Starting phenix.real_space_refine on Sat Feb 24 01:47:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu3_31307/02_2024/7eu3_31307_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu3_31307/02_2024/7eu3_31307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu3_31307/02_2024/7eu3_31307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu3_31307/02_2024/7eu3_31307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu3_31307/02_2024/7eu3_31307_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu3_31307/02_2024/7eu3_31307_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 1 5.49 5 S 204 5.16 5 C 26574 2.51 5 N 6641 2.21 5 O 7351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 248": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 359": "NH1" <-> "NH2" Residue "F ARG 437": "NH1" <-> "NH2" Residue "F ARG 714": "NH1" <-> "NH2" Residue "F ARG 760": "NH1" <-> "NH2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "H GLU 240": "OE1" <-> "OE2" Residue "H GLU 267": "OE1" <-> "OE2" Residue "H ARG 293": "NH1" <-> "NH2" Residue "H GLU 302": "OE1" <-> "OE2" Residue "H GLU 307": "OE1" <-> "OE2" Residue "H ARG 323": "NH1" <-> "NH2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ARG 74": "NH1" <-> "NH2" Residue "J ARG 106": "NH1" <-> "NH2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K GLU 114": "OE1" <-> "OE2" Residue "K ARG 144": "NH1" <-> "NH2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 205": "NH1" <-> "NH2" Residue "L ARG 120": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L ARG 159": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 131": "OE1" <-> "OE2" Residue "M ARG 189": "NH1" <-> "NH2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "N ARG 138": "NH1" <-> "NH2" Residue "N ARG 180": "NH1" <-> "NH2" Residue "N GLU 188": "OE1" <-> "OE2" Residue "N ARG 199": "NH1" <-> "NH2" Residue "N ARG 203": "NH1" <-> "NH2" Residue "N ARG 212": "NH1" <-> "NH2" Residue "1 ARG 96": "NH1" <-> "NH2" Residue "1 ARG 130": "NH1" <-> "NH2" Residue "1 ARG 162": "NH1" <-> "NH2" Residue "1 ARG 167": "NH1" <-> "NH2" Residue "1 ARG 206": "NH1" <-> "NH2" Residue "1 ARG 210": "NH1" <-> "NH2" Residue "1 ARG 212": "NH1" <-> "NH2" Residue "2 GLU 113": "OE1" <-> "OE2" Residue "2 ARG 130": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "2 ARG 190": "NH1" <-> "NH2" Residue "3 ARG 131": "NH1" <-> "NH2" Residue "3 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 188": "NH1" <-> "NH2" Residue "4 ARG 129": "NH1" <-> "NH2" Residue "4 GLU 149": "OE1" <-> "OE2" Residue "4 ARG 173": "NH1" <-> "NH2" Residue "4 ARG 201": "NH1" <-> "NH2" Residue "5 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 ARG 156": "NH1" <-> "NH2" Residue "5 PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 200": "NH1" <-> "NH2" Residue "5 ARG 224": "NH1" <-> "NH2" Residue "5 ARG 227": "NH1" <-> "NH2" Residue "6 ARG 116": "NH1" <-> "NH2" Residue "6 ARG 117": "NH1" <-> "NH2" Residue "6 ARG 155": "NH1" <-> "NH2" Residue "6 ARG 167": "NH1" <-> "NH2" Residue "6 ARG 194": "NH1" <-> "NH2" Residue "6 ARG 219": "NH1" <-> "NH2" Residue "6 GLU 240": "OE1" <-> "OE2" Residue "6 ARG 280": "NH1" <-> "NH2" Residue "6 ARG 288": "NH1" <-> "NH2" Residue "6 ARG 297": "NH1" <-> "NH2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 ARG 349": "NH1" <-> "NH2" Residue "6 ARG 358": "NH1" <-> "NH2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 406": "NH1" <-> "NH2" Residue "6 PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 429": "OE1" <-> "OE2" Residue "6 ARG 430": "NH1" <-> "NH2" Residue "7 ARG 45": "NH1" <-> "NH2" Residue "7 ARG 49": "NH1" <-> "NH2" Residue "7 ARG 65": "NH1" <-> "NH2" Residue "7 ARG 73": "NH1" <-> "NH2" Residue "7 TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 83": "NH1" <-> "NH2" Residue "7 ARG 95": "NH1" <-> "NH2" Residue "7 ARG 110": "NH1" <-> "NH2" Residue "7 GLU 152": "OE1" <-> "OE2" Residue "7 ARG 185": "NH1" <-> "NH2" Residue "7 ARG 202": "NH1" <-> "NH2" Residue "7 ARG 236": "NH1" <-> "NH2" Residue "7 GLU 249": "OE1" <-> "OE2" Residue "7 ARG 251": "NH1" <-> "NH2" Residue "7 ARG 280": "NH1" <-> "NH2" Residue "7 ARG 283": "NH1" <-> "NH2" Residue "7 ARG 304": "NH1" <-> "NH2" Residue "7 GLU 348": "OE1" <-> "OE2" Residue "7 ARG 351": "NH1" <-> "NH2" Residue "9 GLU 157": "OE1" <-> "OE2" Residue "0 ARG 79": "NH1" <-> "NH2" Residue "0 GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40775 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2608 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 330} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3646 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 841 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3874 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 24, 'TRANS': 474} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 750 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5124 Classifications: {'peptide': 671} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 24, 'TRANS': 646} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1260 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 170} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "H" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2991 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 21, 'TRANS': 361} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 96 Chain: "I" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1229 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "J" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1258 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 150} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "K" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1474 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 572 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 61} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 876 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "N" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1154 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "T" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 305 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'TRANS': 60} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'UNK:plan-1': 61} Unresolved non-hydrogen planarities: 61 Chain: "1" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 143} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "2" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 915 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 4, 'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "3" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 989 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "4" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 878 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 119} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "5" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1289 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 164} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "6" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2541 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 18, 'TRANS': 324} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "7" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2311 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 298} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "8" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 828 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 110} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "9" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 617 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "0" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1089 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 11, 'TRANS': 137} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'BCR': 1, 'SQD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38434 SG CYS 8 132 75.038 177.624 129.984 1.00 78.19 S Time building chain proxies: 20.85, per 1000 atoms: 0.51 Number of scatterers: 40775 At special positions: 0 Unit cell: (172.524, 230.032, 186.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 204 16.00 P 1 15.00 O 7351 8.00 N 6641 7.00 C 26574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 410 " - pdb=" SG CYS 6 433 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.48 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 8 201 " pdb="FE3 SF4 8 201 " - pdb=" SG CYS 8 132 " pdb="FE4 SF4 8 201 " - pdb=" SG CYS 8 168 " pdb="FE4 SF4 8 201 " - pdb=" SG CYS 8 135 " Number of angles added : 9 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 188 helices and 20 sheets defined 43.