: 3.503A pdb=" N LYS U 327 " --> pdb=" O LEU U 323 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU U 329 " --> pdb=" O MET U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 346 removed outlier: 4.827A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 4.321A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL U 360 " --> pdb=" O THR U 356 " (cutoff:3.500A) Processing helix chain 'U' and resid 365 through 378 removed outlier: 3.718A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 388 removed outlier: 5.115A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) Processing helix chain 'U' and resid 389 through 396 removed outlier: 3.702A pdb=" N LEU U 393 " --> pdb=" O ASN U 389 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 413 removed outlier: 5.146A pdb=" N LYS U 401 " --> pdb=" O THR U 397 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS U 413 " --> pdb=" O GLY U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 415 through 424 removed outlier: 5.680A pdb=" N ALA U 419 " --> pdb=" O HIS U 415 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU U 420 " --> pdb=" O GLU U 416 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 451 removed outlier: 4.065A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA U 451 " --> pdb=" O GLY U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 3.868A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN U 467 " --> pdb=" O ASN U 463 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 486 removed outlier: 3.677A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER U 478 " --> pdb=" O ARG U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 4.589A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 508 through 521 removed outlier: 3.522A pdb=" N LEU U 514 " --> pdb=" O GLU U 510 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA U 515 " --> pdb=" O ALA U 511 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY U 517 " --> pdb=" O GLY U 513 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 4.298A pdb=" N ILE U 529 " --> pdb=" O ASN U 525 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLU U 530 " --> pdb=" O ALA U 526 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 557 removed outlier: 3.984A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU U 548 " --> pdb=" O ILE U 544 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 574 removed outlier: 3.887A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS U 574 " --> pdb=" O LEU U 570 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.542A pdb=" N TYR U 584 " --> pdb=" O ARG U 580 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.520A pdb=" N VAL U 619 " --> pdb=" O ARG U 615 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 641 removed outlier: 4.269A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 3.521A pdb=" N SER U 638 " --> pdb=" O PRO U 634 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 removed outlier: 3.592A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS U 660 " --> pdb=" O LEU U 656 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA U 661 " --> pdb=" O GLY U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 678 removed outlier: 6.332A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) Proline residue: U 674 - end of helix removed outlier: 4.040A pdb=" N ASP U 678 " --> pdb=" O PRO U 674 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.584A pdb=" N ALA U 687 " --> pdb=" O VAL U 683 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 699 through 704 Proline residue: U 704 - end of helix Processing helix chain 'U' and resid 705 through 719 Processing helix chain 'U' and resid 723 through 739 removed outlier: 3.559A pdb=" N GLY U 729 " --> pdb=" O MET U 725 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY U 735 " --> pdb=" O ILE U 731 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 769 removed outlier: 4.090A pdb=" N VAL U 760 " --> pdb=" O HIS U 756 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL U 763 " --> pdb=" O SER U 759 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) Processing helix chain 'U' and resid 774 through 783 removed outlier: 4.731A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR U 783 " --> pdb=" O LEU U 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 774 through 783' Processing helix chain 'U' and resid 886 through 891 removed outlier: 4.372A pdb=" N LEU U 889 " --> pdb=" O PRO U 886 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS U 890 " --> pdb=" O ALA U 887 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL U 891 " --> pdb=" O GLN U 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 886 through 891' Processing helix chain 'V' and resid 19 through 53 removed outlier: 4.536A pdb=" N GLU V 23 " --> pdb=" O PRO V 19 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN V 24 " --> pdb=" O GLY V 20 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU V 25 " --> pdb=" O GLY V 21 " (cutoff:3.500A) Proline residue: V 26 - end of helix Proline residue: V 29 - end of helix Proline residue: V 32 - end of helix removed outlier: 3.675A pdb=" N MET V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU V 39 " --> pdb=" O VAL V 35 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU V 40 " --> pdb=" O GLU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 76 removed outlier: 3.644A pdb=" N THR V 71 " --> pdb=" O LEU V 67 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU V 73 " --> pdb=" O THR V 69 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP V 74 " --> pdb=" O VAL V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 95 removed outlier: 4.734A pdb=" N LYS V 89 " --> pdb=" O ALA V 85 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU V 90 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Proline residue: V 91 - end of helix removed outlier: 5.283A pdb=" N LEU V 95 " --> pdb=" O PRO V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 121 removed outlier: 3.504A pdb=" N VAL V 112 " --> pdb=" O LEU V 108 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 141 removed outlier: 3.595A pdb=" N PHE V 134 " --> pdb=" O PHE V 130 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU V 137 " --> pdb=" O PRO V 133 " (cutoff:3.500A) Proline residue: V 138 - end of helix removed outlier: 3.955A pdb=" N THR V 141 " --> pdb=" O GLU V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 166 Proline residue: V 158 - end of helix Proline residue: V 161 - end of helix removed outlier: 4.182A pdb=" N TYR V 166 " --> pdb=" O GLU V 162 " (cutoff:3.500A) Processing helix chain 'V' and resid 170 through 192 removed outlier: 4.739A pdb=" N PHE V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET V 192 " --> pdb=" O SER V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 222 removed outlier: 5.026A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR V 218 " --> pdb=" O HIS V 214 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 224 through 239 removed outlier: 5.313A pdb=" N ARG V 228 " --> pdb=" O LEU V 224 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR V 239 " --> pdb=" O LEU V 235 " (cutoff:3.500A) Processing helix chain 'V' and resid 245 through 262 removed outlier: 3.698A pdb=" N THR V 249 " --> pdb=" O ASP V 245 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN V 257 " --> pdb=" O LEU V 253 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER V 262 " --> pdb=" O TYR V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 272 removed outlier: 3.556A pdb=" N LYS V 269 " --> pdb=" O ASP V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 282 through 300 removed outlier: 5.514A pdb=" N ALA V 286 " --> pdb=" O ASN V 282 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG V 287 " --> pdb=" O ASN V 283 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR V 290 " --> pdb=" O ALA V 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 317 removed outlier: 3.515A pdb=" N ALA V 305 " --> pdb=" O GLU V 301 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG V 307 " --> pdb=" O SER V 303 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR V 308 " --> pdb=" O GLU V 304 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS V 315 " --> pdb=" O ASN V 311 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA V 316 " --> pdb=" O ALA V 312 " (cutoff:3.500A) Proline residue: V 317 - end of helix Processing helix chain 'V' and resid 322 through 340 removed outlier: 6.361A pdb=" N GLN V 326 " --> pdb=" O VAL V 322 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE V 333 " --> pdb=" O HIS V 329 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL V 334 " --> pdb=" O LYS V 330 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 370 removed outlier: 5.210A pdb=" N ARG V 355 " --> pdb=" O PRO V 351 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER V 356 " --> pdb=" O SER V 352 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET V 358 " --> pdb=" O LYS V 354 " (cutoff:3.500A) Proline residue: V 359 - end of helix removed outlier: 3.591A pdb=" N ALA V 366 " --> pdb=" O LEU V 362 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY V 370 " --> pdb=" O ALA V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 371 through 383 removed outlier: 4.833A pdb=" N PHE V 375 " --> pdb=" O ASN V 371 " (cutoff:3.500A) Processing helix chain 'V' and resid 384 through 390 removed outlier: 3.590A pdb=" N GLY V 390 " --> pdb=" O PHE V 386 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 414 removed outlier: 4.736A pdb=" N ARG V 399 " --> pdb=" O ILE V 395 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN V 401 " --> pdb=" O ARG V 397 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL V 407 " --> pdb=" O ILE V 403 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 3.661A pdb=" N GLN V 424 " --> pdb=" O ALA V 420 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN V 427 " --> pdb=" O ALA V 423 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 removed outlier: 4.364A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU V 435 " --> pdb=" O PRO V 431 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 496 removed outlier: 6.030A pdb=" N THR V 469 " --> pdb=" O ASP V 465 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG V 470 " --> pdb=" O ILE V 466 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU V 471 " --> pdb=" O TYR V 467 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 3.832A pdb=" N ALA V 475 " --> pdb=" O GLU V 471 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP V 485 " --> pdb=" O SER V 481 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET V 494 " --> pdb=" O SER V 490 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG V 495 " --> pdb=" O VAL V 491 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE V 496 " --> pdb=" O LYS V 492 " (cutoff:3.500A) Processing helix chain 'V' and resid 344 through 349 removed outlier: 5.604A pdb=" N GLN V 347 " --> pdb=" O ASP V 344 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE V 348 " --> pdb=" O ARG V 345 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG V 349 " --> pdb=" O LEU V 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 344 through 349' Processing helix chain 'W' and resid 1 through 16 removed outlier: 3.605A pdb=" N GLY W 5 " --> pdb=" O MET W 1 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL W 14 " --> pdb=" O ASP W 10 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS W 15 " --> pdb=" O GLY W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 38 removed outlier: 4.230A pdb=" N VAL W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) Proline residue: W 29 - end of helix removed outlier: 4.664A pdb=" N GLY W 38 " --> pdb=" O LEU W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 64 Processing helix chain 'W' and resid 68 through 87 removed outlier: 4.087A pdb=" N LYS W 72 " --> pdb=" O VAL W 68 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET W 73 " --> pdb=" O ALA W 69 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU W 76 " --> pdb=" O LYS W 72 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 115 removed outlier: 4.553A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU W 114 " --> pdb=" O THR W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 116 through 134 removed outlier: 4.484A pdb=" N ILE W 120 " --> pdb=" O THR W 116 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU W 133 " --> pdb=" O ARG W 129 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 154 removed outlier: 5.333A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS W 147 " --> pdb=" O ALA W 143 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS W 153 " --> pdb=" O LEU W 149 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU W 154 " --> pdb=" O ALA W 150 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 172 removed outlier: 4.134A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 197 removed outlier: 4.539A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 210 removed outlier: 3.532A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS W 208 " --> pdb=" O ILE W 204 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE W 209 " --> pdb=" O ILE W 205 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN W 210 " --> pdb=" O SER W 206 " (cutoff:3.500A) Processing helix chain 'W' and resid 220 through 238 removed outlier: 4.007A pdb=" N LEU W 224 " --> pdb=" O GLU W 220 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS W 225 " --> pdb=" O LYS W 221 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 258 removed outlier: 4.801A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) Proline residue: W 254 - end of helix removed outlier: 4.585A pdb=" N GLN W 257 " --> pdb=" O THR W 253 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA W 258 " --> pdb=" O PRO W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 260 through 278 removed outlier: 4.396A pdb=" N GLN W 264 " --> pdb=" O SER W 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL W 270 " --> pdb=" O ALA W 266 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA W 277 " --> pdb=" O TYR W 273 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 291 removed outlier: 3.835A pdb=" N SER W 284 " --> pdb=" O ASP W 280 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP W 285 " --> pdb=" O ASN W 281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER W 291 " --> pdb=" O VAL W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 310 removed outlier: 4.213A pdb=" N LYS W 303 " --> pdb=" O ILE W 299 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N THR W 310 " --> pdb=" O LEU W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 330 removed outlier: 5.634A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS W 330 " --> pdb=" O MET W 326 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 removed outlier: 3.643A pdb=" N THR W 338 " --> pdb=" O GLU W 334 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 370 removed outlier: 4.898A pdb=" N GLU W 348 " --> pdb=" O THR W 344 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE W 365 " --> pdb=" O HIS W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 Processing helix chain 'W' and resid 385 through 400 removed outlier: 3.586A pdb=" N SER W 389 " --> pdb=" O SER W 385 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 455 removed outlier: 3.524A pdb=" N MET W 436 " --> pdb=" O LEU W 432 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU W 438 " --> pdb=" O SER W 434 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL W 439 " --> pdb=" O LEU W 435 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN W 440 " --> pdb=" O MET W 436 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS W 444 " --> pdb=" O ASN W 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE W 452 " --> pdb=" O LYS W 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 61 removed outlier: 3.543A pdb=" N ALA X 58 " --> pdb=" O GLY X 54 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY X 61 " --> pdb=" O LEU X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 81 removed outlier: 3.685A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 4.869A pdb=" N ASN X 78 " --> pdb=" O ARG X 74 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE X 80 " --> pdb=" O PHE X 76 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER X 81 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 99 removed outlier: 4.235A pdb=" N ALA X 86 " --> pdb=" O LYS X 82 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG X 87 " --> pdb=" O ALA X 83 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU X 88 " --> pdb=" O LYS X 84 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 removed outlier: 4.029A pdb=" N GLU X 106 " --> pdb=" O ALA X 102 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 141 removed outlier: 3.596A pdb=" N ARG X 126 " --> pdb=" O ARG X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 158 removed outlier: 4.344A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 181 removed outlier: 3.653A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS X 178 " --> pdb=" O SER X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 201 removed outlier: 4.429A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE X 200 " --> pdb=" O THR X 196 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR X 201 " --> pdb=" O ALA X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 205 through 222 removed outlier: 3.530A pdb=" N THR X 209 " --> pdb=" O LYS X 205 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU X 221 " --> pdb=" O ILE X 217 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU X 222 " --> pdb=" O HIS X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 5.310A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR X 229 " --> pdb=" O TRP X 225 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP X 240 " --> pdb=" O PHE X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 4.586A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER X 250 " --> pdb=" O LYS X 246 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU X 251 " --> pdb=" O ALA X 247 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU X 261 " --> pdb=" O CYS X 257 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 274 removed outlier: 4.064A pdb=" N VAL X 267 " --> pdb=" O THR X 263 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY X 273 " --> pdb=" O ALA X 269 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS X 274 " --> pdb=" O LEU X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 275 through 280 removed outlier: 4.641A pdb=" N TYR X 279 " --> pdb=" O LEU X 275 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA X 280 " --> pdb=" O ALA X 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 275 through 280' Processing helix chain 'X' and resid 281 through 297 removed outlier: 3.516A pdb=" N GLU X 285 " --> pdb=" O GLY X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.872A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 340 removed outlier: 5.531A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU X 332 " --> pdb=" O ASP X 328 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG X 337 " --> pdb=" O GLN X 333 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL X 338 " --> pdb=" O ASN X 334 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE X 339 " --> pdb=" O LEU X 335 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.915A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 372 removed outlier: 5.034A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 422 removed outlier: 3.534A pdb=" N GLU X 402 " --> pdb=" O GLU X 398 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR X 403 " --> pdb=" O ALA X 399 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE X 404 " --> pdb=" O ALA X 400 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN X 405 " --> pdb=" O LEU X 401 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS X 417 " --> pdb=" O SER X 413 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 29 removed outlier: 3.989A pdb=" N ILE Y 19 " --> pdb=" O PRO Y 15 " (cutoff:3.500A) Proline residue: Y 29 - end of helix Processing helix chain 'Y' and resid 34 through 48 removed outlier: 3.977A pdb=" N ARG Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Y 41 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET Y 42 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN Y 48 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 60 removed outlier: 5.182A pdb=" N TYR Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR Y 54 " --> pdb=" O MET Y 50 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER Y 60 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 92 removed outlier: 3.676A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP Y 85 " --> pdb=" O LEU Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 114 removed outlier: 3.521A pdb=" N ALA Y 106 " --> pdb=" O ASP Y 102 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 132 removed outlier: 3.901A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR Y 131 " --> pdb=" O THR Y 127 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL Y 132 " --> pdb=" O TYR Y 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 4.395A pdb=" N ARG Y 137 " --> pdb=" O ALA Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 167 removed outlier: 4.089A pdb=" N ILE Y 157 " --> pdb=" O ASP Y 153 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR Y 158 " --> pdb=" O ASN Y 154 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG Y 159 " --> pdb=" O ASP Y 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU Y 162 " --> pdb=" O THR Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 173 removed outlier: 4.143A pdb=" N GLY Y 172 " --> pdb=" O ILE Y 168 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP Y 173 " --> pdb=" O GLU Y 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 168 through 173' Processing helix chain 'Y' and resid 176 through 191 removed outlier: 3.577A pdb=" N GLN Y 184 " --> pdb=" O LEU Y 180 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Y 189 " --> pdb=" O GLY Y 185 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE Y 191 " --> pdb=" O TYR Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 203 removed outlier: 4.742A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE Y 201 " --> pdb=" O ALA Y 197 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP Y 203 " --> pdb=" O GLU Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.864A pdb=" N SER Y 227 " --> pdb=" O THR Y 223 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET Y 228 " --> pdb=" O VAL Y 224 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA Y 230 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU Y 231 " --> pdb=" O SER Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 241 removed outlier: 4.032A pdb=" N LYS Y 239 " --> pdb=" O ASP