Starting phenix.real_space_refine on Tue Mar 12 00:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgz_30676/03_2024/7dgz_30676_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgz_30676/03_2024/7dgz_30676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgz_30676/03_2024/7dgz_30676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgz_30676/03_2024/7dgz_30676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgz_30676/03_2024/7dgz_30676_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgz_30676/03_2024/7dgz_30676_updated.pdb" } resolution = 3.8 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= 0.003 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 16 5.49 5 S 396 5.16 5 C 39318 2.51 5 N 10324 2.21 5 O 10838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 GLU 38": "OE1" <-> "OE2" Residue "3 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 42": "OD1" <-> "OD2" Residue "8 ARG 199": "NH1" <-> "NH2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "O ARG 77": "NH1" <-> "NH2" Residue "R PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 355": "NH1" <-> "NH2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h GLU 64": "OE1" <-> "OE2" Residue "h TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 68": "OE1" <-> "OE2" Residue "j ARG 60": "NH1" <-> "NH2" Residue "1 ARG 195": "NH1" <-> "NH2" Residue "1 GLU 202": "OE1" <-> "OE2" Residue "1 GLU 206": "OE1" <-> "OE2" Residue "1 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 274": "NH1" <-> "NH2" Residue "6 PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 86": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 60921 Number of models: 1 Model: "" Number of chains: 61 Chain: "2" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2582 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 321} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "3" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 104} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 3447 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3439 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 434} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 97 Conformer: "B" Number of residues, atoms: 458, 3439 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 434} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 97 bond proxies already assigned to first conformer: 3516 Chain: "5" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 697 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 92} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1186 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 5, 'PTRANS': 3, 'TRANS': 163} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 94 Chain: "8" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2965 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'CIS': 6, 'PTRANS': 21, 'TRANS': 399} Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 172 Chain: "9" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1535 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 185} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 5183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5183 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 4, 'PTRANS': 32, 'TRANS': 651} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3410 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 401} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1705 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 191} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1200 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 141} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1388 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 183 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PCIS': 3, 'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 89} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 530 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 530 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 652 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 602 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 67} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "O" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 107} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "P" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 78} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1345 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 155} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2407 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 294} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "S" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2299 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 298} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 169 Chain: "T" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 942 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 131} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "U" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1019 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "V" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "W" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 616 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 79} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "X" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 372 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "Y" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 409 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "Z" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 493 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 4, 'PTRANS': 3, 'TRANS': 66} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "a" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "b" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1032 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 4, 'PTRANS': 10, 'TRANS': 124} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "c" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 617 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "d" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 708 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 149 Chain: "f" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1156 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 204 Chain: "h" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 721 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 84} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "i" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 277 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "j" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 892 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "1" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2500 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 294} Chain: "6" Number of atoms: 4765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4765 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "g" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1351 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 159} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "e" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 864 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 15, 'TRANS': 122} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 224 Chain: "M" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 642 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "4" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "Q" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "V" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25676 SG CYS E 152 100.445 72.040 50.806 1.00 33.04 S ATOM 25450 SG CYS E 123 93.519 73.653 53.108 1.00 49.72 S ATOM 25423 SG CYS E 119 89.705 70.071 46.038 1.00 38.03 S ATOM 28590 SG CYS I 115 83.871 57.042 31.348 1.00 39.11 S Time building chain proxies: 25.94, per 1000 atoms: 0.43 Number of scatterers: 60921 At special positions: 0 Unit cell: (224.965, 231.952, 220.773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 396 16.00 P 16 15.00 O 10838 8.00 N 10324 7.00 C 39318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 66 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 56 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 46 " - pdb=" SG CYS Q 56 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 88 " - pdb=" SG CYS Q 100 " distance=2.03 Simple disulfide: pdb=" SG CYS T 18 " - pdb=" SG CYS T 75 " distance=2.03 Simple disulfide: pdb=" SG CYS T 95 " - pdb=" SG CYS T 115 " distance=2.02 Simple disulfide: pdb=" SG CYS d 59 " - pdb=" SG CYS d 90 " distance=2.03 Simple disulfide: pdb=" SG CYS g 113 " - pdb=" SG CYS g 125 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.81 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 9 301 " pdb="FE2 FES 9 301 " - pdb=" SG CYS 9 180 " pdb="FE1 FES 9 301 " - pdb=" SG CYS 9 140 " pdb=" FES A 803 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 75 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 92 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 78 " pdb=" SF4 A 801 " pdb="FE4 SF4 A 801 " - pdb=" NE2 HIS A 124 " pdb="FE2 SF4 A 801 " - pdb=" SG CYS A 128 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 137 " pdb="FE3 SF4 A 801 " - pdb=" SG CYS A 131 " pdb=" SF4 A 802 " pdb="FE1 SF4 A 802 " - pdb=" SG CYS A 182 " pdb="FE4 SF4 A 802 " - pdb=" SG CYS A 226 " pdb="FE3 SF4 A 802 " - pdb=" SG CYS A 179 " pdb=" SF4 D 301 " pdb="FE2 SF4 D 301 " - pdb=" SG CYS D 156 " pdb="FE3 SF4 D 301 " - pdb=" SG CYS D 186 " pdb=" SF4 E 301 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 123 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 152 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 158 " pdb=" SF4 E 302 " pdb="FE2 SF4 E 302 " - pdb=" SG CYS E 119 " pdb="FE3 SF4 E 302 " - pdb=" SG CYS E 162 " pdb="FE1 SF4 E 302 " - pdb=" SG CYS E 113 " Number of angles added : 49 Zn2+ tetrahedral coordination pdb=" ZN I 300 " pdb="ZN ZN I 300 " - pdb=" NE2 HIS I 96 " pdb="ZN ZN I 300 " - pdb=" SG CYS I 115 " 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15014 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 300 helices and 21 sheets defined 35.8% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.01 Creating SS restraints... Processing helix chain '2' and resid 3 through 21 removed outlier: 3.616A pdb=" N ILE 2 7 " --> pdb=" O PRO 2 3 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE 2 13 " --> pdb=" O ILE 2 9 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET 2 14 " --> pdb=" O LEU 2 10 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE 2 18 " --> pdb=" O MET 2 14 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE 2 19 " --> pdb=" O LEU 2 15 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL 2 20 " --> pdb=" O GLY 2 16 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 4.020A pdb=" N PHE 2 33 " --> pdb=" O VAL 2 29 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN 2 36 " --> pdb=" O GLY 2 32 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET 2 37 " --> pdb=" O PHE 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 53 through 60 removed outlier: 3.727A pdb=" N THR 2 57 " --> pdb=" O THR 2 53 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS 2 58 " --> pdb=" O GLU 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 79 removed outlier: 3.876A pdb=" N SER 2 67 " --> pdb=" O GLN 2 63 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET 2 71 " --> pdb=" O SER 2 67 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN 2 77 " --> pdb=" O ALA 2 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET 2 79 " --> pdb=" O ILE 2 75 " (cutoff:3.500A) Processing helix chain '2' and resid 92 through 104 removed outlier: 3.860A pdb=" N LEU 2 97 " --> pdb=" O MET 2 93 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET 2 100 " --> pdb=" O MET 2 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA 2 101 " --> pdb=" O LEU 2 97 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N MET 2 104 " --> pdb=" O MET 2 100 " (cutoff:3.500A) Processing helix chain '2' and resid 114 through 119 removed outlier: 3.741A pdb=" N VAL 2 118 " --> pdb=" O TRP 2 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR 2 119 " --> pdb=" O VAL 2 115 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 114 through 119' Processing helix chain '2' and resid 130 through 132 No H-bonds generated for 'chain '2' and resid 130 through 132' Processing helix chain '2' and resid 145 through 147 No H-bonds generated for 'chain '2' and resid 145 through 147' Processing helix chain '2' and resid 153 through 169 removed outlier: 3.647A pdb=" N SER 2 158 " --> pdb=" O ILE 2 154 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER 2 161 " --> pdb=" O LEU 2 157 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE 2 162 " --> pdb=" O SER 2 158 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU 2 163 " --> pdb=" O VAL 2 159 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP 2 167 " --> pdb=" O LEU 2 163 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY 2 168 " --> pdb=" O ILE 2 164 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY 2 169 " --> pdb=" O GLY 2 165 " (cutoff:3.500A) Processing helix chain '2' and resid 175 through 180 Processing helix chain '2' and resid 188 through 191 No H-bonds generated for 'chain '2' and resid 188 through 191' Processing helix chain '2' and resid 202 through 219 removed outlier: 3.586A pdb=" N MET 2 215 " --> pdb=" O MET 2 211 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET 2 218 " --> pdb=" O THR 2 214 " (cutoff:3.500A) Processing helix chain '2' and resid 228 through 230 No H-bonds generated for 'chain '2' and resid 228 through 230' Processing helix chain '2' and resid 238 through 251 removed outlier: 3.545A pdb=" N VAL 2 242 " --> pdb=" O PRO 2 238 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU 2 248 " --> pdb=" O ILE 2 244 " (cutoff:3.500A) Processing helix chain '2' and resid 261 through 270 removed outlier: 3.647A pdb=" N MET 2 265 " --> pdb=" O MET 2 261 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN 2 268 " --> pdb=" O TRP 2 264 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU 2 269 " --> pdb=" O MET 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 277 through 283 removed outlier: 3.580A pdb=" N PHE 2 281 " --> pdb=" O ILE 2 277 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET 2 282 " --> pdb=" O LEU 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 297 through 302 removed outlier: 5.104A pdb=" N LEU 2 302 " --> pdb=" O TYR 2 298 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 19 removed outlier: 3.564A pdb=" N LEU 3 17 " --> pdb=" O LEU 3 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL 3 18 " --> pdb=" O ALA 3 14 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE 3 19 " --> pdb=" O THR 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 69 removed outlier: 3.679A pdb=" N PHE 3 62 " --> pdb=" O VAL 3 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU 3 67 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU 3 68 " --> pdb=" O LEU 3 64 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE 3 69 " --> pdb=" O PHE 3 65 " (cutoff:3.500A) Processing helix chain '3' and resid 73 through 75 No H-bonds generated for 'chain '3' and resid 73 through 75' Processing helix chain '3' and resid 85 through 107 removed outlier: 3.790A pdb=" N PHE 3 93 " --> pdb=" O THR 3 89 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU 3 94 " --> pdb=" O MET 3 90 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE 3 95 " --> pdb=" O ALA 3 91 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE 3 96 " --> pdb=" O LEU 3 92 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER 3 101 " --> pdb=" O LEU 3 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU 3 102 " --> pdb=" O LEU 3 98 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU 3 105 " --> pdb=" O SER 3 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR 3 107 " --> pdb=" O ALA 3 103 " (cutoff:3.500A) Processing helix chain '4' and resid 5 through 10 removed outlier: 3.574A pdb=" N MET 4 10 " --> pdb=" O ILE 4 6 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 15 No H-bonds generated for 'chain '4' and resid 12 through 15' Processing helix chain '4' and resid 21 through 41 removed outlier: 4.109A pdb=" N ASN 4 26 " --> pdb=" O ILE 4 23 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER 4 27 " --> pdb=" O TRP 4 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR 4 28 " --> pdb=" O VAL 4 25 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA 4 29 " --> pdb=" O ASN 4 26 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS 4 30 " --> pdb=" O SER 4 27 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER 4 31 " --> pdb=" O THR 4 28 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU 4 32 " --> pdb=" O ALA 4 29 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE 4 34 " --> pdb=" O SER 4 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE 4 36 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER 4 38 " --> pdb=" O SER 4 35 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU 4 41 " --> pdb=" O SER 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 73 through 80 removed outlier: 3.739A pdb=" N LEU 4 77 " --> pdb=" O LEU 4 73 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET 4 78 " --> pdb=" O PRO 4 74 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA 4 79 " --> pdb=" O LEU 4 75 " (cutoff:3.500A) Processing helix chain '4' and resid 89 through 108 removed outlier: 3.767A pdb=" N LEU 4 94 " --> pdb=" O THR 4 90 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE 4 96 " --> pdb=" O LYS 4 92 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU 4 99 " --> pdb=" O PHE 4 95 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE 4 105 " --> pdb=" O SER 4 101 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 4 106 " --> pdb=" O LEU 4 102 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET 4 108 " --> pdb=" O LEU 4 104 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 122 removed outlier: 3.577A pdb=" N ILE 4 120 " --> pdb=" O ILE 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 128 through 134 removed outlier: 3.751A pdb=" N ILE 4 132 " --> pdb=" O PRO 4 128 " (cutoff:3.500A) Processing helix chain '4' and resid 145 through 149 Processing helix chain '4' and resid 153 through 168 removed outlier: 3.688A pdb=" N LEU 4 158 " --> pdb=" O LEU 4 154 " (cutoff:3.500A) Proline residue: 4 159 - end of helix removed outlier: 3.592A pdb=" N VAL 4 162 " --> pdb=" O LEU 4 158 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA 4 163 " --> pdb=" O PRO 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 204 removed outlier: 3.545A pdb=" N CYS 4 199 " --> pdb=" O MET 4 195 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA 4 202 " --> pdb=" O ALA 4 198 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE 4 203 " --> pdb=" O CYS 4 199 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET 4 204 " --> pdb=" O MET 4 200 " (cutoff:3.500A) Processing helix chain '4' and resid 216 through 219 No H-bonds generated for 'chain '4' and resid 216 through 219' Processing helix chain '4' and resid 230 through 238 removed outlier: 3.582A pdb=" N LEU 4 235 " --> pdb=" O LEU 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 241 through 246 Processing helix chain '4' and resid 259 through 272 removed outlier: 3.902A pdb=" N LEU 4 264 " --> pdb=" O PRO 4 260 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER 4 265 " --> pdb=" O PHE 4 261 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET 4 269 " --> pdb=" O SER 4 265 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE 4 270 " --> pdb=" O LEU 4 266 " (cutoff:3.500A) Processing helix chain '4' and resid 274 through 276 No H-bonds generated for 'chain '4' and resid 274 through 276' Processing helix chain '4' and resid 282 through 295 removed outlier: 3.574A pdb=" N ILE 4 286 " --> pdb=" O LEU 4 282 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA 4 287 " --> pdb=" O LYS 4 283 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR 4 288 " --> pdb=" O SER 4 284 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER 4 289 " --> pdb=" O LEU 4 285 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL 4 291 " --> pdb=" O ALA 4 287 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS 4 293 " --> pdb=" O SER 4 289 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET 4 294 " --> pdb=" O SER 4 290 " (cutoff:3.500A) Processing helix chain '4' and resid 298 through 301 No H-bonds generated for 'chain '4' and resid 298 through 301' Processing helix chain '4' and resid 309 through 316 removed outlier: 3.609A pdb=" N THR 4 313 " --> pdb=" O TYR 4 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA 4 314 " --> pdb=" O MET 4 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET 4 316 " --> pdb=" O ALA 4 312 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 331 removed outlier: 4.038A pdb=" N SER 4 324 " --> pdb=" O GLY 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 353 through 367 removed outlier: 4.224A pdb=" N THR 4 357 " --> pdb=" O LEU 4 354 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU 4 361 " --> pdb=" O TRP 4 358 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU 4 364 " --> pdb=" O LEU 4 361 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN 4 366 " --> pdb=" O SER 4 363 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU 4 367 " --> pdb=" O LEU 4 364 " (cutoff:3.500A) Processing helix chain '4' and resid 378 through 385 removed outlier: 3.695A pdb=" N MET 4 383 " --> pdb=" O LEU 4 379 " (cutoff:3.500A) Processing helix chain '4' and resid 390 through 411 removed outlier: 3.520A pdb=" N ILE 4 393 " --> pdb=" O ASN 4 390 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU 4 395 " --> pdb=" O THR 4 392 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET 4 396 " --> pdb=" O ILE 4 393 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN 4 399 " --> pdb=" O MET 4 396 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE 4 402 " --> pdb=" O ASN 4 399 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR 4 403 " --> pdb=" O MET 4 400 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER 4 407 " --> pdb=" O ALA 4 404 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU 4 408 " --> pdb=" O LEU 4 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR 4 409 " --> pdb=" O TYR 4 406 " (cutoff:3.500A) Processing helix chain '4' and resid 431 through 435 Processing helix chain '4' and resid 441 through 444 No H-bonds generated for 'chain '4' and resid 441 through 444' Processing helix chain '5' and resid 3 through 8 Processing helix chain '5' and resid 10 through 12 No H-bonds generated for 'chain '5' and resid 10 through 12' Processing helix chain '5' and resid 17 through 19 No H-bonds generated for 'chain '5' and resid 17 through 19' Processing helix chain '5' and resid 26 through 36 removed outlier: 3.592A pdb=" N LEU 5 30 " --> pdb=" O MET 5 27 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU 5 31 " --> pdb=" O SER 5 28 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET 5 36 " --> pdb=" O LEU 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 41 through 50 removed outlier: 4.242A pdb=" N THR 5 47 " --> pdb=" O MET 5 43 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN 5 50 " --> pdb=" O LEU 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 56 through 84 Proline residue: 5 60 - end of helix removed outlier: 3.550A pdb=" N LEU 5 64 " --> pdb=" O ILE 5 61 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE 5 66 " --> pdb=" O LEU 5 63 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA 5 68 " --> pdb=" O VAL 5 65 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU 5 70 " --> pdb=" O ALA 5 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA 5 72 " --> pdb=" O CYS 5 69 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 5 77 " --> pdb=" O GLY 5 74 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL 5 81 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN 5 83 " --> pdb=" O MET 5 80 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR 5 84 " --> pdb=" O VAL 5 81 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 20 removed outlier: 3.693A pdb=" N VAL 7 11 " --> pdb=" O PHE 7 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE 7 12 " --> pdb=" O ILE 7 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL 7 18 " --> pdb=" O VAL 7 14 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE 7 20 " --> pdb=" O GLY 7 16 " (cutoff:3.500A) Processing helix chain '7' and resid 25 through 27 No H-bonds generated for 'chain '7' and resid 25 through 27' Processing helix chain '7' and resid 30 through 44 removed outlier: 4.591A pdb=" N VAL 7 35 " --> pdb=" O LEU 7 31 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 58 removed outlier: 4.237A pdb=" N VAL 7 56 " --> pdb=" O LEU 7 52 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU 7 58 " --> pdb=" O LEU 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 64 through 70 removed outlier: 3.716A pdb=" N GLY 7 69 " --> pdb=" O MET 7 65 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 107 removed outlier: 3.696A pdb=" N GLY 7 91 " --> pdb=" O LYS 7 87 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA 7 92 " --> pdb=" O ALA 7 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL 7 94 " --> pdb=" O LEU 7 90 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR 7 95 " --> pdb=" O GLY 7 91 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY 7 96 " --> pdb=" O ALA 7 92 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU 7 97 " --> pdb=" O PHE 7 93 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N MET 7 99 " --> pdb=" O THR 7 95 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE 7 101 " --> pdb=" O LEU 7 97 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL 7 104 " --> pdb=" O GLU 7 100 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR 7 106 " --> pdb=" O PHE 7 102 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL 7 107 " --> pdb=" O MET 7 103 " (cutoff:3.500A) Processing helix chain '7' and resid 152 through 169 removed outlier: 3.525A pdb=" N VAL 7 156 " --> pdb=" O TRP 7 152 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP 7 159 " --> pdb=" O ILE 7 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU 7 161 " --> pdb=" O THR 7 157 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE 7 163 " --> pdb=" O TRP 7 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL 7 165 " --> pdb=" O LEU 7 161 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL 7 166 " --> pdb=" O LEU 7 162 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE 7 168 " --> pdb=" O GLY 7 164 " (cutoff:3.500A) Processing helix chain '8' and resid 79 through 82 Processing helix chain '8' and resid 95 through 100 removed outlier: 3.698A pdb=" N TRP 8 99 " --> pdb=" O THR 8 95 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER 8 100 " --> pdb=" O GLY 8 96 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 95 through 100' Processing helix chain '8' and resid 130 through 133 No H-bonds generated for 'chain '8' and resid 130 through 133' Processing helix chain '8' and resid 136 through 140 removed outlier: 3.553A pdb=" N GLU 8 140 " --> pdb=" O HIS 8 136 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 136 through 140' Processing helix chain '8' and resid 142 through 149 removed outlier: 3.505A pdb=" N ARG 8 147 " --> pdb=" O LEU 8 143 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA 8 148 " --> pdb=" O VAL 8 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET 8 149 " --> pdb=" O GLY 8 145 " (cutoff:3.500A) Processing helix chain '8' and resid 164 through 176 removed outlier: 3.695A pdb=" N GLN 8 170 " --> pdb=" O ALA 8 166 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 8 174 " --> pdb=" O GLN 8 170 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA 8 176 " --> pdb=" O ALA 8 172 " (cutoff:3.500A) Processing helix chain '8' and resid 212 through 215 No H-bonds generated for 'chain '8' and resid 212 through 215' Processing helix chain '8' and resid 245 through 249 Processing helix chain '8' and resid 251 through 256 Processing helix chain '8' and resid 296 through 301 removed outlier: 3.881A pdb=" N GLU 8 301 " --> pdb=" O LYS 8 297 " (cutoff:3.500A) Processing helix chain '8' and resid 339 through 344 Processing helix chain '8' and resid 363 through 376 removed outlier: 3.847A pdb=" N ILE 8 367 " --> pdb=" O ILE 8 363 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG 8 369 " --> pdb=" O LYS 8 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU 8 370 " --> pdb=" O ALA 8 366 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 8 374 " --> pdb=" O LEU 8 370 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS 8 375 " --> pdb=" O ILE 8 371 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS 8 376 " --> pdb=" O GLU 8 372 " (cutoff:3.500A) Processing helix chain '8' and resid 389 through 401 removed outlier: 3.533A pdb=" N LYS 8 394 " --> pdb=" O ASP 8 390 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL 8 395 " --> pdb=" O TRP 8 391 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA 8 397 " --> pdb=" O ASN 8 393 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG 8 398 " --> pdb=" O LYS 8 394 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG 8 401 " --> pdb=" O ALA 8 397 " (cutoff:3.500A) Processing helix chain '8' and resid 408 through 418 removed outlier: 3.586A pdb=" N SER 8 416 " --> pdb=" O LEU 8 412 " (cutoff:3.500A) Processing helix chain '8' and resid 426 through 439 removed outlier: 4.042A pdb=" N TRP 8 433 " --> pdb=" O ASP 8 429 " (cutoff:3.500A) Proline residue: 8 434 - end of helix removed outlier: 3.645A pdb=" N LEU 8 438 " --> pdb=" O PRO 8 434 " (cutoff:3.500A) Processing helix chain '8' and resid 449 through 457 Processing helix chain '9' and resid 57 through 69 removed outlier: 4.188A pdb=" N LYS 9 61 " --> pdb=" O PRO 9 57 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG 9 62 " --> pdb=" O GLU 9 58 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 9 63 " --> pdb=" O ASN 9 59 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 9 64 " --> pdb=" O TYR 9 60 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA 9 65 " --> pdb=" O LYS 9 61 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE 9 66 " --> pdb=" O ARG 9 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN 9 69 " --> pdb=" O ALA 9 65 " (cutoff:3.500A) Processing helix chain '9' and resid 79 through 90 removed outlier: 3.773A pdb=" N ASP 9 84 " --> pdb=" O LEU 9 80 " (cutoff:3.500A) Processing helix chain '9' and resid 95 through 104 removed outlier: 3.647A pdb=" N VAL 9 101 " --> pdb=" O ALA 9 97 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA 9 102 " --> pdb=" O MET 9 98 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU 9 103 " --> pdb=" O ASN 9 99 " (cutoff:3.500A) Processing helix chain '9' and resid 109 through 117 removed outlier: 3.791A pdb=" N TYR 9 113 " --> pdb=" O MET 9 110 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU 9 114 " --> pdb=" O ARG 9 111 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA 9 116 " --> pdb=" O TYR 9 113 " (cutoff:3.500A) Processing helix chain '9' and resid 138 through 142 Processing helix chain '9' and resid 153 through 156 No H-bonds generated for 'chain '9' and resid 153 through 156' Processing helix chain '9' and resid 198 through 201 No H-bonds generated for 'chain '9' and resid 198 through 201' Processing helix chain '9' and resid 204 through 210 removed outlier: 3.704A pdb=" N ALA 9 210 " --> pdb=" O ASP 9 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.860A pdb=" N GLU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.633A pdb=" N ALA A 186 " --> pdb=" O CYS A 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 187' Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.632A pdb=" N ILE A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 224 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 322 through 332 removed outlier: 4.284A pdb=" N VAL A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.155A pdb=" N GLU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 396' Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 486 through 501 removed outlier: 3.538A pdb=" N ALA A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.899A pdb=" N LEU A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 539 No H-bonds generated for 'chain 'A' and resid 536 through 539' Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.807A pdb=" N ILE A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 624 " --> pdb=" O TRP A 620 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 666 through 673 removed outlier: 3.735A pdb=" N GLU A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 700 through 703 No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 712 through 715 No H-bonds generated for 'chain 'A' and resid 712 through 715' Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 149 through 159 removed outlier: 4.292A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 175 removed outlier: 4.302A pdb=" N ILE B 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 171 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 172 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 174 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 182 through 188 removed outlier: 3.572A pdb=" N ALA B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 187 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 No H-bonds generated for 'chain 'B' and resid 190 through 193' Processing helix chain 'B' and resid 198 through 209 removed outlier: 4.138A pdb=" N GLU B 206 " --> pdb=" O TRP B 202 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.642A pdb=" N VAL B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 255 through 262 removed outlier: 3.842A pdb=" N GLU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 282 through 285 No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 327 through 345 removed outlier: 3.525A pdb=" N LEU B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N CYS B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 341 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 386 removed outlier: 3.606A pdb=" N LYS B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 384 " --> pdb=" O HIS B 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 385 " --> pdb=" O HIS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 4.800A pdb=" N LEU B 435 " --> pdb=" O HIS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 454 removed outlier: 4.101A pdb=" N GLY B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 removed outlier: 3.887A pdb=" N SER C 61 " --> pdb=" O HIS C 57 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.729A pdb=" N VAL C 95 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Proline residue: C 97 - end of helix removed outlier: 3.826A pdb=" N PHE C 101 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 103 " --> pdb=" O THR C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 175 removed outlier: 3.980A pdb=" N ASN C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR C 168 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 170 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU C 171 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP C 173 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 74 through 77 No H-bonds generated for 'chain 'D' and resid 74 through 77' Processing helix chain 'D' and resid 91 through 100 removed outlier: 4.152A pdb=" N GLU D 95 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS D 98 " --> pdb=" O GLU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 removed outlier: 3.563A pdb=" N ARG D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL D 140 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 203 removed outlier: 3.727A pdb=" N LYS D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 62 removed outlier: 3.584A pdb=" N ASP E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 161 No H-bonds generated for 'chain 'E' and resid 158 through 161' Processing helix chain 'E' and resid 187 through 195 removed outlier: 4.515A pdb=" N ASN E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 removed outlier: 3.701A pdb=" N GLN E 206 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 89 No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'G' and resid 135 through 138 No H-bonds generated for 'chain 'G' and resid 135 through 138' Processing helix chain 'H' and resid 6 through 9 No H-bonds generated for 'chain 'H' and resid 6 through 9' Processing helix chain 'H' and resid 34 through 43 removed outlier: 3.560A pdb=" N LYS H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 42 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS H 43 " --> pdb=" O GLU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 55 No H-bonds generated for 'chain 'H' and resid 52 through 55' Processing helix chain 'H' and resid 61 through 67 Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.772A pdb=" N ILE H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG H 81 " --> pdb=" O HIS H 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 30 removed outlier: 3.871A pdb=" N GLY J 8 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 12 " --> pdb=" O GLY J 8 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL J 14 " --> pdb=" O ALA J 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU J 16 " --> pdb=" O MET J 12 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE J 17 " --> pdb=" O GLY J 13 " (cutoff:3.500A) Proline residue: J 19 - end of helix removed outlier: 3.720A pdb=" N ARG J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE J 29 " --> pdb=" O ARG J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 54 removed outlier: 3.529A pdb=" N TYR J 46 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET J 48 " --> pdb=" O GLN J 44 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG J 53 " --> pdb=" O GLU J 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 54 " --> pdb=" O ARG J 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 39 removed outlier: 4.891A pdb=" N GLY K 32 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG K 34 " --> pdb=" O GLN K 31 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE K 37 " --> pdb=" O ARG K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 89 No H-bonds generated for 'chain 'K' and resid 86 through 89' Processing helix chain 'K' and resid 92 through 96 Processing helix chain 'L' and resid 8 through 11 No H-bonds generated for 'chain 'L' and resid 8 through 11' Processing helix chain 'L' and resid 19 through 26 Processing helix chain 'L' and resid 32 through 34 No H-bonds generated for 'chain 'L' and resid 32 through 34' Processing helix chain 'N' and resid 24 through 35 removed outlier: 3.733A pdb=" N THR N 29 " --> pdb=" O LYS N 25 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE N 31 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL N 34 " --> pdb=" O LYS N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 59 removed outlier: 4.207A pdb=" N GLN N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR N 52 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET N 58 " --> pdb=" O GLU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 69 removed outlier: 3.931A pdb=" N GLU N 69 " --> pdb=" O VAL N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 65 through 69' Processing helix chain 'N' and resid 77 through 94 removed outlier: 3.624A pdb=" N LEU N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS N 93 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 41 removed outlier: 4.883A pdb=" N ARG O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU O 35 " --> pdb=" O ARG O 31 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG O 37 " --> pdb=" O ARG O 33 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG O 41 " --> pdb=" O ARG O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 49 No H-bonds generated for 'chain 'O' and resid 46 through 49' Processing helix chain 'O' and resid 56 through 70 removed outlier: 3.566A pdb=" N ARG O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL O 63 " --> pdb=" O GLY O 59 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS O 68 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN O 70 " --> pdb=" O MET O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 94 removed outlier: 3.531A pdb=" N ILE O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU O 90 " --> pdb=" O GLY O 86 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU O 91 " --> pdb=" O LYS O 87 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU O 92 " --> pdb=" O MET O 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE O 