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.70 Creating SS restraints... Processing helix chain 'A' and resid 30 through 56 removed outlier: 4.772A pdb=" N ALA A 55 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.755A pdb=" N PHE A 83 " --> pdb=" O THR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 112 Proline residue: A 101 - end of helix removed outlier: 3.607A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 157 through 168 removed outlier: 4.266A pdb=" N ALA A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 4.079A pdb=" N ALA A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 181 " --> pdb=" O CYS A 177 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 209 No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.688A pdb=" N VAL A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 274 Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.693A pdb=" N ASP A 289 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE A 290 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 291 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 4.231A pdb=" N LYS A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.272A pdb=" N LEU A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 51 removed outlier: 4.098A pdb=" N LEU B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 77 removed outlier: 4.305A pdb=" N SER B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 removed outlier: 3.512A pdb=" N PHE B 100 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) Proline residue: B 113 - end of helix removed outlier: 4.045A pdb=" N GLU B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 144 Processing helix chain 'B' and resid 151 through 160 Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 175 through 204 removed outlier: 3.882A pdb=" N THR B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TYR B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.833A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 removed outlier: 5.391A pdb=" N GLN B 251 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TRP B 252 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Proline residue: B 254 - end of helix removed outlier: 3.952A pdb=" N TYR B 257 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 removed outlier: 5.036A pdb=" N LYS B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 316 removed outlier: 4.501A pdb=" N ASN B 293 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 297 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 299 " --> pdb=" O HIS B 296 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 304 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET B 307 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 309 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY B 310 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU B 312 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU B 313 " --> pdb=" O GLY B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 328 Processing helix chain 'B' and resid 337 through 340 No H-bonds generated for 'chain 'B' and resid 337 through 340' Processing helix chain 'B' and resid 348 through 376 removed outlier: 3.851A pdb=" N SER B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 392 through 406 removed outlier: 3.871A pdb=" N CYS B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 433 through 454 removed outlier: 4.186A pdb=" N TYR B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.761A pdb=" N ILE B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER B 491 " --> pdb=" O CYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'C' and resid 8 through 30 Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 59 through 84 removed outlier: 4.304A pdb=" N MET C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU C 75 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 92 through 113 removed outlier: 3.565A pdb=" N LEU C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.868A pdb=" N TRP D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 103 removed outlier: 4.125A pdb=" N GLY D 88 " --> pdb=" O GLY D 84 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 129 Processing helix chain 'D' and resid 134 through 154 removed outlier: 4.141A pdb=" N GLU D 144 " --> pdb=" O MET D 140 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU D 145 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Proline residue: D 147 - end of helix Processing helix chain 'D' and resid 160 through 186 removed outlier: 3.654A pdb=" N ILE D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D 178 " --> pdb=" O GLY D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 224 removed outlier: 3.897A pdb=" N ALA D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 243 through 249 removed outlier: 3.999A pdb=" N LEU D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 4.208A pdb=" N GLY D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 273 No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.875A pdb=" N ILE D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 320 removed outlier: 3.774A pdb=" N MET D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE D 316 " --> pdb=" O HIS D 312 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 352 removed outlier: 3.728A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 385 removed outlier: 3.612A pdb=" N PHE D 381 " --> pdb=" O MET D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 405 removed outlier: 4.123A pdb=" N ALA D 396 " --> pdb=" O SER D 392 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU D 397 " --> pdb=" O GLY D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 removed outlier: 4.264A pdb=" N THR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY D 425 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET D 426 " --> pdb=" O MET D 422 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) Proline residue: D 430 - end of helix removed outlier: 3.685A pdb=" N SER D 435 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 477 Proline residue: D 471 - end of helix Processing helix chain 'D' and resid 488 through 491 No H-bonds generated for 'chain 'D' and resid 488 through 491' Processing helix chain 'E' and resid 2 through 5 No H-bonds generated for 'chain 'E' and resid 2 through 5' Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.794A pdb=" N VAL E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR E 12 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE E 16 " --> pdb=" O TYR E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 51 removed outlier: 3.754A pdb=" N THR E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE E 48 " --> pdb=" O ASN E 44 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 87 removed outlier: 3.626A pdb=" N LEU E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 58 through 70 removed outlier: 4.331A pdb=" N SER F 63 " --> pdb=" O PRO F 59 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE F 66 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 77 removed outlier: 3.783A pdb=" N LYS F 76 " --> pdb=" O PRO F 72 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 72 through 77' Processing helix chain 'F' and resid 81 through 106 Proline residue: F 85 - end of helix removed outlier: 3.594A pdb=" N LEU F 89 " --> pdb=" O PRO F 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 93 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU F 100 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN F 103 " --> pdb=" O GLN F 99 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 158 removed outlier: 3.902A pdb=" N VAL F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 151 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER F 158 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 181 removed outlier: 3.524A pdb=" N GLY F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 204 removed outlier: 3.996A pdb=" N PHE F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU F 194 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU F 195 " --> pdb=" O PHE F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 242 removed outlier: 3.888A pdb=" N CYS F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLN F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN F 224 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 4.287A pdb=" N GLN F 252 " --> pdb=" O ARG F 248 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 282 removed outlier: 4.425A pdb=" N CYS F 271 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA F 272 " --> pdb=" O THR F 269 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS F 282 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 removed outlier: 4.506A pdb=" N GLU F 297 " --> pdb=" O PRO F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 313 through 328 removed outlier: 4.484A pdb=" N LEU F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU F 319 " --> pdb=" O GLY F 315 " (cutoff:3.500A) Proline residue: F 324 - end of helix removed outlier: 3.613A pdb=" N ILE F 327 " --> pdb=" O LEU F 323 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 350 removed outlier: 3.681A pdb=" N SER F 337 " --> pdb=" O MET F 333 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 378 removed outlier: 4.329A pdb=" N ALA F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR F 371 " --> pdb=" O SER F 367 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 377 " --> pdb=" O MET F 373 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 378 " --> pdb=" O LEU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 411 removed outlier: 4.066A pdb=" N PHE F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR F 393 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU F 398 " --> pdb=" O SER F 394 " (cutoff:3.500A) Proline residue: F 411 - end of helix Processing helix chain 'F' and resid 435 through 448 removed outlier: 4.193A pdb=" N THR F 439 " --> pdb=" O ILE F 435 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE F 440 " --> pdb=" O THR F 436 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER F 446 " --> pdb=" O TRP F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 469 removed outlier: 3.705A pdb=" N GLU F 461 " --> pdb=" O TRP F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 496 removed outlier: 4.952A pdb=" N ILE F 476 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY F 482 " --> pdb=" O SER F 478 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA F 485 " --> pdb=" O ALA F 481 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR F 492 " --> pdb=" O MET F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 591 Processing helix chain 'F' and resid 593 through 599 removed outlier: 5.688A pdb=" N GLY F 598 " --> pdb=" O THR F 594 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 664 Processing helix chain 'F' and resid 686 through 703 removed outlier: 4.625A pdb=" N GLU F 689 " --> pdb=" O PRO F 686 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU F 691 " --> pdb=" O LYS F 688 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP F 692 " --> pdb=" O GLU F 689 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR F 699 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR F 703 " --> pdb=" O SER F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 707 through 729 removed outlier: 3.589A pdb=" N VAL F 715 " --> pdb=" O TYR F 712 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE F 716 " --> pdb=" O THR F 713 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR F 717 " --> pdb=" O ARG F 714 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 718 " --> pdb=" O VAL F 715 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE F 720 " --> pdb=" O THR F 717 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG F 721 " --> pdb=" O LEU F 718 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR F 724 " --> pdb=" O ARG F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 755 removed outlier: 4.124A pdb=" N GLY F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER F 746 " --> pdb=" O VAL F 742 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE F 747 " --> pdb=" O GLY F 743 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU F 751 " --> pdb=" O PHE F 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 776 removed outlier: 3.829A pdb=" N TYR F 771 " --> pdb=" O PHE F 767 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 776 " --> pdb=" O VAL F 772 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 28 removed outlier: 3.500A pdb=" N LEU G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 52 Processing helix chain 'G' and resid 57 through 65 removed outlier: 3.977A pdb=" N GLN G 62 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 80 removed outlier: 3.575A pdb=" N MET G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE G 80 " --> pdb=" O PHE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 117 removed outlier: 4.015A pdb=" N ILE G 105 " --> pdb=" O SER G 101 " (cutoff:3.500A) Proline residue: G 116 - end of helix Processing helix chain 'G' and resid 120 through 123 No H-bonds generated for 'chain 'G' and resid 120 through 123' Processing helix chain 'G' and resid 130 through 132 No H-bonds generated for 'chain 'G' and resid 130 through 132' Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'G' and resid 153 through 174 removed outlier: 4.287A pdb=" N SER G 160 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 56 removed outlier: 4.733A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 79 through 87 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.936A pdb=" N ILE H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 130 through 148 removed outlier: 3.653A pdb=" N PHE H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR H 142 " --> pdb=" O ARG H 138 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 193 removed outlier: 4.259A pdb=" N ASP H 173 " --> pdb=" O TYR H 169 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS H 174 " --> pdb=" O GLY H 170 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS H 175 " --> pdb=" O TRP H 171 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP H 177 " --> pdb=" O ASP H 173 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE H 178 " --> pdb=" O LYS H 174 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU H 183 " --> pdb=" O CYS H 179 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 187 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU H 188 " --> pdb=" O ARG H 184 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR H 189 " --> pdb=" O GLY H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 203 removed outlier: 3.776A pdb=" N ARG H 202 " --> pdb=" O ILE H 198 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 203' Processing helix chain 'H' and resid 211 through 216 Processing helix chain 'H' and resid 222 through 227 removed outlier: 5.079A pdb=" N SER H 227 " --> pdb=" O MET H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 241 No H-bonds generated for 'chain 'H' and resid 239 through 241' Processing helix chain 'H' and resid 257 through 265 Processing helix chain 'H' and resid 268 through 281 removed outlier: 4.218A pdb=" N ILE H 272 " --> pdb=" O SER H 269 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE H 279 " --> pdb=" O GLN H 276 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU H 280 " --> pdb=" O GLN H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 293 Processing helix chain 'H' and resid 365 through 368 No H-bonds generated for 'chain 'H' and resid 365 through 368' Processing helix chain 'H' and resid 374 through 383 Processing helix chain 'I' and resid 5 through 33 removed outlier: 5.184A pdb=" N GLY I 12 " --> pdb=" O PHE I 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN I 13 " --> pdb=" O MET I 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER I 31 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 113 Processing helix chain 'I' and resid 149 through 151 No H-bonds generated for 'chain 'I' and resid 149 through 151' Processing helix chain 'J' and resid 5 through 13 removed outlier: 5.273A pdb=" N LYS J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N HIS J 13 " --> pdb=" O TRP J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 removed outlier: 3.720A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL J 46 " --> pdb=" O VAL J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 115 removed outlier: 4.366A pdb=" N SER J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 115' Processing helix chain 'K' and resid 37 through 51 removed outlier: 4.838A pdb=" N LEU K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN K 43 " --> pdb=" O SER K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 72 Processing helix chain 'K' and resid 78 through 81 Processing helix chain 'K' and resid 109 through 115 removed outlier: 3.801A pdb=" N TYR K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 130 No H-bonds generated for 'chain 'K' and resid 127 through 130' Processing helix chain 'K' and resid 133 through 135 No H-bonds generated for 'chain 'K' and resid 133 through 135' Processing helix chain 'K' and resid 165 through 179 removed outlier: 3.907A pdb=" N LYS K 175 " --> pdb=" O THR K 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS K 176 " --> pdb=" O LYS K 172 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE K 177 " --> pdb=" O LEU K 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER K 178 " --> pdb=" O ARG K 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 108 removed outlier: 3.726A pdb=" N ALA L 104 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 121 removed outlier: 3.684A pdb=" N ILE L 114 " --> pdb=" O VAL L 110 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN L 117 " --> pdb=" O PRO L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 4.318A pdb=" N GLN L 134 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE L 135 " --> pdb=" O TYR L 132 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET L 136 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N PHE L 141 " --> pdb=" O THR L 138 " (cutoff:3.500A) Proline residue: L 143 - end of helix Processing helix chain 'M' and resid 137 through 151 removed outlier: 3.997A pdb=" N MET M 142 " --> pdb=" O GLU M 138 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL M 143 " --> pdb=" O THR M 139 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN M 148 " --> pdb=" O TYR M 144 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP M 149 " --> pdb=" O ASN M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 180 removed outlier: 4.335A pdb=" N ASP M 170 " --> pdb=" O LEU M 166 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS M 173 " --> pdb=" O SER M 169 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE M 175 " --> pdb=" O LEU M 171 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG M 176 " --> pdb=" O