Y 235 " (cutoff:3.500A) Processing helix chain 'Y' and resid 244 through 254 removed outlier: 4.115A pdb=" N VAL Y 249 " --> pdb=" O GLU Y 245 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 Processing helix chain 'Y' and resid 268 through 285 removed outlier: 3.722A pdb=" N PHE Y 272 " --> pdb=" O TYR Y 268 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS Y 283 " --> pdb=" O GLU Y 279 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 310 removed outlier: 4.926A pdb=" N ARG Y 293 " --> pdb=" O ALA Y 289 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR Y 294 " --> pdb=" O PRO Y 290 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 322 removed outlier: 3.609A pdb=" N MET Y 319 " --> pdb=" O THR Y 315 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 5.382A pdb=" N ILE Y 330 " --> pdb=" O GLY Y 326 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 388 removed outlier: 6.210A pdb=" N TRP Y 364 " --> pdb=" O ASP Y 360 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN Y 365 " --> pdb=" O SER Y 361 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 28 removed outlier: 4.597A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU Z 17 " --> pdb=" O PRO Z 13 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER Z 18 " --> pdb=" O LEU Z 14 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL Z 20 " --> pdb=" O LEU Z 16 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 removed outlier: 3.619A pdb=" N GLY Z 80 " --> pdb=" O GLU Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 4.887A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU Z 111 " --> pdb=" O ALA Z 107 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Proline residue: Z 117 - end of helix Processing helix chain 'Z' and resid 166 through 177 removed outlier: 6.665A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU Z 175 " --> pdb=" O GLY Z 171 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG Z 177 " --> pdb=" O GLU Z 173 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 217 removed outlier: 6.448A pdb=" N ARG Z 190 " --> pdb=" O THR Z 186 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE Z 191 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU Z 201 " --> pdb=" O GLY Z 197 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER Z 203 " --> pdb=" O LYS Z 199 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS Z 214 " --> pdb=" O SER Z 210 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA Z 216 " --> pdb=" O LEU Z 212 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR Z 217 " --> pdb=" O GLU Z 213 " (cutoff:3.500A) Processing helix chain 'Z' and resid 223 through 236 removed outlier: 3.879A pdb=" N TYR Z 228 " --> pdb=" O HIS Z 224 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP Z 232 " --> pdb=" O TYR Z 228 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE Z 234 " --> pdb=" O LEU Z 230 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN Z 235 " --> pdb=" O GLN Z 231 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU Z 236 " --> pdb=" O ASP Z 232 " (cutoff:3.500A) Processing helix chain 'Z' and resid 241 through 289 removed outlier: 3.528A pdb=" N PHE Z 245 " --> pdb=" O SER Z 241 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Z 265 " --> pdb=" O TYR Z 261 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER Z 268 " --> pdb=" O SER Z 264 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL Z 270 " --> pdb=" O ILE Z 266 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Z 271 " --> pdb=" O ARG Z 267 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN Z 278 " --> pdb=" O ASN Z 274 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Z 285 " --> pdb=" O ALA Z 281 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 12 removed outlier: 3.598A pdb=" N LEU a 8 " --> pdb=" O VAL a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 32 removed outlier: 4.494A pdb=" N VAL a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS a 32 " --> pdb=" O LEU a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 5.427A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR a 38 " --> pdb=" O TRP a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 removed outlier: 3.914A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 removed outlier: 3.718A pdb=" N LEU a 76 " --> pdb=" O ASN a 72 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR a 88 " --> pdb=" O VAL a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 105 removed outlier: 4.148A pdb=" N LEU a 94 " --> pdb=" O PRO a 90 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL a 104 " --> pdb=" O THR a 100 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 123 removed outlier: 4.947A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR a 116 " --> pdb=" O ILE a 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU a 121 " --> pdb=" O ALA a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 143 removed outlier: 4.101A pdb=" N VAL a 138 " --> pdb=" O THR a 134 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 164 removed outlier: 6.681A pdb=" N HIS a 152 " --> pdb=" O VAL a 148 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN a 164 " --> pdb=" O SER a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 184 removed outlier: 3.641A pdb=" N TYR a 173 " --> pdb=" O HIS a 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU a 180 " --> pdb=" O ALA a 176 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 5.196A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY a 207 " --> pdb=" O ALA a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 215 through 220 removed outlier: 5.182A pdb=" N HIS a 219 " --> pdb=" O GLU a 215 " (cutoff:3.500A) Proline residue: a 220 - end of helix No H-bonds generated for 'chain 'a' and resid 215 through 220' Processing helix chain 'a' and resid 221 through 226 removed outlier: 5.247A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.148A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE a 240 " --> pdb=" O THR a 236 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.983A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 285 removed outlier: 5.063A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE a 282 " --> pdb=" O MET a 278 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG a 284 " --> pdb=" O MET a 280 " (cutoff:3.500A) Proline residue: a 285 - end of helix Processing helix chain 'a' and resid 292 through 301 removed outlier: 3.997A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 318 removed outlier: 3.625A pdb=" N VAL a 307 " --> pdb=" O THR a 303 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 376 removed outlier: 4.178A pdb=" N GLY a 348 " --> pdb=" O GLN a 344 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET a 349 " --> pdb=" O GLN a 345 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 67 through 76 removed outlier: 5.364A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 100 removed outlier: 3.903A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG b 100 " --> pdb=" O ALA b 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 removed outlier: 3.520A pdb=" N LEU b 124 " --> pdb=" O ASN b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 162 removed outlier: 3.815A pdb=" N ASN b 161 " --> pdb=" O VAL b 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY b 162 " --> pdb=" O ASN b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 187 removed outlier: 4.631A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'b' and resid 13 through 19 removed outlier: 3.626A pdb=" N MET b 16 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG b 17 " --> pdb=" O GLU b 14 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN b 18 " --> pdb=" O TYR b 15 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY b 19 " --> pdb=" O MET b 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 13 through 19' Processing helix chain 'c' and resid 34 through 49 removed outlier: 3.687A pdb=" N LEU c 38 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU c 39 " --> pdb=" O SER c 35 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY c 48 " --> pdb=" O HIS c 44 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 88 removed outlier: 4.367A pdb=" N VAL c 87 " --> pdb=" O SER c 83 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP c 88 " --> pdb=" O VAL c 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 83 through 88' Processing helix chain 'c' and resid 89 through 103 removed outlier: 4.089A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR c 102 " --> pdb=" O MET c 98 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 removed outlier: 4.270A pdb=" N ASN c 128 " --> pdb=" O GLY c 124 " (cutoff:3.500A) Processing helix chain 'c' and resid 146 through 151 removed outlier: 5.433A pdb=" N VAL c 151 " --> pdb=" O PRO c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 195 removed outlier: 3.977A pdb=" N ILE c 193 " --> pdb=" O ILE c 189 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY c 195 " --> pdb=" O ALA c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 211 through 222 removed outlier: 6.901A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 220 " --> pdb=" O MET c 216 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 removed outlier: 4.342A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR c 230 " --> pdb=" O MET c 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 224 through 230' Processing helix chain 'c' and resid 234 through 260 removed outlier: 3.832A pdb=" N CYS c 238 " --> pdb=" O TYR c 234 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS c 239 " --> pdb=" O SER c 235 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU c 242 " --> pdb=" O CYS c 238 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER c 243 " --> pdb=" O LYS c 239 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL c 244 " --> pdb=" O HIS c 240 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL c 245 " --> pdb=" O ASN c 241 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS c 246 " --> pdb=" O GLU c 242 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU c 247 " --> pdb=" O SER c 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 275 removed outlier: 3.515A pdb=" N ILE c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL c 275 " --> pdb=" O ALA c 271 " (cutoff:3.500A) Processing helix chain 'c' and resid 280 through 310 removed outlier: 5.196A pdb=" N LEU c 284 " --> pdb=" O PRO c 280 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU c 285 " --> pdb=" O LYS c 281 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU c 286 " --> pdb=" O ARG c 282 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS c 287 " --> pdb=" O HIS c 283 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN c 295 " --> pdb=" O LEU c 291 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 183 removed outlier: 5.337A pdb=" N LEU c 181 " --> pdb=" O THR c 178 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY c 182 " --> pdb=" O SER c 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 33 removed outlier: 3.976A pdb=" N GLY d 20 " --> pdb=" O LEU d 16 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 33 " --> pdb=" O VAL d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 66 removed outlier: 3.691A pdb=" N GLN d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU d 48 " --> pdb=" O THR d 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 84 removed outlier: 3.673A pdb=" N GLU d 72 " --> pdb=" O ILE d 68 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP d 84 " --> pdb=" O CYS d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 110 removed outlier: 3.735A pdb=" N ASN d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 120 removed outlier: 3.542A pdb=" N LEU d 119 " --> pdb=" O PHE d 115 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix Processing helix chain 'd' and resid 147 through 158 removed outlier: 3.501A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE d 152 " --> pdb=" O TYR d 148 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 184 removed outlier: 3.657A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP d 176 " --> pdb=" O ASP d 172 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 198 removed outlier: 3.624A pdb=" N ALA d 194 " --> pdb=" O LEU d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 213 removed outlier: 4.313A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 238 through 255 removed outlier: 4.099A pdb=" N LEU d 242 " --> pdb=" O PRO d 238 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET d 255 " --> pdb=" O ARG d 251 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 52 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.446A pdb=" N THR e 69 " --> pdb=" O TYR e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 59 through 64 removed outlier: 4.368A pdb=" N GLY e 64 " --> pdb=" O GLU e 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 59 through 64' Processing helix chain 'f' and resid 7 through 23 removed outlier: 3.870A pdb=" N VAL f 11 " --> pdb=" O ASP f 7 " (cutoff:3.500A) Proline residue: f 13 - end of helix Proline residue: f 17 - end of helix Proline residue: f 21 - end of helix Processing helix chain 'f' and resid 27 through 48 removed outlier: 3.793A pdb=" N GLU f 32 " --> pdb=" O PRO f 28 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG f 34 " --> pdb=" O GLY f 30 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS f 41 " --> pdb=" O GLY f 37 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU f 47 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU f 48 " --> pdb=" O GLU f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 62 removed outlier: 3.918A pdb=" N MET f 58 " --> pdb=" O ASP f 54 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU f 59 " --> pdb=" O GLU f 55 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU f 61 " --> pdb=" O GLU f 57 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG f 62 " --> pdb=" O MET f 58 " (cutoff:3.500A) Processing helix chain 'f' and resid 63 through 72 Processing helix chain 'f' and resid 79 through 95 removed outlier: 3.759A pdb=" N ARG f 83 " --> pdb=" O ARG f 79 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER f 84 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER f 88 " --> pdb=" O SER f 84 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL f 92 " --> pdb=" O SER f 88 " (cutoff:3.500A) Proline residue: f 93 - end of helix Processing helix chain 'f' and resid 101 through 114 removed outlier: 4.723A pdb=" N LYS f 105 " --> pdb=" O PRO f 101 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS f 107 " --> pdb=" O TYR f 103 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU f 108 " --> pdb=" O GLY f 104 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR f 110 " --> pdb=" O LEU f 106 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASN f 112 " --> pdb=" O GLU f 108 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N MET f 113 " --> pdb=" O ILE f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 117 through 123 removed outlier: 4.778A pdb=" N PHE f 121 " --> pdb=" O GLU f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 149 removed outlier: 3.769A pdb=" N LEU f 140 " --> pdb=" O GLU f 136 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR f 142 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 153 through 173 removed outlier: 3.671A pdb=" N TYR f 158 " --> pdb=" O TRP f 154 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL f 159 " --> pdb=" O GLY f 155 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS f 161 " --> pdb=" O GLU f 157 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN f 171 " --> pdb=" O ALA f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 177 through 191 removed outlier: 4.021A pdb=" N ARG f 181 " --> pdb=" O GLU f 177 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU f 182 " --> pdb=" O LYS f 178 " (cutoff:3.500A) Proline residue: f 183 - end of helix removed outlier: 3.847A pdb=" N VAL f 188 " --> pdb=" O LEU f 184 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLU f 190 " --> pdb=" O THR f 186 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE f 191 " --> pdb=" O LEU f 187 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 209 removed outlier: 4.392A pdb=" N ALA f 200 " --> pdb=" O MET f 196 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET f 209 " --> pdb=" O CYS f 205 " (cutoff:3.500A) Processing helix chain 'f' and resid 210 through 227 removed outlier: 6.067A pdb=" N VAL f 214 " --> pdb=" O GLU f 210 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP f 215 " --> pdb=" O ILE f 211 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE f 221 " --> pdb=" O LEU f 217 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR f 226 " --> pdb=" O ASP f 222 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA f 227 " --> pdb=" O GLU f 223 " (cutoff:3.500A) Processing helix chain 'f' and resid 228 through 245 removed outlier: 3.901A pdb=" N CYS f 236 " --> pdb=" O TYR f 232 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL f 237 " --> pdb=" O LEU f 233 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 4.088A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) Processing helix chain 'f' and resid 254 through 262 removed outlier: 4.611A pdb=" N SER f 260 " --> pdb=" O PHE f 256 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE f 262 " --> pdb=" O LYS f 258 " (cutoff:3.500A) Processing helix chain 'f' and resid 265 through 280 removed outlier: 3.609A pdb=" N ALA f 269 " --> pdb=" O ALA f 265 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU f 279 " --> pdb=" O MET f 275 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP f 280 " --> pdb=" O GLU f 276 " (cutoff:3.500A) Processing helix chain 'f' and resid 283 through 294 removed outlier: 4.037A pdb=" N LYS f 292 " --> pdb=" O VAL f 288 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN f 293 " --> pdb=" O VAL f 289 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 301 through 306 removed outlier: 4.621A pdb=" N LEU f 305 " --> pdb=" O HIS f 301 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU f 306 " --> pdb=" O GLY f 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 301 through 306' Processing helix chain 'f' and resid 315 through 334 removed outlier: 4.063A pdb=" N GLU f 319 " --> pdb=" O GLU f 315 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL f 324 " --> pdb=" O ILE f 320 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLN f 325 " --> pdb=" O MET f 321 " (cutoff:3.500A) Processing helix chain 'f' and resid 335 through 340 removed outlier: 3.884A pdb=" N MET f 340 " --> pdb=" O GLU f 336 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 359 removed outlier: 4.482A pdb=" N LYS f 350 " --> pdb=" O ASP f 346 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS f 352 " --> pdb=" O ILE f 348 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU f 353 " --> pdb=" O TYR f 349 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU f 354 " --> pdb=" O LYS f 350 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN f 355 " --> pdb=" O THR f 351 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASN f 356 " --> pdb=" O HIS f 352 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG f 357 " --> pdb=" O LEU f 353 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE f 358 " --> pdb=" O GLU f 354 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLY f 359 " --> pdb=" O ASN f 355 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 380 removed outlier: 4.105A pdb=" N ASN f 371 " --> pdb=" O SER f 367 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU f 372 " --> pdb=" O ALA f 368 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA f 373 " --> pdb=" O ARG f 369 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER f 375 " --> pdb=" O ASN f 371 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE f 376 " --> pdb=" O LEU f 372 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL f 377 " --> pdb=" O ALA f 373 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN f 378 " --> pdb=" O SER f 374 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 402 removed outlier: 3.516A pdb=" N TYR f 400 " --> pdb=" O ASN f 396 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 403 through 419 removed outlier: 3.857A pdb=" N LEU f 414 " --> pdb=" O ALA f 410 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET f 416 " --> pdb=" O ALA f 412 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 424 through 434 removed outlier: 3.582A pdb=" N ILE f 429 " --> pdb=" O GLY f 425 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 3.580A pdb=" N LYS f 441 " --> pdb=" O GLU f 437 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU f 446 " --> pdb=" O SER f 442 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY f 449 " --> pdb=" O LEU f 445 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE f 450 " --> pdb=" O LEU f 446 " (cutoff:3.500A) Processing helix chain 'f' and resid 463 through 472 removed outlier: 3.916A pdb=" N SER f 467 " --> pdb=" O LEU f 463 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS f 472 " --> pdb=" O ASP f 468 " (cutoff:3.500A) Processing helix chain 'f' and resid 475 through 490 removed outlier: 4.103A pdb=" N LEU f 479 " --> pdb=" O ASN f 475 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER f 481 " --> pdb=" O MET f 477 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE f 482 " --> pdb=" O ARG f 478 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE f 483 " --> pdb=" O LEU f 479 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY f 484 " --> pdb=" O GLY f 480 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU f 485 " --> pdb=" O SER f 481 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY f 486 " --> pdb=" O ILE f 482 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 508 removed outlier: 4.311A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) Proline residue: f 503 - end of helix removed outlier: 4.751A pdb=" N SER f 508 " --> pdb=" O VAL f 504 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 527 removed outlier: 3.794A pdb=" N ILE f 525 " --> pdb=" O ALA f 521 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA f 526 " --> pdb=" O CYS f 522 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 549 removed outlier: 4.151A pdb=" N VAL f 534 " --> pdb=" O CYS f 530 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN f 540 " --> pdb=" O SER f 536 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER f 546 " --> pdb=" O ILE f 542 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU f 547 " --> pdb=" O MET f 543 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR f 548 " --> pdb=" O GLU f 544 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (cutoff:3.500A) Processing helix chain 'f' and resid 551 through 567 removed outlier: 