94 " --> pdb=" O LEU O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 106 No H-bonds generated for 'chain 'O' and resid 104 through 106' Processing helix chain 'O' and resid 118 through 123 removed outlier: 3.673A pdb=" N TYR O 123 " --> pdb=" O LEU O 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 11 removed outlier: 3.715A pdb=" N LEU P 11 " --> pdb=" O PHE P 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 7 through 11' Processing helix chain 'Q' and resid 22 through 27 Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 39 through 45 removed outlier: 3.550A pdb=" N LEU Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 77 removed outlier: 3.708A pdb=" N ASN Q 64 " --> pdb=" O GLY Q 60 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS Q 66 " --> pdb=" O LEU Q 62 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Q 69 " --> pdb=" O GLN Q 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG Q 76 " --> pdb=" O ARG Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 90 removed outlier: 3.943A pdb=" N GLU Q 84 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 107 removed outlier: 3.967A pdb=" N ALA Q 105 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN Q 106 " --> pdb=" O GLN Q 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 76 removed outlier: 4.020A pdb=" N TYR R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS R 72 " --> pdb=" O TYR R 68 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG R 75 " --> pdb=" O ASN R 71 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET R 76 " --> pdb=" O HIS R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 143 through 145 No H-bonds generated for 'chain 'R' and resid 143 through 145' Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 155 through 158 No H-bonds generated for 'chain 'R' and resid 155 through 158' Processing helix chain 'R' and resid 185 through 189 Processing helix chain 'R' and resid 242 through 252 removed outlier: 3.534A pdb=" N ILE R 249 " --> pdb=" O VAL R 245 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE R 250 " --> pdb=" O THR R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 284 removed outlier: 3.574A pdb=" N VAL R 283 " --> pdb=" O TYR R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 319 No H-bonds generated for 'chain 'R' and resid 317 through 319' Processing helix chain 'S' and resid 79 through 81 No H-bonds generated for 'chain 'S' and resid 79 through 81' Processing helix chain 'S' and resid 105 through 107 No H-bonds generated for 'chain 'S' and resid 105 through 107' Processing helix chain 'S' and resid 118 through 141 removed outlier: 3.763A pdb=" N TRP S 122 " --> pdb=" O ARG S 118 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN S 130 " --> pdb=" O SER S 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR S 131 " --> pdb=" O ARG S 127 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU S 135 " --> pdb=" O TYR S 131 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU S 136 " --> pdb=" O ALA S 132 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU S 139 " --> pdb=" O LEU S 135 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER S 140 " --> pdb=" O GLU S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 153 through 163 removed outlier: 3.917A pdb=" N PHE S 157 " --> pdb=" O ASP S 154 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET S 161 " --> pdb=" O LEU S 158 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG S 163 " --> pdb=" O ALA S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 182 removed outlier: 4.001A pdb=" N LYS S 180 " --> pdb=" O ASN S 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 201 through 208 removed outlier: 4.223A pdb=" N ILE S 206 " --> pdb=" O GLN S 203 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS S 208 " --> pdb=" O ARG S 205 " (cutoff:3.500A) Processing helix chain 'S' and resid 219 through 227 removed outlier: 4.103A pdb=" N ASP S 224 " --> pdb=" O ALA S 220 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE S 225 " --> pdb=" O TYR S 221 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU S 226 " --> pdb=" O LEU S 222 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 237 No H-bonds generated for 'chain 'S' and resid 234 through 237' Processing helix chain 'S' and resid 261 through 268 removed outlier: 3.518A pdb=" N TYR S 266 " --> pdb=" O GLU S 262 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS S 268 " --> pdb=" O LEU S 264 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 9 Processing helix chain 'T' and resid 18 through 42 removed outlier: 3.990A pdb=" N THR T 22 " --> pdb=" O CYS T 18 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER T 27 " --> pdb=" O TYR T 23 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE T 28 " --> pdb=" O ALA T 24 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY T 29 " --> pdb=" O THR T 25 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY T 33 " --> pdb=" O GLY T 29 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL T 35 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR T 39 " --> pdb=" O VAL T 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER T 40 " --> pdb=" O VAL T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 70 removed outlier: 3.702A pdb=" N ALA T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA T 65 " --> pdb=" O PHE T 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY T 67 " --> pdb=" O ALA T 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE T 69 " --> pdb=" O ALA T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 79 removed outlier: 3.665A pdb=" N SER T 77 " --> pdb=" O THR T 73 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN T 79 " --> pdb=" O CYS T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 103 removed outlier: 4.212A pdb=" N ALA T 96 " --> pdb=" O ILE T 92 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE T 100 " --> pdb=" O ALA T 96 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU T 101 " --> pdb=" O GLY T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 3.511A pdb=" N TYR T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET T 118 " --> pdb=" O ALA T 114 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA T 123 " --> pdb=" O GLY T 119 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU T 124 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL T 125 " --> pdb=" O THR T 121 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS T 126 " --> pdb=" O ALA T 122 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN T 129 " --> pdb=" O VAL T 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 14 removed outlier: 3.946A pdb=" N GLN U 12 " --> pdb=" O LYS U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 27 removed outlier: 4.515A pdb=" N VAL U 26 " --> pdb=" O GLY U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 88 No H-bonds generated for 'chain 'U' and resid 86 through 88' Processing helix chain 'V' and resid 38 through 49 removed outlier: 3.736A pdb=" N PHE V 45 " --> pdb=" O GLY V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 70 removed outlier: 3.567A pdb=" N ARG V 59 " --> pdb=" O ARG V 55 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE V 62 " --> pdb=" O ARG V 58 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG V 68 " --> pdb=" O ASP V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 77 No H-bonds generated for 'chain 'V' and resid 74 through 77' Processing helix chain 'V' and resid 80 through 95 removed outlier: 3.596A pdb=" N LEU V 84 " --> pdb=" O ASP V 80 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU V 94 " --> pdb=" O ASN V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 124 No H-bonds generated for 'chain 'V' and resid 121 through 124' Processing helix chain 'V' and resid 132 through 137 Processing helix chain 'W' and resid 79 through 89 removed outlier: 3.709A pdb=" N VAL W 83 " --> pdb=" O ILE W 79 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU W 87 " --> pdb=" O VAL W 83 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS W 88 " --> pdb=" O LEU W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 125 removed outlier: 4.935A pdb=" N ALA W 121 " --> pdb=" O ILE W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 134 No H-bonds generated for 'chain 'W' and resid 132 through 134' Processing helix chain 'W' and resid 136 through 139 removed outlier: 3.759A pdb=" N MET W 139 " --> pdb=" O GLU W 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 136 through 139' Processing helix chain 'W' and resid 143 through 151 removed outlier: 4.154A pdb=" N TYR W 147 " --> pdb=" O GLU W 143 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE W 148 " --> pdb=" O ILE W 144 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA W 149 " --> pdb=" O VAL W 145 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP W 150 " --> pdb=" O ASP W 146 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 28 removed outlier: 3.810A pdb=" N VAL X 21 " --> pdb=" O MET X 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 57 through 69 removed outlier: 3.526A pdb=" N PHE Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA Y 66 " --> pdb=" O GLU Y 62 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET Y 68 " --> pdb=" O PHE Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 76 No H-bonds generated for 'chain 'Y' and resid 73 through 76' Processing helix chain 'Z' and resid 28 through 37 removed outlier: 3.622A pdb=" N GLN Z 33 " --> pdb=" O GLU Z 30 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU Z 36 " --> pdb=" O GLN Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 67 No H-bonds generated for 'chain 'Z' and resid 64 through 67' Processing helix chain 'a' and resid 31 through 33 No H-bonds generated for 'chain 'a' and resid 31 through 33' Processing helix chain 'a' and resid 37 through 51 Processing helix chain 'a' and resid 63 through 69 Processing helix chain 'a' and resid 88 through 92 removed outlier: 3.871A pdb=" N ALA a 91 " --> pdb=" O LEU a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 105 removed outlier: 3.766A pdb=" N PHE a 100 " --> pdb=" O GLY a 96 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR a 102 " --> pdb=" O LEU a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 117 removed outlier: 3.550A pdb=" N LEU a 115 " --> pdb=" O ARG a 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 66 Processing helix chain 'b' and resid 69 through 77 removed outlier: 3.575A pdb=" N TYR b 74 " --> pdb=" O LEU b 70 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU b 76 " --> pdb=" O ARG b 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU b 77 " --> pdb=" O PHE b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 85 removed outlier: 3.566A pdb=" N ILE b 84 " --> pdb=" O ILE b 80 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY b 85 " --> pdb=" O PRO b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 92 Processing helix chain 'b' and resid 116 through 125 removed outlier: 4.076A pdb=" N TRP b 120 " --> pdb=" O PRO b 116 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA b 122 " --> pdb=" O SER b 118 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG b 123 " --> pdb=" O ARG b 119 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR b 124 " --> pdb=" O TRP b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 156 removed outlier: 3.936A pdb=" N LEU b 154 " --> pdb=" O ARG b 150 " (cutoff:3.500A) Processing helix chain 'b' and resid 176 through 178 No H-bonds generated for 'chain 'b' and resid 176 through 178' Processing helix chain 'c' and resid 7 through 9 No H-bonds generated for 'chain 'c' and resid 7 through 9' Processing helix chain 'c' and resid 19 through 26 Processing helix chain 'c' and resid 69 through 90 removed outlier: 3.628A pdb=" N THR c 73 " --> pdb=" O ILE c 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS c 74 " --> pdb=" O PHE c 70 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL c 75 " --> pdb=" O ALA c 71 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU c 76 " --> pdb=" O PHE c 72 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE c 77 " --> pdb=" O THR c 73 " (cutoff:3.500A) Proline residue: c 78 - end of helix removed outlier: 3.613A pdb=" N TYR c 84 " --> pdb=" O TRP c 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU c 86 " --> pdb=" O ILE c 82 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR c 88 " --> pdb=" O TYR c 84 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N HIS c 89 " --> pdb=" O TYR c 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 48 Processing helix chain 'd' and resid 61 through 66 Processing helix chain 'd' and resid 68 through 72 Processing helix chain 'd' and resid 81 through 99 Processing helix chain 'd' and resid 101 through 108 removed outlier: 4.231A pdb=" N ARG d 107 " --> pdb=" O GLU d 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 28 removed outlier: 3.790A pdb=" N LEU f 19 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG f 22 " --> pdb=" O ARG f 18 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU f 24 " --> pdb=" O TYR f 20 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU f 27 " --> pdb=" O ALA f 23 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 39 Processing helix chain 'f' and resid 41 through 48 removed outlier: 3.918A pdb=" N ARG f 47 " --> pdb=" O LEU f 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE f 48 " --> pdb=" O LEU f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 58 through 63 removed outlier: 5.575A pdb=" N LEU f 63 " --> pdb=" O LYS f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 116 through 130 removed outlier: 3.921A pdb=" N GLU f 123 " --> pdb=" O PHE f 119 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN f 124 " --> pdb=" O ALA f 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP f 125 " --> pdb=" O LYS f 121 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS f 126 " --> pdb=" O ARG f 122 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS f 127 " --> pdb=" O GLU f 123 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU f 128 " --> pdb=" O GLN f 124 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG f 129 " --> pdb=" O TRP f 125 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 143 removed outlier: 3.724A pdb=" N GLN f 141 " --> pdb=" O VAL f 137 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU f 142 " --> pdb=" O LYS f 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 90 removed outlier: 3.663A pdb=" N VAL h 89 " --> pdb=" O ASN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 105 Processing helix chain 'h' and resid 112 through 114 No H-bonds generated for 'chain 'h' and resid 112 through 114' Processing helix chain 'h' and resid 116 through 131 removed outlier: 3.869A pdb=" N ARG h 120 " --> pdb=" O GLU h 116 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL h 126 " --> pdb=" O ALA h 122 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS h 127 " --> pdb=" O GLU h 123 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG h 129 " --> pdb=" O LEU h 125 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 72 removed outlier: 3.709A pdb=" N SER i 51 " --> pdb=" O THR i 47 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL i 52 " --> pdb=" O LEU i 48 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR i 69 " --> pdb=" O ASP i 65 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS i 70 " --> pdb=" O VAL i 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 20 removed outlier: 3.648A pdb=" N ARG j 19 " --> pdb=" O ASP j 16 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER j 20 " --> pdb=" O GLU j 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 16 through 20' Processing helix chain 'j' and resid 29 through 47 removed outlier: 5.010A pdb=" N GLY j 35 " --> pdb=" O LEU j 31 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY j 38 " --> pdb=" O VAL j 34 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU j 43 " --> pdb=" O TYR j 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 61 No H-bonds generated for 'chain 'j' and resid 58 through 61' Processing helix chain 'j' and resid 64 through 95 removed outlier: 3.552A pdb=" N VAL j 69 " --> pdb=" O ILE j 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS j 77 " --> pdb=" O TYR j 73 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG j 78 " --> pdb=" O TYR j 74 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN j 79 " --> pdb=" O LEU j 75 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR j 81 " --> pdb=" O LYS j 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR j 83 " --> pdb=" O GLN j 79 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP j 89 " --> pdb=" O VAL j 85 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER j 92 " --> pdb=" O HIS j 88 " (cutoff:3.500A) Processing helix chain 'j' and resid 98 through 100 No H-bonds generated for 'chain 'j' and resid 98 through 100' Processing helix chain '1' and resid 3 through 21 removed outlier: 3.668A pdb=" N LEU 1 7 " --> pdb=" O MET 1 3 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE 1 11 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) Proline residue: 1 12 - end of helix removed outlier: 3.900A pdb=" N LEU 1 15 " --> pdb=" O ILE 1 11 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA 1 16 " --> pdb=" O PRO 1 12 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU 1 20 " --> pdb=" O ALA 1 16 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR 1 21 " --> pdb=" O VAL 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 23 through 30 removed outlier: 3.590A pdb=" N VAL 1 27 " --> pdb=" O VAL 1 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU 1 28 " --> pdb=" O GLU 1 24 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 50 No H-bonds generated for 'chain '1' and resid 47 through 50' Processing helix chain '1' and resid 53 through 57 Processing helix chain '1' and resid 74 through 86 removed outlier: 3.628A pdb=" N LEU 1 79 " --> pdb=" O PRO 1 75 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU 1 81 " --> pdb=" O MET 1 77 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET 1 85 " --> pdb=" O LEU 1 81 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TRP 1 86 " --> pdb=" O ALA 1 82 " (cutoff:3.500A) Processing helix chain '1' and resid 102 through 109 removed outlier: 3.883A pdb=" N LEU 1 106 " --> pdb=" O VAL 1 102 " (cutoff:3.500A) Processing helix chain '1' and resid 111 through 122 removed outlier: 3.517A pdb=" N ILE 1 116 " --> pdb=" O VAL 1 113 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU 1 117 " --> pdb=" O TYR 1 114 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER 1 119 " --> pdb=" O ILE 1 116 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY 1 120 " --> pdb=" O LEU 1 117 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA 1 122 " --> pdb=" O SER 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 133 through 141 removed outlier: 4.396A pdb=" N GLN 1 138 " --> pdb=" O ARG 1 134 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR 1 139 " --> pdb=" O ALA 1 135 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER 1 141 " --> pdb=" O ALA 1 137 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 157 removed outlier: 4.153A pdb=" N VAL 1 153 " --> pdb=" O ILE 1 149 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU 1 154 " --> pdb=" O LEU 1 150 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N MET 1 156 " --> pdb=" O SER 1 152 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 169 removed outlier: 4.499A pdb=" N GLN 1 169 " --> pdb=" O LEU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 179 through 192 removed outlier: 3.541A pdb=" N MET 1 183 " --> pdb=" O TRP 1 179 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET 1 184 " --> pdb=" O PRO 1 180 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE 1 186 " --> pdb=" O ALA 1 182 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER 1 188 " --> pdb=" O MET 1 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR 1 189 " --> pdb=" O TRP 1 185 " (cutoff:3.500A) Processing helix chain '1' and resid 219 through 238 removed outlier: 4.534A pdb=" N PHE 1 224 " --> pdb=" O ALA 1 221 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA 1 226 " --> pdb=" O PHE 1 223 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE 1 231 " --> pdb=" O TYR 1 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE 1 232 " --> pdb=" O ALA 1 229 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET 1 234 " --> pdb=" O ILE 1 231 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN 1 235 " --> pdb=" O ILE 1 232 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE 1 236 " --> pdb=" O MET 1 233 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR 1 238 " --> pdb=" O ASN 1 235 " (cutoff:3.500A) Processing helix chain '1' and resid 253 through 274 removed outlier: 3.787A pdb=" N ILE 1 257 " --> pdb=" O GLU 1 253 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN 1 258 " --> pdb=" O LEU 1 254 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE 1 261 " --> pdb=" O ILE 1 257 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS 1 262 " --> pdb=" O ASN 1 258 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU 1 265 " --> pdb=" O ILE 1 261 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER 1 269 " --> pdb=" O LEU 1 265 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE 1 270 " --> pdb=" O LEU 1 266 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU 1 271 " --> pdb=" O THR 1 267 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG 1 274 " --> pdb=" O PHE 1 270 " (cutoff:3.500A) Processing helix chain '1' and resid 283 through 287 Processing helix chain '1' and resid 294 through 309 removed outlier: 3.561A pdb=" N SER 1 306 " --> pdb=" O MET 1 302 " (cutoff:3.500A) Proline residue: 1 308 - end of helix Processing helix chain '6' and resid 9 through 23 removed outlier: 4.186A pdb=" N LEU 6 15 " --> pdb=" O THR 6 11 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR 6 16 " --> pdb=" O LEU 6 12 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET 6 17 " --> pdb=" O LEU 6 13 " (cutoff:3.500A) Proline residue: 6 18 - end of helix removed outlier: 4.200A pdb=" N MET 6 22 " --> pdb=" O PRO 6 18 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER 6 23 " --> pdb=" O ILE 6 19 " (cutoff:3.500A) Processing helix chain '6' and resid 32 through 57 removed outlier: 3.554A pdb=" N VAL 6 36 " --> pdb=" O TYR 6 32 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR 6 42 " --> pdb=" O THR 6 38 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA 6 43 " --> pdb=" O ALA 6 39 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE 6 45 " --> pdb=" O SER 6 41 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR 6 46 " --> pdb=" O TYR 6 42 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE 6 49 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) Proline residue: 6 50 - end of helix removed outlier: 3.631A pdb=" N HIS 6 56 " --> pdb=" O MET 6 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER 6 57 " --> pdb=" O MET 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 89 through 107 removed outlier: 3.529A pdb=" N VAL 6 96 " --> pdb=" O VAL 6 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR 6 97 " --> pdb=" O ALA 6 93 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET 6 101 " --> pdb=" O THR 6 97 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU 6 102 " --> pdb=" O TRP 6 98 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE 6 103 " --> pdb=" O SER 6 99 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER 6 104 " --> pdb=" O ILE 6 100 " (cutoff:3.500A) Processing helix chain '6' and resid 114 through 132 removed outlier: 4.353A pdb=" N LEU 6 122 " --> pdb=" O PHE 6 118 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU 6 131 " --> pdb=" O THR 6 127 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL 6 132 " --> pdb=" O MET 6 128 " (cutoff:3.500A) Processing helix chain '6' and resid 137 through 155 removed outlier: 3.640A pdb=" N VAL 6 147 " --> pdb=" O GLY 6 143 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY 6 148 " --> pdb=" O TRP 6 144 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE 6 149 " --> pdb=" O GLU 6 145 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE 6 152 " --> pdb=" O GLY 6 148 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU 6 154 " --> pdb=" O MET 6 150 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 193 removed outlier: 3.817A pdb=" N ASN 6 175 " --> pdb=" O ALA 6 171 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG 6 176 " --> pdb=" O ILE 6 172 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY 6 181 " --> pdb=" O ILE 6 177 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE 6 182 " --> pdb=" O GLY 6 178 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE 6 189 " --> pdb=" O ALA 6 185 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU 6 190 " --> pdb=" O MET 6 186 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR 6 191 " --> pdb=" O ALA 6 187 " (cutoff:3.500A) Processing helix chain '6' and resid 198 through 202 removed outlier: 3.571A pdb=" N PHE 6 202 " --> pdb=" O LEU 6 198 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 198 through 202' Processing helix chain '6' and resid 210 through 223 removed outlier: 4.113A pdb=" N ILE 6 214 " --> pdb=" O ASN 6 210 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY 6 215 " --> pdb=" O MET 6 211 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS 6 223 " --> pdb=" O ALA 6 219 " (cutoff:3.500A) Processing helix chain '6' and resid 230 through 238 removed outlier: 3.564A pdb=" N LEU 6 233 " --> pdb=" O HIS 6 230 " (cutoff:3.500A) Proline residue: 6 234 - end of helix removed outlier: 4.402A pdb=" N MET 6 237 " --> pdb=" O PRO 6 234 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU 6 238 " --> pdb=" O SER 6 235 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 230 through 238' Processing helix chain '6' and resid 241 through 247 Processing helix chain '6' and resid 258 through 262 Processing helix chain '6' and resid 264 through 267 No H-bonds generated for 'chain '6' and resid 264 through 267' Processing helix chain '6' and resid 271 through 292 removed outlier: 3.839A pdb=" N SER 6 275 " --> pdb=" O LYS 6 271 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE 6 276 " --> pdb=" O TYR 6 272 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR 6 284 " --> pdb=" O LEU 6 280 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR 6 285 " --> pdb=" O GLY 6 281 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU 6 286 " --> pdb=" O ALA 6 282 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS 6 291 " --> pdb=" O PHE 6 287 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA 6 292 " --> pdb=" O THR 6 288 " (cutoff:3.500A) Processing helix chain '6' and resid 298 through 313 removed outlier: 3.709A pdb=" N SER 6 307 " --> pdb=" O ALA 6 303 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU 6 310 " --> pdb=" O THR 6 306 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY 6 311 " --> pdb=" O SER 6 307 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU 6 312 " --> pdb=" O SER 6 308 " (cutoff:3.500A) Processing helix chain '6' and resid 315 through 318 No H-bonds generated for 'chain '6' and resid 315 through 318' Processing helix chain '6' and resid 322 through 347 removed outlier: 3.508A pdb=" N HIS 6 328 " --> pdb=" O LEU 6 324 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE 6 329 " --> pdb=" O ALA 6 325 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS 6 330 " --> pdb=" O PHE 6 326 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE 6 334 " --> pdb=" O CYS 6 330 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE 6 335 " --> pdb=" O THR 6 331 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS 6 336 " --> pdb=" O HIS 6 332 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA 6 337 " --> pdb=" O ALA 6 333 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET 6 338 " --> pdb=" O PHE 6 334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET 6 341 " --> pdb=" O ALA 6 337 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER 6 345 " --> pdb=" O MET 6 341 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE 6 346 " --> pdb=" O CYS 6 342 " (cutoff:3.500A) Processing helix chain '6' and resid 367 through 379 removed outlier: 3.623A pdb=" N THR 6 371 " --> pdb=" O PRO 6 367 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL 6 375 " --> pdb=" O THR 6 371 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY 6 376 " --> pdb=" O ALA 6 372 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU 6 378 " --> pdb=" O ILE 6 374 " (cutoff:3.500A) Processing helix chain '6' and resid 387 through 396 removed outlier: 4.164A pdb=" N TYR 6 390 " --> pdb=" O THR 6 387 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS 6 392 " --> pdb=" O PHE 6 389 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASP 6 393 " --> pdb=" O TYR 6 390 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU 6 394 " --> pdb=" O SER 6 391 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE 6 396 " --> pdb=" O ASP 6 393 " (cutoff:3.500A) Processing helix chain '6' and resid 409 through 430 removed outlier: 5.386A pdb=" N ILE 6 414 " --> pdb=" O LEU 6 410 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 6 415 " --> pdb=" O MET 6 411 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER 6 417 " --> pdb=" O LEU 6 413 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE 6 418 " --> pdb=" O ILE 6 414 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA 6 420 " --> pdb=" O THR 6 416 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE 6 421 " --> pdb=" O SER 6 417 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR 6 422 " --> pdb=" O PHE 6 418 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER 6 423 " --> pdb=" O THR 6 419 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR 6 424 " --> pdb=" O ALA 6 420 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 6 425 " --> pdb=" O ILE 6 421 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE 6 426 " --> pdb=" O TYR 6 422 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE 6 427 " --> pdb=" O SER 6 423 " (cutoff:3.500A) Processing helix chain '6' and resid 448 through 462 removed outlier: 3.670A pdb=" N ARG 6 456 " --> pdb=" O ASN 6 452 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 6 457 " --> pdb=" O SER 6 453 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE 6 459 " --> pdb=" O LYS 6 455 " (cutoff:3.500A) Processing helix chain '6' and resid 465 through 468 No H-bonds generated for 'chain '6' and resid 465 through 468' Processing helix chain '6' and resid 489 through 505 removed outlier: 3.607A pdb=" N THR 6 494 " --> pdb=" O ALA 6 490 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY 6 497 " --> pdb=" O VAL 6 493 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE 6 498 " --> pdb=" O THR 6 494 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE 6 499 " --> pdb=" O ILE 6 495 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU 6 502 " --> pdb=" O PHE 6 498 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 6 504 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) Processing helix chain '6' and resid 529 through 535 removed outlier: 4.078A pdb=" N ARG 6 535 " --> pdb=" O THR 6 531 " (cutoff:3.500A) Processing helix chain '6' and resid 537 through 540 No H-bonds generated for 'chain '6' and resid 537 through 540' Processing helix chain '6' and resid 544 through 547 No H-bonds generated for 'chain '6' and resid 544 through 547' Processing helix chain '6' and resid 563 through 572 removed outlier: 3.805A pdb=" N SER 6 567 " --> pdb=" O PRO 6 563 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET 6 571 " --> pdb=" O SER 6 567 " (cutoff:3.500A) Processing helix chain '6' and resid 584 through 600 removed outlier: 3.966A pdb=" N PHE 6 588 " --> pdb=" O ILE 6 584 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU 6 589 " --> pdb=" O LYS 6 585 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER 6 590 " --> pdb=" O LEU 6 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU 6 592 " --> pdb=" O PHE 6 588 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE 6 593 " --> pdb=" O LEU 6 589 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR 6 594 " --> pdb=" O SER 6 590 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET 6 599 " --> pdb=" O ILE 6 595 " (cutoff:3.500A) Processing helix chain '6' and resid 603 through 605 No H-bonds generated for 'chain '6' and resid 603 through 605' Processing helix chain 'g' and resid 30 through 56 removed outlier: 4.030A pdb=" N LYS g 35 " --> pdb=" O THR g 31 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA g 36 " --> pdb=" O TYR g 32 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP g 38 " --> pdb=" O THR g 34 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU g 40 " --> pdb=" O ALA g 36 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL g 41 " --> pdb=" O PHE g 37 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG g 43 " --> pdb=" O LEU g 39 " (cutoff:3.500A) Proline residue: g 44 - end of helix removed outlier: 3.555A pdb=" N LEU g 47 " --> pdb=" O ARG g 43 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL g 48 " --> pdb=" O PRO g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 117 removed outlier: 4.194A pdb=" N GLU g 89 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG g 94 " --> pdb=" O MET g 90 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL g 98 " --> pdb=" O ARG g 94 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP g 99 " --> pdb=" O ASP g 95 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU g 101 " --> pdb=" O LYS g 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL g 103 " --> pdb=" O ASP g 99 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS g 113 " --> pdb=" O ARG g 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN g 114 " --> pdb=" O LEU g 110 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN g 115 " --> pdb=" O LYS g 111 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG g 116 " --> pdb=" O ALA g 112 " (cutoff:3.500A) Processing helix chain 'g' and resid 128 through 134 removed outlier: 4.007A pdb=" N THR g 133 " --> pdb=" O LEU g 129 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN g 134 " --> pdb=" O GLU g 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 140 through 143 No H-bonds generated for 'chain 'g' and resid 140 through 143' Processing helix chain 'g' and resid 161 through 167 Processing helix chain 'e' and resid 44 through 46 No H-bonds generated for 'chain 'e' and resid 44 through 46' Processing helix chain 'e' and resid 128 through 139 removed outlier: 3.728A pdb=" N GLY e 135 " --> pdb=" O LYS e 131 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE e 136 " --> pdb=" O HIS e 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 21 removed outlier: 3.634A pdb=" N ARG M 14 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU M 16 " --> pdb=" O LYS M 12 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS M 20 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU M 21 " --> pdb=" O TYR M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 54 removed outlier: 4.014A pdb=" N ILE M 50 " --> pdb=" O ASP M 46 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET M 52 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA M 53 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N MET M 54 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 68 Processing helix chain 'M' and resid 73 through 84 Processing sheet with id= A, first strand: chain '8' and resid 240 through 243 removed outlier: 7.220A pdb=" N TYR 8 112 " --> pdb=" O THR 8 241 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ALA 8 243 " --> pdb=" O TYR 8 112 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL 8 114 " --> pdb=" O ALA 8 243 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA 8 153 " --> pdb=" O LEU 8 113 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL 8 115 " --> pdb=" O ALA 8 153 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR 8 155 " --> pdb=" O VAL 8 115 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE 8 196 " --> pdb=" O ILE 8 156 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE 8 158 " --> pdb=" O PHE 8 196 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL 8 198 " --> pdb=" O ILE 8 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '8' and resid 273 through 277 removed outlier: 3.715A pdb=" N GLU 8 290 " --> pdb=" O LYS 8 274 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL 8 288 " --> pdb=" O PHE 8 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '8' and resid 316 through 318 removed outlier: 3.624A pdb=" N ALA 8 316 " --> pdb=" O MET 8 357 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE 8 355 " --> pdb=" O ILE 8 318 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '9' and resid 130 through 135 removed outlier: 3.568A pdb=" N THR 9 170 " --> pdb=" O TYR 9 130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL 9 174 " --> pdb=" O VAL 9 134 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 32 through 35 Processing sheet with id= F, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= G, first strand: chain 'A' and resid 198 through 200 Processing sheet with id= H, first strand: chain 'A' and resid 246 through 250 removed outlier: 3.785A pdb=" N THR A 265 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 248 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 338 through 341 removed outlier: 6.402A pdb=" N MET A 544 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 341 " --> pdb=" O MET A 544 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE A 546 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 582 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY A 570 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU A 584 " --> pdb=" O GLY A 570 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 513 through 515 removed outlier: 8.723A pdb=" N ASN A 514 " --> pdb=" O PRO A 472 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 474 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 399 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 475 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 401 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS A 428 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 402 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA A 430 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP A 443 " --> pdb=" O LEU A 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.922A pdb=" N ARG B 96 " --> pdb=" O HIS B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 98 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 407 through 411 Processing sheet with id= M, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.876A pdb=" N ILE C 143 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER C 141 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 86 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR C 148 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 77 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 122 through 125 removed outlier: 6.525A pdb=" N TYR D 149 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL D 125 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL D 151 " --> pdb=" O VAL D 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 129 through 134 removed outlier: 3.527A pdb=" N ARG E 144 " --> pdb=" O GLU E 131 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLU E 133 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR E 142 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 78 through 81 removed outlier: 3.535A pdb=" N MET G 99 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU G 126 " --> pdb=" O MET G 99 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 84 through 86 removed outlier: 3.530A pdb=" N ILE I 85 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.040A pdb=" N GLU K 18 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG K 68 " --> pdb=" O GLU K 18 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'R' and resid 81 through 84 removed outlier: 5.389A pdb=" N ILE R 104 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS R 84 " --> pdb=" O ILE R 104 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N MET R 106 " --> pdb=" O HIS R 84 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'R' and resid 167 through 169 removed outlier: 6.778A pdb=" N ILE R 201 " --> pdb=" O SER R 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'R' and resid 205 through 207 1095 hydrogen bonds defined for protein. 2876 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: 15.70 Time building geometry restraints manager: 19.