GLU M 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 89 removed outlier: 3.516A pdb=" N ARG N 87 " --> pdb=" O ARG N 83 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU N 88 " --> pdb=" O TYR N 84 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 110 No H-bonds generated for 'chain 'N' and resid 107 through 110' Processing helix chain 'N' and resid 136 through 141 Processing helix chain 'N' and resid 186 through 191 Processing helix chain 'N' and resid 194 through 197 No H-bonds generated for 'chain 'N' and resid 194 through 197' Processing helix chain 'N' and resid 219 through 222 No H-bonds generated for 'chain 'N' and resid 219 through 222' Processing helix chain '1' and resid 129 through 131 No H-bonds generated for 'chain '1' and resid 129 through 131' Processing helix chain '1' and resid 135 through 138 No H-bonds generated for 'chain '1' and resid 135 through 138' Processing helix chain '1' and resid 140 through 143 No H-bonds generated for 'chain '1' and resid 140 through 143' Processing helix chain '1' and resid 205 through 207 No H-bonds generated for 'chain '1' and resid 205 through 207' Processing helix chain '1' and resid 212 through 219 removed outlier: 4.167A pdb=" N VAL 1 217 " --> pdb=" O ASN 1 213 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL 1 218 " --> pdb=" O LYS 1 214 " (cutoff:3.500A) Processing helix chain '2' and resid 115 through 128 removed outlier: 3.687A pdb=" N ARG 2 120 " --> pdb=" O ALA 2 116 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA 2 123 " --> pdb=" O ILE 2 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU 2 124 " --> pdb=" O ARG 2 120 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR 2 128 " --> pdb=" O GLU 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 134 Processing helix chain '2' and resid 140 through 152 removed outlier: 4.339A pdb=" N VAL 2 145 " --> pdb=" O VAL 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 155 through 158 No H-bonds generated for 'chain '2' and resid 155 through 158' Processing helix chain '2' and resid 175 through 185 removed outlier: 4.643A pdb=" N MET 2 182 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR 2 183 " --> pdb=" O VAL 2 179 " (cutoff:3.500A) Processing helix chain '2' and resid 187 through 190 No H-bonds generated for 'chain '2' and resid 187 through 190' Processing helix chain '2' and resid 195 through 203 removed outlier: 3.764A pdb=" N LYS 2 203 " --> pdb=" O LEU 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 205 through 211 removed outlier: 4.449A pdb=" N ASP 2 210 " --> pdb=" O LYS 2 206 " (cutoff:3.500A) Processing helix chain '3' and resid 129 through 134 Processing helix chain '3' and resid 136 through 142 removed outlier: 4.828A pdb=" N GLU 3 141 " --> pdb=" O LEU 3 137 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP 3 142 " --> pdb=" O LEU 3 138 " (cutoff:3.500A) Processing helix chain '3' and resid 152 through 172 removed outlier: 4.727A pdb=" N ARG 3 157 " --> pdb=" O ASN 3 153 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU 3 158 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE 3 162 " --> pdb=" O LEU 3 158 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE 3 163 " --> pdb=" O LYS 3 159 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP 3 168 " --> pdb=" O TYR 3 164 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 202 Proline residue: 3 181 - end of helix removed outlier: 4.023A pdb=" N GLU 3 194 " --> pdb=" O PHE 3 190 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR 3 202 " --> pdb=" O ALA 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 206 through 225 removed outlier: 3.996A pdb=" N ASP 3 214 " --> pdb=" O SER 3 210 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU 3 221 " --> pdb=" O LEU 3 217 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET 3 223 " --> pdb=" O LEU 3 219 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR 3 224 " --> pdb=" O GLN 3 220 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 185 No H-bonds generated for 'chain '4' and resid 183 through 185' Processing helix chain '4' and resid 201 through 206 Processing helix chain '5' and resid 105 through 114 Processing helix chain '5' and resid 211 through 218 Processing helix chain '6' and resid 127 through 142 removed outlier: 3.990A pdb=" N LEU 6 131 " --> pdb=" O TYR 6 127 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE 6 132 " --> pdb=" O GLU 6 128 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE 6 133 " --> pdb=" O ASN 6 129 " (cutoff:3.500A) Proline residue: 6 134 - end of helix Processing helix chain '6' and resid 154 through 161 removed outlier: 3.856A pdb=" N GLN 6 158 " --> pdb=" O ALA 6 154 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL 6 159 " --> pdb=" O ARG 6 155 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR 6 160 " --> pdb=" O GLY 6 156 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU 6 161 " --> pdb=" O LYS 6 157 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 154 through 161' Processing helix chain '6' and resid 183 through 194 removed outlier: 4.292A pdb=" N ASN 6 193 " --> pdb=" O GLY 6 189 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG 6 194 " --> pdb=" O VAL 6 190 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 215 Processing helix chain '6' and resid 257 through 260 No H-bonds generated for 'chain '6' and resid 257 through 260' Processing helix chain '6' and resid 285 through 297 removed outlier: 3.945A pdb=" N VAL 6 291 " --> pdb=" O LEU 6 287 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU 6 292 " --> pdb=" O ARG 6 288 " (cutoff:3.500A) Processing helix chain '6' and resid 332 through 340 removed outlier: 4.107A pdb=" N GLU 6 340 " --> pdb=" O GLU 6 336 " (cutoff:3.500A) Processing helix chain '6' and resid 359 through 361 No H-bonds generated for 'chain '6' and resid 359 through 361' Processing helix chain '6' and resid 363 through 365 No H-bonds generated for 'chain '6' and resid 363 through 365' Processing helix chain '6' and resid 383 through 387 Processing helix chain '6' and resid 398 through 405 Processing helix chain '6' and resid 418 through 422 Processing helix chain '6' and resid 448 through 457 removed outlier: 4.190A pdb=" N ASP 6 457 " --> pdb=" O LYS 6 453 " (cutoff:3.500A) Processing helix chain '8' and resid 104 through 111 removed outlier: 3.576A pdb=" N ALA 8 111 " --> pdb=" O ILE 8 107 " (cutoff:3.500A) Processing helix chain '8' and resid 151 through 156 Processing helix chain '9' and resid 108 through 114 removed outlier: 3.812A pdb=" N PHE 9 112 " --> pdb=" O PHE 9 108 " (cutoff:3.500A) Processing helix chain '9' and resid 118 through 120 No H-bonds generated for 'chain '9' and resid 118 through 120' Processing helix chain '9' and resid 144 through 147 No H-bonds generated for 'chain '9' and resid 144 through 147' Processing helix chain '9' and resid 151 through 164 Processing helix chain '0' and resid 109 through 114 removed outlier: 3.899A pdb=" N GLU 0 114 " --> pdb=" O GLU 0 110 " (cutoff:3.500A) Processing helix chain '0' and resid 125 through 131 removed outlier: 4.049A pdb=" N SER 0 130 " --> pdb=" O GLN 0 126 " (cutoff:3.500A) Processing helix chain '0' and resid 134 through 137 No H-bonds generated for 'chain '0' and resid 134 through 137' Processing helix chain '0' and resid 139 through 141 No H-bonds generated for 'chain '0' and resid 139 through 141' Processing helix chain '0' and resid 147 through 165 removed outlier: 3.600A pdb=" N ALA 0 155 " --> pdb=" O TYR 0 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS 0 162 " --> pdb=" O ILE 0 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE 0 164 " --> pdb=" O VAL 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 172 through 174 No H-bonds generated for 'chain '0' and resid 172 through 174' Processing helix chain '0' and resid 177 through 180 No H-bonds generated for 'chain '0' and resid 177 through 180' Processing helix chain '0' and resid 186 through 190 Processing helix chain '0' and resid 194 through 196 No H-bonds generated for 'chain '0' and resid 194 through 196' Processing sheet with id= A, first strand: chain 'F' and resid 111 through 120 removed outlier: 3.898A pdb=" N TYR F 111 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU F 125 " --> pdb=" O TRP F 117 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL F 119 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 12 through 14 removed outlier: 3.888A pdb=" N ARG H 27 " --> pdb=" O ILE H 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 51 through 53 removed outlier: 3.859A pdb=" N VAL J 85 " --> pdb=" O LEU J 72 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 215 through 217 removed outlier: 6.666A pdb=" N VAL N 204 " --> pdb=" O LEU N 70 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE N 72 " --> pdb=" O VAL N 204 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA N 206 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 78 through 80 removed outlier: 3.501A pdb=" N TYR 1 89 " --> pdb=" O TYR 1 80 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 118 through 120 Processing sheet with id= G, first strand: chain '1' and resid 