4.209A pdb=" N ALA f 555 " --> pdb=" O LYS f 551 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TRP f 557 " --> pdb=" O THR f 553 " (cutoff:3.500A) Proline residue: f 559 - end of helix removed outlier: 4.007A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) Processing helix chain 'f' and resid 572 through 583 removed outlier: 4.143A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU f 580 " --> pdb=" O ILE f 576 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL f 583 " --> pdb=" O ALA f 579 " (cutoff:3.500A) Processing helix chain 'f' and resid 585 through 601 removed outlier: 5.225A pdb=" N ALA f 591 " --> pdb=" O PHE f 587 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN f 592 " --> pdb=" O ARG f 588 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR f 593 " --> pdb=" O SER f 589 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU f 594 " --> pdb=" O PHE f 590 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL f 595 " --> pdb=" O ALA f 591 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP f 596 " --> pdb=" O ASN f 592 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL f 597 " --> pdb=" O THR f 593 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA f 599 " --> pdb=" O VAL f 595 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 615 removed outlier: 3.532A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN f 611 " --> pdb=" O LEU f 607 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE f 615 " --> pdb=" O GLN f 611 " (cutoff:3.500A) Processing helix chain 'f' and resid 625 through 643 removed outlier: 4.132A pdb=" N ASP f 638 " --> pdb=" O LYS f 634 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS f 639 " --> pdb=" O LYS f 635 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS f 640 " --> pdb=" O ASP f 636 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU f 641 " --> pdb=" O LYS f 637 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ALA f 642 " --> pdb=" O ASP f 638 " (cutoff:3.500A) Proline residue: f 643 - end of helix Processing helix chain 'f' and resid 645 through 658 removed outlier: 3.724A pdb=" N HIS f 649 " --> pdb=" O ASP f 645 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN f 650 " --> pdb=" O MET f 646 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE f 657 " --> pdb=" O ALA f 653 " (cutoff:3.500A) Processing helix chain 'f' and resid 672 through 679 removed outlier: 4.331A pdb=" N LEU f 679 " --> pdb=" O PHE f 675 " (cutoff:3.500A) Processing helix chain 'f' and resid 683 through 695 Proline residue: f 691 - end of helix Processing helix chain 'f' and resid 702 through 716 removed outlier: 4.748A pdb=" N ILE f 706 " --> pdb=" O PRO f 702 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER f 714 " --> pdb=" O LEU f 710 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N HIS f 715 " --> pdb=" O SER f 711 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASP f 716 " --> pdb=" O LYS f 712 " (cutoff:3.500A) Processing helix chain 'f' and resid 722 through 736 removed outlier: 3.650A pdb=" N ALA f 728 " --> pdb=" O ASN f 724 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY f 735 " --> pdb=" O MET f 731 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR f 736 " --> pdb=" O VAL f 732 " (cutoff:3.500A) Processing helix chain 'f' and resid 742 through 755 removed outlier: 3.967A pdb=" N GLN f 747 " --> pdb=" O ALA f 743 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA f 753 " --> pdb=" O ALA f 749 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS f 754 " --> pdb=" O GLN f 750 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP f 755 " --> pdb=" O TYR f 751 " (cutoff:3.500A) Processing helix chain 'f' and resid 774 through 786 Proline residue: f 780 - end of helix removed outlier: 5.347A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) Processing helix chain 'f' and resid 794 through 801 removed outlier: 4.423A pdb=" N THR f 798 " --> pdb=" O ALA f 794 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU f 800 " --> pdb=" O LEU f 796 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 6.158A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.931A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 159 through 166 removed outlier: 4.374A pdb=" N MET A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.968A pdb=" N ILE A 184 " --> pdb=" O CYS A 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 205 removed outlier: 4.411A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.648A pdb=" N ALA A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.882A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 247' Processing helix chain 'A' and resid 251 through 268 removed outlier: 4.956A pdb=" N ARG A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 309 removed outlier: 4.534A pdb=" N ARG A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 363 removed outlier: 6.287A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 5.152A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.710A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.696A pdb=" N PHE A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.013A pdb=" N VAL A 177 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY A 178 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 removed outlier: 4.691A pdb=" N SER B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 6.078A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 175' Processing helix chain 'B' and resid 190 through 206 removed outlier: 3.633A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 208 through 215 removed outlier: 4.268A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.778A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.644A pdb=" N VAL B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.914A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 318 removed outlier: 5.624A pdb=" N GLU B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.846A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.068A pdb=" N LYS B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.241A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 removed outlier: 3.520A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 426 removed outlier: 3.725A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 68 removed outlier: 3.979A pdb=" N LYS C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ALA C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER C 18 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLY C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 27 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 removed outlier: 4.811A pdb=" N MET C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 139' Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.930A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 179 removed outlier: 3.675A pdb=" N LEU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY C 179 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 208 removed outlier: 4.939A pdb=" N ALA C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 242 removed outlier: 4.324A pdb=" N GLY C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 231 " --> pdb=" O GLY C 227 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 removed outlier: 5.237A pdb=" N ARG C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 4.358A pdb=" N LEU C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 302 through 307' Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.207A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 6.173A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.965A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 removed outlier: 7.019A pdb=" N LYS C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 406 " --> pdb=" O LYS C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 398 through 406' Processing helix chain 'C' and resid 215 through 221 removed outlier: 3.507A pdb=" N GLU C 218 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL C 220 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN C 221 " --> pdb=" O GLU C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 221' Processing helix chain 'D' and resid 40 through 85 removed outlier: 4.295A pdb=" N TYR D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D 45 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.098A pdb=" N GLN D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 195 Processing helix chain 'D' and resid 211 through 223 removed outlier: 4.919A pdb=" N LEU D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 279 through 297 removed outlier: 4.329A pdb=" N ARG D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 removed outlier: 4.590A pdb=" N LEU D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASP D 318 " --> pdb=" O ALA D 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 318' Processing helix chain 'D' and resid 338 through 353 removed outlier: 6.760A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 366 removed outlier: 3.515A pdb=" N VAL D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 360 through 366' Processing helix chain 'D' and resid 371 through 390 removed outlier: 3.774A pdb=" N ILE D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 376 " --> pdb=" O GLY D 372 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 388 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 408 removed outlier: 5.297A pdb=" N GLU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 4.116A pdb=" N ILE D 167 " --> pdb=" O TYR D 164 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY D 168 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 52 removed outlier: 4.056A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 12 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS E 14 " --> pdb=" O GLN E 10 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS E 15 " --> pdb=" O ASP E 11 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.982A pdb=" N LEU E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 93' Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.509A pdb=" N TYR E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN E 121 " --> pdb=" O PRO E 117 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU E 125 " --> pdb=" O ASN E 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 116 through 125' Processing helix chain 'E' and resid 138 through 154 removed outlier: 3.784A pdb=" N VAL E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.668A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 191 removed outlier: 3.652A pdb=" N LEU E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 6.908A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.470A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.509A pdb=" N ILE E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 removed outlier: 4.156A pdb=" N ARG E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 305 through 318 removed outlier: 6.232A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 339 through 358 removed outlier: 3.573A pdb=" N GLY E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.797A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 372 " --> pdb=" O MET E 368 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 35 removed outlier: 3.608A pdb=" N ILE F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 85 removed outlier: 5.098A pdb=" N ILE F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG F 44 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.963A pdb=" N LYS F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.534A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY F 189 " --> pdb=" O TYR F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'F' and resid 191 through 208 removed outlier: 4.833A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 removed outlier: 4.006A pdb=" N GLU F 213 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY F 216 " --> pdb=" O PHE F 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 209 through 216' Processing helix chain 'F' and resid 232 through 245 removed outlier: 5.495A pdb=" N ALA F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR F 244 " --> pdb=" O CYS F 240 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 258 removed outlier: 4.475A pdb=" N LEU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 258' Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.788A pdb=" N LYS F 266 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG F 269 " --> pdb=" O ALA F 265 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS F 276 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 293 removed outlier: 4.828A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 5.383A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG F 308 " --> pdb=" O ARG F 304 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 4.249A pdb=" N LEU F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 339 through 344' Processing helix chain 'F' and resid 358 through 372 removed outlier: 4.430A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 5.280A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 removed outlier: 3.515A pdb=" N GLY F 404 " --> pdb=" O CYS F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.752A pdb=" N TYR F 420 " --> pdb=" O THR F 416 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 427 " --> pdb=" O GLY F 423 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN F 428 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 removed outlier: 4.817A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 5.174A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 67' Processing helix chain 'G' and resid 83 through 105 removed outlier: 3.547A pdb=" N SER G 87 " --> pdb=" O MET G 83 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG G 93 " --> pdb=" O SER G 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA G 99 " --> pdb=" O ARG G 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 129 removed outlier: 3.827A pdb=" N CYS G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 116 " --> pdb=" O ASP G 112 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 4.348A pdb=" N SER G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 5.663A pdb=" N THR G 194 " --> pdb=" O THR G 190 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 removed outlier: 5.056A pdb=" N GLU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 36 removed outlier: 4.818A pdb=" N GLU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS g 30 " --> pdb=" O GLU g 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 5.173A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 67' Processing helix chain 'g' and resid 83 through 105 removed outlier: 3.547A pdb=" N SER g 87 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER g 89 " --> pdb=" O ALA g 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG g 93 " --> pdb=" O SER g 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS g 102 " --> pdb=" O ALA g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 110 through 129 removed outlier: 3.825A pdb=" N CYS g 115 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS g 116 " --> pdb=" O ASP g 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE g 121 " --> pdb=" O ARG g 117 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 4.347A pdb=" N SER g 175 " --> pdb=" O LYS g 171 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER g 177 " --> pdb=" O THR g 173 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 5.663A pdb=" N THR g 194 " --> pdb=" O THR g 190 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 231 through 244 removed outlier: 5.055A pdb=" N GLU g 244 " --> pdb=" O VAL g 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.890A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 63 removed outlier: 4.619A pdb=" N VAL H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N HIS H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 63' Processing helix chain 'H' and resid 80 through 101 removed outlier: 3.597A pdb=" N ARG H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 86 " --> pdb=" O ASP H 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN H 95 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 125 removed outlier: 3.524A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY H 125 " --> pdb=" O TYR H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.473A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE H 199 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 removed outlier: 4.167A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 209' Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.519A pdb=" N VAL H 226 " --> pdb=" O THR H 222 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.889A pdb=" N GLU h 23 " --> pdb=" O LEU h 19 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 4.619A pdb=" N VAL h 62 " --> pdb=" O ASP h 58 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N HIS h 63 " --> pdb=" O GLU h 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 58 through 63' Processing helix chain 'h' and resid 80 through 101 removed outlier: 3.596A pdb=" N ARG h 84 " --> pdb=" O GLY h 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU h 86 " --> pdb=" O ASP h 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN h 95 " --> pdb=" O ARG h 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR h 97 " --> pdb=" O LEU h 93 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 125 removed outlier: 3.525A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER h 124 " --> pdb=" O GLU h 120 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY h 125 " --> pdb=" O TYR h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 4.473A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE h 199 " --> pdb=" O LEU h 195 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 209 removed outlier: 4.168A pdb=" N ILE h 208 " --> pdb=" O THR h 204 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU h 209 " --> pdb=" O GLU h 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 204 through 209' Processing helix chain 'h' and resid 222 through 231 removed outlier: 3.519A pdb=" N VAL h 226 " --> pdb=" O THR h 222 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA h 231 " --> pdb=" O LYS h 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 29 removed outlier: 5.141A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR I 23 " --> pdb=" O TYR I 19 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA I 24 " --> pdb=" O GLN I 20 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY I 29 " --> pdb=" O MET I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 removed outlier: 3.623A pdb=" N VAL I 85 " --> pdb=" O SER I 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN I 95 " --> pdb=" O ARG I 91 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 124 removed outlier: 3.669A pdb=" N ALA I 113 " --> pdb=" O GLN I 109 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 4.715A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR I 179 " --> pdb=" O LEU I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 201 removed outlier: 4.925A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS I 199 " --> pdb=" O LYS I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 212 removed outlier: 3.945A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 230 through 251 removed outlier: 4.037A pdb=" N ARG I 249 " --> pdb=" O ALA I 245 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 29 removed outlier: 5.142A pdb=" N GLU i 22 " --> pdb=" O LEU i 18 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR i 23 " --> pdb=" O TYR i 19 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA i 24 " --> pdb=" O GLN i 20 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY i 29 " --> pdb=" O MET i 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.623A pdb=" N VAL i 85 " --> pdb=" O SER i 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU i 92 " --> pdb=" O ASN i 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN i 95 " --> pdb=" O ARG i 91 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU i 98 " --> pdb=" O ALA i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.670A pdb=" N ALA i 113 " --> pdb=" O GLN i 109 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE i 117 " --> pdb=" O ALA i 113 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR i 122 " --> pdb=" O LYS i 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE i 124 " --> pdb=" O ALA i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 removed outlier: 4.713A pdb=" N ALA i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR i 179 " --> pdb=" O LEU i 175 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 201 removed outlier: 4.924A pdb=" N LEU i 190 " --> pdb=" O LEU i 186 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS i 199 " --> pdb=" O LYS i 195 " (cutoff:3.500A) Processing helix chain 'i' and resid 207 through 212 removed outlier: 3.944A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU i 212 " --> pdb=" O ALA i 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 207 through 212' Processing helix chain 'i' and resid 230 through 251 removed outlier: 4.037A pdb=" N ARG i 249 " --> pdb=" O ALA i 245 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU i 250 " --> pdb=" O LYS i 246 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS i 251 " --> pdb=" O ALA i 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 30 removed outlier: 5.366A pdb=" N GLU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 5.265A pdb=" N VAL J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG J 60 " --> pdb=" O GLU J 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 55 through 60' Processing helix chain 'J' and resid 76 through 98 removed outlier: 4.117A pdb=" N ALA J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 83 " --> pdb=" O ASP J 79 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG J 95 " --> pdb=" O CYS J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 121 removed outlier: 3.527A pdb=" N ILE J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 108 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.926A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN J 175 " --> pdb=" O PHE J 171 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR J 176 " --> pdb=" O LEU J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 removed outlier: 4.167A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 199 removed outlier: 3.557A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 239 removed outlier: 3.872A pdb=" N GLU J 238 " --> pdb=" O LYS J 234 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN J 239 " --> pdb=" O GLU J 235 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 30 removed outlier: 5.365A pdb=" N GLU j 20 " --> pdb=" O LEU j 16 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU j 24 " --> pdb=" O