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 24930 1.39 - 1.62: 36749 1.62 - 1.84: 663 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 62422 Sorted by residual: bond pdb=" C1D NAP R 601 " pdb=" O4D NAP R 601 " ideal model delta sigma weight residual 1.375 1.631 -0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C1B NAP R 601 " pdb=" C2B NAP R 601 " ideal model delta sigma weight residual 1.528 1.291 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1D NAP R 601 " pdb=" C2D NAP R 601 " ideal model delta sigma weight residual 1.533 1.315 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP R 601 " pdb=" O4B NAP R 601 " ideal model delta sigma weight residual 1.400 1.611 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C4D NAP R 601 " pdb=" O4D NAP R 601 " ideal model delta sigma weight residual 1.447 1.295 0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 62417 not shown) Histogram of bond angle deviations from ideal: 73.21 - 88.15: 74 88.15 - 103.08: 698 103.08 - 118.02: 46450 118.02 - 132.95: 37517 132.95 - 147.89: 218 Bond angle restraints: 84957 Sorted by residual: angle pdb=" S1 FES A 803 " pdb="FE2 FES A 803 " pdb=" S2 FES A 803 " ideal model delta sigma weight residual 104.33 88.52 15.81 1.14e+00 7.69e-01 1.92e+02 angle pdb=" S1 FES A 803 " pdb="FE1 FES A 803 " pdb=" S2 FES A 803 " ideal model delta sigma weight residual 104.33 88.27 16.06 1.20e+00 6.94e-01 1.79e+02 angle pdb=" S1 FES 9 301 " pdb="FE2 FES 9 301 " pdb=" S2 FES 9 301 " ideal model delta sigma weight residual 104.33 89.57 14.76 1.14e+00 7.69e-01 1.68e+02 angle pdb="FE1 FES 9 301 " pdb=" S2 FES 9 301 " pdb="FE2 FES 9 301 " ideal model delta sigma weight residual 75.66 90.14 -14.48 1.14e+00 7.69e-01 1.61e+02 angle pdb=" S1 FES 9 301 " pdb="FE1 FES 9 301 " pdb=" S2 FES 9 301 " ideal model delta sigma weight residual 104.33 89.57 14.76 1.20e+00 6.94e-01 1.51e+02 ... (remaining 84952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.10: 36413 30.10 - 60.20: 837 60.20 - 90.30: 42 90.30 - 120.39: 0 120.39 - 150.49: 2 Dihedral angle restraints: 37294 sinusoidal: 14046 harmonic: 23248 Sorted by residual: dihedral pdb=" CA GLU I 106 " pdb=" C GLU I 106 " pdb=" N THR I 107 " pdb=" CA THR I 107 " ideal model delta harmonic sigma weight residual 180.00 94.01 85.99 0 5.00e+00 4.00e-02 2.96e+02 dihedral pdb=" CA TRP V 142 " pdb=" C TRP V 142 " pdb=" N TYR V 143 " pdb=" CA TYR V 143 " ideal model delta harmonic sigma weight residual 180.00 109.04 70.96 0 5.00e+00 4.00e-02 2.01e+02 dihedral pdb=" CA ARG e 81 " pdb=" C ARG e 81 " pdb=" N SER e 82 " pdb=" CA SER e 82 " ideal model delta harmonic sigma weight residual -180.00 -116.21 -63.79 0 5.00e+00 4.00e-02 1.63e+02 ... (remaining 37291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 8686 0.108 - 0.216: 792 0.216 - 0.323: 73 0.323 - 0.431: 12 0.431 - 0.539: 4 Chirality restraints: 9567 Sorted by residual: chirality pdb=" CA ASP e 87 " pdb=" N ASP e 87 " pdb=" C ASP e 87 " pdb=" CB ASP e 87 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.26e+00 chirality pdb=" CA HIS B 92 " pdb=" N HIS B 92 " pdb=" C HIS B 92 " pdb=" CB HIS B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA HIS e 94 " pdb=" N HIS e 94 " pdb=" C HIS e 94 " pdb=" CB HIS e 94 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 9564 not shown) Planarity restraints: 10757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 3 42 " -0.135 5.00e-02 4.00e+02 2.15e-01 7.40e+01 pdb=" N PRO 3 43 " 0.371 5.00e-02 4.00e+02 pdb=" CA PRO 3 43 " -0.143 5.00e-02 4.00e+02 pdb=" CD PRO 3 43 " -0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 3 35 " 0.105 5.00e-02 4.00e+02 1.64e-01 4.31e+01 pdb=" N PRO 3 36 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO 3 36 " 0.099 5.00e-02 4.00e+02 pdb=" CD PRO 3 36 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 128 " 0.097 5.00e-02 4.00e+02 1.47e-01 3.46e+01 pdb=" N PRO A 129 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.077 5.00e-02 4.00e+02 ... (remaining 10754 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 26 1.97 - 2.70: 2779 2.70 - 3.44: 84073 3.44 - 4.17: 133402 4.17 - 4.90: 228964 Nonbonded interactions: 449244 Sorted by model distance: nonbonded pdb=" OE1 GLU 1 204 " pdb=" CD ARG 1 279 " model vdw 1.238 3.440 nonbonded pdb=" O ARG 1 195 " pdb=" OD1 ASP 1 199 " model vdw 1.439 3.040 nonbonded pdb=" O ASN 6 506 " pdb=" N ASN 6 510 " model vdw 1.491 2.520 nonbonded pdb=" CG LYS 3 33 " pdb=" OH TYR 3 37 " model vdw 1.519 3.440 nonbonded pdb=" O PHE W 104 " pdb=" CB LEU W 108 " model vdw 1.555 3.440 ... (remaining 449239 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 'M' and (resid 6 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 or (resid 22 through 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 27 or (resid 28 and (n \ ame N or name CA or name C or name O or name CB )) or resid 29 through 30 or (re \ sid 31 and (name N or name CA or name C or name O or name CB )) or resid 32 thro \ ugh 34 or (resid 35 and (name N or name CA or name C or name O or name CB )) or \ resid 36 through 38 or (resid 39 and (name N or name CA or name C or name O or n \ ame CB )) or resid 40 through 44 or (resid 45 through 46 and (name N or name CA \ or name C or name O or name CB )) or resid 47 through 51 or (resid 52 through 53 \ and (name N or name CA or name C or name O or name CB )) or resid 54 through 55 \ or (resid 56 and (name N or name CA or name C or name O or name CB )) or resid \ 57 through 65 or (resid 66 through 67 and (name N or name CA or name C or name O \ or name CB )) or resid 68 through 69 or (resid 70 and (name N or name CA or nam \ e C or name O or name CB )) or resid 71 through 72 or (resid 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 and (name N or \ name CA or name C or name O or name CB )) or resid 76 through 77 or (resid 78 a \ nd (name N or name CA or name C or name O or name CB )) or resid 79 through 81 o \ r (resid 82 and (name N or name CA or name C or name O or name CB )) or resid 83 \ or (resid 84 through 85 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'W' and resid 74 through 153) } 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=0.50 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: 1.250 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: 0.040 Extract box with map and model: 7.070 Check model and map are aligned: 0.670 Set scattering table: 0.430 Process input model: 135.300 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.240 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.256 62422 Z= 0.539 Angle : 1.427 35.552 84957 Z= 0.785 Chirality : 0.067 0.539 9567 Planarity : 0.009 0.215 10757 Dihedral : 12.683 150.493 22256 Min Nonbonded Distance : 1.238 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 1.47 % Allowed : 17.60 % Favored : 80.93 % Rotamer: Outliers : 1.31 % Allowed : 3.04 % Favored : 95.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.92 % Twisted Proline : 2.57 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.15 (0.07), residues: 7895 helix: -4.39 (0.05), residues: 3035 sheet: -3.27 (0.25), residues: 318 loop : -4.10 (0.08), residues: 4542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP V 142 HIS 0.024 0.002 HIS A 124 PHE 0.045 0.003 PHE 2 111 TYR 0.073 0.003 TYR V 143 ARG 0.011 0.001 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1281 time to evaluate : 5.425 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: 2 45 MET cc_start: 0.7927 (mmp) cc_final: 0.7650 (tpp) REVERT: 3 42 ASP cc_start: 0.3159 (OUTLIER) cc_final: 0.2872 (m-30) REVERT: 4 161 LEU cc_start: 0.8730 (mt) cc_final: 0.8437 (mt) REVERT: 5 73 LEU cc_start: 0.8899 (tt) cc_final: 0.8578 (tt) REVERT: 7 34 ILE cc_start: 0.8170 (mm) cc_final: 0.7750 (mt) REVERT: B 375 MET cc_start: 0.8888 (tpt) cc_final: 0.8528 (tpp) REVERT: B 443 MET cc_start: 0.7759 (mtp) cc_final: 0.7509 (mtp) REVERT: B 460 GLU cc_start: 0.6301 (tm-30) cc_final: 0.5943 (tm-30) REVERT: D 107 ASP cc_start: 0.8027 (t0) cc_final: 0.7719 (t0) REVERT: D 191 GLU cc_start: 0.7299 (tp30) cc_final: 0.6992 (tp30) REVERT: E 74 LEU cc_start: 0.8806 (tp) cc_final: 0.8588 (tp) REVERT: G 59 LEU cc_start: 0.7113 (mt) cc_final: 0.6791 (tp) REVERT: I 52 ARG cc_start: 0.7567 (mmt90) cc_final: 0.6016 (tmm160) REVERT: I 65 GLU cc_start: 0.6809 (mp0) cc_final: 0.6590 (mp0) REVERT: N 7 LYS cc_start: 0.7658 (pttm) cc_final: 0.7099 (tptt) REVERT: O 26 ASN cc_start: 0.7451 (m-40) cc_final: 0.7211 (m-40) REVERT: R 206 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6194 (pp) REVERT: R 324 THR cc_start: 0.8222 (m) cc_final: 0.7729 (m) REVERT: S 38 THR cc_start: 0.5232 (m) cc_final: 0.5010 (m) REVERT: T 81 ARG cc_start: 0.7610 (mmt-90) cc_final: 0.6502 (mtp-110) REVERT: f 56 ASP cc_start: 0.6188 (m-30) cc_final: 0.5768 (p0) REVERT: h 64 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7331 (pm20) REVERT: h 68 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6339 (tt0) REVERT: j 90 MET cc_start: 0.7511 (ttp) cc_final: 0.7231 (ttt) REVERT: 1 214 GLU cc_start: 0.7804 (tp30) cc_final: 0.7428 (tp30) REVERT: 1 228 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7416 (t80) REVERT: 1 232 ILE cc_start: 0.8804 (pt) cc_final: 0.8559 (mt) REVERT: 6 518 ASN cc_start: 0.4872 (OUTLIER) cc_final: 0.4609 (m110) REVERT: 6 520 PHE cc_start: 0.5753 (OUTLIER) cc_final: 0.5286 (m-80) REVERT: 6 544 MET cc_start: 0.5396 (ttp) cc_final: 0.4770 (tpt) REVERT: M 57 GLU cc_start: 0.4128 (tt0) cc_final: 0.3739 (tt0) outliers start: 77 outliers final: 36 residues processed: 1346 average time/residue: 0.6014 time to fit residues: 1332.0770 Evaluate side-chains 781 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 738 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 27 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 33 LYS Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain B residue 61 TRP Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 200 PRO Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain h residue 63 ASP Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain h residue 68 GLU Chi-restraints excluded: chain h residue 69 LYS Chi-restraints excluded: chain h residue 70 ASN Chi-restraints excluded: chain 1 residue 89 LEU Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 208 VAL Chi-restraints excluded: chain 1 residue 211 PHE Chi-restraints excluded: chain 1 residue 225 MET Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 514 HIS Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 518 ASN Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 524 THR Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain g residue 15 ARG Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 92 TRP Chi-restraints excluded: chain e residue 160 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 656 optimal weight: 2.9990 chunk 588 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 397 optimal weight: 0.7980 chunk 314 optimal weight: 6.9990 chunk 609 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 370 optimal weight: 7.9990 chunk 453 optimal weight: 5.9990 chunk 705 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 49 ASN 2 172 GLN 3 10 ASN ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 43 ASN 4 168 GLN 5 25 HIS 8 281 HIS 8 422 HIS A 142 GLN A 309 ASN A 334 GLN A 359 ASN A 571 HIS A 666 GLN B 112 HIS B 160 ASN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 250 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN B 381 HIS C 249 GLN D 158 ASN E 192 ASN E 204 ASN H 82 GLN L 46 ASN N 111 GLN P 9 GLN R 150 GLN ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 HIS S 317 GLN f 62 GLN i 62 HIS j 88 HIS ** 1 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 292 ASN 1 317 GLN 6 170 GLN 6 226 GLN 6 270 ASN 6 479 GLN e 94 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 62422 Z= 0.244 Angle : 0.886 13.766 84957 Z= 0.454 Chirality : 0.047 0.272 9567 Planarity : 0.007 0.107 10757 Dihedral : 11.806 146.621 9218 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.67 % Allowed : 16.77 % Favored : 82.56 % Rotamer: Outliers : 3.12 % Allowed : 10.76 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.99 % Twisted Proline : 2.36 % Twisted General : 0.44 % 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: -5.27 (0.08), residues: 7895 helix: -3.28 (0.07), residues: 3129 sheet: -2.83 (0.28), residues: 291 loop : -3.88 (0.08), residues: 4475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP V 142 HIS 0.012 0.001 HIS 6 230 PHE 0.054 0.002 PHE Z 63 TYR 0.031 0.002 TYR V 143 ARG 0.010 0.001 ARG 4 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 822 time to evaluate : 5.425 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: 2 87 MET cc_start: 0.7522 (ptt) cc_final: 0.7180 (ptt) REVERT: 2 135 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8229 (mmtm) REVERT: 3 41 PHE cc_start: 0.2880 (t80) cc_final: 0.2679 (t80) REVERT: 3 90 MET cc_start: 0.6753 (tpp) cc_final: 0.6537 (tpp) REVERT: 4 346 ARG cc_start: 0.7531 (mtm110) cc_final: 0.6974 (ptt90) REVERT: 7 21 SER cc_start: 0.8203 (m) cc_final: 0.7724 (t) REVERT: 7 70 TYR cc_start: 0.7159 (t80) cc_final: 0.6613 (t80) REVERT: A 302 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8187 (pp) REVERT: A 341 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7896 (pt) REVERT: B 52 MET cc_start: 0.5365 (tpp) cc_final: 0.4868 (tpp) REVERT: B 323 ARG cc_start: 0.7524 (ptp90) cc_final: 0.7322 (ptt-90) REVERT: D 107 ASP cc_start: 0.7988 (t0) cc_final: 0.7723 (t0) REVERT: G 59 LEU cc_start: 0.7244 (mt) cc_final: 0.6872 (tp) REVERT: H 10 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7573 (pp) REVERT: H 38 LYS cc_start: 0.7440 (pttt) cc_final: 0.7064 (pttp) REVERT: I 52 ARG cc_start: 0.7514 (mmt90) cc_final: 0.6206 (tmm160) REVERT: L 40 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7883 (pttm) REVERT: L 46 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8887 (t0) REVERT: Q 159 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7049 (mmmt) REVERT: R 150 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7067 (mm110) REVERT: R 195 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5552 (t80) REVERT: R 206 ILE cc_start: 0.6351 (OUTLIER) cc_final: 0.5914 (pp) REVERT: R 272 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6227 (tp) REVERT: R 324 THR cc_start: 0.8106 (m) cc_final: 0.7668 (m) REVERT: T 19 HIS cc_start: 0.7072 (m-70) cc_final: 0.6723 (m90) REVERT: T 58 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.4575 (ptt180) REVERT: T 81 ARG cc_start: 0.7323 (mmt-90) cc_final: 0.6649 (mtp-110) REVERT: W 110 LEU cc_start: 0.1337 (OUTLIER) cc_final: -0.0090 (tp) REVERT: Z 63 PHE cc_start: 0.7165 (t80) cc_final: 0.6964 (t80) REVERT: b 160 MET cc_start: 0.5618 (tpp) cc_final: 0.5137 (tpt) REVERT: c 38 GLN cc_start: 0.6478 (mp10) cc_final: 0.6183 (mm-40) REVERT: f 56 ASP cc_start: 0.6121 (m-30) cc_final: 0.5611 (p0) REVERT: f 150 ARG cc_start: 0.6790 (mmp80) cc_final: 0.5543 (mmt90) REVERT: h 64 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6672 (pp20) REVERT: 1 70 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7091 (ttp) REVERT: 1 85 MET cc_start: 0.8456 (ttm) cc_final: 0.8098 (ttm) REVERT: 1 121 TRP cc_start: 0.8000 (t60) cc_final: 0.7727 (t60) REVERT: 1 233 MET cc_start: 0.8004 (tmm) cc_final: 0.7781 (tmm) REVERT: 6 170 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: 6 230 HIS cc_start: 0.7834 (p-80) cc_final: 0.7579 (p-80) REVERT: 6 304 PHE cc_start: 0.7803 (m-80) cc_final: 0.7217 (m-80) REVERT: 6 456 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.5625 (ttp-170) REVERT: 6 518 ASN cc_start: 0.4720 (OUTLIER) cc_final: 0.4496 (m110) REVERT: 6 520 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.5256 (m-80) REVERT: 6 544 MET cc_start: 0.5194 (ttp) cc_final: 0.4634 (tpt) outliers start: 184 outliers final: 90 residues processed: 961 average time/residue: 0.5401 time to fit residues: 892.9782 Evaluate side-chains 814 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 706 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 244 ILE Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 27 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 126 LEU Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 7 residue 50 SER Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 150 GLN Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain S residue 180 LYS Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 109 ILE Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 63 ASP Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain h residue 68 GLU Chi-restraints excluded: chain h residue 103 SER Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 16 ASP Chi-restraints excluded: chain j residue 37 LEU Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain 1 residue 70 MET Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 211 PHE Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 170 GLN Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 496 LEU Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 518 ASN Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain 6 residue 576 LEU Chi-restraints excluded: chain g residue 15 ARG Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 92 TRP Chi-restraints excluded: chain e residue 160 GLN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 392 optimal weight: 5.9990 chunk 218 optimal weight: 0.0870 chunk 587 optimal weight: 6.9990 chunk 480 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 706 optimal weight: 2.9990 chunk 763 optimal weight: 8.9990 chunk 629 optimal weight: 1.9990 chunk 700 optimal weight: 0.1980 chunk 240 optimal weight: 0.9980 chunk 567 optimal weight: 8.