152 through 156 Processing sheet with id= H, first strand: chain '1' and resid 159 through 161 Processing sheet with id= I, first strand: chain '4' and resid 164 through 167 removed outlier: 3.528A pdb=" N VAL 4 164 " --> pdb=" O ILE 4 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '4' and resid 221 through 225 Processing sheet with id= K, first strand: chain '4' and resid 171 through 173 removed outlier: 3.945A pdb=" N ASP 4 181 " --> pdb=" O ALA 4 172 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '5' and resid 237 through 239 removed outlier: 4.217A pdb=" N ILE 5 82 " --> pdb=" O GLY 5 93 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY 5 93 " --> pdb=" O ILE 5 82 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE 5 84 " --> pdb=" O ASN 5 91 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN 5 91 " --> pdb=" O ILE 5 84 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY 5 98 " --> pdb=" O VAL 5 207 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL 5 207 " --> pdb=" O GLY 5 98 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '5' and resid 130 through 132 removed outlier: 3.669A pdb=" N ARG 5 130 " --> pdb=" O GLN 5 138 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '6' and resid 198 through 200 removed outlier: 3.857A pdb=" N MET 6 198 " --> pdb=" O ARG 6 117 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS 6 119 " --> pdb=" O MET 6 198 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU 6 147 " --> pdb=" O VAL 6 118 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N CYS 6 120 " --> pdb=" O LEU 6 147 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP 6 149 " --> pdb=" O CYS 6 120 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '6' and resid 392 through 394 Processing sheet with id= P, first strand: chain '7' and resid 52 through 55 removed outlier: 3.816A pdb=" N SER 7 81 " --> pdb=" O GLN 7 71 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG 7 73 " --> pdb=" O VAL 7 79 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL 7 79 " --> pdb=" O ARG 7 73 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '7' and resid 137 through 139 removed outlier: 3.858A pdb=" N GLU 7 152 " --> pdb=" O ALA 7 139 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET 7 173 " --> pdb=" O ILE 7 356 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY 7 352 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 196 through 198 Processing sheet with id= S, first strand: chain '7' and resid 269 through 272 removed outlier: 4.107A pdb=" N VAL 7 269 " --> pdb=" O SER 7 317 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU 7 315 " --> pdb=" O ARG 7 271 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '8' and resid 93 through 96 removed outlier: 6.289A pdb=" N GLN 8 184 " --> pdb=" O VAL 8 139 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL 8 139 " --> pdb=" O GLN 8 184 " (cutoff:3.500A) 1389 hydrogen bonds defined for protein. 3879 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: 11.42 Time building geometry restraints manager: 16.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 14916 1.38 - 1.57: 26508 1.57 - 1.76: 7 1.76 - 1.95: 324 1.95 - 2.14: 12 Bond restraints: 41767 Sorted by residual: bond pdb=" C6 SQD F 803 " pdb=" S SQD F 803 " ideal model delta sigma weight residual 1.840 1.660 0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C6 SQD F 802 " pdb=" S SQD F 802 " ideal model delta sigma weight residual 1.840 1.662 0.178 2.00e-02 2.50e+03 7.96e+01 bond pdb=" C7 LHG D 601 " pdb=" O7 LHG D 601 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C23 LHG D 601 " pdb=" O8 LHG D 601 " ideal model delta sigma weight residual 1.328 1.450 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" O8 SQD F 802 " pdb=" S SQD F 802 " ideal model delta sigma weight residual 1.514 1.634 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 41762 not shown) Histogram of bond angle deviations from ideal: 89.07 - 98.40: 24 98.40 - 107.72: 1708 107.72 - 117.04: 27108 117.04 - 126.36: 27342 126.36 - 135.69: 696 Bond angle restraints: 56878 Sorted by residual: angle pdb=" N LYS N 157 " pdb=" CA LYS N 157 " pdb=" C LYS N 157 " ideal model delta sigma weight residual 108.34 131.24 -22.90 1.31e+00 5.83e-01 3.06e+02 angle pdb=" C GLU C 49 " pdb=" N PRO C 50 " pdb=" CA PRO C 50 " ideal model delta sigma weight residual 119.90 102.80 17.10 1.02e+00 9.61e-01 2.81e+02 angle pdb=" C GLN 6 274 " pdb=" N PRO 6 275 " pdb=" CA PRO 6 275 " ideal model delta sigma weight residual 119.84 135.69 -15.85 1.25e+00 6.40e-01 1.61e+02 angle pdb="FE2 SF4 8 201 " pdb=" S1 SF4 8 201 " pdb="FE4 SF4 8 201 " ideal model delta sigma weight residual 73.70 90.89 -17.19 1.50e+00 4.44e-01 1.31e+02 angle pdb="FE2 SF4 8 201 " pdb=" S3 SF4 8 201 " pdb="FE4 SF4 8 201 " ideal model delta sigma weight residual 73.70 90.87 -17.17 1.50e+00 4.44e-01 1.31e+02 ... (remaining 56873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 22698 23.00 - 46.01: 1490 46.01 - 69.01: 124 69.01 - 92.02: 32 92.02 - 115.02: 2 Dihedral angle restraints: 24346 sinusoidal: 8770 harmonic: 15576 Sorted by residual: dihedral pdb=" CA ASN 5 86 " pdb=" C ASN 5 86 " pdb=" N PRO 5 87 " pdb=" CA PRO 5 87 " ideal model delta harmonic sigma weight residual 180.00 134.90 45.10 0 5.00e+00 4.00e-02 8.14e+01 dihedral pdb=" CA PRO N 125 " pdb=" C PRO N 125 " pdb=" N VAL N 126 " pdb=" CA VAL N 126 " ideal model delta harmonic sigma weight residual 180.00 -135.13 -44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA TRP 6 178 " pdb=" C TRP 6 178 " pdb=" N PRO 6 179 " pdb=" CA PRO 6 179 " ideal model delta harmonic sigma weight residual -180.00 -136.93 -43.07 0 5.00e+00 4.00e-02 7.42e+01 ... (remaining 24343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 6468 0.170 - 0.341: 23 0.341 - 0.511: 0 0.511 - 0.681: 2 0.681 - 0.852: 4 Chirality restraints: 6497 Sorted by residual: chirality pdb="FE4 SF4 8 201 " pdb=" S1 SF4 8 201 " pdb=" S2 SF4 8 201 " pdb=" S3 SF4 8 201 " both_signs ideal model delta sigma weight residual False 10.55 9.70 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb="FE1 SF4 8 201 " pdb=" S2 SF4 8 201 " pdb=" S3 SF4 8 201 " pdb=" S4 SF4 8 201 " both_signs ideal model delta sigma weight residual False -10.55 -9.71 -0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb="FE2 SF4 8 201 " pdb=" S1 SF4 8 201 " pdb=" S3 SF4 8 201 " pdb=" S4 SF4 8 201 " both_signs ideal model delta sigma weight residual False 10.55 9.72 0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 6494 not shown) Planarity restraints: 7182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN 6 274 " 0.034 2.00e-02 2.50e+03 6.75e-02 4.55e+01 pdb=" C GLN 6 274 " -0.117 2.00e-02 2.50e+03 pdb=" O GLN 6 274 " 0.044 2.00e-02 2.50e+03 pdb=" N PRO 6 275 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 122 " 0.031 2.00e-02 2.50e+03 5.97e-02 3.56e+01 pdb=" C THR I 122 " -0.103 2.00e-02 2.50e+03 pdb=" O THR I 122 " 0.038 2.00e-02 2.50e+03 pdb=" N GLU I 123 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 480 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASP D 480 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP D 480 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE D 481 " -0.022 2.00e-02 2.50e+03 ... (remaining 7179 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 150 2.43 - 3.05: 28224 3.05 - 3.67: 61086 3.67 - 4.28: 86990 4.28 - 4.90: 139841 Nonbonded interactions: 316291 Sorted by model distance: nonbonded pdb=" O LEU 8 123 " pdb=" O LEU 8 124 " model vdw 1.818 3.040 nonbonded pdb=" O GLU C 49 " pdb=" C PRO C 50 " model vdw 2.080 3.270 nonbonded pdb=" C LEU 8 123 " pdb=" O LEU 8 124 " model vdw 2.146 3.270 nonbonded pdb=" CA GLY C 47 " pdb=" ND2 ASN H 14 " model vdw 2.174 3.520 nonbonded pdb=" OG SER J 68 " pdb=" OH TYR J 123 " model vdw 2.210 2.440 ... (remaining 316286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 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: 0.030 Extract box with map and model: 20.490 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 106.350 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.005 0.180 41767 Z= 0.320 Angle : 0.877 22.898 56878 Z= 0.495 Chirality : 0.052 0.852 6497 Planarity : 0.005 0.092 7182 Dihedral : 14.842 115.021 14371 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 14.98 % Favored : 84.56 % Rotamer: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 2.38 % 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: -4.98 (0.09), residues: 5280 helix: -2.25 (0.09), residues: 2399 sheet: -3.25 (0.25), residues: 335 loop : -4.52 (0.10), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP 8 164 HIS 0.007 0.001 HIS F 407 PHE 0.030 0.001 PHE 9 105 TYR 0.026 0.001 TYR F 516 ARG 0.003 0.000 ARG J 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 736 time to evaluate : 4.993 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: A 133 TRP cc_start: 0.8794 (t60) cc_final: 0.8439 (t60) REVERT: A 166 GLN cc_start: 0.8472 (pp30) cc_final: 0.8084 (pp30) REVERT: A 302 MET cc_start: 0.2849 (tpt) cc_final: 0.2461 (tmm) REVERT: A 325 TRP cc_start: 0.6831 (m100) cc_final: 0.6357 (m100) REVERT: B 47 MET cc_start: 0.8016 (tmm) cc_final: 0.7461 (mtp) REVERT: B 124 MET cc_start: 0.7728 (mmm) cc_final: 0.7421 (ttm) REVERT: B 320 MET cc_start: 0.8901 (tpp) cc_final: 0.8237 (tpp) REVERT: B 323 MET cc_start: 0.8215 (ttp) cc_final: 0.7890 (ttp) REVERT: B 448 LEU cc_start: 0.9044 (mm) cc_final: 0.8745 (mm) REVERT: D 118 MET cc_start: 0.8366 (tpp) cc_final: 0.7991 (tpp) REVERT: D 214 TYR cc_start: 0.8425 (t80) cc_final: 0.7626 (t80) REVERT: D 276 PHE cc_start: 0.8277 (t80) cc_final: 0.8015 (t80) REVERT: D 371 MET cc_start: 0.8555 (ptp) cc_final: 0.8321 (ptp) REVERT: D 488 ASP cc_start: 0.8382 (m-30) cc_final: 0.8172 (m-30) REVERT: F 71 ILE cc_start: 0.9102 (mt) cc_final: 0.8886 (tt) REVERT: F 198 MET cc_start: 0.8797 (tmm) cc_final: 0.8569 (tmm) REVERT: F 371 TYR cc_start: 0.8435 (m-80) cc_final: 0.8212 (m-80) REVERT: F 373 MET cc_start: 0.8799 (tpp) cc_final: 0.8454 (tpp) REVERT: G 105 ILE cc_start: 0.9262 (mm) cc_final: 0.9004 (mt) REVERT: G 112 MET cc_start: 0.8233 (tpp) cc_final: 0.7971 (tpp) REVERT: H 378 MET cc_start: 0.6022 (tpt) cc_final: 0.5201 (mmm) REVERT: I 17 ARG cc_start: 0.4597 (mtm-85) cc_final: 0.4254 (ptp-170) REVERT: I 84 ARG cc_start: 0.5241 (tpp-160) cc_final: 0.3603 (ttt180) REVERT: I 107 CYS cc_start: 0.7243 (t) cc_final: 0.6795 (t) REVERT: I 109 ASN cc_start: 0.7624 (m-40) cc_final: 0.7399 (m-40) REVERT: I 118 CYS cc_start: 0.6890 (t) cc_final: 0.6487 (p) REVERT: I 121 MET cc_start: 0.2649 (ptp) cc_final: 0.1773 (pmm) REVERT: K 48 TRP cc_start: 0.6842 (t60) cc_final: 0.6526 (t60) REVERT: K 54 LEU cc_start: 0.7876 (pt) cc_final: 0.7241 (tt) REVERT: K 93 ASP cc_start: 0.6499 (p0) cc_final: 0.5752 (p0) REVERT: K 121 TYR cc_start: 0.6240 (m-80) cc_final: 0.5798 (m-80) REVERT: K 134 MET cc_start: 0.5842 (ppp) cc_final: 0.5111 (ppp) REVERT: K 144 ARG cc_start: 0.3730 (mpt180) cc_final: 0.3203 (mmt180) REVERT: K 205 ARG cc_start: 0.1397 (tpm170) cc_final: 0.0950 (tpm170) REVERT: 1 108 LYS cc_start: 0.7798 (mptt) cc_final: 0.7528 (mptt) REVERT: 2 100 TYR cc_start: 0.8513 (t80) cc_final: 0.8223 (t80) REVERT: 2 213 GLU cc_start: 0.8336 (tp30) cc_final: 0.7809 (tm-30) REVERT: 3 202 THR cc_start: 0.9062 (p) cc_final: 0.8857 (p) REVERT: 3 226 MET cc_start: 0.8211 (ppp) cc_final: 0.7588 (ptm) REVERT: 4 249 GLU cc_start: 0.8545 (pp20) cc_final: 0.7844 (pp20) REVERT: 5 182 THR cc_start: 0.8548 (m) cc_final: 0.8336 (p) REVERT: 5 241 PRO cc_start: 0.5398 (Cg_endo) cc_final: 0.5034 (Cg_exo) REVERT: 6 214 PHE cc_start: 0.8934 (t80) cc_final: 0.8621 (t80) REVERT: 6 220 GLU cc_start: 0.7859 (tt0) cc_final: 0.7304 (tp30) REVERT: 6 312 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6284 (tp30) REVERT: 7 149 VAL cc_start: 0.8466 (m) cc_final: 0.8150 (m) REVERT: 7 301 LEU cc_start: 0.8554 (mt) cc_final: 0.8307 (mp) REVERT: 7 308 MET cc_start: 0.4499 (mtt) cc_final: 0.4233 (mtt) REVERT: 8 113 ILE cc_start: 0.8726 (pt) cc_final: 0.8485 (pt) REVERT: 8 123 LEU cc_start: 0.9008 (mm) cc_final: 0.8803 (mt) REVERT: 0 69 ASP cc_start: 0.7701 (t0) cc_final: 0.7469 (t0) REVERT: 0 158 ILE cc_start: 0.9335 (tp) cc_final: 0.8950 (tp) REVERT: 0 198 ASP cc_start: 0.5322 (p0) cc_final: 0.5060 (p0) outliers start: 2 outliers final: 0 residues processed: 736 average time/residue: 0.5145 time to fit residues: 622.0682 Evaluate side-chains 503 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 4.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 4.9990 chunk 400 optimal weight: 8.9990 chunk 222 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 413 optimal weight: 9.9990 chunk 160 optimal weight: 0.5980 chunk 251 optimal weight: 7.9990 chunk 308 optimal weight: 0.0010 chunk 479 optimal weight: 5.9990 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 358 GLN B 222 GLN B 317 GLN B 362 ASN D 125 GLN F 218 GLN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN H 367 GLN I 32 HIS I 58 HIS I 139 GLN J 13 HIS K 91 GLN M 145 ASN ** M 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 GLN 1 141 ASN 5 86 ASN 5 206 GLN 6 129 ASN 6 381 GLN 6 401 GLN ** 7 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 184 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 41767 Z= 0.247 Angle : 0.736 11.460 56878 Z= 0.375 Chirality : 0.046 0.212 6497 Planarity : 0.005 0.092 7182 Dihedral : 7.959 104.887 5901 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.89 % Favored : 83.94 % Rotamer: Outliers : 1.92 % Allowed : 13.94 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % 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: -3.96 (0.11), residues: 5280 helix: -1.26 (0.10), residues: 2410 sheet: -2.91 (0.25), residues: 364 loop : -4.14 (0.11), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 8 164 HIS 0.008 0.001 HIS F 407 PHE 0.031 0.002 PHE I 85 TYR 0.028 0.002 TYR F 516 ARG 0.011 0.000 ARG 6 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 546 time to evaluate : 4.345 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: A 133 TRP cc_start: 0.8783 (t60) cc_final: 0.8422 (t60) REVERT: A 302 MET cc_start: 0.3153 (tpt) cc_final: 0.2903 (tmm) REVERT: B 47 MET cc_start: 0.7929 (tmm) cc_final: 0.7651 (mtt) REVERT: B 124 MET cc_start: 0.7640 (mmm) cc_final: 0.7328 (ttm) REVERT: B 320 MET cc_start: 0.8929 (tpp) cc_final: 0.8220 (tpp) REVERT: B 323 MET cc_start: 0.8237 (ttp) cc_final: 0.7901 (ttp) REVERT: B 448 LEU cc_start: 0.9129 (mm) cc_final: 0.8722 (mm) REVERT: D 118 MET cc_start: 0.8606 (tpp) cc_final: 0.8117 (tpp) REVERT: D 214 TYR cc_start: 0.8517 (t80) cc_final: 0.7763 (t80) REVERT: D 276 PHE cc_start: 0.8193 (t80) cc_final: 0.7894 (t80) REVERT: D 371 MET cc_start: 0.8270 (ptp) cc_final: 0.7965 (ptp) REVERT: E 53 ASP cc_start: 0.8326 (m-30) cc_final: 0.8085 (t0) REVERT: F 198 MET cc_start: 0.8813 (tmm) cc_final: 0.8537 (tmm) REVERT: F 371 TYR cc_start: 0.8465 (m-80) cc_final: 0.8252 (m-80) REVERT: F 373 MET cc_start: 0.8994 (tpp) cc_final: 0.8620 (tpp) REVERT: G 105 ILE cc_start: 0.9264 (mm) cc_final: 0.8967 (mt) REVERT: G 112 MET cc_start: 0.8265 (tpp) cc_final: 0.7995 (tpp) REVERT: H 76 MET cc_start: 0.6659 (tpp) cc_final: 0.5761 (tmm) REVERT: H 77 PHE cc_start: 0.4680 (m-80) cc_final: 0.4283 (m-10) REVERT: I 17 ARG cc_start: 0.4566 (mtm-85) cc_final: 0.4241 (ptp-170) REVERT: I 58 HIS cc_start: 0.7292 (t70) cc_final: 0.7034 (t-170) REVERT: I 84 ARG cc_start: 0.5257 (tpp-160) cc_final: 0.3736 (ttt180) REVERT: I 107 CYS cc_start: 0.7296 (t) cc_final: 0.6916 (t) REVERT: I 109 ASN cc_start: 0.7646 (m-40) cc_final: 0.7423 (m-40) REVERT: I 118 CYS cc_start: 0.6964 (t) cc_final: 0.6379 (p) REVERT: I 126 GLU cc_start: 0.5207 (mm-30) cc_final: 0.4276 (pp20) REVERT: J 70 TYR cc_start: 0.1917 (t80) cc_final: 0.1641 (t80) REVERT: J 105 TRP cc_start: 0.4850 (p90) cc_final: 0.3674 (p90) REVERT: J 143 LEU cc_start: 0.7067 (mm) cc_final: 0.6800 (mm) REVERT: K 48 TRP cc_start: 0.6874 (t60) cc_final: 0.6583 (t60) REVERT: K 121 TYR cc_start: 0.6548 (m-80) cc_final: 0.6046 (m-80) REVERT: K 134 MET cc_start: 0.5910 (ppp) cc_final: 0.5414 (ppp) REVERT: K 144 ARG cc_start: 0.3652 (mpt180) cc_final: 0.3028 (mmt180) REVERT: K 205 ARG cc_start: 0.1404 (tpm170) cc_final: 0.0691 (tpt170) REVERT: N 83 ARG cc_start: 0.6586 (tmm-80) cc_final: 0.6323 (tmm160) REVERT: N 195 LEU cc_start: 0.5218 (mm) cc_final: 0.4901 (mt) REVERT: 2 100 TYR cc_start: 0.8451 (t80) cc_final: 0.8199 (t80) REVERT: 2 213 GLU cc_start: 0.8391 (tp30) cc_final: 0.7957 (tm-30) REVERT: 3 226 MET cc_start: 0.7948 (ppp) cc_final: 0.7700 (ptm) REVERT: 4 249 GLU cc_start: 0.8482 (pp20) cc_final: 0.7798 (pp20) REVERT: 5 162 ASN cc_start: 0.8879 (t0) cc_final: 0.8647 (t0) REVERT: 5 182 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8296 (p) REVERT: 5 241 PRO cc_start: 0.5123 (Cg_endo) cc_final: 0.4874 (Cg_exo) REVERT: 6 220 GLU cc_start: 0.7802 (tt0) cc_final: 0.7170 (tp30) REVERT: 7 149 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8161 (m) REVERT: 7 185 ARG cc_start: 0.7975 (ptt-90) cc_final: 0.7728 (ttp-110) REVERT: 7 292 PHE cc_start: 0.7696 (t80) cc_final: 0.7337 (t80) REVERT: 7 308 MET cc_start: 0.4651 (mtt) cc_final: 0.4409 (mtt) REVERT: 8 113 ILE cc_start: 0.8760 (pt) cc_final: 0.8519 (pt) REVERT: 9 161 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7864 (ttm110) REVERT: 0 69 ASP cc_start: 0.7475 (t0) cc_final: 0.7236 (t0) REVERT: 0 158 ILE cc_start: 0.9320 (tp) cc_final: 0.9019 (tp) outliers start: 77 outliers final: 48 residues processed: 594 average time/residue: 0.5066 time to fit residues: 500.7268 Evaluate side-chains 541 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 491 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 742 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 2 residue 140 TYR Chi-restraints excluded: chain 3 residue 136 ASP Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 86 ASN Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 182 THR Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 155 ASP Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 197 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 399 optimal weight: 0.9980 chunk 326 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 480 optimal weight: 5.9990 chunk 518 optimal weight: 3.9990 chunk 427 optimal weight: 6.9990 chunk 476 