GLU j 20 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 5.266A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG j 60 " --> pdb=" O GLU j 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 55 through 60' Processing helix chain 'j' and resid 76 through 98 removed outlier: 4.117A pdb=" N ALA j 80 " --> pdb=" O LEU j 76 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE j 82 " --> pdb=" O ALA j 78 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL j 83 " --> pdb=" O ASP j 79 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL j 89 " --> pdb=" O ASN j 85 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG j 95 " --> pdb=" O CYS j 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 121 removed outlier: 3.527A pdb=" N ILE j 107 " --> pdb=" O THR j 103 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR j 108 " --> pdb=" O VAL j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 3.926A pdb=" N VAL j 168 " --> pdb=" O GLY j 164 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN j 175 " --> pdb=" O PHE j 171 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR j 176 " --> pdb=" O LEU j 172 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 183 removed outlier: 4.166A pdb=" N ILE j 181 " --> pdb=" O THR j 177 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR j 183 " --> pdb=" O GLU j 179 " (cutoff:3.500A) Processing helix chain 'j' and resid 184 through 199 removed outlier: 3.557A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 239 removed outlier: 3.873A pdb=" N GLU j 238 " --> pdb=" O LYS j 234 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN j 239 " --> pdb=" O GLU j 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 35 removed outlier: 4.023A pdb=" N GLU K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU K 29 " --> pdb=" O GLU K 25 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.574A pdb=" N ILE K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 65' Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.842A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 123 removed outlier: 3.511A pdb=" N THR K 113 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA K 115 " --> pdb=" O SER K 111 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE K 123 " --> pdb=" O LEU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 185 removed outlier: 3.720A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR K 185 " --> pdb=" O LEU K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 removed outlier: 3.522A pdb=" N LEU K 199 " --> pdb=" O ILE K 195 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE K 200 " --> pdb=" O LYS K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 230 through 241 removed outlier: 5.848A pdb=" N GLU K 235 " --> pdb=" O LYS K 231 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU K 236 " --> pdb=" O GLU K 232 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 35 removed outlier: 4.023A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU k 29 " --> pdb=" O GLU k 25 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE k 31 " --> pdb=" O ALA k 27 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER k 35 " --> pdb=" O ILE k 31 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 65 removed outlier: 4.575A pdb=" N ILE k 64 " --> pdb=" O GLU k 60 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU k 65 " --> pdb=" O PRO k 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 60 through 65' Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.842A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR k 96 " --> pdb=" O ALA k 92 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 123 removed outlier: 3.510A pdb=" N THR k 113 " --> pdb=" O VAL k 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA k 115 " --> pdb=" O SER k 111 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN k 122 " --> pdb=" O ASN k 118 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE k 123 " --> pdb=" O LEU k 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 174 through 185 removed outlier: 3.720A pdb=" N VAL k 184 " --> pdb=" O SER k 180 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR k 185 " --> pdb=" O LEU k 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 removed outlier: 3.521A pdb=" N LEU k 199 " --> pdb=" O ILE k 195 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE k 200 " --> pdb=" O LYS k 196 " (cutoff:3.500A) Processing helix chain 'k' and resid 230 through 241 removed outlier: 5.848A pdb=" N GLU k 235 " --> pdb=" O LYS k 231 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU k 236 " --> pdb=" O GLU k 232 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 33 removed outlier: 3.781A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER L 33 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 122 removed outlier: 3.662A pdb=" N SER L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN L 117 " --> pdb=" O GLY L 113 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 164 through 180 removed outlier: 4.265A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG L 174 " --> pdb=" O THR L 170 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 5.278A pdb=" N LEU L 187 " --> pdb=" O ASN L 183 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG L 193 " --> pdb=" O LYS L 189 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 206 through 211 removed outlier: 7.126A pdb=" N VAL L 210 " --> pdb=" O THR L 206 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER L 211 " --> pdb=" O THR L 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 206 through 211' Processing helix chain 'L' and resid 226 through 234 removed outlier: 5.957A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 4.552A pdb=" N GLU L 234 " --> pdb=" O SER L 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 226 through 234' Processing helix chain 'L' and resid 4 through 9 removed outlier: 4.646A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP L 9 " --> pdb=" O TYR L 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 33 removed outlier: 3.781A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU l 27 " --> pdb=" O GLU l 23 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL l 29 " --> pdb=" O ALA l 25 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER l 33 " --> pdb=" O VAL l 29 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 Processing helix chain 'l' and resid 104 through 122 removed outlier: 3.661A pdb=" N SER l 110 " --> pdb=" O SER l 106 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU l 111 " --> pdb=" O ARG l 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN l 117 " --> pdb=" O GLY l 113 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix Processing helix chain 'l' and resid 164 through 180 removed outlier: 4.264A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG l 174 " --> pdb=" O THR l 170 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 5.278A pdb=" N LEU l 187 " --> pdb=" O ASN l 183 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY l 191 " --> pdb=" O LEU l 187 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG l 193 " --> pdb=" O LYS l 189 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU l 197 " --> pdb=" O ARG l 193 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU l 199 " --> pdb=" O LEU l 195 " (cutoff:3.500A) Proline residue: l 200 - end of helix Processing helix chain 'l' and resid 206 through 211 removed outlier: 7.127A pdb=" N VAL l 210 " --> pdb=" O THR l 206 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N SER l 211 " --> pdb=" O THR l 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 206 through 211' Processing helix chain 'l' and resid 226 through 234 removed outlier: 5.958A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 4.553A pdb=" N GLU l 234 " --> pdb=" O SER l 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 226 through 234' Processing helix chain 'l' and resid 4 through 9 removed outlier: 4.646A pdb=" N ASN l 8 " --> pdb=" O GLN l 5 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP l 9 " --> pdb=" O TYR l 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 34 removed outlier: 3.662A pdb=" N LYS M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER M 34 " --> pdb=" O VAL M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 removed outlier: 3.543A pdb=" N SER M 86 " --> pdb=" O ALA M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.824A pdb=" N TYR M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 180 removed outlier: 3.503A pdb=" N THR M 174 " --> pdb=" O GLN M 170 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU M 177 " --> pdb=" O LYS M 173 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLN M 180 " --> pdb=" O ILE M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 201 removed outlier: 4.046A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N HIS M 201 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 242 removed outlier: 3.964A pdb=" N LYS M 237 " --> pdb=" O GLU M 233 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU M 241 " --> pdb=" O LYS M 237 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER M 242 " --> pdb=" O TYR M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 10 removed outlier: 5.206A pdb=" N ASP M 8 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU M 9 " --> pdb=" O GLY M 6 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N SER M 10 " --> pdb=" O TYR M 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 5 through 10' Processing helix chain 'm' and resid 20 through 34 removed outlier: 3.662A pdb=" N LYS m 28 " --> pdb=" O GLU m 24 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL m 30 " --> pdb=" O ALA m 26 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER m 34 " --> pdb=" O VAL m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 102 removed outlier: 3.542A pdb=" N SER m 86 " --> pdb=" O ALA m 82 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 125 removed outlier: 3.825A pdb=" N TYR m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR m 125 " --> pdb=" O ALA m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 169 through 180 removed outlier: 3.502A pdb=" N THR m 174 " --> pdb=" O GLN m 170 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU m 175 " --> pdb=" O ALA m 171 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU m 177 " --> pdb=" O LYS m 173 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLN m 180 " --> pdb=" O ILE m 176 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 201 removed outlier: 4.047A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS m 195 " --> pdb=" O LYS m 191 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE m 196 " --> pdb=" O GLU m 192 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N HIS m 201 " --> pdb=" O ILE m 197 " (cutoff:3.500A) Processing helix chain 'm' and resid 233 through 242 removed outlier: 3.964A pdb=" N LYS m 237 " --> pdb=" O GLU m 233 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU m 241 " --> pdb=" O LYS m 237 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER m 242 " --> pdb=" O TYR m 238 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 10 removed outlier: 5.205A pdb=" N ASP m 8 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU m 9 " --> pdb=" O GLY m 6 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER m 10 " --> pdb=" O TYR m 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 5 through 10' Processing helix chain 'N' and resid 48 through 71 removed outlier: 4.260A pdb=" N THR N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 91 removed outlier: 3.541A pdb=" N PHE N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.639A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 removed outlier: 3.664A pdb=" N ALA N 163 " --> pdb=" O ALA N 159 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 71 removed outlier: 4.259A pdb=" N THR n 52 " --> pdb=" O SER n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.541A pdb=" N PHE n 83 " --> pdb=" O ALA n 79 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.639A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 removed outlier: 3.665A pdb=" N ALA n 163 " --> pdb=" O ALA n 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.569A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.692A pdb=" N VAL O 137 " --> pdb=" O ALA O 133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE O 142 " --> pdb=" O PHE O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 removed outlier: 3.739A pdb=" N ASP O 166 " --> pdb=" O GLY O 162 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.568A pdb=" N ARG o 89 " --> pdb=" O GLN o 85 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.692A pdb=" N VAL o 137 " --> pdb=" O ALA o 133 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE o 142 " --> pdb=" O PHE o 138 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 removed outlier: 3.739A pdb=" N ASP o 166 " --> pdb=" O GLY o 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 8 removed outlier: 5.010A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY P 8 " --> pdb=" O MET P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 79 removed outlier: 3.648A pdb=" N LEU P 73 " --> pdb=" O PHE P 69 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.245A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 153 removed outlier: 3.715A pdb=" N MET P 146 " --> pdb=" O CYS P 142 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 3.574A pdb=" N ASN P 173 " --> pdb=" O GLN P 169 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP P 176 " --> pdb=" O LEU P 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 5.010A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY p 8 " --> pdb=" O MET p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 79 removed outlier: 3.649A pdb=" N LEU p 73 " --> pdb=" O PHE p 69 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY p 79 " --> pdb=" O GLU p 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.245A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 153 removed outlier: 3.715A pdb=" N MET p 146 " --> pdb=" O CYS p 142 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 3.574A pdb=" N ASN p 173 " --> pdb=" O GLN p 169 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP p 176 " --> pdb=" O LEU p 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 72 removed outlier: 7.368A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 95 removed outlier: 3.589A pdb=" N ASN Q 87 " --> pdb=" O PHE Q 83 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG Q 95 " --> pdb=" O CYS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 147 removed outlier: 4.451A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Q 140 " --> pdb=" O ALA Q 136 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR Q 147 " --> pdb=" O LEU Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 170 removed outlier: 3.775A pdb=" N GLU Q 166 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU Q 167 " --> pdb=" O CYS Q 163 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) Processing helix chain 'q' and resid 49 through 72 removed outlier: 7.368A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN q 55 " --> pdb=" O GLY q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 95 removed outlier: 3.588A pdb=" N ASN q 87 " --> pdb=" O PHE q 83 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG q 95 " --> pdb=" O CYS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 134 through 147 removed outlier: 4.451A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU q 140 " --> pdb=" O ALA q 136 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR q 147 " --> pdb=" O LEU q 143 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 170 removed outlier: 3.776A pdb=" N GLU q 166 " --> pdb=" O LYS q 162 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU q 167 " --> pdb=" O CYS q 163 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN q 168 " --> pdb=" O LEU q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 71 removed outlier: 3.530A pdb=" N ARG R 57 " --> pdb=" O SER R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 91 removed outlier: 3.947A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.863A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 removed outlier: 3.510A pdb=" N ARG R 166 " --> pdb=" O GLN R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 201 removed outlier: 3.635A pdb=" N SER R 200 " --> pdb=" O HIS R 196 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY R 201 " --> pdb=" O GLU R 197 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 71 removed outlier: 3.530A pdb=" N ARG r 57 " --> pdb=" O SER r 53 " (cutoff:3.500A) Processing helix chain 'r' and resid 75 through 91 removed outlier: 3.948A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.862A pdb=" N GLY r 137 " --> pdb=" O VAL r 133 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL r 138 " --> pdb=" O TYR r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 removed outlier: 3.510A pdb=" N ARG r 166 " --> pdb=" O GLN r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 191 through 201 removed outlier: 3.635A pdb=" N SER r 200 " --> pdb=" O HIS r 196 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY r 201 " --> pdb=" O GLU r 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 79 removed outlier: 3.546A pdb=" N LYS S 66 " --> pdb=" O LEU S 62 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS S 73 " --> pdb=" O GLU S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.745A pdb=" N THR S 94 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 removed outlier: 3.914A pdb=" N LEU S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.610A pdb=" N PHE S 179 " --> pdb=" O VAL S 175 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE S 180 " --> pdb=" O LYS S 176 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 79 removed outlier: 3.546A pdb=" N LYS s 66 " --> pdb=" O LEU s 62 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS s 73 " --> pdb=" O GLU s 69 " (cutoff:3.500A) Processing helix chain 's' and resid 84 through 100 removed outlier: 3.745A pdb=" N THR s 94 " --> pdb=" O ALA s 90 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 removed outlier: 3.914A pdb=" N LEU s 145 " --> pdb=" O ALA s 141 " (cutoff:3.500A) Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 removed outlier: 3.611A pdb=" N PHE s 179 " --> pdb=" O VAL s 175 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE s 180 " --> pdb=" O LYS s 176 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 3.641A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.726A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 157 removed outlier: 4.225A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.712A pdb=" N VAL T 153 " --> pdb=" O LEU T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 161 through 180 removed outlier: 3.811A pdb=" N ASP T 180 " --> pdb=" O LEU T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 215 removed outlier: 5.664A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 209 through 215' Processing helix chain 't' and resid 56 through 78 removed outlier: 3.642A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.726A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 157 removed outlier: 4.226A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix removed outlier: 3.713A pdb=" N VAL t 153 " --> pdb=" O LEU t 149 " (cutoff:3.500A) Processing helix chain 't' and resid 161 through 180 removed outlier: 3.811A pdb=" N ASP t 180 " --> pdb=" O LEU t 176 " (cutoff:3.500A) Processing helix chain 't' and resid 209 through 215 removed outlier: 5.665A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing sheet with id= 1, first strand: chain 'V' and resid 449 through 452 removed outlier: 3.835A pdb=" N SER V 450 " --> pdb=" O GLN V 459 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'X' and resid 376 through 380 removed outlier: 3.582A pdb=" N VAL X 384 " --> pdb=" O ASP X 379 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'Z' and resid 47 through 50 removed outlier: 3.841A pdb=" N VAL Z 50 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL Z 9 " --> pdb=" O THR Z 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL Z 11 " --> pdb=" O GLU Z 161 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'Z' and resid 52 through 55 removed outlier: 4.911A pdb=" N ASN Z 52 " --> pdb=" O LEU Z 40 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR Z 95 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'Z' and resid 120 through 124 removed outlier: 4.124A pdb=" N LEU Z 121 " --> pdb=" O TYR Z 138 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'a' and resid 320 through 326 removed outlier: 5.128A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'b' and resid 47 through 53 removed outlier: 4.245A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG b 108 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 29 through 33 Processing sheet with id= 9, first strand: chain 'c' and resid 141 through 145 Processing sheet with id= 10, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.443A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.945A pdb=" N VAL A 212 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 107 through 112 removed outlier: 4.366A pdb=" N SER B 149 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 161 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 246 through 251 removed outlier: 3.639A pdb=" N PHE B 283 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 326 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 330 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 349 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 71 through 77 removed outlier: 6.573A pdb=" N ALA C 115 " --> pdb=" O HIS C 124 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR C 122 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 84 through 90 No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'C' and resid 209 through 214 removed outlier: 3.962A pdb=" N LYS C 290 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 294 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY C 190 " --> pdb=" O THR C 295 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 102 through 105 removed outlier: 6.991A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA D 128 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 226 through 231 removed outlier: 5.060A pdb=" N ALA D 226 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE D 261 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 260 " --> pdb=" O ASN D 304 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 306 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 310 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG D 200 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 78 through 81 removed outlier: 