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 268 GLN 3 28 ASN 4 374 ASN 5 25 HIS ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN E 192 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 GLN ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 124 ASN 6 67 HIS 6 328 HIS 6 479 GLN e 94 HIS e 132 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 62422 Z= 0.205 Angle : 0.818 12.194 84957 Z= 0.413 Chirality : 0.045 0.296 9567 Planarity : 0.006 0.129 10757 Dihedral : 10.870 149.424 9181 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 16.61 % Favored : 82.91 % Rotamer: Outliers : 3.21 % Allowed : 12.39 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.98 % Twisted Proline : 2.14 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.08), residues: 7895 helix: -2.61 (0.08), residues: 3123 sheet: -2.48 (0.28), residues: 294 loop : -3.72 (0.08), residues: 4478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP V 142 HIS 0.009 0.001 HIS 6 230 PHE 0.048 0.002 PHE Z 63 TYR 0.040 0.001 TYR M 17 ARG 0.013 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 803 time to evaluate : 5.455 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: 2 87 MET cc_start: 0.7483 (ptt) cc_final: 0.7135 (ptt) REVERT: 2 135 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7850 (mmtt) REVERT: 4 346 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7041 (ptt90) REVERT: 7 21 SER cc_start: 0.8431 (m) cc_final: 0.7777 (t) REVERT: 7 70 TYR cc_start: 0.7270 (t80) cc_final: 0.6792 (t80) REVERT: A 94 MET cc_start: 0.5964 (ttp) cc_final: 0.5700 (ttp) REVERT: A 302 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8143 (pp) REVERT: A 341 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7866 (pt) REVERT: B 443 MET cc_start: 0.7452 (mtp) cc_final: 0.6930 (mtp) REVERT: B 460 GLU cc_start: 0.6384 (tm-30) cc_final: 0.6149 (tm-30) REVERT: G 59 LEU cc_start: 0.7222 (mt) cc_final: 0.6818 (tp) REVERT: H 10 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7332 (pp) REVERT: H 38 LYS cc_start: 0.7451 (pttt) cc_final: 0.7090 (pttp) REVERT: I 52 ARG cc_start: 0.7503 (mmt90) cc_final: 0.6185 (tmm160) REVERT: L 40 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8172 (pttm) REVERT: O 26 ASN cc_start: 0.6764 (m-40) cc_final: 0.6340 (t0) REVERT: Q 159 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7127 (mmmt) REVERT: R 206 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5847 (pp) REVERT: R 324 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7532 (m) REVERT: T 19 HIS cc_start: 0.7058 (m-70) cc_final: 0.6731 (m90) REVERT: T 58 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.4477 (ptt180) REVERT: W 110 LEU cc_start: -0.0057 (OUTLIER) cc_final: -0.1114 (tp) REVERT: W 130 ILE cc_start: 0.5849 (mt) cc_final: 0.5566 (mt) REVERT: b 160 MET cc_start: 0.5641 (tpp) cc_final: 0.5121 (tpt) REVERT: f 56 ASP cc_start: 0.6019 (m-30) cc_final: 0.5400 (p0) REVERT: f 150 ARG cc_start: 0.6598 (mmp80) cc_final: 0.5475 (mmt90) REVERT: h 64 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6907 (pp20) REVERT: h 68 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6342 (mt-10) REVERT: 1 121 TRP cc_start: 0.8091 (t60) cc_final: 0.7861 (t60) REVERT: 1 228 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6847 (t80) REVERT: 6 170 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: 6 208 ASP cc_start: 0.6667 (t0) cc_final: 0.6350 (p0) REVERT: 6 304 PHE cc_start: 0.7825 (m-80) cc_final: 0.7292 (m-80) REVERT: 6 456 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.4678 (ttp-170) REVERT: 6 518 ASN cc_start: 0.4697 (OUTLIER) cc_final: 0.4464 (m-40) REVERT: 6 520 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.5219 (m-80) REVERT: 6 533 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7028 (tmm) REVERT: 6 540 MET cc_start: 0.6622 (ppp) cc_final: 0.6344 (ppp) REVERT: 6 544 MET cc_start: 0.5036 (ttp) cc_final: 0.4485 (tpt) REVERT: 6 571 MET cc_start: 0.8095 (ttp) cc_final: 0.7843 (ttt) REVERT: 6 572 LYS cc_start: 0.7618 (mmpt) cc_final: 0.7415 (mttm) REVERT: e 128 LEU cc_start: 0.6331 (tp) cc_final: 0.6049 (tp) outliers start: 189 outliers final: 106 residues processed: 942 average time/residue: 0.5502 time to fit residues: 900.0617 Evaluate side-chains 835 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 712 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 244 ILE Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 175 ASN Chi-restraints excluded: chain 4 residue 228 SER Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 80 MET Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 7 residue 149 TYR Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain 8 residue 410 ASP Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain O residue 25 MET Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 324 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 125 VAL Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 63 ASP Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain h residue 68 GLU Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 16 ASP Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 70 MET Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 211 PHE Chi-restraints excluded: chain 1 residue 223 PHE Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 96 VAL Chi-restraints excluded: chain 6 residue 170 GLN Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 479 GLN Chi-restraints excluded: chain 6 residue 496 LEU Chi-restraints excluded: chain 6 residue 518 ASN Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 533 MET Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain g residue 52 ILE Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 92 TRP Chi-restraints excluded: chain e residue 119 THR Chi-restraints excluded: chain e residue 160 GLN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 698 optimal weight: 6.9990 chunk 531 optimal weight: 6.9990 chunk 366 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 337 optimal weight: 8.9990 chunk 474 optimal weight: 7.9990 chunk 709 optimal weight: 8.9990 chunk 751 optimal weight: 0.9980 chunk 370 optimal weight: 3.9990 chunk 672 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 25 HIS 5 92 ASN ** 9 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 131 HIS ** 9 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS Q 103 GLN ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 230 ASN 1 287 HIS ** 6 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 94 HIS e 132 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 62422 Z= 0.246 Angle : 0.810 13.312 84957 Z= 0.408 Chirality : 0.046 0.250 9567 Planarity : 0.006 0.105 10757 Dihedral : 10.416 149.599 9169 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.48 % Allowed : 17.33 % Favored : 82.19 % Rotamer: Outliers : 3.65 % Allowed : 13.46 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.99 % Twisted Proline : 1.71 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.08), residues: 7895 helix: -2.14 (0.08), residues: 3146 sheet: -2.35 (0.27), residues: 309 loop : -3.64 (0.09), residues: 4440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 2 264 HIS 0.009 0.001 HIS 6 230 PHE 0.040 0.002 PHE Z 63 TYR 0.028 0.001 TYR B 141 ARG 0.007 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 743 time to evaluate : 5.536 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: 2 45 MET cc_start: 0.7100 (mmm) cc_final: 0.6872 (mmm) REVERT: 2 87 MET cc_start: 0.7227 (ptt) cc_final: 0.6881 (ptt) REVERT: 2 108 MET cc_start: 0.7737 (mmt) cc_final: 0.7506 (mmt) REVERT: 2 187 MET cc_start: 0.7956 (mmm) cc_final: 0.7756 (mmm) REVERT: 3 32 GLU cc_start: 0.3766 (OUTLIER) cc_final: 0.3499 (pt0) REVERT: 3 100 VAL cc_start: 0.9077 (m) cc_final: 0.8774 (p) REVERT: 4 346 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7084 (ptt90) REVERT: 7 21 SER cc_start: 0.8356 (m) cc_final: 0.7774 (t) REVERT: 7 70 TYR cc_start: 0.7338 (t80) cc_final: 0.6904 (t80) REVERT: A 94 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.5636 (ttp) REVERT: A 302 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8290 (pp) REVERT: A 341 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7914 (pt) REVERT: A 359 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7355 (t0) REVERT: B 211 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8648 (m-10) REVERT: B 371 MET cc_start: 0.8171 (ptm) cc_final: 0.7741 (ttp) REVERT: G 59 LEU cc_start: 0.7243 (mt) cc_final: 0.6746 (tp) REVERT: H 10 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7331 (pp) REVERT: H 38 LYS cc_start: 0.7488 (pttt) cc_final: 0.7156 (pttp) REVERT: I 52 ARG cc_start: 0.7679 (mmt90) cc_final: 0.6238 (tmm160) REVERT: L 40 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8255 (pttm) REVERT: R 195 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5618 (t80) REVERT: R 206 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.5935 (pp) REVERT: R 324 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7498 (m) REVERT: S 272 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6225 (mt) REVERT: T 19 HIS cc_start: 0.7069 (m-70) cc_final: 0.6714 (m90) REVERT: T 58 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.4486 (ptt180) REVERT: T 99 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7982 (mm) REVERT: W 110 LEU cc_start: 0.0526 (OUTLIER) cc_final: -0.0340 (tp) REVERT: W 130 ILE cc_start: 0.5731 (mt) cc_final: 0.5472 (mt) REVERT: b 160 MET cc_start: 0.5967 (tpp) cc_final: 0.5427 (tpt) REVERT: f 56 ASP cc_start: 0.6190 (m-30) cc_final: 0.5438 (p0) REVERT: f 150 ARG cc_start: 0.6653 (mmp80) cc_final: 0.5464 (mmt90) REVERT: h 64 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6710 (pp20) REVERT: 1 121 TRP cc_start: 0.8127 (t60) cc_final: 0.7873 (t60) REVERT: 1 156 MET cc_start: 0.7495 (tpp) cc_final: 0.7108 (tpp) REVERT: 1 211 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7179 (t80) REVERT: 1 228 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.7296 (t80) REVERT: 6 53 MET cc_start: 0.7124 (mtp) cc_final: 0.6858 (mtm) REVERT: 6 170 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: 6 208 ASP cc_start: 0.6490 (t0) cc_final: 0.6242 (p0) REVERT: 6 304 PHE cc_start: 0.7922 (m-80) cc_final: 0.7415 (m-80) REVERT: 6 314 MET cc_start: 0.8253 (mmm) cc_final: 0.7920 (tpp) REVERT: 6 456 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6227 (ttp-110) REVERT: 6 520 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.5210 (m-80) REVERT: 6 533 MET cc_start: 0.7448 (mtp) cc_final: 0.7079 (tmm) REVERT: 6 544 MET cc_start: 0.5065 (ttp) cc_final: 0.4476 (tpt) REVERT: 6 571 MET cc_start: 0.8057 (ttp) cc_final: 0.7846 (ttm) REVERT: 6 572 LYS cc_start: 0.7744 (mmpt) cc_final: 0.7474 (mttm) outliers start: 215 outliers final: 137 residues processed: 897 average time/residue: 0.5286 time to fit residues: 824.5404 Evaluate side-chains 844 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 686 time to evaluate : 5.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 4 residue 175 ASN Chi-restraints excluded: chain 4 residue 199 CYS Chi-restraints excluded: chain 4 residue 228 SER Chi-restraints excluded: chain 4 residue 323 SER Chi-restraints excluded: chain 4 residue 343 ILE Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 75 LEU Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 80 MET Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 90 VAL Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 149 TYR Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain 8 residue 156 ILE Chi-restraints excluded: chain 8 residue 410 ASP Chi-restraints excluded: chain 9 residue 83 LEU Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 222 TRP Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 324 THR Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain S residue 272 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 63 ASP Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 16 ASP Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain j residue 80 ASP Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 70 MET Chi-restraints excluded: chain 1 residue 96 ILE Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 208 VAL Chi-restraints excluded: chain 1 residue 211 PHE Chi-restraints excluded: chain 1 residue 223 PHE Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 294 LEU Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 96 VAL Chi-restraints excluded: chain 6 residue 170 GLN Chi-restraints excluded: chain 6 residue 246 LEU Chi-restraints excluded: chain 6 residue 387 THR Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 496 LEU Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain g residue 52 ILE Chi-restraints excluded: chain e residue 75 TYR Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 92 TRP Chi-restraints excluded: chain e residue 119 THR Chi-restraints excluded: chain e residue 160 GLN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 625 optimal weight: 2.9990 chunk 426 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 559 optimal weight: 30.0000 chunk 309 optimal weight: 0.0020 chunk 640 optimal weight: 1.9990 chunk 519 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 383 optimal weight: 5.9990 chunk 674 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 28 ASN 5 25 HIS ** 8 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 74 HIS ** 9 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS D 158 ASN E 192 ASN G 92 ASN L 46 ASN Q 95 GLN ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 94 HIS e 132 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 62422 Z= 0.198 Angle : 0.776 11.888 84957 Z= 0.389 Chirality : 0.045 0.252 9567 Planarity : 0.005 0.127 10757 Dihedral : 9.942 151.386 9163 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.14 % Favored : 83.49 % Rotamer: Outliers : 3.85 % Allowed : 14.17 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.98 % Twisted Proline : 1.71 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.09), residues: 7895 helix: -1.81 (0.09), residues: 3171 sheet: -2.25 (0.27), residues: 316 loop : -3.54 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 2 264 HIS 0.007 0.001 HIS 6 230 PHE 0.058 0.001 PHE Z 63 TYR 0.040 0.001 TYR M 17 ARG 0.006 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 760 time to evaluate : 5.479 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: 2 87 MET cc_start: 0.7212 (ptt) cc_final: 0.6850 (ptt) REVERT: 3 32 GLU cc_start: 0.4249 (OUTLIER) cc_final: 0.3881 (pt0) REVERT: 3 100 VAL cc_start: 0.9073 (m) cc_final: 0.8826 (p) REVERT: 4 98 MET cc_start: 0.7733 (tpp) cc_final: 0.7519 (tpp) REVERT: 4 228 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7803 (m) REVERT: 4 346 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7057 (ptt90) REVERT: 4 413 MET cc_start: 0.6654 (tmm) cc_final: 0.6435 (ppp) REVERT: 7 21 SER cc_start: 0.8287 (m) cc_final: 0.7642 (t) REVERT: 7 70 TYR cc_start: 0.7399 (t80) cc_final: 0.7184 (t80) REVERT: A 94 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5701 (ttp) REVERT: A 302 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8142 (pp) REVERT: A 341 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7876 (pt) REVERT: A 359 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7296 (t0) REVERT: B 211 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8566 (m-10) REVERT: B 371 MET cc_start: 0.8206 (ptm) cc_final: 0.7805 (ttp) REVERT: D 107 ASP cc_start: 0.7826 (t0) cc_final: 0.7539 (t0) REVERT: G 59 LEU cc_start: 0.7162 (mt) cc_final: 0.6697 (tp) REVERT: H 10 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7150 (pp) REVERT: H 38 LYS cc_start: 0.7483 (pttt) cc_final: 0.7108 (pttp) REVERT: I 52 ARG cc_start: 0.7753 (mmt90) cc_final: 0.6084 (tmm160) REVERT: L 40 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8195 (pttm) REVERT: O 26 ASN cc_start: 0.7260 (m-40) cc_final: 0.6859 (t0) REVERT: Q 159 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6862 (mmmt) REVERT: R 195 PHE cc_start: 0.5904 (OUTLIER) cc_final: 0.5577 (t80) REVERT: R 206 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5883 (pp) REVERT: R 324 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7290 (m) REVERT: S 272 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.6001 (mt) REVERT: T 19 HIS cc_start: 0.6953 (m-70) cc_final: 0.6637 (m90) REVERT: T 58 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.4528 (ptt180) REVERT: T 99 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7818 (mm) REVERT: U 49 TYR cc_start: 0.8430 (m-80) cc_final: 0.8012 (m-80) REVERT: V 120 MET cc_start: 0.7858 (tpp) cc_final: 0.7650 (tpp) REVERT: V 127 LEU cc_start: 0.3188 (OUTLIER) cc_final: 0.2915 (pp) REVERT: W 110 LEU cc_start: 0.0314 (OUTLIER) cc_final: -0.0172 (tp) REVERT: W 130 ILE cc_start: 0.6029 (mt) cc_final: 0.5753 (mt) REVERT: b 153 GLU cc_start: 0.8034 (tp30) cc_final: 0.7672 (tp30) REVERT: b 160 MET cc_start: 0.5713 (tpp) cc_final: 0.5233 (tpt) REVERT: f 56 ASP cc_start: 0.6147 (m-30) cc_final: 0.5444 (p0) REVERT: f 150 ARG cc_start: 0.6548 (mmp80) cc_final: 0.5499 (mmt90) REVERT: h 64 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6793 (pp20) REVERT: 1 121 TRP cc_start: 0.7957 (t60) cc_final: 0.7695 (t60) REVERT: 1 156 MET cc_start: 0.7450 (tpp) cc_final: 0.7168 (tpp) REVERT: 1 228 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.7129 (t80) REVERT: 6 170 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: 6 257 ILE cc_start: 0.6622 (pp) cc_final: 0.6283 (pp) REVERT: 6 304 PHE cc_start: 0.7895 (m-80) cc_final: 0.7376 (m-80) REVERT: 6 314 MET cc_start: 0.8140 (mmm) cc_final: 0.7514 (tpp) REVERT: 6 336 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8491 (mmpt) REVERT: 6 456 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5931 (ttp-110) REVERT: 6 520 PHE cc_start: 0.5506 (OUTLIER) cc_final: 0.5003 (m-80) REVERT: 6 533 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6947 (tmm) REVERT: 6 544 MET cc_start: 0.4716 (ttp) cc_final: 0.4333 (tpt) REVERT: 6 571 MET cc_start: 0.8049 (ttp) cc_final: 0.7821 (ttm) REVERT: 6 572 LYS cc_start: 0.7714 (mmpt) cc_final: 0.7445 (mttm) outliers start: 227 outliers final: 137 residues processed: 927 average time/residue: 0.5352 time to fit residues: 863.6636 Evaluate side-chains 855 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 693 time to evaluate : 5.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 175 LEU Chi-restraints excluded: chain 2 residue 184 ILE Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 175 ASN Chi-restraints excluded: chain 4 residue 199 CYS Chi-restraints excluded: chain 4 residue 228 SER Chi-restraints excluded: chain 4 residue 325 MET Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 75 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 90 VAL Chi-restraints excluded: chain 7 residue 2 MET Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 7 residue 74 MET Chi-restraints excluded: chain 7 residue 149 TYR Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain 8 residue 410 ASP Chi-restraints excluded: chain 9 residue 83 LEU Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 169 PHE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 222 TRP Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 324 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain S residue 272 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 115 CYS Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 38 GLN Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 62 GLU Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 70 MET Chi-restraints excluded: chain 1 residue 96 ILE Chi-restraints excluded: chain 1 residue 138 GLN Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 208 VAL Chi-restraints excluded: chain 1 residue 223 PHE Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 280 PHE Chi-restraints excluded: chain 1 residue 294 LEU Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 96 VAL Chi-restraints excluded: chain 6 residue 170 GLN Chi-restraints excluded: chain 6 residue 261 ILE Chi-restraints excluded: chain 6 residue 336 LYS Chi-restraints excluded: chain 6 residue 387 THR Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 496 LEU Chi-restraints excluded: chain 6 residue 513 TYR Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 533 MET Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain e residue 75 TYR Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 119 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 252 optimal weight: 10.0000 chunk 676 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 440 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 751 optimal weight: 4.9990 chunk 624 optimal weight: 0.0000 chunk 348 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 394 optimal weight: 9.9990 overall best weight: 2.