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 385 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN E 39 ASN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN ** M 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS 6 401 GLN ** 7 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 41767 Z= 0.242 Angle : 0.715 12.181 56878 Z= 0.364 Chirality : 0.045 0.204 6497 Planarity : 0.005 0.094 7182 Dihedral : 7.755 105.663 5901 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.47 % Favored : 84.39 % Rotamer: Outliers : 2.84 % Allowed : 16.58 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % Twisted General : 0.14 % 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: -3.50 (0.11), residues: 5280 helix: -0.82 (0.10), residues: 2390 sheet: -2.74 (0.25), residues: 379 loop : -3.92 (0.11), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP H 217 HIS 0.009 0.001 HIS F 407 PHE 0.025 0.002 PHE 9 105 TYR 0.020 0.001 TYR 9 150 ARG 0.008 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 515 time to evaluate : 4.720 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: A 133 TRP cc_start: 0.8830 (t60) cc_final: 0.8461 (t60) REVERT: A 199 LYS cc_start: 0.8176 (ptmt) cc_final: 0.7888 (ptmt) REVERT: A 302 MET cc_start: 0.2955 (tpt) cc_final: 0.2722 (tmm) REVERT: B 47 MET cc_start: 0.7849 (tmm) cc_final: 0.7617 (mtt) REVERT: B 320 MET cc_start: 0.8974 (tpp) cc_final: 0.8758 (tpp) REVERT: B 323 MET cc_start: 0.8158 (ttp) cc_final: 0.7868 (ttp) REVERT: B 448 LEU cc_start: 0.9095 (mm) cc_final: 0.8672 (mm) REVERT: C 98 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8288 (mm) REVERT: D 118 MET cc_start: 0.8602 (tpp) cc_final: 0.8264 (tpp) REVERT: D 214 TYR cc_start: 0.8572 (t80) cc_final: 0.7770 (t80) REVERT: D 371 MET cc_start: 0.8492 (ptp) cc_final: 0.8113 (ptp) REVERT: D 488 ASP cc_start: 0.8689 (m-30) cc_final: 0.8278 (m-30) REVERT: E 53 ASP cc_start: 0.8341 (m-30) cc_final: 0.8124 (t0) REVERT: F 198 MET cc_start: 0.8826 (tmm) cc_final: 0.8544 (tmm) REVERT: F 373 MET cc_start: 0.9017 (tpp) cc_final: 0.8608 (tpp) REVERT: G 21 LEU cc_start: 0.8350 (tp) cc_final: 0.7929 (mt) REVERT: G 105 ILE cc_start: 0.9281 (mm) cc_final: 0.8944 (mt) REVERT: G 112 MET cc_start: 0.8269 (tpp) cc_final: 0.7964 (tpp) REVERT: H 76 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6521 (tmm) REVERT: H 77 PHE cc_start: 0.5225 (m-80) cc_final: 0.4898 (m-80) REVERT: I 17 ARG cc_start: 0.4525 (mtm-85) cc_final: 0.4161 (ptp-170) REVERT: I 84 ARG cc_start: 0.5330 (tpp-160) cc_final: 0.3801 (ttt180) REVERT: I 126 GLU cc_start: 0.5159 (mm-30) cc_final: 0.4130 (pp20) REVERT: J 72 LEU cc_start: 0.1105 (OUTLIER) cc_final: 0.0859 (mp) REVERT: J 143 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6900 (mm) REVERT: K 28 LEU cc_start: 0.5144 (OUTLIER) cc_final: 0.4837 (mt) REVERT: K 48 TRP cc_start: 0.6751 (t60) cc_final: 0.6468 (t60) REVERT: K 54 LEU cc_start: 0.7981 (pt) cc_final: 0.7691 (tt) REVERT: K 121 TYR cc_start: 0.6593 (m-80) cc_final: 0.6103 (m-80) REVERT: K 134 MET cc_start: 0.5895 (ppp) cc_final: 0.5544 (ppp) REVERT: K 144 ARG cc_start: 0.3883 (mpt180) cc_final: 0.3454 (mmt180) REVERT: K 205 ARG cc_start: 0.1401 (tpm170) cc_final: 0.0709 (tpt170) REVERT: N 76 HIS cc_start: 0.7390 (m-70) cc_final: 0.7147 (m90) REVERT: N 83 ARG cc_start: 0.6905 (tmm-80) cc_final: 0.6624 (tmm160) REVERT: N 199 ARG cc_start: 0.6459 (ttp80) cc_final: 0.5995 (tmm-80) REVERT: 2 100 TYR cc_start: 0.8414 (t80) cc_final: 0.8141 (t80) REVERT: 2 213 GLU cc_start: 0.8292 (tp30) cc_final: 0.7847 (tm-30) REVERT: 4 249 GLU cc_start: 0.8477 (pp20) cc_final: 0.7764 (pp20) REVERT: 5 162 ASN cc_start: 0.8935 (t0) cc_final: 0.8669 (t0) REVERT: 5 182 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8447 (p) REVERT: 5 241 PRO cc_start: 0.5187 (Cg_endo) cc_final: 0.4969 (Cg_exo) REVERT: 6 220 GLU cc_start: 0.7832 (tt0) cc_final: 0.7257 (tp30) REVERT: 7 185 ARG cc_start: 0.7934 (ptt-90) cc_final: 0.7665 (ttp-110) REVERT: 7 292 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7474 (t80) REVERT: 0 69 ASP cc_start: 0.7539 (t0) cc_final: 0.7280 (t0) REVERT: 0 158 ILE cc_start: 0.9324 (tp) cc_final: 0.9029 (tp) REVERT: 0 200 TRP cc_start: 0.5520 (p90) cc_final: 0.3848 (t-100) outliers start: 114 outliers final: 71 residues processed: 593 average time/residue: 0.4910 time to fit residues: 487.9347 Evaluate side-chains 561 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 483 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 182 THR Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 6 residue 129 ASN Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 99 HIS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 8 residue 135 CYS Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 197 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 3.9990 chunk 361 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 53 optimal weight: 0.0970 chunk 229 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 482 optimal weight: 0.2980 chunk 510 optimal weight: 0.0970 chunk 251 optimal weight: 0.9980 chunk 456 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.8978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN H 84 ASN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN J 50 ASN ** 5 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41767 Z= 0.180 Angle : 0.673 11.261 56878 Z= 0.341 Chirality : 0.044 0.188 6497 Planarity : 0.005 0.089 7182 Dihedral : 7.432 101.013 5901 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.60 % Favored : 85.27 % Rotamer: Outliers : 2.64 % Allowed : 18.50 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.11), residues: 5280 helix: -0.53 (0.11), residues: 2396 sheet: -2.45 (0.26), residues: 366 loop : -3.80 (0.11), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 217 HIS 0.007 0.001 HIS F 407 PHE 0.023 0.001 PHE K 65 TYR 0.019 0.001 TYR F 487 ARG 0.007 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 546 time to evaluate : 4.772 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: A 120 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6570 (t-170) REVERT: A 133 TRP cc_start: 0.8812 (t60) cc_final: 0.8457 (t60) REVERT: A 146 MET cc_start: 0.7719 (ttp) cc_final: 0.7500 (ptm) REVERT: B 47 MET cc_start: 0.7790 (tmm) cc_final: 0.7582 (mtt) REVERT: B 124 MET cc_start: 0.7646 (ttm) cc_final: 0.7248 (ttm) REVERT: B 172 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8469 (tmt170) REVERT: B 448 LEU cc_start: 0.9044 (mm) cc_final: 0.8580 (mm) REVERT: D 118 MET cc_start: 0.8597 (tpp) cc_final: 0.8318 (tpp) REVERT: F 123 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6967 (p90) REVERT: F 174 ASN cc_start: 0.8940 (t0) cc_final: 0.8564 (t0) REVERT: F 198 MET cc_start: 0.8839 (tmm) cc_final: 0.8548 (tmm) REVERT: F 371 TYR cc_start: 0.8235 (m-80) cc_final: 0.7991 (m-80) REVERT: F 373 MET cc_start: 0.8983 (tpp) cc_final: 0.8549 (tpp) REVERT: G 21 LEU cc_start: 0.8337 (tp) cc_final: 0.7877 (mt) REVERT: G 105 ILE cc_start: 0.9271 (mm) cc_final: 0.8926 (mt) REVERT: G 112 MET cc_start: 0.8213 (tpp) cc_final: 0.7837 (tpp) REVERT: H 76 MET cc_start: 0.6863 (tpp) cc_final: 0.6457 (tmm) REVERT: H 77 PHE cc_start: 0.5430 (m-80) cc_final: 0.5093 (m-80) REVERT: H 142 TYR cc_start: 0.5405 (m-10) cc_final: 0.5075 (m-10) REVERT: H 237 ASP cc_start: 0.8089 (t0) cc_final: 0.7652 (t0) REVERT: I 84 ARG cc_start: 0.5371 (tpp-160) cc_final: 0.3907 (ttt180) REVERT: K 28 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4459 (mt) REVERT: K 54 LEU cc_start: 0.8099 (pt) cc_final: 0.7782 (tt) REVERT: K 121 TYR cc_start: 0.6595 (m-80) cc_final: 0.6119 (m-80) REVERT: K 144 ARG cc_start: 0.3738 (mpt180) cc_final: 0.3340 (mmt180) REVERT: K 205 ARG cc_start: 0.1401 (tpm170) cc_final: 0.0707 (tpt170) REVERT: N 76 HIS cc_start: 0.7389 (m-70) cc_final: 0.7130 (m90) REVERT: N 83 ARG cc_start: 0.7084 (tmm-80) cc_final: 0.6651 (tmt170) REVERT: N 199 ARG cc_start: 0.6276 (ttp80) cc_final: 0.5888 (tmm-80) REVERT: 2 100 TYR cc_start: 0.8313 (t80) cc_final: 0.8058 (t80) REVERT: 2 136 MET cc_start: 0.5745 (tpt) cc_final: 0.5225 (tpt) REVERT: 2 213 GLU cc_start: 0.8235 (tp30) cc_final: 0.7774 (tm-30) REVERT: 4 249 GLU cc_start: 0.8370 (pp20) cc_final: 0.7681 (pp20) REVERT: 5 162 ASN cc_start: 0.8914 (t0) cc_final: 0.8641 (t0) REVERT: 5 241 PRO cc_start: 0.4976 (Cg_endo) cc_final: 0.4765 (Cg_exo) REVERT: 6 220 GLU cc_start: 0.7733 (tt0) cc_final: 0.7129 (tp30) REVERT: 6 354 MET cc_start: 0.8170 (tpp) cc_final: 0.7045 (tpp) REVERT: 7 185 ARG cc_start: 0.7931 (ptt-90) cc_final: 0.7631 (ttp-110) REVERT: 7 285 TYR cc_start: 0.6861 (m-80) cc_final: 0.6610 (m-80) REVERT: 7 292 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7367 (t80) REVERT: 8 113 ILE cc_start: 0.8513 (pt) cc_final: 0.8265 (pt) REVERT: 0 69 ASP cc_start: 0.7430 (t0) cc_final: 0.7087 (t0) REVERT: 0 158 ILE cc_start: 0.9325 (tp) cc_final: 0.9063 (tp) REVERT: 0 179 ILE cc_start: 0.8338 (tt) cc_final: 0.8087 (mm) REVERT: 0 200 TRP cc_start: 0.5494 (p90) cc_final: 0.3834 (t-100) outliers start: 106 outliers final: 65 residues processed: 625 average time/residue: 0.5011 time to fit residues: 525.8041 Evaluate side-chains 554 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 