7.042A pdb=" N ILE E 70 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR E 96 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 194 through 198 removed outlier: 5.954A pdb=" N LYS E 168 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET E 275 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS E 170 " --> pdb=" O MET E 275 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 171 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR E 173 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 301 " --> pdb=" O TYR E 173 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 95 through 98 removed outlier: 4.030A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL F 123 " --> pdb=" O GLU F 95 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 222 through 227 Processing sheet with id= 23, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.085A pdb=" N THR F 247 " --> pdb=" O PRO F 280 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE F 282 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER F 281 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE F 285 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'F' and resid 121 through 126 removed outlier: 3.833A pdb=" N ALA F 122 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.117A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET G 80 " --> pdb=" O HIS G 68 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR G 81 " --> pdb=" O CYS G 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET G 138 " --> pdb=" O CYS G 154 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY G 142 " --> pdb=" O GLN G 150 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'G' and resid 164 through 169 removed outlier: 6.491A pdb=" N LYS G 164 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE G 50 " --> pdb=" O GLY G 218 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G 228 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.116A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET g 80 " --> pdb=" O HIS g 68 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY g 77 " --> pdb=" O ILE g 141 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR g 81 " --> pdb=" O CYS g 137 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET g 138 " --> pdb=" O CYS g 154 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY g 142 " --> pdb=" O GLN g 150 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'g' and resid 164 through 169 removed outlier: 6.491A pdb=" N LYS g 164 " --> pdb=" O ARG g 43 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE g 50 " --> pdb=" O GLY g 218 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG g 228 " --> pdb=" O VAL g 219 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.560A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'H' and resid 160 through 164 removed outlier: 5.214A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.560A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER h 133 " --> pdb=" O SER h 77 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'h' and resid 160 through 164 removed outlier: 5.214A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'I' and resid 33 through 38 removed outlier: 5.267A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU I 48 " --> pdb=" O THR I 33 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE I 37 " --> pdb=" O LEU I 44 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'I' and resid 72 through 78 removed outlier: 3.510A pdb=" N ALA I 73 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER I 75 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'i' and resid 33 through 38 removed outlier: 5.267A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU i 48 " --> pdb=" O THR i 33 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE i 37 " --> pdb=" O LEU i 44 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'i' and resid 72 through 78 removed outlier: 3.510A pdb=" N ALA i 73 " --> pdb=" O ILE i 137 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER i 75 " --> pdb=" O LEU i 135 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN i 155 " --> pdb=" O ASP i 151 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'J' and resid 62 through 65 removed outlier: 3.648A pdb=" N CYS J 63 " --> pdb=" O MET J 71 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER J 130 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA J 131 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG J 143 " --> pdb=" O GLY J 135 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'J' and resid 158 through 162 removed outlier: 3.507A pdb=" N GLY J 34 " --> pdb=" O ASN J 159 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE J 161 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA J 32 " --> pdb=" O ILE J 161 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'j' and resid 62 through 65 removed outlier: 3.648A pdb=" N CYS j 63 " --> pdb=" O MET j 71 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL j 69 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER j 130 " --> pdb=" O ALA j 74 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA j 131 " --> pdb=" O THR j 147 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG j 143 " --> pdb=" O GLY j 135 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'j' and resid 158 through 162 removed outlier: 3.507A pdb=" N GLY j 34 " --> pdb=" O ASN j 159 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE j 161 " --> pdb=" O ALA j 32 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA j 32 " --> pdb=" O ILE j 161 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.375A pdb=" N LYS K 66 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET K 78 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL K 68 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY K 144 " --> pdb=" O GLY K 75 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU K 141 " --> pdb=" O MET K 156 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP K 157 " --> pdb=" O THR K 161 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR K 161 " --> pdb=" O ASP K 157 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'K' and resid 167 through 171 removed outlier: 5.050A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASN K 214 " --> pdb=" O LYS K 52 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'k' and resid 66 through 70 removed outlier: 6.375A pdb=" N LYS k 66 " --> pdb=" O MET k 78 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET k 78 " --> pdb=" O LYS k 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL k 68 " --> pdb=" O CYS k 76 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY k 144 " --> pdb=" O GLY k 75 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU k 141 " --> pdb=" O MET k 156 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP k 157 " --> pdb=" O THR k 161 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR k 161 " --> pdb=" O ASP k 157 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'k' and resid 167 through 171 removed outlier: 5.050A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN k 214 " --> pdb=" O LYS k 52 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'L' and resid 34 through 39 removed outlier: 4.791A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL L 215 " --> pdb=" O ALA L 44 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'L' and resid 69 through 76 removed outlier: 6.043A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU L 133 " --> pdb=" O SER L 73 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY L 131 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU L 132 " --> pdb=" O THR L 147 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 34 through 39 removed outlier: 4.790A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL l 215 " --> pdb=" O ALA l 44 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'l' and resid 69 through 76 removed outlier: 6.043A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU l 133 " --> pdb=" O SER l 73 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY l 131 " --> pdb=" O ALA l 75 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU l 132 " --> pdb=" O THR l 147 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'M' and resid 66 through 69 removed outlier: 3.840A pdb=" N PHE M 67 " --> pdb=" O MET M 75 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY M 138 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET M 136 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN M 147 " --> pdb=" O SER M 139 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.471A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA M 208 " --> pdb=" O VAL M 53 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'm' and resid 66 through 69 removed outlier: 3.841A pdb=" N PHE m 67 " --> pdb=" O MET m 75 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY m 138 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET m 136 " --> pdb=" O ALA m 76 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN m 147 " --> pdb=" O SER m 139 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'm' and resid 162 through 166 removed outlier: 4.470A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA m 208 " --> pdb=" O VAL m 53 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.814A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.416A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE N 174 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.815A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.417A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE n 174 " --> pdb=" O LEU n 189 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.448A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.429A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP O 17 " --> pdb=" O THR O 2 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.447A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.428A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP o 17 " --> pdb=" O THR o 2 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'P' and resid 42 through 45 removed outlier: 5.521A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU P 106 " --> pdb=" O ALA P 54 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.480A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP P 25 " --> pdb=" O ALA P 10 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.521A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU p 106 " --> pdb=" O ALA p 54 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.480A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP p 25 " --> pdb=" O ALA p 10 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.540A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA Q 105 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU Q 45 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU Q 103 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL Q 47 " --> pdb=" O ASN Q 101 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Q' and resid 129 through 133 removed outlier: 3.742A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP Q 18 " --> pdb=" O TYR Q 3 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY Q 187 " --> pdb=" O ASP Q 184 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.538A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA q 105 " --> pdb=" O LEU q 43 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU q 45 " --> pdb=" O LEU q 103 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU q 103 " --> pdb=" O LEU q 45 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL q 47 " --> pdb=" O ASN q 101 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 129 through 133 removed outlier: 3.742A pdb=" N LEU q 4 " --> pdb=" O HIS q 132 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP q 18 " --> pdb=" O TYR q 3 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL q 180 " --> pdb=" O LEU q 191 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY q 187 " --> pdb=" O ASP q 184 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'R' and resid 34 through 37 removed outlier: 6.453A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA R 46 " --> pdb=" O GLY R 98 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.109A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY R 11 " --> pdb=" O PHE R 8 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.453A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA r 46 " --> pdb=" O GLY r 98 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.108A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.858A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'S' and resid 135 through 139 removed outlier: 6.082A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP S 26 " --> pdb=" O THR S 11 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 's' and resid 43 through 46 removed outlier: 6.858A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 's' and resid 135 through 139 removed outlier: 6.081A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'T' and resid 42 through 45 removed outlier: 3.548A pdb=" N VAL T 45 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR T 109 " --> pdb=" O SER T 54 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.107A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA T 23 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE T 189 " --> pdb=" O GLU T 200 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY T 196 " --> pdb=" O THR T 193 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 't' and resid 42 through 45 removed outlier: 3.548A pdb=" N VAL t 45 " --> pdb=" O THR t 49 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR t 109 " --> pdb=" O SER t 54 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 't' and resid 136 through 139 removed outlier: 4.107A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA t 23 " --> pdb=" O LEU t 12 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) 4887 hydrogen bonds defined for protein. 14571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 50.25 Time building geometry restraints manager: 34.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 30262 1.33 - 1.46: 22566 1.46 - 1.58: 51668 1.58 - 1.71: 18 1.71 - 1.83: 1002 Bond restraints: 105516 Sorted by residual: bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C5 ATP E 401 " pdb=" C6 ATP E 401 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.02e+01 ... (remaining 105511 not shown) Histogram of bond angle deviations from ideal: 96.43 - 104.99: 1820 104.99 - 113.54: 59776 113.54 - 122.10: 61567 122.10 - 130.65: 19093 130.65 - 139.21: 457 Bond angle restraints: 142713 Sorted by residual: angle pdb=" PA ATP E 401 " pdb=" O3A ATP E 401 " pdb=" PB ATP E 401 " ideal model delta sigma weight residual 136.83 113.60 23.23 1.00e+00 1.00e+00 5.40e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.91 20.96 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.25 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 121.19 18.68 1.00e+00 1.00e+00 3.49e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.60 16.23 1.00e+00 1.00e+00 2.63e+02 ... (remaining 142708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 63617 35.42 - 70.84: 596 70.84 - 106.27: 75 106.27 - 141.69: 1 141.69 - 177.11: 2 Dihedral angle restraints: 64291 sinusoidal: 25577 harmonic: 38714 Sorted by residual: dihedral pdb=" CA ARG f 807 " pdb=" C ARG f 807 " pdb=" N ASN f 808 " pdb=" CA ASN f 808 " ideal model delta harmonic sigma weight residual -180.00 -114.25 -65.75 0 5.00e+00 4.00e-02 1.73e+02 dihedral pdb=" CA GLN E 226 " pdb=" C GLN E 226 " pdb=" N PRO E 227 " pdb=" CA PRO E 227 " ideal model delta harmonic sigma weight residual -180.00 -120.76 -59.24 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA ARG A 284 " pdb=" C ARG A 284 " pdb=" N PHE A 285 " pdb=" CA PHE A 285 " ideal model delta harmonic sigma weight residual -180.00 -122.29 -57.71 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 64288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 14034 0.081 - 0.161: 2032 0.161 - 0.242: 146 0.242 - 0.322: 13 0.322 - 0.403: 4 Chirality restraints: 16229 Sorted by residual: chirality pdb=" CB ILE f 809 " pdb=" CA ILE f 809 " pdb=" CG1 ILE f 809 " pdb=" CG2 ILE f 809 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA THR E 247 " pdb=" N THR E 247 " pdb=" C THR E 247 " pdb=" CB THR E 247 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB VAL f 852 " pdb=" CA VAL f 852 " pdb=" CG1 VAL f 852 " pdb=" CG2 VAL f 852 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 16226 not shown) Planarity restraints: 18467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP f 755 " 0.078 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO f 756 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO f 756 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO f 756 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 226 " 0.065 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO E 227 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO E 227 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 227 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 284 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ARG A 284 " -0.067 2.00e-02 2.50e+03 pdb=" O ARG A 284 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE A 285 " 0.023 2.00e-02 2.50e+03 ... (remaining 18464 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 156 2.38 - 3.01: 51208 3.01 - 3.64: 156247 3.64 - 4.27: 227960 4.27 - 4.90: 372854 Nonbonded interactions: 808425 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 1.749 2.230 nonbonded pdb=" NE2 GLN W 456 " pdb=" OXT GLN W 456 " model vdw 1.984 2.520 nonbonded pdb=" OH TYR V 467 " pdb=" OH TYR X 397 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR c 178 " pdb=" OD1 ASN c 180 " model vdw 2.228 2.440 nonbonded pdb=" CD GLN W 456 " pdb=" OXT GLN W 456 " model vdw 2.232 3.270 ... (remaining 808420 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 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 13.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 45.340 Check model and map are aligned: 1.180 Set scattering table: 0.710 Process input model: 279.970 Find NCS groups from input model: 7.170 Set up NCS constraints: 1.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 351.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 105516 Z= 0.486 Angle : 1.104 23.235 142713 Z= 0.633 Chirality : 0.056 0.403 16229 Planarity : 0.007 0.119 18467 Dihedral : 11.319 177.111 39371 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.60 % Favored : 91.07 % Rotamer: Outliers : 0.82 % Allowed : 4.59 % Favored : 94.59 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.08 % Twisted Proline : 1.29 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.05), residues: 13216 helix: -3.65 (0.04), residues: 5867 sheet: -2.03 (0.12), residues: 1832 loop : -3.55 (0.07), residues: 5517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP M 215 HIS 0.015 0.003 HIS C 205 PHE 0.058 0.004 PHE m 102 TYR 0.062 0.003 TYR f 681 ARG 0.020 0.001 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1344 time to evaluate : 9.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 27 LEU cc_start: 0.8185 (mt) cc_final: 0.7953 (tp) REVERT: U 120 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7799 (pm20) REVERT: U 176 MET cc_start: 0.7400 (mmp) cc_final: 0.7114 (mmt) REVERT: U 188 MET cc_start: 0.4991 (tpp) cc_final: 0.2937 (tpp) REVERT: U 427 LEU cc_start: 0.7905 (mp) cc_final: 0.7667 (tp) REVERT: U 819 VAL cc_start: 0.5398 (OUTLIER) cc_final: 0.4857 (p) REVERT: V 181 TYR cc_start: 0.8836 (m-10) cc_final: 0.8583 (m-10) REVERT: V 247 GLN cc_start: 0.8637 (tt0) cc_final: 0.8140 (tm-30) REVERT: V 396 ILE cc_start: 0.8079 (tp) cc_final: 0.7875 (mm) REVERT: W 1 MET cc_start: 0.6473 (tpt) cc_final: 0.5921 (tmm) REVERT: W 135 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.4458 (mmtt) REVERT: W 233 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8591 (mm) REVERT: W 241 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7819 (mt) REVERT: X 395 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9075 (pttp) REVERT: Y 364 TRP cc_start: 0.8535 (t-100) cc_final: 0.7884 (t-100) REVERT: Z 8 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8126 (tppt) REVERT: Z 81 MET cc_start: 0.8688 (mtt) cc_final: 0.7583 (mtt) REVERT: Z 88 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.8280 (ttp80) REVERT: Z 91 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8010 (mt) REVERT: a 81 LEU cc_start: 0.7603 (pp) cc_final: 0.7332 (tt) REVERT: a 87 MET cc_start: 0.4674 (mtp) cc_final: 0.3844 (ptt) REVERT: a 136 GLU cc_start: 0.9020 (tt0) cc_final: 0.8650 (pp20) REVERT: b 15 TYR cc_start: 0.6414 (m-10) cc_final: 0.6107 (m-10) REVERT: b 178 SER cc_start: 0.3772 (t) cc_final: 0.3527 (p) REVERT: c 57 MET cc_start: 0.8855 (ttp) cc_final: 0.8587 (ttm) REVERT: c 95 MET cc_start: 0.9062 (tpt) cc_final: 0.8812 (mmm) REVERT: c 105 PRO cc_start: 0.8586 (Cg_endo) cc_final: 0.7722 (Cg_exo) REVERT: c 226 MET cc_start: 0.7233 (pmm) cc_final: 0.6466 (pmm) REVERT: d 1 MET cc_start: 0.4664 (ttt) cc_final: 0.3760 (mtt) REVERT: d 61 TRP cc_start: 0.7283 (m-10) cc_final: 0.7018 (m-90) REVERT: d 111 ARG cc_start: 0.7391 (mmt-90) cc_final: 0.7118 (mmt90) REVERT: d 118 GLU cc_start: 0.8782 (tm-30) cc_final: 0.7717 (tm-30) REVERT: f 180 GLN cc_start: 0.2526 (mt0) cc_final: 0.1980 (mp10) REVERT: f 184 LEU cc_start: 0.2715 (mp) cc_final: 0.2307 (mm) REVERT: f 761 MET cc_start: 0.3811 (tpt) cc_final: 0.2823 (mmt) REVERT: A 256 MET cc_start: 0.6938 (mmt) cc_final: 0.6736 (mtp) REVERT: A 262 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8362 (pt0) REVERT: A 280 ILE cc_start: 0.6564 (pp) cc_final: 0.6193 (tt) REVERT: A 299 MET cc_start: 0.9179 (tmt) cc_final: 0.8889 (tmm) REVERT: B 333 ARG cc_start: 0.8608 (ptp-170) cc_final: 0.7969 (ppt90) REVERT: B 372 MET cc_start: -0.1285 (ptm) cc_final: -0.2927 (ttt) REVERT: C 72 TYR cc_start: 0.8947 (m-10) cc_final: 0.8664 (m-10) REVERT: C 273 MET cc_start: 0.8928 (ttp) cc_final: 0.8457 (ttp) REVERT: C 387 VAL cc_start: 0.9258 (t) cc_final: 0.9053 (p) REVERT: C 399 MET cc_start: 0.6453 (mmt) cc_final: 0.5770 (tpp) REVERT: E 277 MET cc_start: 0.8341 (mmt) cc_final: 0.7656 (mmt) REVERT: F 224 LEU cc_start: 0.9573 (tp) cc_final: 0.9224 (tp) REVERT: I 25 MET cc_start: 0.8242 (mtp) cc_final: 0.8016 (mtm) REVERT: J 176 TYR cc_start: 0.6153 (m-10) cc_final: 0.5928 (m-10) REVERT: P 171 MET cc_start: 0.8844 (mmm) cc_final: 0.8546 (mmt) REVERT: S 118 LYS cc_start: 0.8707 (mttp) cc_final: 0.8212 (mttm) REVERT: T 103 MET cc_start: 0.8754 (mmm) cc_final: 0.8418 (mmm) REVERT: g 73 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8840 (t) REVERT: g 212 PRO cc_start: 0.7789 (Cg_exo) cc_final: 0.7536 (Cg_endo) REVERT: j 159 ASN cc_start: 0.7542 (t0) cc_final: 0.7305 (m110) REVERT: k 78 MET cc_start: 0.8071 (ptp) cc_final: 0.7814 (ppp) REVERT: l 26 MET cc_start: 0.8626 (mmt) cc_final: 0.8264 (mmm) REVERT: t 96 MET cc_start: 0.9095 (mmp) cc_final: 0.8812 (mmm) outliers start: 91 outliers final: 24 residues processed: 1429 average time/residue: 1.0066 time to fit residues: 2392.9272 Evaluate side-chains 709 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 678 time to evaluate : 9.