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 10 ASN 3 28 ASN 4 333 ASN 5 25 HIS ** 8 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN L 46 ASN ** P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 ASN 1 235 ASN ** 1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 170 GLN ** 6 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 HIS ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 62422 Z= 0.250 Angle : 0.792 17.714 84957 Z= 0.397 Chirality : 0.045 0.233 9567 Planarity : 0.005 0.103 10757 Dihedral : 9.748 150.527 9152 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 17.60 % Favored : 81.99 % Rotamer: Outliers : 4.26 % Allowed : 14.68 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.99 % Twisted Proline : 1.71 % Twisted General : 0.17 % 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: -3.91 (0.09), residues: 7895 helix: -1.63 (0.09), residues: 3194 sheet: -2.14 (0.27), residues: 336 loop : -3.55 (0.09), residues: 4365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP 2 264 HIS 0.008 0.001 HIS S 190 PHE 0.047 0.002 PHE Z 63 TYR 0.025 0.001 TYR V 143 ARG 0.007 0.000 ARG I 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 716 time to evaluate : 5.419 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: 2 87 MET cc_start: 0.7372 (ptt) cc_final: 0.7102 (ptt) REVERT: 3 32 GLU cc_start: 0.4327 (OUTLIER) cc_final: 0.3897 (pt0) REVERT: 3 100 VAL cc_start: 0.9121 (m) cc_final: 0.8909 (p) REVERT: 4 36 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6961 (t80) REVERT: 4 346 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7082 (ptt90) REVERT: 7 70 TYR cc_start: 0.7436 (t80) cc_final: 0.7187 (t80) REVERT: A 77 MET cc_start: 0.8812 (tpp) cc_final: 0.8545 (tpp) REVERT: A 94 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5800 (ttp) REVERT: A 117 MET cc_start: 0.8557 (tmm) cc_final: 0.8129 (tmm) REVERT: A 265 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 302 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8292 (pp) REVERT: A 341 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 359 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7243 (t0) REVERT: B 211 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: B 460 GLU cc_start: 0.5820 (tm-30) cc_final: 0.5538 (tm-30) REVERT: D 96 MET cc_start: 0.8199 (ttp) cc_final: 0.7937 (ttp) REVERT: D 107 ASP cc_start: 0.7971 (t0) cc_final: 0.7649 (t0) REVERT: G 59 LEU cc_start: 0.7257 (mt) cc_final: 0.6721 (tp) REVERT: G 94 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8559 (m) REVERT: H 10 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7165 (pp) REVERT: H 38 LYS cc_start: 0.7552 (pttt) cc_final: 0.7205 (pttp) REVERT: H 86 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7419 (pp) REVERT: I 52 ARG cc_start: 0.7737 (mmt90) cc_final: 0.6214 (tmm160) REVERT: L 40 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8261 (pttm) REVERT: O 26 ASN cc_start: 0.6991 (m-40) cc_final: 0.6570 (t0) REVERT: R 195 PHE cc_start: 0.5659 (OUTLIER) cc_final: 0.5366 (t80) REVERT: R 206 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6237 (pp) REVERT: R 324 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7634 (m) REVERT: S 138 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8107 (mp) REVERT: T 19 HIS cc_start: 0.6982 (m-70) cc_final: 0.6660 (m90) REVERT: T 58 ARG cc_start: 0.5633 (OUTLIER) cc_final: 0.4739 (ptt180) REVERT: T 99 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7859 (mm) REVERT: U 49 TYR cc_start: 0.8454 (m-80) cc_final: 0.8013 (m-80) REVERT: V 127 LEU cc_start: 0.3527 (OUTLIER) cc_final: 0.3249 (pp) REVERT: W 110 LEU cc_start: 0.0470 (OUTLIER) cc_final: 0.0153 (tp) REVERT: W 130 ILE cc_start: 0.6066 (mt) cc_final: 0.5807 (mt) REVERT: f 56 ASP cc_start: 0.6194 (m-30) cc_final: 0.5522 (p0) REVERT: h 64 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6676 (pp20) REVERT: 1 121 TRP cc_start: 0.8093 (t60) cc_final: 0.7825 (t60) REVERT: 1 156 MET cc_start: 0.7505 (tpp) cc_final: 0.7245 (tpp) REVERT: 1 228 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7135 (t80) REVERT: 6 19 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8830 (mp) REVERT: 6 170 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: 6 257 ILE cc_start: 0.6636 (pp) cc_final: 0.6341 (pp) REVERT: 6 304 PHE cc_start: 0.7907 (m-80) cc_final: 0.7441 (m-80) REVERT: 6 314 MET cc_start: 0.8201 (mmm) cc_final: 0.7574 (tpp) REVERT: 6 336 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8688 (mmpt) REVERT: 6 456 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6052 (ttp-110) REVERT: 6 520 PHE cc_start: 0.5498 (OUTLIER) cc_final: 0.4979 (m-80) REVERT: 6 533 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7084 (tmm) REVERT: 6 544 MET cc_start: 0.4947 (ttp) cc_final: 0.4423 (tpt) REVERT: 6 571 MET cc_start: 0.8143 (ttp) cc_final: 0.7925 (ttm) REVERT: 6 572 LYS cc_start: 0.7781 (mmpt) cc_final: 0.7458 (mttm) REVERT: g 28 ASN cc_start: 0.1173 (OUTLIER) cc_final: 0.0676 (m-40) outliers start: 251 outliers final: 157 residues processed: 896 average time/residue: 0.5346 time to fit residues: 836.3038 Evaluate side-chains 866 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 680 time to evaluate : 5.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 86 VAL Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 175 LEU Chi-restraints excluded: chain 2 residue 184 ILE Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 36 PHE Chi-restraints excluded: chain 4 residue 109 THR Chi-restraints excluded: chain 4 residue 195 MET Chi-restraints excluded: chain 4 residue 199 CYS Chi-restraints excluded: chain 4 residue 228 SER Chi-restraints excluded: chain 4 residue 297 VAL Chi-restraints excluded: chain 4 residue 323 SER Chi-restraints excluded: chain 4 residue 325 MET Chi-restraints excluded: chain 4 residue 333 ASN Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 75 LEU Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 90 VAL Chi-restraints excluded: chain 7 residue 2 MET Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 7 residue 149 TYR Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain 8 residue 156 ILE Chi-restraints excluded: chain 8 residue 410 ASP Chi-restraints excluded: chain 9 residue 83 LEU Chi-restraints excluded: chain 9 residue 123 ASN Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 141 MET Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 155 CYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain Q residue 169 PHE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 324 THR Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 95 CYS Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 115 CYS Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 78 ASP Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain a residue 79 ASN Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 132 ASN Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 62 ARG Chi-restraints excluded: chain 1 residue 70 MET Chi-restraints excluded: chain 1 residue 96 ILE Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 145 THR Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 208 VAL Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 294 LEU Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 19 ILE Chi-restraints excluded: chain 6 residue 96 VAL Chi-restraints excluded: chain 6 residue 170 GLN Chi-restraints excluded: chain 6 residue 246 LEU Chi-restraints excluded: chain 6 residue 261 ILE Chi-restraints excluded: chain 6 residue 336 LYS Chi-restraints excluded: chain 6 residue 387 THR Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 414 ILE Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 496 LEU Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 533 MET Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 113 CYS Chi-restraints excluded: chain e residue 75 TYR Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 119 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 724 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 428 optimal weight: 10.0000 chunk 548 optimal weight: 9.9990 chunk 425 optimal weight: 7.9990 chunk 632 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 chunk 748 optimal weight: 10.0000 chunk 468 optimal weight: 0.0770 chunk 456 optimal weight: 7.9990 chunk 345 optimal weight: 1.9990 overall best weight: 1.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** 8 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 ASN 1 5 ASN ** 1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 HIS ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 62422 Z= 0.210 Angle : 0.778 14.646 84957 Z= 0.387 Chirality : 0.045 0.235 9567 Planarity : 0.005 0.100 10757 Dihedral : 9.558 151.717 9152 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.42 % Favored : 83.22 % Rotamer: Outliers : 4.02 % Allowed : 15.45 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.98 % Twisted Proline : 1.50 % Twisted General : 0.17 % 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: -3.78 (0.09), residues: 7895 helix: -1.52 (0.09), residues: 3177 sheet: -2.00 (0.27), residues: 342 loop : -3.48 (0.09), residues: 4376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 2 264 HIS 0.016 0.001 HIS 6 534 PHE 0.039 0.001 PHE 1 293 TYR 0.038 0.001 TYR M 17 ARG 0.012 0.000 ARG M 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 729 time to evaluate : 5.495 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: 2 87 MET cc_start: 0.7428 (ptt) cc_final: 0.7047 (ptt) REVERT: 3 32 GLU cc_start: 0.4237 (OUTLIER) cc_final: 0.3877 (pt0) REVERT: 4 36 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6929 (t80) REVERT: 4 346 ARG cc_start: 0.7593 (mtm110) cc_final: 0.7075 (ptt90) REVERT: 5 80 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7203 (mpp) REVERT: 7 70 TYR cc_start: 0.7441 (t80) cc_final: 0.7206 (t80) REVERT: A 77 MET cc_start: 0.8791 (tpp) cc_final: 0.8514 (tpp) REVERT: A 94 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5705 (ttp) REVERT: A 117 MET cc_start: 0.8609 (tmm) cc_final: 0.8181 (tmm) REVERT: A 265 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8619 (p) REVERT: A 302 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 341 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7817 (pt) REVERT: A 359 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7237 (t0) REVERT: B 211 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8665 (m-10) REVERT: B 460 GLU cc_start: 0.5888 (tm-30) cc_final: 0.5659 (tm-30) REVERT: D 107 ASP cc_start: 0.7913 (t0) cc_final: 0.7642 (t0) REVERT: G 59 LEU cc_start: 0.7208 (mt) cc_final: 0.6675 (tp) REVERT: G 94 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8557 (m) REVERT: H 10 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7141 (pp) REVERT: H 38 LYS cc_start: 0.7449 (pttt) cc_final: 0.7092 (pttp) REVERT: H 86 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7401 (pp) REVERT: I 52 ARG cc_start: 0.7739 (mmt90) cc_final: 0.6145 (tmm160) REVERT: L 40 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8179 (pttm) REVERT: N 111 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6641 (mt0) REVERT: O 26 ASN cc_start: 0.6839 (m-40) cc_final: 0.6512 (t0) REVERT: R 195 PHE cc_start: 0.5579 (OUTLIER) cc_final: 0.5271 (t80) REVERT: R 206 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6231 (pp) REVERT: R 309 PRO cc_start: 0.6068 (Cg_endo) cc_final: 0.5833 (Cg_exo) REVERT: R 324 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7403 (m) REVERT: T 19 HIS cc_start: 0.6943 (m-70) cc_final: 0.6634 (m90) REVERT: T 58 ARG cc_start: 0.5621 (OUTLIER) cc_final: 0.4765 (ptt180) REVERT: T 99 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7807 (mm) REVERT: U 49 TYR cc_start: 0.8437 (m-80) cc_final: 0.7975 (m-80) REVERT: V 10 MET cc_start: 0.7897 (mmp) cc_final: 0.7380 (mmp) REVERT: V 127 LEU cc_start: 0.3128 (OUTLIER) cc_final: 0.2828 (pp) REVERT: W 110 LEU cc_start: 0.0174 (OUTLIER) cc_final: -0.0047 (tp) REVERT: W 130 ILE cc_start: 0.5897 (mt) cc_final: 0.5655 (mt) REVERT: b 137 MET cc_start: 0.8378 (mmm) cc_final: 0.8084 (mmm) REVERT: f 56 ASP cc_start: 0.6160 (m-30) cc_final: 0.5650 (p0) REVERT: h 64 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6684 (pp20) REVERT: 1 85 MET cc_start: 0.8681 (ttm) cc_final: 0.8427 (mtp) REVERT: 1 156 MET cc_start: 0.7554 (tpp) cc_final: 0.7332 (tpp) REVERT: 1 228 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.7102 (t80) REVERT: 6 192 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.7536 (m110) REVERT: 6 257 ILE cc_start: 0.6774 (pp) cc_final: 0.6472 (pp) REVERT: 6 304 PHE cc_start: 0.7835 (m-80) cc_final: 0.7369 (m-80) REVERT: 6 314 MET cc_start: 0.8180 (mmm) cc_final: 0.7557 (tpp) REVERT: 6 336 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8677 (mmpt) REVERT: 6 456 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6151 (ttp-110) REVERT: 6 520 PHE cc_start: 0.5459 (OUTLIER) cc_final: 0.4995 (m-80) REVERT: 6 533 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7084 (tmm) REVERT: 6 544 MET cc_start: 0.4845 (ttp) cc_final: 0.4368 (tpt) REVERT: 6 572 LYS cc_start: 0.7748 (mmpt) cc_final: 0.7415 (mttm) REVERT: g 28 ASN cc_start: 0.1217 (OUTLIER) cc_final: 0.0731 (m-40) REVERT: M 52 MET cc_start: 0.7541 (tpt) cc_final: 0.6655 (tpp) outliers start: 237 outliers final: 154 residues processed: 904 average time/residue: 0.5325 time to fit residues: 837.6343 Evaluate side-chains 883 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 700 time to evaluate : 5.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 86 VAL Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 175 LEU Chi-restraints excluded: chain 2 residue 184 ILE Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 36 PHE Chi-restraints excluded: chain 4 residue 109 THR Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 4 residue 195 MET Chi-restraints excluded: chain 4 residue 199 CYS Chi-restraints excluded: chain 4 residue 204 MET Chi-restraints excluded: chain 4 residue 297 VAL Chi-restraints excluded: chain 4 residue 323 SER Chi-restraints excluded: chain 4 residue 325 MET Chi-restraints excluded: chain 4 residue 343 ILE Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 75 LEU Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 80 MET Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 90 VAL Chi-restraints excluded: chain 7 residue 2 MET Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 7 residue 54 LEU Chi-restraints excluded: chain 7 residue 74 MET Chi-restraints excluded: chain 7 residue 149 TYR Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain 8 residue 156 ILE Chi-restraints excluded: chain 8 residue 410 ASP Chi-restraints excluded: chain 9 residue 83 LEU Chi-restraints excluded: chain 9 residue 123 ASN Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain 9 residue 205 ILE Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 155 CYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain Q residue 169 PHE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 324 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 95 CYS Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 115 CYS Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 78 ASP Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 38 GLN Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain h residue 67 TYR Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 62 ARG Chi-restraints excluded: chain 1 residue 138 GLN Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 208 VAL Chi-restraints excluded: chain 1 residue 223 PHE Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 294 LEU Chi-restraints excluded: chain 6 residue 192 ASN Chi-restraints excluded: chain 6 residue 261 ILE Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 336 LYS Chi-restraints excluded: chain 6 residue 387 THR Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 414 ILE Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 513 TYR Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 533 MET Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 113 CYS Chi-restraints excluded: chain e residue 75 TYR Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 119 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 463 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 447 optimal weight: 0.0770 chunk 225 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 476 optimal weight: 7.9990 chunk 510 optimal weight: 6.9990 chunk 370 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 588 optimal weight: 9.9990 overall best weight: 4.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 36 ASN 3 10 ASN 3 28 ASN 8 168 ASN ** 8 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 HIS B 87 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 ASN ** 1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 HIS ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 62422 Z= 0.342 Angle : 0.852 16.470 84957 Z= 0.427 Chirality : 0.048 0.261 9567 Planarity : 0.006 0.103 10757 Dihedral : 9.734 148.579 9148 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.43 % Allowed : 18.89 % Favored : 80.68 % Rotamer: Outliers : 4.12 % Allowed : 15.79 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.99 % Twisted Proline : 1.28 % Twisted General : 0.19 % 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: -3.84 (0.09), residues: 7895 helix: -1.53 (0.09), residues: 3171 sheet: -2.14 (0.27), residues: 340 loop : -3.54 (0.09), residues: 4384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP 2 264 HIS 0.008 0.001 HIS B 381 PHE 0.037 0.002 PHE 1 293 TYR 0.033 0.002 TYR V 143 ARG 0.009 0.001 ARG 1 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 680 time to evaluate : 5.636 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: 2 87 MET cc_start: 0.7610 (ptt) cc_final: 0.7307 (ptt) REVERT: 3 32 GLU cc_start: 0.4417 (OUTLIER) cc_final: 0.4021 (pt0) REVERT: 4 36 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7224 (t80) REVERT: 4 346 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7097 (ptt90) REVERT: 5 80 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7335 (mpp) REVERT: 7 70 TYR cc_start: 0.7481 (t80) cc_final: 0.7180 (t80) REVERT: 9 74 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7190 (t-90) REVERT: 9 98 MET cc_start: 0.7957 (ttp) cc_final: 0.7698 (mtp) REVERT: A 94 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.6020 (ttp) REVERT: A 265 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8644 (p) REVERT: A 302 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8453 (pp) REVERT: A 341 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7799 (pt) REVERT: A 359 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7545 (t0) REVERT: B 211 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8700 (m-10) REVERT: B 460 GLU cc_start: 0.6225 (tm-30) cc_final: 0.5981 (tm-30) REVERT: G 59 LEU cc_start: 0.7366 (mt) cc_final: 0.6756 (tp) REVERT: H 10 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7401 (pp) REVERT: H 38 LYS cc_start: 0.7494 (pttt) cc_final: 0.7240 (pttp) REVERT: H 86 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7631 (pp) REVERT: I 52 ARG cc_start: 0.7930 (mmt90) cc_final: 0.6403 (tmm160) REVERT: L 40 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8163 (pttm) REVERT: N 111 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6698 (mt0) REVERT: Q 159 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6879 (mmmt) REVERT: R 195 PHE cc_start: 0.5748 (OUTLIER) cc_final: 0.5397 (t80) REVERT: R 324 THR cc_start: 0.8195 (m) cc_final: 0.7773 (m) REVERT: T 58 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.4940 (ptt180) REVERT: T 99 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7832 (mm) REVERT: V 127 LEU cc_start: 0.3610 (OUTLIER) cc_final: 0.3283 (pp) REVERT: W 110 LEU cc_start: 0.0173 (OUTLIER) cc_final: -0.0245 (tp) REVERT: W 130 ILE cc_start: 0.5991 (mt) cc_final: 0.5741 (mt) REVERT: h 64 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6614 (pp20) REVERT: j 90 MET cc_start: 0.7278 (ttt) cc_final: 0.6925 (ttp) REVERT: 1 85 MET cc_start: 0.8676 (ttm) cc_final: 0.8432 (mtp) REVERT: 1 156 MET cc_start: 0.7624 (tpp) cc_final: 0.7334 (tpp) REVERT: 1 228 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7239 (t80) REVERT: 1 233 MET cc_start: 0.8268 (tmm) cc_final: 0.8044 (tmm) REVERT: 1 280 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8235 (m-10) REVERT: 1 310 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8228 (tm) REVERT: 6 19 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8791 (mp) REVERT: 6 304 PHE cc_start: 0.7953 (m-80) cc_final: 0.7449 (m-80) REVERT: 6 314 MET cc_start: 0.8302 (mmm) cc_final: 0.7742 (tpp) REVERT: 6 336 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8816 (mmpt) REVERT: 6 456 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6308 (ttp-110) REVERT: 6 520 PHE cc_start: 0.5565 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: 6 533 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7133 (tmm) REVERT: 6 544 MET cc_start: 0.5329 (ttp) cc_final: 0.4763 (tpt) REVERT: 6 572 LYS cc_start: 0.8057 (mmpt) cc_final: 0.7675 (mttm) REVERT: M 52 MET cc_start: 0.7555 (tpt) cc_final: 0.6909 (tpp) outliers start: 243 outliers final: 171 residues processed: 860 average time/residue: 0.5491 time to fit residues: 842.9051 Evaluate side-chains 856 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 656 time to evaluate : 5.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 86 VAL Chi-restraints excluded: chain 2 residue 100 MET Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 175 LEU Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 36 PHE Chi-restraints excluded: chain 4 residue 109 THR Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 4 residue 195 MET Chi-restraints excluded: chain 4 residue 199 CYS Chi-restraints excluded: chain 4 residue 297 VAL Chi-restraints excluded: chain 4 residue 323 SER Chi-restraints excluded: chain 4 residue 325 MET Chi-restraints excluded: chain 4 residue 343 ILE Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 75 LEU Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 80 MET Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 90 VAL Chi-restraints excluded: chain 7 residue 2 MET Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 7 residue 54 LEU Chi-restraints excluded: chain 7 residue 149 TYR Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain 8 residue 156 ILE Chi-restraints excluded: chain 8 residue 410 ASP Chi-restraints excluded: chain 9 residue 74 HIS Chi-restraints excluded: chain 9 residue 83 LEU Chi-restraints excluded: chain 9 residue 123 ASN Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 141 MET Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain 9 residue 205 ILE Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 155 CYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 169 PHE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 95 CYS Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 115 CYS Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 78 ASP Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 147 TYR Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 132 ASN Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain h residue 67 TYR Chi-restraints excluded: chain h residue 68 GLU Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 62 ARG Chi-restraints excluded: chain 1 residue 91 MET Chi-restraints excluded: chain 1 residue 138 GLN Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 208 VAL Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 280 PHE Chi-restraints excluded: chain 1 residue 294 LEU Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 19 ILE Chi-restraints excluded: chain 6 residue 96 VAL Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 180 ILE Chi-restraints excluded: chain 6 residue 261 ILE Chi-restraints excluded: chain 6 residue 336 LYS Chi-restraints excluded: chain 6 residue 338 MET Chi-restraints excluded: chain 6 residue 387 THR Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 513 TYR Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 533 MET Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain 6 residue 603 ASN Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 113 CYS Chi-restraints excluded: chain e residue 75 TYR Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 119 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 681 optimal weight: 5.9990 chunk 717 optimal weight: 5.9990 chunk 654 optimal weight: 6.9990 chunk 697 optimal weight: 0.9990 chunk 420 optimal weight: 5.9990 chunk 304 optimal weight: 0.7980 chunk 548 optimal weight: 0.0970 chunk 214 optimal weight: 9.9990 chunk 630 optimal weight: 7.9990 chunk 660 optimal weight: 6.9990 chunk 695 optimal weight: 5.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 48 HIS 3 28 ASN ** 8 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 139 GLN 6 170 GLN ** 6 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 HIS ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 62422 Z= 0.253 Angle : 0.820 16.123 84957 Z= 0.407 Chirality : 0.046 0.268 9567 Planarity : 0.005 0.097 10757 Dihedral : 9.569 149.624 9146 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 17.25 % Favored : 82.39 % Rotamer: Outliers : 3.53 % Allowed : 16.74 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.98 % Twisted Proline : 1.28 % Twisted General : 0.19 % 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: -3.74 (0.09), residues: 7895 helix: -1.42 (0.09), residues: 3166 sheet: -2.09 (0.28), residues: 342 loop : -3.51 (0.09), residues: 4387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP 2 264 HIS 0.007 0.001 HIS S 190 PHE 0.034 0.002 PHE 1 293 TYR 0.032 0.001 TYR V 143 ARG 0.007 0.000 ARG f 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 690 time to evaluate : 5.545 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: 2 71 MET cc_start: 0.7030 (tpp) cc_final: 0.6752 (mmm) REVERT: 2 87 MET cc_start: 0.7314 (ptt) cc_final: 0.6956 (ptt) REVERT: 3 32 GLU cc_start: 0.4434 (OUTLIER) cc_final: 0.4022 (pt0) REVERT: 4 36 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7192 (t80) REVERT: 4 346 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7129 (ptt90) REVERT: 5 80 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7322 (mpp) REVERT: 7 70 TYR cc_start: 0.7428 (t80) cc_final: 0.7156 (t80) REVERT: 9 98 MET cc_start: 0.7808 (ttp) cc_final: 0.7536 (mtp) REVERT: A 77 MET cc_start: 0.8773 (tpp) cc_final: 0.8544 (tpp) REVERT: A 94 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.5903 (ttp) REVERT: A 117 MET cc_start: 0.8682 (tmm) cc_final: 0.8390 (tmm) REVERT: A 265 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8653 (p) REVERT: A 302 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8270 (pp) REVERT: A 341 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7833 (pt) REVERT: A 359 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7489 (t0) REVERT: B 211 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8768 (m-10) REVERT: B 460 GLU cc_start: 0.6212 (tm-30) cc_final: 0.5942 (tm-30) REVERT: D 107 ASP cc_start: 0.8165 (t0) cc_final: 0.7806 (t0) REVERT: G 59 LEU cc_start: 0.7143 (mt) cc_final: 0.6530 (tp) REVERT: H 10 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7396 (pp) REVERT: H 38 LYS cc_start: 0.7509 (pttt) cc_final: 0.7263 (pttp) REVERT: H 86 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7526 (pp) REVERT: I 52 ARG cc_start: 0.7880 (mmt90) cc_final: 0.6352 (tmm160) REVERT: L 40 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8010 (pttm) REVERT: N 111 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6753 (mt0) REVERT: P 108 GLN cc_start: 0.6680 (pm20) cc_final: 0.6406 (pt0) REVERT: Q 159 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6786 (mmmt) REVERT: R 195 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5478 (t80) REVERT: R 324 THR cc_start: 0.7955 (m) cc_final: 0.7459 (m) REVERT: T 58 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.4746 (ptt180) REVERT: T 99 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7657 (mm) REVERT: U 4 LEU cc_start: 0.7054 (mp) cc_final: 0.6815 (mp) REVERT: U 49 TYR cc_start: 0.8360 (m-80) cc_final: 0.7928 (m-80) REVERT: W 110 LEU cc_start: 0.0171 (OUTLIER) cc_final: -0.0238 (tp) REVERT: W 130 ILE cc_start: 0.5925 (mt) cc_final: 0.5684 (mt) REVERT: b 137 MET cc_start: 0.8393 (mmm) cc_final: 0.8071 (mmm) REVERT: h 64 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6631 (pp20) REVERT: 1 85 MET cc_start: 0.8674 (ttm) cc_final: 0.8439 (mtp) REVERT: 1 156 MET cc_start: 0.7542 (tpp) cc_final: 0.7322 (tpp) REVERT: 1 228 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7142 (t80) REVERT: 1 280 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: 1 310 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8212 (tm) REVERT: 6 304 PHE cc_start: 0.7885 (m-80) cc_final: 0.7463 (m-80) REVERT: 6 314 MET cc_start: 0.8289 (mmm) cc_final: 0.7719 (tpp) REVERT: 6 336 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8790 (mmpt) REVERT: 6 456 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6287 (ttp-110) REVERT: 6 520 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.5068 (m-80) REVERT: 6 533 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7100 (tmm) REVERT: 6 544 MET cc_start: 0.5107 (ttp) cc_final: 0.4565 (tpt) REVERT: 6 572 LYS cc_start: 0.7816 (mmpt) cc_final: 0.7579 (mttm) REVERT: g 28 ASN cc_start: 0.1190 (OUTLIER) cc_final: 0.0647 (m-40) outliers start: 208 outliers final: 164 residues processed: 846 average time/residue: 0.5391 time to fit residues: 797.7865 Evaluate side-chains 861 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 670 time to evaluate : 5.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 86 VAL Chi-restraints excluded: chain 2 residue 100 MET Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 175 LEU Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 36 PHE Chi-restraints excluded: chain 4 residue 109 THR Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 4 residue 297 VAL Chi-restraints excluded: chain 4 residue 323 SER Chi-restraints excluded: chain 4 residue 325 MET Chi-restraints excluded: chain 4 residue 343 ILE Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 75 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 80 MET Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 90 VAL Chi-restraints excluded: chain 7 residue 2 MET Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 7 residue 54 LEU Chi-restraints excluded: chain 7 residue 149 TYR Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain 8 residue 156 ILE Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 355 ILE Chi-restraints excluded: chain 8 residue 410 ASP Chi-restraints excluded: chain 9 residue 83 LEU Chi-restraints excluded: chain 9 residue 123 ASN Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain 9 residue 205 ILE Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 155 CYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 169 PHE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 95 CYS Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 115 CYS Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 78 ASP Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 143 TYR Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 147 TYR Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain h residue 67 TYR Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 62 ARG Chi-restraints excluded: chain 1 residue 138 GLN Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 208 VAL Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 280 PHE Chi-restraints excluded: chain 1 residue 294 LEU Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 96 VAL Chi-restraints excluded: chain 6 residue 254 VAL Chi-restraints excluded: chain 6 residue 261 ILE Chi-restraints excluded: chain 6 residue 336 LYS Chi-restraints excluded: chain 6 residue 338 MET Chi-restraints excluded: chain 6 residue 387 THR Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 414 ILE Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 513 TYR Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 533 MET Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain 6 residue 561 ILE Chi-restraints excluded: chain 6 residue 603 ASN Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 113 CYS Chi-restraints excluded: chain e residue 75 TYR Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 119 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 458 optimal weight: 9.9990 chunk 737 optimal weight: 0.9990 chunk 450 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 513 optimal weight: 9.9990 chunk 774 optimal weight: 7.9990 chunk 712 optimal weight: 6.9990 chunk 616 optimal weight: 10.0000 chunk 64 optimal weight: 0.0870 chunk 476 optimal weight: 8.9990 chunk 377 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** 8 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN ** S 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 170 GLN ** 6 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 HIS ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 62422 Z= 0.277 Angle : 0.831 15.749 84957 Z= 0.413 Chirality : 0.046 0.294 9567 Planarity : 0.006 0.095 10757 Dihedral : 9.489 149.368 9146 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.37 % Allowed : 18.70 % Favored : 80.93 % Rotamer: Outliers : 3.51 % Allowed : 17.03 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.99 % Twisted Proline : 1.28 % Twisted General : 0.17 % 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: -3.71 (0.09), residues: 7895 helix: -1.37 (0.09), residues: 3160 sheet: -2.04 (0.28), residues: 342 loop : -3.51 (0.09), residues: 4393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 2 264 HIS 0.007 0.001 HIS Q 143 PHE 0.032 0.002 PHE 1 293 TYR 0.030 0.002 TYR V 143 ARG 0.005 0.000 ARG Q 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15790 Ramachandran restraints generated. 7895 Oldfield, 0 Emsley, 7895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 676 time to evaluate : 5.599 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: 2 87 MET cc_start: 0.7353 (ptt) cc_final: 0.6994 (ptt) REVERT: 3 32 GLU cc_start: 0.4386 (OUTLIER) cc_final: 0.3977 (pt0) REVERT: 4 36 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7213 (t80) REVERT: 4 346 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7144 (ptt90) REVERT: 5 6 MET cc_start: 0.6626 (mmp) cc_final: 0.6424 (mtm) REVERT: 5 80 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7288 (mpp) REVERT: 7 70 TYR cc_start: 0.7445 (t80) cc_final: 0.7169 (t80) REVERT: 9 98 MET cc_start: 0.7840 (ttp) cc_final: 0.7578 (mtp) REVERT: A 77 MET cc_start: 0.8848 (tpp) cc_final: 0.8594 (tpp) REVERT: A 94 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.6046 (ttp) REVERT: A 117 MET cc_start: 0.8713 (tmm) cc_final: 0.8362 (tmm) REVERT: A 265 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 302 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8332 (pp) REVERT: A 341 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7772 (pt) REVERT: A 359 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7562 (t0) REVERT: B 211 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8729 (m-10) REVERT: B 320 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.6905 (mt) REVERT: B 420 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 460 GLU cc_start: 0.6250 (tm-30) cc_final: 0.5976 (tm-30) REVERT: G 59 LEU cc_start: 0.7189 (mt) cc_final: 0.6538 (tp) REVERT: H 10 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7341 (pp) REVERT: H 38 LYS cc_start: 0.7576 (pttt) cc_final: 0.7089 (pttm) REVERT: H 86 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7593 (pp) REVERT: I 52 ARG cc_start: 0.7901 (mmt90) cc_final: 0.6390 (tmm160) REVERT: L 40 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8065 (pttm) REVERT: L 82 LYS cc_start: 0.5551 (mttt) cc_final: 0.5119 (mptt) REVERT: N 111 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6736 (mt0) REVERT: Q 121 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6460 (p0) REVERT: Q 159 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6758 (mmmt) REVERT: R 195 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.5504 (t80) REVERT: R 309 PRO cc_start: 0.6159 (Cg_endo) cc_final: 0.5896 (Cg_exo) REVERT: R 324 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7561 (m) REVERT: T 58 ARG cc_start: 0.5762 (OUTLIER) cc_final: 0.4705 (ptt180) REVERT: T 99 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7592 (mm) REVERT: U 4 LEU cc_start: 0.7203 (mp) cc_final: 0.6943 (mp) REVERT: U 49 TYR cc_start: 0.8375 (m-80) cc_final: 0.7970 (m-80) REVERT: V 127 LEU cc_start: 0.3220 (OUTLIER) cc_final: 0.2949 (pp) REVERT: W 110 LEU cc_start: 0.0546 (OUTLIER) cc_final: 0.0005 (tp) REVERT: W 130 ILE cc_start: 0.5965 (mt) cc_final: 0.5733 (mt) REVERT: b 137 MET cc_start: 0.8424 (mmm) cc_final: 0.8090 (mmm) REVERT: h 64 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: 1 85 MET cc_start: 0.8686 (ttm) cc_final: 0.8477 (mtp) REVERT: 1 228 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7125 (t80) REVERT: 1 280 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8214 (m-10) REVERT: 1 310 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8095 (tm) REVERT: 6 88 MET cc_start: 0.6057 (pmm) cc_final: 0.5814 (pmm) REVERT: 6 304 PHE cc_start: 0.7916 (m-80) cc_final: 0.7470 (m-80) REVERT: 6 456 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6325 (ttp-110) REVERT: 6 520 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.5064 (m-80) REVERT: 6 544 MET cc_start: 0.5260 (ttp) cc_final: 0.4655 (tpt) REVERT: 6 572 LYS cc_start: 0.7961 (mmpt) cc_final: 0.7624 (mttm) REVERT: M 52 MET cc_start: 0.7612 (tpt) cc_final: 0.7027 (tpp) outliers start: 207 outliers final: 162 residues processed: 830 average time/residue: 0.5864 time to fit residues: 855.8605 Evaluate side-chains 852 residues out of total 6970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 661 time to evaluate : 5.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 86 VAL Chi-restraints excluded: chain 2 residue 100 MET Chi-restraints excluded: chain 2 residue 162 ILE Chi-restraints excluded: chain 2 residue 175 LEU Chi-restraints excluded: chain 2 residue 184 ILE Chi-restraints excluded: chain 2 residue 284 ILE Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 32 GLU Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 36 PHE Chi-restraints excluded: chain 4 residue 109 THR Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 4 residue 297 VAL Chi-restraints excluded: chain 4 residue 323 SER Chi-restraints excluded: chain 4 residue 325 MET Chi-restraints excluded: chain 4 residue 343 ILE Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 61 ILE Chi-restraints excluded: chain 5 residue 75 LEU Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 78 LEU Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 80 MET Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 90 VAL Chi-restraints excluded: chain 7 residue 2 MET Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 7 residue 54 LEU Chi-restraints excluded: chain 7 residue 149 TYR Chi-restraints excluded: chain 7 residue 171 ILE Chi-restraints excluded: chain 8 residue 156 ILE Chi-restraints excluded: chain 8 residue 204 TYR Chi-restraints excluded: chain 8 residue 355 ILE Chi-restraints excluded: chain 8 residue 410 ASP Chi-restraints excluded: chain 9 residue 83 LEU Chi-restraints excluded: chain 9 residue 123 ASN Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 141 MET Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain 9 residue 205 ILE Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 155 CYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 17 TRP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 121 ASP Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 169 PHE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 324 THR Chi-restraints excluded: chain S residue 86 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 216 LYS Chi-restraints excluded: chain T residue 58 ARG Chi-restraints excluded: chain T residue 89 ASN Chi-restraints excluded: chain T residue 95 CYS Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 115 CYS Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 78 ASP Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 143 TYR Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 147 TYR Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain f residue 30 TRP Chi-restraints excluded: chain f residue 81 ILE Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain h residue 67 TYR Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 62 ARG Chi-restraints excluded: chain 1 residue 138 GLN Chi-restraints excluded: chain 1 residue 143 GLU Chi-restraints excluded: chain 1 residue 201 THR Chi-restraints excluded: chain 1 residue 208 VAL Chi-restraints excluded: chain 1 residue 228 TYR Chi-restraints excluded: chain 1 residue 280 PHE Chi-restraints excluded: chain 1 residue 294 LEU Chi-restraints excluded: chain 1 residue 310 LEU Chi-restraints excluded: chain 6 residue 254 VAL Chi-restraints excluded: chain 6 residue 261 ILE Chi-restraints excluded: chain 6 residue 338 MET Chi-restraints excluded: chain 6 residue 387 THR Chi-restraints excluded: chain 6 residue 412 THR Chi-restraints excluded: chain 6 residue 456 ARG Chi-restraints excluded: chain 6 residue 513 TYR Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 520 PHE Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 525 LEU Chi-restraints excluded: chain 6 residue 551 SER Chi-restraints excluded: chain 6 residue 561 ILE Chi-restraints excluded: chain 6 residue 603 ASN Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 113 CYS Chi-restraints excluded: chain e residue 75 TYR Chi-restraints excluded: chain e residue 89 TRP Chi-restraints excluded: chain e residue 119 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 489 optimal weight: 7.9990 chunk 656 optimal weight: 0.7980 chunk 188 optimal weight: 0.0870 chunk 568 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 617 optimal weight: 0.9990 chunk 258 optimal weight: 7.9990 chunk 633 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 ASN ** 1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 HIS ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.084259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.072533 restraints weight = 260362.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.073811 restraints weight = 298552.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.073509 restraints weight = 133248.353| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 62422 Z= 0.194 Angle : 0.805 15.635 84957 Z= 0.396 Chirality : 0.045 0.287 9567 Planarity : 0.005 0.092 10757 Dihedral : 9.224 152.050 9146 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.77 % Favored : 83.90 % Rotamer: Outliers : 2.92 % Allowed : 17.81 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.98 % Twisted Proline : 1.28 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.09), residues: 7895 helix: -1.25 (0.09), residues: 3147 sheet: -1.80 (0.29), residues: 336 loop : -3.44 (0.09), residues: 4412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 2 264 HIS 0.007 0.001 HIS S 190 PHE 0.034 0.001 PHE I 67 TYR 0.028 0.001 TYR V 143 ARG 0.006 0.000 ARG f 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13631.46 seconds wall clock time: 239 minutes 52.82 seconds (14392.82 seconds total)