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 233 LEU Chi-restraints excluded: chain W residue 239 SER Chi-restraints excluded: chain W residue 241 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 8 LYS Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 806 VAL Chi-restraints excluded: chain f residue 822 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain i residue 228 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 1112 optimal weight: 0.0870 chunk 998 optimal weight: 6.9990 chunk 553 optimal weight: 20.0000 chunk 340 optimal weight: 40.0000 chunk 673 optimal weight: 2.9990 chunk 533 optimal weight: 6.9990 chunk 1032 optimal weight: 0.9980 chunk 399 optimal weight: 50.0000 chunk 627 optimal weight: 2.9990 chunk 768 optimal weight: 5.9990 chunk 1195 optimal weight: 8.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 70 HIS U 107 HIS U 111 GLN U 207 ASN U 412 HIS ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 541 HIS ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN U 888 GLN V 33 GLN V 318 GLN V 453 HIS V 473 GLN V 487 HIS W 86 ASN W 96 GLN W 107 GLN W 203 GLN W 235 GLN ** W 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 257 GLN X 178 HIS ** X 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 48 ASN Y 71 ASN Z 72 HIS Z 225 GLN ** Z 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN a 144 ASN a 152 HIS ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 ASN a 249 GLN a 332 HIS a 370 GLN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 197 ASN c 199 HIS c 237 HIS d 47 GLN ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 GLN f 112 ASN f 118 ASN ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 213 GLN ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN ** f 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 396 ASN f 531 ASN f 565 ASN f 614 HIS f 619 HIS f 737 ASN ** f 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 782 HIS f 815 HIS ** f 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 117 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS B 332 ASN B 416 ASN C 40 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN C 279 GLN C 398 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS D 257 ASN D 302 ASN D 353 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 243 GLN F 315 ASN H 102 GLN H 112 GLN I 20 GLN I 53 HIS I 84 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 GLN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 ASN M 97 ASN ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 165 ASN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN Q 132 HIS S 151 ASN h 102 GLN i 53 HIS i 84 ASN ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 119 GLN ** i 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 116 GLN ** j 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 154 GLN o 165 ASN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN q 132 HIS q 174 ASN r 62 GLN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 105516 Z= 0.201 Angle : 0.693 18.805 142713 Z= 0.359 Chirality : 0.043 0.207 16229 Planarity : 0.005 0.112 18467 Dihedral : 6.794 171.781 14693 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.18 % Rotamer: Outliers : 1.79 % Allowed : 8.57 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.08 % Twisted Proline : 0.43 % 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: -3.04 (0.06), residues: 13216 helix: -1.14 (0.06), residues: 6106 sheet: -1.41 (0.12), residues: 1788 loop : -3.28 (0.07), residues: 5322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP Y 286 HIS 0.020 0.001 HIS Y 344 PHE 0.025 0.002 PHE m 102 TYR 0.027 0.001 TYR f 681 ARG 0.016 0.001 ARG c 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 741 time to evaluate : 9.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 27 LEU cc_start: 0.8109 (mt) cc_final: 0.7862 (tp) REVERT: U 120 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7853 (pm20) REVERT: U 176 MET cc_start: 0.7295 (mmp) cc_final: 0.7037 (mmt) REVERT: U 757 MET cc_start: 0.7444 (tpp) cc_final: 0.7167 (tpp) REVERT: U 819 VAL cc_start: 0.5205 (OUTLIER) cc_final: 0.4506 (p) REVERT: V 146 GLN cc_start: 0.4779 (OUTLIER) cc_final: 0.4324 (pm20) REVERT: V 264 TYR cc_start: 0.8582 (t80) cc_final: 0.8306 (m-80) REVERT: W 73 MET cc_start: 0.8861 (tmm) cc_final: 0.8526 (ppp) REVERT: W 130 MET cc_start: 0.3880 (mtt) cc_final: 0.3575 (mtt) REVERT: W 135 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.3998 (mmtt) REVERT: W 177 MET cc_start: 0.5728 (tpp) cc_final: 0.5511 (mmt) REVERT: X 260 MET cc_start: 0.9229 (mmt) cc_final: 0.8997 (mmm) REVERT: Y 167 LEU cc_start: 0.7070 (tt) cc_final: 0.6696 (mp) REVERT: Y 364 TRP cc_start: 0.8451 (t-100) cc_final: 0.8191 (t-100) REVERT: Z 78 MET cc_start: 0.8531 (mmm) cc_final: 0.8181 (mmm) REVERT: Z 88 ARG cc_start: 0.8565 (tpp-160) cc_final: 0.8243 (ttp80) REVERT: Z 91 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8029 (mt) REVERT: Z 267 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7990 (ttp80) REVERT: b 178 SER cc_start: 0.3285 (t) cc_final: 0.3041 (p) REVERT: c 51 MET cc_start: 0.7823 (mpp) cc_final: 0.6180 (tmm) REVERT: c 105 PRO cc_start: 0.8040 (Cg_endo) cc_final: 0.7727 (Cg_exo) REVERT: d 1 MET cc_start: 0.4338 (ttt) cc_final: 0.4116 (mtt) REVERT: f 131 MET cc_start: -0.0744 (tpp) cc_final: -0.0995 (mpp) REVERT: f 133 MET cc_start: 0.1382 (tmm) cc_final: 0.0833 (ttm) REVERT: f 180 GLN cc_start: 0.2722 (mt0) cc_final: 0.2169 (mp10) REVERT: f 615 ILE cc_start: 0.5608 (OUTLIER) cc_final: 0.5357 (tp) REVERT: f 731 MET cc_start: 0.3418 (ptt) cc_final: 0.2759 (ttt) REVERT: A 164 MET cc_start: 0.1760 (mmm) cc_final: 0.0434 (mtt) REVERT: A 262 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8464 (pt0) REVERT: A 280 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6085 (tt) REVERT: A 299 MET cc_start: 0.9262 (tmt) cc_final: 0.9024 (tmm) REVERT: B 164 MET cc_start: 0.5572 (pmm) cc_final: 0.5189 (ppp) REVERT: C 139 MET cc_start: 0.7275 (mtt) cc_final: 0.6974 (mpp) REVERT: C 293 MET cc_start: 0.6702 (mpp) cc_final: 0.6487 (mpp) REVERT: C 399 MET cc_start: 0.6438 (mmt) cc_final: 0.5659 (tpp) REVERT: D 68 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8665 (tm) REVERT: J 176 TYR cc_start: 0.6131 (m-10) cc_final: 0.5827 (m-10) REVERT: K 226 PHE cc_start: 0.7622 (p90) cc_final: 0.7265 (p90) REVERT: L 88 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8291 (mpp) REVERT: T 103 MET cc_start: 0.8795 (mmm) cc_final: 0.8521 (mmm) REVERT: h 10 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6430 (pp) REVERT: i 25 MET cc_start: 0.8381 (ptm) cc_final: 0.8164 (ptp) REVERT: j 159 ASN cc_start: 0.7392 (t0) cc_final: 0.7006 (m110) REVERT: l 26 MET cc_start: 0.8665 (mmt) cc_final: 0.8338 (mmm) REVERT: p 90 MET cc_start: 0.8759 (ttp) cc_final: 0.8472 (ttp) REVERT: s 158 MET cc_start: 0.6973 (mtm) cc_final: 0.6758 (mtm) outliers start: 198 outliers final: 73 residues processed: 902 average time/residue: 0.9082 time to fit residues: 1425.3939 Evaluate side-chains 687 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 604 time to evaluate : 9.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 712 LEU Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 146 GLN Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 251 LEU Chi-restraints excluded: chain V residue 392 TYR Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 239 SER Chi-restraints excluded: chain W residue 241 LEU Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 194 PHE Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain d residue 62 SER Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 576 ILE Chi-restraints excluded: chain f residue 615 ILE Chi-restraints excluded: chain f residue 806 VAL Chi-restraints excluded: chain f residue 822 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 186 ASP Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 205 LEU Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 120 MET Chi-restraints excluded: chain q residue 24 ASN Chi-restraints excluded: chain r residue 62 GLN Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 664 optimal weight: 6.9990 chunk 371 optimal weight: 30.0000 chunk 995 optimal weight: 10.0000 chunk 814 optimal weight: 20.0000 chunk 329 optimal weight: 0.0000 chunk 1198 optimal weight: 7.9990 chunk 1294 optimal weight: 10.0000 chunk 1067 optimal weight: 5.9990 chunk 1188 optimal weight: 2.9990 chunk 408 optimal weight: 30.0000 chunk 961 optimal weight: 20.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN W 106 GLN ** W 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 362 ASN ** X 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 213 GLN X 380 GLN X 405 GLN ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 HIS Z 12 HIS Z 96 HIS Z 229 GLN ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 10 GLN ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 219 HIS a 257 GLN b 137 ASN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 387 GLN f 752 HIS ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN L 117 GLN M 97 ASN N 71 ASN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 HIS i 30 HIS ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 154 HIS ** j 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 ASN n 66 HIS ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 174 ASN r 62 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 105516 Z= 0.250 Angle : 0.662 20.601 142713 Z= 0.341 Chirality : 0.043 0.232 16229 Planarity : 0.005 0.104 18467 Dihedral : 6.392 176.431 14676 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.84 % Rotamer: Outliers : 2.01 % Allowed : 9.60 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.07), residues: 13216 helix: 0.02 (0.07), residues: 6091 sheet: -1.10 (0.12), residues: 1836 loop : -3.07 (0.08), residues: 5289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 100 HIS 0.014 0.001 HIS Y 344 PHE 0.025 0.002 PHE m 102 TYR 0.029 0.002 TYR X 201 ARG 0.015 0.001 ARG E 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 629 time to evaluate : 9.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 27 LEU cc_start: 0.7949 (mt) cc_final: 0.7665 (tp) REVERT: U 120 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7867 (pm20) REVERT: U 588 MET cc_start: 0.8391 (ttt) cc_final: 0.8156 (ttt) REVERT: U 757 MET cc_start: 0.7538 (tpp) cc_final: 0.7170 (tpp) REVERT: U 819 VAL cc_start: 0.5356 (OUTLIER) cc_final: 0.4857 (p) REVERT: V 146 GLN cc_start: 0.4738 (OUTLIER) cc_final: 0.4447 (pm20) REVERT: V 264 TYR cc_start: 0.8632 (t80) cc_final: 0.8325 (m-80) REVERT: W 60 MET cc_start: 0.0142 (mpp) cc_final: -0.0292 (mtm) REVERT: W 73 MET cc_start: 0.8851 (tmm) cc_final: 0.8581 (ppp) REVERT: W 177 MET cc_start: 0.5752 (tpp) cc_final: 0.5519 (mmt) REVERT: W 230 MET cc_start: 0.7859 (tpp) cc_final: 0.7529 (tpp) REVERT: W 281 ASN cc_start: 0.8924 (t0) cc_final: 0.8642 (p0) REVERT: Y 163 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8212 (ptpp) REVERT: Y 167 LEU cc_start: 0.7224 (tt) cc_final: 0.6841 (mp) REVERT: Z 78 MET cc_start: 0.8387 (mmm) cc_final: 0.8112 (mmm) REVERT: Z 81 MET cc_start: 0.9104 (mtt) cc_final: 0.8869 (mtt) REVERT: Z 88 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.8227 (ttp80) REVERT: Z 91 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8038 (mt) REVERT: Z 267 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7866 (ttp80) REVERT: b 178 SER cc_start: 0.3387 (t) cc_final: 0.3061 (p) REVERT: c 51 MET cc_start: 0.7994 (mpp) cc_final: 0.6387 (tmm) REVERT: c 95 MET cc_start: 0.8864 (mmm) cc_final: 0.8658 (mmm) REVERT: c 160 PHE cc_start: 0.7120 (m-80) cc_final: 0.6859 (m-10) REVERT: c 250 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8581 (mm-30) REVERT: d 1 MET cc_start: 0.4351 (ttt) cc_final: 0.4102 (mtt) REVERT: d 61 TRP cc_start: 0.7342 (m-10) cc_final: 0.6798 (m-10) REVERT: f 126 ILE cc_start: -0.1019 (OUTLIER) cc_final: -0.1309 (pt) REVERT: f 133 MET cc_start: 0.1314 (tmm) cc_final: 0.0923 (ttm) REVERT: f 512 MET cc_start: 0.3812 (tpt) cc_final: 0.3192 (ptt) REVERT: f 615 ILE cc_start: 0.5635 (OUTLIER) cc_final: 0.5426 (tp) REVERT: f 670 MET cc_start: 0.0010 (tpt) cc_final: -0.0317 (tpt) REVERT: A 280 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.5874 (tt) REVERT: A 299 MET cc_start: 0.9240 (tmt) cc_final: 0.9022 (tmm) REVERT: B 164 MET cc_start: 0.5625 (pmm) cc_final: 0.5250 (ppp) REVERT: B 333 ARG cc_start: 0.8686 (ptp-170) cc_final: 0.8245 (ptt90) REVERT: C 139 MET cc_start: 0.7736 (mtt) cc_final: 0.7430 (mpp) REVERT: C 150 MET cc_start: 0.8219 (ptp) cc_final: 0.8007 (ptm) REVERT: C 220 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8496 (t) REVERT: C 399 MET cc_start: 0.6559 (mmt) cc_final: 0.6142 (mmt) REVERT: E 232 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8354 (ttm) REVERT: E 277 MET cc_start: 0.8227 (mmp) cc_final: 0.7691 (mmm) REVERT: F 421 MET cc_start: 0.2602 (mmm) cc_final: 0.2042 (mmm) REVERT: J 176 TYR cc_start: 0.6215 (m-10) cc_final: 0.5697 (m-10) REVERT: L 88 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8380 (mpp) REVERT: h 10 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6621 (pp) REVERT: i 25 MET cc_start: 0.8489 (ptm) cc_final: 0.8248 (ptp) REVERT: j 159 ASN cc_start: 0.7742 (t0) cc_final: 0.7320 (m110) REVERT: l 26 MET cc_start: 0.8682 (mmt) cc_final: 0.8330 (mmm) REVERT: q 118 MET cc_start: 0.8599 (tpp) cc_final: 0.8040 (ttm) outliers start: 222 outliers final: 99 residues processed: 818 average time/residue: 0.8956 time to fit residues: 1309.3663 Evaluate side-chains 686 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 575 time to evaluate : 9.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 712 LEU Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 146 GLN Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 396 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 239 SER Chi-restraints excluded: chain X residue 156 GLU Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 158 ASN Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 235 SER Chi-restraints excluded: chain d residue 62 SER Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 188 LYS Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain f residue 126 ILE Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 381 VAL Chi-restraints excluded: chain f residue 576 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 615 ILE Chi-restraints excluded: chain f residue 741 LEU Chi-restraints excluded: chain f residue 806 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 168 SER Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 48 LEU Chi-restraints excluded: chain k residue 148 GLU Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain q residue 24 ASN Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 1183 optimal weight: 5.9990 chunk 900 optimal weight: 5.9990 chunk 621 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 571 optimal weight: 2.9990 chunk 804 optimal weight: 5.9990 chunk 1202 optimal weight: 4.9990 chunk 1273 optimal weight: 3.9990 chunk 628 optimal weight: 7.9990 chunk 1139 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 711 GLN V 168 GLN V 177 ASN ** W 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 HIS ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 148 GLN ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 866 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 HIS Q 65 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN S 160 ASN ** T 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 95 GLN ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 175 ASN m 72 HIS ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 105516 Z= 0.195 Angle : 0.612 20.696 142713 Z= 0.312 Chirality : 0.043 0.312 16229 Planarity : 0.004 0.114 18467 Dihedral : 6.105 177.256 14673 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.79 % Favored : 92.12 % Rotamer: Outliers : 2.03 % Allowed : 10.48 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.07), residues: 13216 helix: 0.49 (0.07), residues: 6140 sheet: -0.96 (0.12), residues: 1873 loop : -2.94 (0.08), residues: 5203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP d 9 HIS 0.014 0.001 HIS Z 174 PHE 0.022 0.001 PHE m 102 TYR 0.020 0.001 TYR X 201 ARG 0.011 0.000 ARG F 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 615 time to evaluate : 9.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 27 LEU cc_start: 0.7857 (mt) cc_final: 0.7543 (tp) REVERT: U 120 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7854 (pm20) REVERT: U 588 MET cc_start: 0.8341 (ttt) cc_final: 0.8140 (ttt) REVERT: U 725 MET cc_start: 0.8138 (ppp) cc_final: 0.7800 (tmm) REVERT: U 757 MET cc_start: 0.7533 (tpp) cc_final: 0.7167 (tpp) REVERT: U 819 VAL cc_start: 0.5247 (OUTLIER) cc_final: 0.4744 (p) REVERT: V 264 TYR cc_start: 0.8626 (t80) cc_final: 0.8329 (m-80) REVERT: W 177 MET cc_start: 0.5785 (tpp) cc_final: 0.5549 (mmt) REVERT: W 230 MET cc_start: 0.7893 (tpp) cc_final: 0.7572 (tpp) REVERT: W 281 ASN cc_start: 0.8913 (t0) cc_final: 0.8681 (p0) REVERT: Z 7 GLN cc_start: 0.6580 (pt0) cc_final: 0.6289 (tm-30) REVERT: Z 78 MET cc_start: 0.8399 (mmm) cc_final: 0.8154 (mmm) REVERT: Z 88 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8221 (ttp80) REVERT: Z 267 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7754 (ttp80) REVERT: b 178 SER cc_start: 0.2953 (t) cc_final: 0.2671 (p) REVERT: d 52 ARG cc_start: 0.5730 (OUTLIER) cc_final: 0.5473 (ptp-170) REVERT: d 61 TRP cc_start: 0.7302 (m-10) cc_final: 0.6789 (m-10) REVERT: f 133 MET cc_start: 0.1233 (tmm) cc_final: 0.0764 (ttm) REVERT: f 297 MET cc_start: 0.0691 (tpp) cc_final: 0.0406 (ptt) REVERT: f 512 MET cc_start: 0.3540 (tpt) cc_final: 0.2789 (ptp) REVERT: f 595 VAL cc_start: 0.2467 (OUTLIER) cc_final: 0.2236 (t) REVERT: f 670 MET cc_start: -0.0181 (tpt) cc_final: -0.0824 (tpp) REVERT: f 694 LEU cc_start: -0.1593 (OUTLIER) cc_final: -0.1901 (mt) REVERT: f 727 PHE cc_start: 0.4779 (t80) cc_final: 0.4574 (t80) REVERT: A 280 ILE cc_start: 0.6594 (OUTLIER) cc_final: 0.5963 (tt) REVERT: A 299 MET cc_start: 0.9241 (tmt) cc_final: 0.9029 (tmm) REVERT: B 164 MET cc_start: 0.5615 (pmm) cc_final: 0.5250 (ppp) REVERT: B 174 MET cc_start: 0.0460 (mmt) cc_final: 0.0147 (tpp) REVERT: B 312 LEU cc_start: 0.8917 (mm) cc_final: 0.8676 (pp) REVERT: B 355 LEU cc_start: 0.6836 (tp) cc_final: 0.6615 (tp) REVERT: C 72 TYR cc_start: 0.8651 (m-10) cc_final: 0.8324 (m-80) REVERT: C 139 MET cc_start: 0.7656 (mtt) cc_final: 0.7376 (mpp) REVERT: C 150 MET cc_start: 0.8279 (ptp) cc_final: 0.8067 (ptm) REVERT: C 220 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8485 (t) REVERT: C 351 MET cc_start: 0.7863 (mmm) cc_final: 0.7537 (tpp) REVERT: C 399 MET cc_start: 0.6427 (mmt) cc_final: 0.6192 (mmm) REVERT: E 277 MET cc_start: 0.8225 (mmp) cc_final: 0.7955 (mmp) REVERT: G 155 ASP cc_start: 0.8254 (t0) cc_final: 0.7978 (t0) REVERT: J 176 TYR cc_start: 0.6273 (m-10) cc_final: 0.6062 (m-10) REVERT: L 88 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8418 (mpp) REVERT: i 3 ARG cc_start: 0.6891 (mmm160) cc_final: 0.6471 (mmp80) REVERT: i 25 MET cc_start: 0.8463 (ptm) cc_final: 0.8229 (ptp) REVERT: l 26 MET cc_start: 0.8616 (mmt) cc_final: 0.8271 (mmm) REVERT: n 116 MET cc_start: 0.8406 (mtp) cc_final: 0.8204 (mtp) REVERT: q 58 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8120 (mm-30) REVERT: q 118 MET cc_start: 0.8590 (tpp) cc_final: 0.8214 (ttm) outliers start: 224 outliers final: 111 residues processed: 814 average time/residue: 0.8775 time to fit residues: 1265.6239 Evaluate side-chains 691 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 572 time to evaluate : 9.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 224 LEU Chi-restraints excluded: chain V residue 245 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain X residue 156 GLU Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 237 ARG Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 158 ASN Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 235 SER Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 188 LYS Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 381 VAL Chi-restraints excluded: chain f residue 576 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 595 VAL Chi-restraints excluded: chain f residue 694 LEU Chi-restraints excluded: chain f residue 732 VAL Chi-restraints excluded: chain f residue 741 LEU Chi-restraints excluded: chain f residue 806 VAL Chi-restraints excluded: chain f residue 809 ILE Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 205 LEU Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 120 MET Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain q residue 24 ASN Chi-restraints excluded: chain q residue 177 THR Chi-restraints excluded: chain r residue 136 TYR Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 1060 optimal weight: 0.8980 chunk 722 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 947 optimal weight: 10.0000 chunk 525 optimal weight: 6.9990 chunk 1086 optimal weight: 1.9990 chunk 879 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 650 optimal weight: 20.0000 chunk 1142 optimal weight: 3.9990 chunk 321 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 111 GLN U 115 ASN ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN V 168 GLN W 84 ASN ** W 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 71 ASN Y 291 HIS ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 10 GLN ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 56 ASN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 GLN d 102 ASN ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN T 69 GLN T 81 HIS q 82 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 105516 Z= 0.157 Angle : 0.586 20.071 142713 Z= 0.296 Chirality : 0.042 0.244 16229 Planarity : 0.004 0.104 18467 Dihedral : 5.882 174.948 14669 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.28 % Rotamer: Outliers : 1.97 % Allowed : 11.05 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.07), residues: 13216 helix: 0.81 (0.07), residues: 6122 sheet: -0.79 (0.12), residues: 1872 loop : -2.81 (0.08), residues: 5222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 215 HIS 0.009 0.001 HIS Y 344 PHE 0.018 0.001 PHE m 102 TYR 0.022 0.001 TYR d 82 ARG 0.008 0.000 ARG c 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 619 time to evaluate : 9.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 27 LEU cc_start: 0.7832 (mt) cc_final: 0.7517 (tp) REVERT: U 120 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7871 (pm20) REVERT: U 206 MET cc_start: 0.8472 (mmm) cc_final: 0.8266 (mmm) REVERT: U 757 MET cc_start: 0.7528 (tpp) cc_final: 0.7176 (tpp) REVERT: U 819 VAL cc_start: 0.5264 (OUTLIER) cc_final: 0.4767 (p) REVERT: V 264 TYR cc_start: 0.8628 (t80) cc_final: 0.8328 (m-80) REVERT: V 299 GLN cc_start: 0.8793 (tp40) cc_final: 0.8519 (tm-30) REVERT: V 309 MET cc_start: 0.6139 (ttt) cc_final: 0.5928 (ppp) REVERT: V 358 MET cc_start: 0.7531 (pmm) cc_final: 0.7323 (pmm) REVERT: W 60 MET cc_start: -0.0408 (mpp) cc_final: -0.0807 (mtm) REVERT: W 130 MET cc_start: 0.3837 (mtt) cc_final: 0.3409 (mmm) REVERT: W 177 MET cc_start: 0.5659 (tpp) cc_final: 0.5434 (mmt) REVERT: W 230 MET cc_start: 0.7898 (tpp) cc_final: 0.7524 (tpp) REVERT: W 281 ASN cc_start: 0.8901 (t0) cc_final: 0.8683 (p0) REVERT: W 366 MET cc_start: 0.8909 (ptp) cc_final: 0.8639 (ptp) REVERT: Z 7 GLN cc_start: 0.6641 (pt0) cc_final: 0.6364 (tm-30) REVERT: Z 81 MET cc_start: 0.8880 (mtt) cc_final: 0.8535 (mtt) REVERT: Z 88 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8328 (tmm-80) REVERT: Z 267 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7758 (ttp80) REVERT: a 87 MET cc_start: 0.2785 (mtt) cc_final: 0.1644 (ptt) REVERT: b 107 MET cc_start: 0.4780 (mtp) cc_final: 0.4501 (pmm) REVERT: b 178 SER cc_start: 0.2891 (t) cc_final: 0.2563 (p) REVERT: c 51 MET cc_start: 0.7973 (mpp) cc_final: 0.5967 (tmm) REVERT: c 269 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8275 (mp10) REVERT: d 61 TRP cc_start: 0.7207 (m-10) cc_final: 0.6703 (m-10) REVERT: d 95 MET cc_start: 0.7183 (tpt) cc_final: 0.6625 (mmt) REVERT: d 121 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6812 (ptt-90) REVERT: d 255 MET cc_start: 0.7699 (mtp) cc_final: 0.7467 (mtp) REVERT: f 58 MET cc_start: -0.0419 (mtt) cc_final: -0.1142 (ttt) REVERT: f 133 MET cc_start: 0.1313 (tmm) cc_final: 0.0828 (ttm) REVERT: f 497 VAL cc_start: -0.5789 (OUTLIER) cc_final: -0.6207 (t) REVERT: f 512 MET cc_start: 0.3503 (tpt) cc_final: 0.2841 (ptp) REVERT: f 595 VAL cc_start: 0.2447 (OUTLIER) cc_final: 0.2217 (t) REVERT: f 670 MET cc_start: -0.0270 (tpt) cc_final: -0.0723 (tpp) REVERT: f 694 LEU cc_start: -0.1725 (OUTLIER) cc_final: -0.2029 (mt) REVERT: f 727 PHE cc_start: 0.4793 (t80) cc_final: 0.4581 (t80) REVERT: f 830 LEU cc_start: 0.2215 (OUTLIER) cc_final: 0.1395 (pt) REVERT: A 280 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6084 (tt) REVERT: A 299 MET cc_start: 0.9215 (tmt) cc_final: 0.8997 (tmm) REVERT: B 164 MET cc_start: 0.5607 (pmm) cc_final: 0.5238 (ppp) REVERT: C 72 TYR cc_start: 0.8563 (m-10) cc_final: 0.8166 (m-10) REVERT: C 139 MET cc_start: 0.7709 (mtt) cc_final: 0.7433 (mpp) REVERT: C 150 MET cc_start: 0.8324 (ptp) cc_final: 0.8105 (ptm) REVERT: C 220 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8434 (t) REVERT: C 293 MET cc_start: 0.7407 (tmm) cc_final: 0.6302 (tmm) REVERT: C 399 MET cc_start: 0.6406 (mmt) cc_final: 0.5979 (mmt) REVERT: D 238 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7842 (ptpp) REVERT: E 208 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8373 (pt) REVERT: E 264 MET cc_start: 0.8867 (ppp) cc_final: 0.8613 (ppp) REVERT: E 277 MET cc_start: 0.8183 (mmp) cc_final: 0.7743 (mmm) REVERT: F 421 MET cc_start: 0.2994 (mmm) cc_final: 0.2411 (mmm) REVERT: G 32 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9020 (mt) REVERT: J 176 TYR cc_start: 0.6285 (m-10) cc_final: 0.6050 (m-10) REVERT: L 88 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8480 (mpp) REVERT: M 77 VAL cc_start: 0.9130 (m) cc_final: 0.8798 (m) REVERT: i 3 ARG cc_start: 0.6928 (mmm160) cc_final: 0.6103 (mmp80) REVERT: k 206 MET cc_start: 0.8371 (mtp) cc_final: 0.7700 (ttm) REVERT: l 26 MET cc_start: 0.8666 (mmt) cc_final: 0.8330 (mmm) REVERT: n 116 MET cc_start: 0.8340 (mtp) cc_final: 0.7980 (mtp) REVERT: q 118 MET cc_start: 0.8501 (tpp) cc_final: 0.8250 (ttm) outliers start: 218 outliers final: 116 residues processed: 815 average time/residue: 0.8959 time to fit residues: 1290.2632 Evaluate side-chains 700 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 571 time to evaluate : 9.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 124 LYS Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 224 LEU Chi-restraints excluded: chain V residue 239 THR Chi-restraints excluded: chain V residue 245 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain X residue 156 GLU Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 237 ARG Chi-restraints excluded: chain Y residue 325 VAL Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 158 ASN Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 121 ARG Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 497 VAL Chi-restraints excluded: chain f residue 576 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 595 VAL Chi-restraints excluded: chain f residue 694 LEU Chi-restraints excluded: chain f residue 732 VAL Chi-restraints excluded: chain f residue 741 LEU Chi-restraints excluded: chain f residue 806 VAL Chi-restraints excluded: chain f residue 809 ILE Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 106 GLN Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 148 GLU Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 195 LEU Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain r residue 136 TYR Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 428 optimal weight: 0.0670 chunk 1146 optimal weight: 0.0170 chunk 251 optimal weight: 30.0000 chunk 747 optimal weight: 1.9990 chunk 314 optimal weight: 20.0000 chunk 1274 optimal weight: 10.0000 chunk 1057 optimal weight: 9.9990 chunk 589 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 421 optimal weight: 0.0980 chunk 668 optimal weight: 5.9990 overall best weight: 1.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 115 ASN ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 362 ASN ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 135 HIS D 312 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN m 110 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 105516 Z= 0.149 Angle : 0.578 21.942 142713 Z= 0.291 Chirality : 0.042 0.211 16229 Planarity : 0.004 0.104 18467 Dihedral : 5.748 170.784 14668 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.49 % Favored : 92.43 % Rotamer: Outliers : 1.87 % Allowed : 11.56 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.08), residues: 13216 helix: 0.98 (0.07), residues: 6131 sheet: -0.67 (0.12), residues: 1873 loop : -2.73 (0.08), residues: 5212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 215 HIS 0.009 0.001 HIS Z 157 PHE 0.023 0.001 PHE m 102 TYR 0.022 0.001 TYR X 201 ARG 0.011 0.000 ARG F 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 614 time to evaluate : 9.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 27 LEU cc_start: 0.7799 (mt) cc_final: 0.7469 (tp) REVERT: U 120 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7882 (pm20) REVERT: U 176 MET cc_start: 0.7395 (mmp) cc_final: 0.6002 (ppp) REVERT: U 188 MET cc_start: 0.5756 (tpp) cc_final: 0.5538 (mmm) REVERT: U 725 MET cc_start: 0.8138 (ppp) cc_final: 0.7808 (tmm) REVERT: U 757 MET cc_start: 0.7543 (tpp) cc_final: 0.7211 (tpp) REVERT: U 819 VAL cc_start: 0.5257 (OUTLIER) cc_final: 0.4753 (p) REVERT: V 264 TYR cc_start: 0.8618 (t80) cc_final: 0.8330 (m-80) REVERT: V 299 GLN cc_start: 0.8806 (tp40) cc_final: 0.8473 (tm-30) REVERT: V 309 MET cc_start: 0.6136 (ttt) cc_final: 0.5888 (ppp) REVERT: V 358 MET cc_start: 0.7410 (pmm) cc_final: 0.7193 (pmm) REVERT: W 130 MET cc_start: 0.3855 (mtt) cc_final: 0.3424 (mmm) REVERT: W 177 MET cc_start: 0.5687 (tpp) cc_final: 0.5470 (mmt) REVERT: W 230 MET cc_start: 0.7873 (tpp) cc_final: 0.7506 (tpp) REVERT: W 281 ASN cc_start: 0.8916 (t0) cc_final: 0.8689 (p0) REVERT: Z 7 GLN cc_start: 0.6706 (pt0) cc_final: 0.6401 (tm-30) REVERT: Z 81 MET cc_start: 0.8858 (mtt) cc_final: 0.8652 (mtm) REVERT: Z 88 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8300 (tmm-80) REVERT: Z 267 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7708 (ttp80) REVERT: a 87 MET cc_start: 0.2801 (mtt) cc_final: 0.1619 (ptt) REVERT: b 16 MET cc_start: 0.2430 (tpp) cc_final: 0.2140 (tpp) REVERT: b 57 ASP cc_start: 0.7862 (m-30) cc_final: 0.7540 (p0) REVERT: b 178 SER cc_start: 0.2622 (t) cc_final: 0.2346 (p) REVERT: c 51 MET cc_start: 0.7992 (mpp) cc_final: 0.5940 (tmm) REVERT: c 216 MET cc_start: 0.7607 (ppp) cc_final: 0.7241 (ppp) REVERT: d 61 TRP cc_start: 0.7187 (m-10) cc_final: 0.6694 (m-10) REVERT: d 95 MET cc_start: 0.7302 (tpt) cc_final: 0.6764 (mmt) REVERT: d 121 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6790 (ptt-90) REVERT: d 204 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8154 (pttt) REVERT: d 255 MET cc_start: 0.7670 (mtp) cc_final: 0.7425 (mtp) REVERT: f 133 MET cc_start: 0.1328 (tmm) cc_final: 0.0495 (ttt) REVERT: f 458 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6214 (mm-30) REVERT: f 482 ILE cc_start: 0.0409 (OUTLIER) cc_final: -0.0379 (mm) REVERT: f 497 VAL cc_start: -0.5975 (OUTLIER) cc_final: -0.6228 (t) REVERT: f 512 MET cc_start: 0.3470 (tpt) cc_final: 0.3081 (ptp) REVERT: f 595 VAL cc_start: 0.2347 (OUTLIER) cc_final: 0.2110 (t) REVERT: f 670 MET cc_start: -0.0353 (tpt) cc_final: -0.0844 (tpp) REVERT: f 694 LEU cc_start: -0.1734 (OUTLIER) cc_final: -0.2028 (mt) REVERT: f 727 PHE cc_start: 0.4763 (t80) cc_final: 0.4546 (t80) REVERT: A 280 ILE cc_start: 0.6673 (OUTLIER) cc_final: 0.6065 (tt) REVERT: A 299 MET cc_start: 0.9209 (tmt) cc_final: 0.8996 (tmm) REVERT: B 164 MET cc_start: 0.5698 (pmm) cc_final: 0.5325 (ppp) REVERT: B 312 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8672 (pp) REVERT: B 385 MET cc_start: 0.8022 (mmt) cc_final: 0.7688 (mmp) REVERT: B 421 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8860 (tmmt) REVERT: C 72 TYR cc_start: 0.8639 (m-10) cc_final: 0.8248 (m-10) REVERT: C 150 MET cc_start: 0.8358 (ptp) cc_final: 0.8128 (ptm) REVERT: C 220 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8431 (t) REVERT: C 293 MET cc_start: 0.7526 (tmm) cc_final: 0.6201 (tmm) REVERT: C 301 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7539 (tt) REVERT: C 351 MET cc_start: 0.7966 (tpp) cc_final: 0.7646 (tpp) REVERT: C 399 MET cc_start: 0.6381 (mmt) cc_final: 0.5972 (mmt) REVERT: D 238 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7777 (ptpp) REVERT: D 352 MET cc_start: 0.8257 (mtp) cc_final: 0.7850 (tpp) REVERT: E 232 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8271 (ttm) REVERT: E 264 MET cc_start: 0.8811 (ppp) cc_final: 0.8521 (ppp) REVERT: E 277 MET cc_start: 0.8128 (mmp) cc_final: 0.7732 (mmm) REVERT: F 56 LYS cc_start: 0.6502 (tptp) cc_final: 0.6292 (mttp) REVERT: F 69 MET cc_start: 0.7230 (tpp) cc_final: 0.7014 (tpt) REVERT: G 32 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8964 (mt) REVERT: J 173 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7941 (mm-30) REVERT: K 156 MET cc_start: 0.8541 (tpp) cc_final: 0.7921 (tpt) REVERT: L 88 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8537 (mpp) REVERT: M 77 VAL cc_start: 0.9051 (m) cc_final: 0.8643 (m) REVERT: i 3 ARG cc_start: 0.6558 (mmm160) cc_final: 0.6252 (mmp80) REVERT: k 206 MET cc_start: 0.8379 (mtp) cc_final: 0.7774 (ttm) REVERT: l 26 MET cc_start: 0.8636 (mmt) cc_final: 0.8236 (mmm) REVERT: n 9 ASP cc_start: 0.8430 (p0) cc_final: 0.8007 (p0) REVERT: q 58 GLU cc_start: 0.8194 (tp30) cc_final: 0.7885 (tp30) outliers start: 206 outliers final: 126 residues processed: 794 average time/residue: 0.8867 time to fit residues: 1241.6541 Evaluate side-chains 717 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 573 time to evaluate : 9.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 124 LYS Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 224 LEU Chi-restraints excluded: chain V residue 239 THR Chi-restraints excluded: chain V residue 245 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 271 VAL Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain X residue 156 GLU Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 237 ARG Chi-restraints excluded: chain Y residue 325 VAL Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 158 ASN Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 121 ARG Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 381 VAL Chi-restraints excluded: chain f residue 458 GLU Chi-restraints excluded: chain f residue 482 ILE Chi-restraints excluded: chain f residue 497 VAL Chi-restraints excluded: chain f residue 576 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 595 VAL Chi-restraints excluded: chain f residue 638 ASP Chi-restraints excluded: chain f residue 694 LEU Chi-restraints excluded: chain f residue 732 VAL Chi-restraints excluded: chain f residue 741 LEU Chi-restraints excluded: chain f residue 806 VAL Chi-restraints excluded: chain f residue 809 ILE Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 106 GLN Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 148 GLU Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 195 LEU Chi-restraints excluded: chain l residue 205 LEU Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain r residue 136 TYR Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 1228 optimal weight: 0.0770 chunk 143 optimal weight: 0.0000 chunk 726 optimal weight: 6.9990 chunk 930 optimal weight: 8.9990 chunk 720 optimal weight: 10.0000 chunk 1072 optimal weight: 6.9990 chunk 711 optimal weight: 0.9990 chunk 1269 optimal weight: 7.9990 chunk 794 optimal weight: 10.0000 chunk 773 optimal weight: 7.9990 chunk 586 optimal weight: 8.9990 overall best weight: 3.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN U 749 GLN ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 ASN ** W 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 10 GLN ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 ASN ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN i 119 GLN q 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 105516 Z= 0.176 Angle : 0.592 24.251 142713 Z= 0.298 Chirality : 0.042 0.252 16229 Planarity : 0.004 0.098 18467 Dihedral : 5.654 155.542 14668 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.75 % Favored : 92.18 % Rotamer: Outliers : 1.99 % Allowed : 11.89 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.08), residues: 13216 helix: 1.10 (0.07), residues: 6135 sheet: -0.60 (0.12), residues: 1866 loop : -2.66 (0.08), residues: 5215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 215 HIS 0.008 0.001 HIS Z 157 PHE 0.020 0.001 PHE V 147 TYR 0.023 0.001 TYR g 96 ARG 0.009 0.000 ARG F 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 583 time to evaluate : 9.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 27 LEU cc_start: 0.7812 (mt) cc_final: 0.7494 (tp) REVERT: U 120 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7924 (pm20) REVERT: U 176 MET cc_start: 0.7403 (mmp) cc_final: 0.7169 (mmt) REVERT: U 188 MET cc_start: 0.5798 (tpp) cc_final: 0.5593 (mmm) REVERT: U 351 MET cc_start: 0.8681 (mtp) cc_final: 0.8311 (ptt) REVERT: U 725 MET cc_start: 0.8150 (ppp) cc_final: 0.7871 (tmm) REVERT: U 757 MET cc_start: 0.7566 (tpp) cc_final: 0.7251 (tpp) REVERT: U 819 VAL cc_start: 0.5248 (OUTLIER) cc_final: 0.4807 (p) REVERT: V 264 TYR cc_start: 0.8635 (t80) cc_final: 0.8344 (m-80) REVERT: V 358 MET cc_start: 0.7249 (pmm) cc_final: 0.7016 (pmm) REVERT: W 177 MET cc_start: 0.5775 (tpp) cc_final: 0.5130 (mmt) REVERT: W 230 MET cc_start: 0.7867 (tpp) cc_final: 0.7495 (tpp) REVERT: W 281 ASN cc_start: 0.8968 (t0) cc_final: 0.8734 (p0) REVERT: Y 167 LEU cc_start: 0.7046 (pp) cc_final: 0.6609 (tt) REVERT: Z 7 GLN cc_start: 0.6803 (pt0) cc_final: 0.6414 (tm-30) REVERT: Z 88 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8311 (tmm-80) REVERT: Z 267 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7685 (ttp80) REVERT: a 87 MET cc_start: 0.2750 (mtt) cc_final: 0.1566 (ptt) REVERT: b 48 ASN cc_start: 0.6038 (OUTLIER) cc_final: 0.5821 (p0) REVERT: b 178 SER cc_start: 0.2539 (t) cc_final: 0.2216 (p) REVERT: d 61 TRP cc_start: 0.7226 (m-10) cc_final: 0.6736 (m-10) REVERT: d 110 ASN cc_start: 0.7173 (t0) cc_final: 0.6960 (t0) REVERT: d 121 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6905 (ptt-90) REVERT: d 201 ASN cc_start: 0.6459 (p0) cc_final: 0.6113 (m-40) REVERT: d 204 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8149 (pttt) REVERT: d 255 MET cc_start: 0.7690 (mtp) cc_final: 0.7474 (mtp) REVERT: f 133 MET cc_start: 0.1170 (tmm) cc_final: 0.0350 (ttt) REVERT: f 140 LEU cc_start: 0.4058 (OUTLIER) cc_final: 0.3826 (tm) REVERT: f 458 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6175 (mm-30) REVERT: f 482 ILE cc_start: 0.0369 (OUTLIER) cc_final: -0.0722 (mm) REVERT: f 497 VAL cc_start: -0.5894 (OUTLIER) cc_final: -0.6151 (t) REVERT: f 595 VAL cc_start: 0.2321 (OUTLIER) cc_final: 0.2091 (t) REVERT: f 670 MET cc_start: -0.0478 (tpt) cc_final: -0.1024 (tpp) REVERT: f 694 LEU cc_start: -0.1760 (OUTLIER) cc_final: -0.2053 (mt) REVERT: f 727 PHE cc_start: 0.4844 (t80) cc_final: 0.4639 (t80) REVERT: A 280 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.5970 (tt) REVERT: A 299 MET cc_start: 0.9205 (tmt) cc_final: 0.8994 (tmm) REVERT: C 72 TYR cc_start: 0.8660 (m-10) cc_final: 0.8317 (m-80) REVERT: C 139 MET cc_start: 0.7810 (mtt) cc_final: 0.7402 (mpp) REVERT: C 150 MET cc_start: 0.8378 (ptp) cc_final: 0.8132 (ptm) REVERT: C 220 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8410 (t) REVERT: C 399 MET cc_start: 0.6439 (mmt) cc_final: 0.6103 (mmt) REVERT: D 238 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7832 (ptpp) REVERT: E 264 MET cc_start: 0.8759 (ppp) cc_final: 0.8510 (ppp) REVERT: E 277 MET cc_start: 0.8147 (mmp) cc_final: 0.7707 (mmm) REVERT: F 373 MET cc_start: 0.7443 (tpt) cc_final: 0.7237 (tpt) REVERT: F 421 MET cc_start: 0.2949 (mmm) cc_final: 0.2260 (mmm) REVERT: G 32 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8963 (mt) REVERT: K 228 MET cc_start: 0.6925 (ppp) cc_final: 0.6432 (ppp) REVERT: L 88 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8550 (mpp) REVERT: L 180 MET cc_start: 0.8158 (tpp) cc_final: 0.7788 (tpp) REVERT: M 230 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7160 (t70) REVERT: N 4 MET cc_start: 0.8279 (ttt) cc_final: 0.8050 (ttt) REVERT: N 164 MET cc_start: 0.8686 (mtp) cc_final: 0.8468 (mtp) REVERT: i 3 ARG cc_start: 0.6557 (mmm160) cc_final: 0.6263 (mmp80) REVERT: k 206 MET cc_start: 0.8387 (mtp) cc_final: 0.7808 (ttm) REVERT: l 26 MET cc_start: 0.8631 (mmt) cc_final: 0.8277 (mmm) REVERT: q 58 GLU cc_start: 0.8250 (tp30) cc_final: 0.7931 (tp30) outliers start: 220 outliers final: 144 residues processed: 779 average time/residue: 0.9220 time to fit residues: 1263.6401 Evaluate side-chains 729 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 568 time to evaluate : 9.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 224 LEU Chi-restraints excluded: chain V residue 239 THR Chi-restraints excluded: chain V residue 245 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 128 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 256 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain X residue 156 GLU Chi-restraints excluded: chain X residue 202 CYS Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 159 ARG Chi-restraints excluded: chain Y residue 194 PHE Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 237 ARG Chi-restraints excluded: chain Y residue 325 VAL Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 158 ASN Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 121 ARG Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 140 LEU Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 381 VAL Chi-restraints excluded: chain f residue 458 GLU Chi-restraints excluded: chain f residue 482 ILE Chi-restraints excluded: chain f residue 497 VAL Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 595 VAL Chi-restraints excluded: chain f residue 638 ASP Chi-restraints excluded: chain f residue 694 LEU Chi-restraints excluded: chain f residue 732 VAL Chi-restraints excluded: chain f residue 806 VAL Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 106 GLN Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 46 CYS Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain g residue 219 VAL Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 148 GLU Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain l residue 195 LEU Chi-restraints excluded: chain l residue 205 LEU Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain r residue 136 TYR Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 785 optimal weight: 1.9990 chunk 506 optimal weight: 20.0000 chunk 758 optimal weight: 0.6980 chunk 382 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 807 optimal weight: 3.9990 chunk 864 optimal weight: 5.9990 chunk 627 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 997 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 149 GLN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 670 ASN U 707 ASN V 124 ASN ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN X 406 ASN ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 291 GLN ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 71 HIS h 109 GLN q 168 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 105516 Z= 0.216 Angle : 0.624 22.796 142713 Z= 0.314 Chirality : 0.042 0.313 16229 Planarity : 0.004 0.115 18467 Dihedral : 5.643 122.505 14668 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 1.91 % Allowed : 12.27 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.08), residues: 13216 helix: 1.11 (0.07), residues: 6150 sheet: -0.58 (0.12), residues: 1891 loop : -2.65 (0.08), residues: 5175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 215 HIS 0.008 0.001 HIS Z 157 PHE 0.022 0.001 PHE m 102 TYR 0.021 0.001 TYR X 201 ARG 0.008 0.000 ARG F 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 575 time to evaluate : 9.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 ASP cc_start: 0.7587 (p0) cc_final: 0.6879 (m-30) REVERT: U 24 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5983 (tt) REVERT: U 120 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7932 (pm20) REVERT: U 176 MET cc_start: 0.7424 (mmp) cc_final: 0.7194 (mmt) REVERT: U 351 MET cc_start: 0.8700 (mtp) cc_final: 0.8317 (ptt) REVERT: U 695 MET cc_start: 0.8228 (mmp) cc_final: 0.7582 (mmt) REVERT: U 819 VAL cc_start: 0.5304 (OUTLIER) cc_final: 0.4857 (p) REVERT: V 264 TYR cc_start: 0.8672 (t80) cc_final: 0.8360 (m-80) REVERT: V 299 GLN cc_start: 0.8727 (tp40) cc_final: 0.8465 (tm-30) REVERT: V 358 MET cc_start: 0.7210 (pmm) cc_final: 0.6960 (pmm) REVERT: W 73 MET cc_start: 0.8689 (tmm) cc_final: 0.8354 (ppp) REVERT: W 88 MET cc_start: 0.3826 (mmt) cc_final: 0.2886 (ppp) REVERT: W 130 MET cc_start: 0.3767 (mtt) cc_final: 0.3482 (mpp) REVERT: W 177 MET cc_start: 0.5837 (tpp) cc_final: 0.5592 (mmt) REVERT: W 190 MET cc_start: 0.6827 (ptp) cc_final: 0.6414 (ptp) REVERT: W 230 MET cc_start: 0.7938 (tpp) cc_final: 0.7555 (tpp) REVERT: Y 167 LEU cc_start: 0.7108 (pp) cc_final: 0.6806 (tt) REVERT: Z 88 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8343 (tmm-80) REVERT: a 87 MET cc_start: 0.2735 (mtt) cc_final: 0.1592 (ptt) REVERT: b 16 MET cc_start: 0.2359 (tpp) cc_final: 0.1959 (tpp) REVERT: c 41 MET cc_start: 0.9158 (mmm) cc_final: 0.8841 (mmm) REVERT: c 51 MET cc_start: 0.7878 (mpp) cc_final: 0.7123 (pmm) REVERT: d 121 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6946 (ptt-90) REVERT: d 201 ASN cc_start: 0.6692 (p0) cc_final: 0.6370 (m-40) REVERT: d 204 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8199 (pttt) REVERT: d 255 MET cc_start: 0.7747 (mtp) cc_final: 0.7529 (mtp) REVERT: e 6 GLN cc_start: 0.7318 (pt0) cc_final: 0.7053 (pm20) REVERT: f 133 MET cc_start: 0.1243 (tmm) cc_final: 0.0438 (ttt) REVERT: f 140 LEU cc_start: 0.4087 (OUTLIER) cc_final: 0.3861 (tm) REVERT: f 306 GLU cc_start: -0.0327 (mt-10) cc_final: -0.0703 (pt0) REVERT: f 458 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6049 (mm-30) REVERT: f 482 ILE cc_start: 0.0380 (OUTLIER) cc_final: -0.0323 (mm) REVERT: f 497 VAL cc_start: -0.5829 (OUTLIER) cc_final: -0.6103 (t) REVERT: f 670 MET cc_start: -0.0487 (tpt) cc_final: -0.1098 (tpp) REVERT: f 694 LEU cc_start: -0.1789 (OUTLIER) cc_final: -0.2073 (mt) REVERT: f 727 PHE cc_start: 0.4876 (t80) cc_final: 0.4675 (t80) REVERT: A 280 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.5891 (tt) REVERT: A 299 MET cc_start: 0.9201 (tmt) cc_final: 0.8976 (tmm) REVERT: B 255 LEU cc_start: 0.7063 (tp) cc_final: 0.6749 (mm) REVERT: B 421 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8876 (tmmt) REVERT: C 72 TYR cc_start: 0.8649 (m-10) cc_final: 0.8284 (m-10) REVERT: C 139 MET cc_start: 0.7847 (mtt) cc_final: 0.7469 (mpp) REVERT: C 150 MET cc_start: 0.8405 (ptp) cc_final: 0.8134 (ptm) REVERT: C 220 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8411 (t) REVERT: C 399 MET cc_start: 0.6442 (mmt) cc_final: 0.6088 (mmt) REVERT: D 238 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7792 (ptpp) REVERT: D 299 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: E 235 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8688 (tp) REVERT: E 277 MET cc_start: 0.8159 (mmp) cc_final: 0.7949 (mmm) REVERT: G 32 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8993 (mt) REVERT: K 228 MET cc_start: 0.6972 (ppp) cc_final: 0.6649 (ppp) REVERT: L 6 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6858 (p90) REVERT: L 88 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8549 (mpp) REVERT: L 180 MET cc_start: 0.8183 (tpp) cc_final: 0.7753 (tpp) REVERT: M 230 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7180 (t70) REVERT: i 3 ARG cc_start: 0.6592 (mmm160) cc_final: 0.6202 (mmp80) REVERT: k 206 MET cc_start: 0.8359 (mtp) cc_final: 0.7804 (ttm) REVERT: l 26 MET cc_start: 0.8628 (mmt) cc_final: 0.8258 (mmm) REVERT: m 181 MET cc_start: 0.8414 (mmm) cc_final: 0.8153 (mmm) REVERT: q 58 GLU cc_start: 0.8281 (tp30) cc_final: 0.7978 (tp30) outliers start: 211 outliers final: 148 residues processed: 765 average time/residue: 0.8846 time to fit residues: 1201.9138 Evaluate side-chains 719 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 552 time to evaluate : 9.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 141 THR Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 224 LEU Chi-restraints excluded: chain V residue 239 THR Chi-restraints excluded: chain V residue 245 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 128 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 239 SER Chi-restraints excluded: chain W residue 256 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain W residue 409 LEU Chi-restraints excluded: chain X residue 156 GLU Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 237 ARG Chi-restraints excluded: chain Y residue 325 VAL Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 158 ASN Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 235 SER Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 121 ARG Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 140 LEU Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 381 VAL Chi-restraints excluded: chain f residue 458 GLU Chi-restraints excluded: chain f residue 482 ILE Chi-restraints excluded: chain f residue 497 VAL Chi-restraints excluded: chain f residue 576 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 638 ASP Chi-restraints excluded: chain f residue 694 LEU Chi-restraints excluded: chain f residue 732 VAL Chi-restraints excluded: chain f residue 778 LEU Chi-restraints excluded: chain f residue 806 VAL Chi-restraints excluded: chain f residue 809 ILE Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain L residue 6 TYR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 106 GLN Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 46 CYS Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 155 TYR Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 148 GLU Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain l residue 205 LEU Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain q residue 24 ASN Chi-restraints excluded: chain r residue 136 TYR Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 1154 optimal weight: 6.9990 chunk 1216 optimal weight: 7.9990 chunk 1109 optimal weight: 0.0980 chunk 1182 optimal weight: 5.9990 chunk 1215 optimal weight: 0.8980 chunk 711 optimal weight: 2.9990 chunk 515 optimal weight: 10.0000 chunk 928 optimal weight: 8.9990 chunk 363 optimal weight: 30.0000 chunk 1068 optimal weight: 8.9990 chunk 1118 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 475 ASN ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 HIS Q 65 GLN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 105516 Z= 0.185 Angle : 0.610 23.358 142713 Z= 0.305 Chirality : 0.042 0.319 16229 Planarity : 0.004 0.111 18467 Dihedral : 5.559 112.452 14668 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.69 % Favored : 92.24 % Rotamer: Outliers : 1.66 % Allowed : 12.69 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.08), residues: 13216 helix: 1.14 (0.07), residues: 6158 sheet: -0.55 (0.12), residues: 1892 loop : -2.59 (0.08), residues: 5166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 215 HIS 0.013 0.001 HIS B 120 PHE 0.019 0.001 PHE m 102 TYR 0.031 0.001 TYR X 201 ARG 0.009 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 564 time to evaluate : 9.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 ASP cc_start: 0.7719 (p0) cc_final: 0.7010 (m-30) REVERT: U 24 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5970 (tt) REVERT: U 695 MET cc_start: 0.8227 (mmp) cc_final: 0.7553 (mmt) REVERT: U 725 MET cc_start: 0.8264 (ppp) cc_final: 0.8005 (tmm) REVERT: U 819 VAL cc_start: 0.5307 (OUTLIER) cc_final: 0.4875 (p) REVERT: V 264 TYR cc_start: 0.8588 (t80) cc_final: 0.8387 (m-80) REVERT: V 358 MET cc_start: 0.7154 (pmm) cc_final: 0.6899 (pmm) REVERT: W 88 MET cc_start: 0.3840 (mmt) cc_final: 0.3075 (ppp) REVERT: W 130 MET cc_start: 0.4017 (mtt) cc_final: 0.3505 (mmm) REVERT: W 177 MET cc_start: 0.5784 (tpp) cc_final: 0.5549 (mmt) REVERT: W 230 MET cc_start: 0.7939 (tpp) cc_final: 0.7569 (tpp) REVERT: Y 167 LEU cc_start: 0.7100 (pp) cc_final: 0.6821 (tt) REVERT: Z 7 GLN cc_start: 0.6816 (pt0) cc_final: 0.6305 (tm-30) REVERT: Z 88 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8276 (tmm-80) REVERT: Z 257 MET cc_start: 0.9080 (tpp) cc_final: 0.8780 (tpp) REVERT: b 16 MET cc_start: 0.2244 (tpp) cc_final: 0.1912 (tpp) REVERT: c 41 MET cc_start: 0.9205 (mmm) cc_final: 0.8875 (mmm) REVERT: c 167 MET cc_start: 0.3825 (ttt) cc_final: 0.3569 (ttt) REVERT: c 216 MET cc_start: 0.7668 (ppp) cc_final: 0.7259 (ppp) REVERT: d 121 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6793 (ptt-90) REVERT: d 201 ASN cc_start: 0.6652 (p0) cc_final: 0.6403 (m110) REVERT: d 204 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8188 (pttt) REVERT: d 255 MET cc_start: 0.7775 (mtp) cc_final: 0.7460 (mtp) REVERT: e 6 GLN cc_start: 0.7314 (pt0) cc_final: 0.7030 (pm20) REVERT: f 133 MET cc_start: 0.1167 (tmm) cc_final: 0.0399 (ttt) REVERT: f 140 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.3831 (tm) REVERT: f 215 ASP cc_start: 0.2344 (p0) cc_final: 0.1892 (t70) REVERT: f 458 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5945 (mm-30) REVERT: f 482 ILE cc_start: 0.0316 (OUTLIER) cc_final: -0.0372 (mm) REVERT: f 497 VAL cc_start: -0.5799 (OUTLIER) cc_final: -0.6074 (t) REVERT: f 670 MET cc_start: -0.0485 (tpt) cc_final: -0.1100 (tpp) REVERT: f 694 LEU cc_start: -0.1842 (OUTLIER) cc_final: -0.2119 (mt) REVERT: f 727 PHE cc_start: 0.4918 (t80) cc_final: 0.4713 (t80) REVERT: A 280 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.5837 (tt) REVERT: A 299 MET cc_start: 0.9204 (tmt) cc_final: 0.9003 (tmm) REVERT: B 255 LEU cc_start: 0.7243 (tp) cc_final: 0.6918 (mp) REVERT: B 421 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8814 (tmmt) REVERT: C 72 TYR cc_start: 0.8640 (m-10) cc_final: 0.8300 (m-10) REVERT: C 139 MET cc_start: 0.7824 (mtt) cc_final: 0.7459 (mpp) REVERT: C 150 MET cc_start: 0.8399 (ptp) cc_final: 0.8132 (ptm) REVERT: C 220 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8427 (t) REVERT: C 399 MET cc_start: 0.6458 (mmt) cc_final: 0.6121 (mmt) REVERT: D 238 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7719 (ptpp) REVERT: E 185 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7903 (mtp85) REVERT: E 232 MET cc_start: 0.8557 (ttm) cc_final: 0.8189 (mtm) REVERT: E 235 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8651 (tp) REVERT: E 277 MET cc_start: 0.8175 (mmp) cc_final: 0.7935 (mmm) REVERT: F 69 MET cc_start: 0.7394 (tpp) cc_final: 0.7125 (tpt) REVERT: F 421 MET cc_start: 0.3480 (mmt) cc_final: 0.2829 (mmm) REVERT: G 32 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8948 (mt) REVERT: G 209 ASP cc_start: 0.7443 (t0) cc_final: 0.6837 (t0) REVERT: K 228 MET cc_start: 0.6963 (ppp) cc_final: 0.6687 (ppp) REVERT: L 88 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8559 (mpp) REVERT: L 180 MET cc_start: 0.8222 (tpp) cc_final: 0.7814 (tpp) REVERT: M 230 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7182 (t70) REVERT: N 164 MET cc_start: 0.8709 (mtp) cc_final: 0.8500 (mtp) REVERT: i 3 ARG cc_start: 0.6521 (mmm160) cc_final: 0.6241 (mmp80) REVERT: k 206 MET cc_start: 0.8331 (mtp) cc_final: 0.7794 (ttm) REVERT: q 58 GLU cc_start: 0.8279 (tp30) cc_final: 0.7969 (tp30) outliers start: 183 outliers final: 146 residues processed: 723 average time/residue: 0.8723 time to fit residues: 1119.7406 Evaluate side-chains 716 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 552 time to evaluate : 9.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 130 PHE Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 224 LEU Chi-restraints excluded: chain V residue 239 THR Chi-restraints excluded: chain V residue 245 ASP Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 128 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 239 SER Chi-restraints excluded: chain W residue 256 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain X residue 156 GLU Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 159 ARG Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 325 VAL Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 226 ILE Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 158 ASN Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 235 SER Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 121 ARG Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 140 LEU Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 381 VAL Chi-restraints excluded: chain f residue 458 GLU Chi-restraints excluded: chain f residue 482 ILE Chi-restraints excluded: chain f residue 497 VAL Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 584 SER Chi-restraints excluded: chain f residue 638 ASP Chi-restraints excluded: chain f residue 694 LEU Chi-restraints excluded: chain f residue 732 VAL Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 185 ARG Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 159 ASN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 106 GLN Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 46 CYS Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain S residue 105 TYR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 155 TYR Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 148 GLU Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain l residue 205 LEU Chi-restraints excluded: chain n residue 44 CYS Chi-restraints excluded: chain n residue 121 VAL Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain r residue 136 TYR Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 1178 optimal weight: 9.9990 chunk 776 optimal weight: 8.9990 chunk 1250 optimal weight: 9.9990 chunk 763 optimal weight: 6.9990 chunk 593 optimal weight: 20.0000 chunk 869 optimal weight: 7.9990 chunk 1312 optimal weight: 7.9990 chunk 1207 optimal weight: 2.9990 chunk 1044 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 807 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 91 ASN ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 258 GLN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 464 GLN U 596 ASN ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 361 HIS ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 178 ASN ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 GLN ** f 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 782 HIS ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 238 HIS J 122 ASN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN ** M 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 HIS ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 152 GLN h 112 GLN ** m 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 66 HIS r 70 ASN t 65 GLN t 89 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 105516 Z= 0.312 Angle : 0.707 22.351 142713 Z= 0.359 Chirality : 0.045 0.324 16229 Planarity : 0.005 0.115 18467 Dihedral : 5.895 107.129 14667 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.02 % Favored : 90.91 % Rotamer: Outliers : 1.67 % Allowed : 12.78 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.07), residues: 13216 helix: 0.88 (0.07), residues: 6186 sheet: -0.59 (0.12), residues: 1861 loop : -2.70 (0.08), residues: 5169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 156 HIS 0.013 0.001 HIS B 120 PHE 0.023 0.002 PHE m 102 TYR 0.025 0.002 TYR X 201 ARG 0.007 0.001 ARG F 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26432 Ramachandran restraints generated. 13216 Oldfield, 0 Emsley, 13216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 561 time to evaluate : 9.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 24 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6037 (tp) REVERT: U 725 MET cc_start: 0.8244 (ppp) cc_final: 0.7983 (tmm) REVERT: U 819 VAL cc_start: 0.5448 (OUTLIER) cc_final: 0.4995 (p) REVERT: V 264 TYR cc_start: 0.8610 (t80) cc_final: 0.8368 (m-80) REVERT: V 299 GLN cc_start: 0.8763 (tp40) cc_final: 0.8516 (tm-30) REVERT: V 358 MET cc_start: 0.7129 (pmm) cc_final: 0.6869 (pmm) REVERT: W 16 MET cc_start: 0.1023 (tpt) cc_final: 0.0700 (tpt) REVERT: W 73 MET cc_start: 0.8784 (tmm) cc_final: 0.8301 (ppp) REVERT: W 88 MET cc_start: 0.3973 (mmt) cc_final: 0.3208 (ppp) REVERT: W 177 MET cc_start: 0.5998 (tpp) cc_final: 0.5497 (mmm) REVERT: W 230 MET cc_start: 0.7950 (tpp) cc_final: 0.7697 (tpp) REVERT: Y 167 LEU cc_start: 0.7288 (pp) cc_final: 0.7039 (tt) REVERT: Z 88 ARG cc_start: 0.8705 (tpp-160) cc_final: 0.8273 (tmm-80) REVERT: Z 112 MET cc_start: 0.8544 (ttm) cc_final: 0.8320 (ppp) REVERT: Z 257 MET cc_start: 0.9106 (tpp) cc_final: 0.8811 (tpp) REVERT: Z 267 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7795 (ttp80) REVERT: b 16 MET cc_start: 0.2200 (tpp) cc_final: 0.1971 (tpp) REVERT: c 41 MET cc_start: 0.9271 (mmm) cc_final: 0.8921 (mmm) REVERT: d 121 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6979 (ptt-90) REVERT: d 204 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8168 (pttt) REVERT: e 1 MET cc_start: 0.5038 (tpp) cc_final: 0.4148 (tpt) REVERT: e 6 GLN cc_start: 0.7295 (pt0) cc_final: 0.6828 (pm20) REVERT: f 133 MET cc_start: 0.1310 (tmm) cc_final: 0.0717 (ttm) REVERT: f 140 LEU cc_start: 0.3989 (OUTLIER) cc_final: 0.3745 (tm) REVERT: f 482 ILE cc_start: 0.0375 (OUTLIER) cc_final: -0.0604 (mm) REVERT: f 497 VAL cc_start: -0.5824 (OUTLIER) cc_final: -0.6153 (t) REVERT: f 670 MET cc_start: -0.0345 (tpt) cc_final: -0.0996 (tpp) REVERT: f 694 LEU cc_start: -0.1847 (OUTLIER) cc_final: -0.2101 (mt) REVERT: f 727 PHE cc_start: 0.4938 (t80) cc_final: 0.4720 (t80) REVERT: A 280 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.5579 (tt) REVERT: A 299 MET cc_start: 0.9213 (tmt) cc_final: 0.9003 (tmm) REVERT: B 107 MET cc_start: 0.7935 (mpp) cc_final: 0.7728 (mpp) REVERT: B 255 LEU cc_start: 0.7286 (tp) cc_final: 0.7027 (mm) REVERT: C 72 TYR cc_start: 0.8586 (m-10) cc_final: 0.8145 (m-10) REVERT: C 150 MET cc_start: 0.8403 (ptp) cc_final: 0.8155 (ptm) REVERT: C 220 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8471 (t) REVERT: C 293 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7048 (tpt) REVERT: C 399 MET cc_start: 0.6498 (mmt) cc_final: 0.6239 (mmm) REVERT: D 299 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: E 235 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8759 (tp) REVERT: E 264 MET cc_start: 0.8868 (ppp) cc_final: 0.8580 (ppp) REVERT: E 277 MET cc_start: 0.8254 (mmp) cc_final: 0.7966 (mmm) REVERT: F 421 MET cc_start: 0.3713 (mmm) cc_final: 0.2825 (mmm) REVERT: G 32 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9072 (mt) REVERT: G 209 ASP cc_start: 0.7531 (t0) cc_final: 0.6998 (t0) REVERT: L 88 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8537 (mpp) REVERT: M 230 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7286 (t70) REVERT: i 3 ARG cc_start: 0.6584 (mmm160) cc_final: 0.6267 (mmp80) REVERT: j 71 MET cc_start: 0.9024 (ttp) cc_final: 0.8747 (ttp) REVERT: k 206 MET cc_start: 0.8334 (mtp) cc_final: 0.7770 (ttm) REVERT: l 88 MET cc_start: 0.9108 (mmm) cc_final: 0.8897 (mmm) REVERT: p 90 MET cc_start: 0.8743 (ttp) cc_final: 0.8505 (ttm) REVERT: q 38 MET cc_start: 0.8920 (mmm) cc_final: 0.8355 (mpp) REVERT: q 58 GLU cc_start: 0.8279 (tp30) cc_final: 0.7967 (tp30) outliers start: 184 outliers final: 143 residues processed: 726 average time/residue: 0.8735 time to fit residues: 1128.4957 Evaluate side-chains 704 residues out of total 11352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 544 time to evaluate : 9.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 PHE Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 246 TYR Chi-restraints excluded: chain U residue 463 ASN Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 130 PHE Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 224 LEU Chi-restraints excluded: chain V residue 239 THR Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 128 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 239 SER Chi-restraints excluded: chain W residue 256 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain X residue 156 GLU Chi-restraints excluded: chain X residue 274 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 325 VAL Chi-restraints excluded: chain Y residue 378 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 226 ILE Chi-restraints excluded: chain Z residue 267 ARG Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain b residue 158 ASN Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 235 SER Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 121 ARG Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 140 LEU Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 381 VAL Chi-restraints excluded: chain f residue 482 ILE Chi-restraints excluded: chain f residue 497 VAL Chi-restraints excluded: chain f residue 576 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 584 SER Chi-restraints excluded: chain f residue 638 ASP Chi-restraints excluded: chain f residue 694 LEU Chi-restraints excluded: chain f residue 732 VAL Chi-restraints excluded: chain f residue 778 LEU Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 106 GLN Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 138 PHE Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 110 HIS Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 155 TYR Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain k residue 148 GLU Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 205 LEU Chi-restraints excluded: chain n residue 44 CYS Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 132 VAL Chi-restraints excluded: chain q residue 24 ASN Chi-restraints excluded: chain q residue 177 THR Chi-restraints excluded: chain r residue 136 TYR Chi-restraints excluded: chain s residue 127 VAL Chi-restraints excluded: chain s residue 191 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1317 random chunks: chunk 640 optimal weight: 3.9990 chunk 829 optimal weight: 9.9990 chunk 1112 optimal weight: 5.9990 chunk 320 optimal weight: 10.0000 chunk 963 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 chunk 1046 optimal weight: 4.9990 chunk 437 optimal weight: 40.0000 chunk 1074 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 377 HIS ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 201 ASN ** f 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.055653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.041150 restraints weight = 1001710.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.042180 restraints weight = 599112.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.041989 restraints weight = 361366.057| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 105516 Z= 0.229 Angle : 0.655 22.507 142713 Z= 0.329 Chirality : 0.043 0.326 16229 Planarity : 0.004 0.114 18467 Dihedral : 5.782 110.118 14667 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.98 % Favored : 91.94 % Rotamer: Outliers : 1.67 % Allowed : 12.88 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.09 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.07), residues: 13216 helix: 0.97 (0.07), residues: 6165 sheet: -0.58 (0.12), residues: 1880 loop : -2.62 (0.08), residues: 5171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 215 HIS 0.008 0.001 HIS D 222 PHE 0.021 0.001 PHE m 102 TYR 0.034 0.001 TYR X 201 ARG 0.006 0.000 ARG F 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23018.25 seconds wall clock time: 408 minutes 14.60 seconds (24494.60 seconds total)