485 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain 1 residue 94 ASP Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 208 GLU Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 145 VAL Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 0.7980 chunk 289 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 380 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 435 optimal weight: 1.9990 chunk 352 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 260 optimal weight: 5.9990 chunk 458 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** 5 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 401 GLN ** 7 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41767 Z= 0.193 Angle : 0.677 12.676 56878 Z= 0.341 Chirality : 0.044 0.242 6497 Planarity : 0.005 0.083 7182 Dihedral : 7.246 89.547 5901 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.45 % Favored : 85.44 % Rotamer: Outliers : 3.49 % Allowed : 19.30 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.11), residues: 5280 helix: -0.35 (0.11), residues: 2389 sheet: -2.35 (0.26), residues: 376 loop : -3.70 (0.11), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 217 HIS 0.008 0.001 HIS F 407 PHE 0.024 0.001 PHE K 65 TYR 0.028 0.001 TYR 2 140 ARG 0.009 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 511 time to evaluate : 4.995 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: A 120 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6560 (t-170) REVERT: A 133 TRP cc_start: 0.8821 (t60) cc_final: 0.8494 (t60) REVERT: A 302 MET cc_start: 0.2467 (tmm) cc_final: 0.2189 (ppp) REVERT: B 124 MET cc_start: 0.7743 (ttm) cc_final: 0.7406 (ttm) REVERT: B 172 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8470 (tmt170) REVERT: B 265 VAL cc_start: 0.8832 (t) cc_final: 0.8557 (t) REVERT: B 320 MET cc_start: 0.8808 (tpp) cc_final: 0.8400 (tpp) REVERT: B 448 LEU cc_start: 0.9027 (mm) cc_final: 0.8548 (mm) REVERT: C 98 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8321 (mm) REVERT: D 118 MET cc_start: 0.8681 (tpp) cc_final: 0.8243 (tpp) REVERT: D 271 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7457 (p-80) REVERT: F 71 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8965 (tp) REVERT: F 123 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6889 (p90) REVERT: F 174 ASN cc_start: 0.8955 (t0) cc_final: 0.8589 (t0) REVERT: F 198 MET cc_start: 0.8815 (tmm) cc_final: 0.8523 (tmm) REVERT: F 371 TYR cc_start: 0.8182 (m-80) cc_final: 0.7884 (m-80) REVERT: F 373 MET cc_start: 0.8995 (tpp) cc_final: 0.8548 (tpp) REVERT: G 21 LEU cc_start: 0.8311 (tp) cc_final: 0.7898 (mt) REVERT: G 105 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8999 (mt) REVERT: G 112 MET cc_start: 0.8116 (tpp) cc_final: 0.7769 (tpp) REVERT: H 51 MET cc_start: 0.6771 (mmt) cc_final: 0.6453 (mmt) REVERT: H 76 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6498 (tmm) REVERT: H 77 PHE cc_start: 0.5716 (m-80) cc_final: 0.5313 (m-80) REVERT: H 132 PHE cc_start: 0.7838 (m-80) cc_final: 0.7408 (m-10) REVERT: H 142 TYR cc_start: 0.5654 (m-10) cc_final: 0.5369 (m-80) REVERT: I 84 ARG cc_start: 0.5177 (tpp-160) cc_final: 0.3870 (ttt180) REVERT: I 114 CYS cc_start: 0.1665 (OUTLIER) cc_final: 0.0892 (m) REVERT: I 129 THR cc_start: 0.4819 (p) cc_final: 0.4594 (p) REVERT: K 28 LEU cc_start: 0.5068 (OUTLIER) cc_final: 0.4468 (mt) REVERT: K 121 TYR cc_start: 0.6581 (m-80) cc_final: 0.6107 (m-80) REVERT: K 144 ARG cc_start: 0.3627 (mpt180) cc_final: 0.3284 (mmt180) REVERT: K 205 ARG cc_start: 0.1379 (tpm170) cc_final: 0.0737 (tpt170) REVERT: N 76 HIS cc_start: 0.7563 (m-70) cc_final: 0.7300 (m90) REVERT: N 83 ARG cc_start: 0.7193 (tmm-80) cc_final: 0.6752 (tmt170) REVERT: N 199 ARG cc_start: 0.6004 (ttp80) cc_final: 0.5803 (tmm-80) REVERT: 2 100 TYR cc_start: 0.8353 (t80) cc_final: 0.8085 (t80) REVERT: 2 213 GLU cc_start: 0.8233 (tp30) cc_final: 0.7765 (tm-30) REVERT: 4 249 GLU cc_start: 0.8345 (pp20) cc_final: 0.7957 (pt0) REVERT: 5 162 ASN cc_start: 0.8969 (t0) cc_final: 0.8739 (t0) REVERT: 5 182 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8396 (p) REVERT: 6 220 GLU cc_start: 0.7714 (tt0) cc_final: 0.7116 (tp30) REVERT: 6 385 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.7993 (tt) REVERT: 7 185 ARG cc_start: 0.7918 (ptt-90) cc_final: 0.7610 (ttp-110) REVERT: 7 292 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7514 (t80) REVERT: 0 69 ASP cc_start: 0.7279 (t0) cc_final: 0.6918 (t0) REVERT: 0 158 ILE cc_start: 0.9283 (tp) cc_final: 0.9000 (tp) REVERT: 0 179 ILE cc_start: 0.8311 (tt) cc_final: 0.8053 (mm) REVERT: 0 200 TRP cc_start: 0.5492 (p90) cc_final: 0.3850 (t-100) outliers start: 140 outliers final: 89 residues processed: 612 average time/residue: 0.5020 time to fit residues: 516.3829 Evaluate side-chains 588 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 487 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain 1 residue 94 ASP Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 4 residue 216 MET Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 182 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 6 residue 129 ASN Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 176 ASP Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 208 GLU Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 8 residue 135 CYS Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 145 VAL Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 5.9990 chunk 459 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 299 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 510 optimal weight: 3.9990 chunk 424 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 42 optimal weight: 0.0570 chunk 168 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS F 465 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 401 GLN ** 7 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41767 Z= 0.258 Angle : 0.704 11.533 56878 Z= 0.355 Chirality : 0.045 0.209 6497 Planarity : 0.005 0.085 7182 Dihedral : 7.170 83.764 5901 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.74 % Favored : 84.11 % Rotamer: Outliers : 3.67 % Allowed : 19.60 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.19 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.11), residues: 5280 helix: -0.32 (0.11), residues: 2379 sheet: -2.26 (0.27), residues: 363 loop : -3.64 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP H 217 HIS 0.011 0.001 HIS F 407 PHE 0.027 0.001 PHE K 65 TYR 0.022 0.001 TYR 2 140 ARG 0.009 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 493 time to evaluate : 4.774 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: A 133 TRP cc_start: 0.8829 (t60) cc_final: 0.8474 (t60) REVERT: A 146 MET cc_start: 0.7806 (ttp) cc_final: 0.7597 (ptm) REVERT: A 302 MET cc_start: 0.2480 (tmm) cc_final: 0.2200 (ppp) REVERT: B 124 MET cc_start: 0.7814 (ttm) cc_final: 0.7376 (ttm) REVERT: B 172 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8516 (tmt170) REVERT: B 265 VAL cc_start: 0.8867 (t) cc_final: 0.8589 (t) REVERT: B 323 MET cc_start: 0.8132 (ttp) cc_final: 0.7888 (ttp) REVERT: B 448 LEU cc_start: 0.9020 (mm) cc_final: 0.8522 (mm) REVERT: C 98 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8341 (mm) REVERT: D 118 MET cc_start: 0.8713 (tpp) cc_final: 0.8324 (tpp) REVERT: D 271 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7545 (p-80) REVERT: F 71 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8935 (tp) REVERT: F 123 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7182 (p90) REVERT: F 198 MET cc_start: 0.8818 (tmm) cc_final: 0.8512 (tmm) REVERT: F 282 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8521 (tppp) REVERT: F 371 TYR cc_start: 0.8346 (m-80) cc_final: 0.8135 (m-80) REVERT: F 373 MET cc_start: 0.9079 (tpp) cc_final: 0.8603 (tpp) REVERT: F 488 MET cc_start: 0.9011 (tpp) cc_final: 0.8766 (tpp) REVERT: G 21 LEU cc_start: 0.8428 (tp) cc_final: 0.7983 (mt) REVERT: G 66 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6384 (t80) REVERT: G 105 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8981 (mt) REVERT: G 112 MET cc_start: 0.8129 (tpp) cc_final: 0.7736 (tpp) REVERT: H 76 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6427 (tmm) REVERT: H 77 PHE cc_start: 0.5838 (m-80) cc_final: 0.5437 (m-80) REVERT: H 132 PHE cc_start: 0.7929 (m-80) cc_final: 0.7569 (m-10) REVERT: H 142 TYR cc_start: 0.5502 (m-10) cc_final: 0.5190 (m-10) REVERT: H 237 ASP cc_start: 0.8113 (t0) cc_final: 0.7674 (t0) REVERT: H 350 TRP cc_start: 0.4715 (t60) cc_final: 0.4470 (t60) REVERT: I 84 ARG cc_start: 0.4803 (tpp-160) cc_final: 0.3614 (ttt180) REVERT: I 114 CYS cc_start: 0.1543 (OUTLIER) cc_final: 0.1025 (m) REVERT: J 106 ARG cc_start: 0.4430 (OUTLIER) cc_final: 0.4188 (mtm-85) REVERT: K 28 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4364 (mt) REVERT: K 121 TYR cc_start: 0.6219 (m-80) cc_final: 0.5823 (m-80) REVERT: K 144 ARG cc_start: 0.3935 (mpt180) cc_final: 0.3507 (mmt180) REVERT: K 205 ARG cc_start: 0.1349 (tpm170) cc_final: 0.0761 (tpt170) REVERT: N 76 HIS cc_start: 0.7394 (m-70) cc_final: 0.7136 (m90) REVERT: N 83 ARG cc_start: 0.7219 (tmm-80) cc_final: 0.6766 (tmt170) REVERT: 2 100 TYR cc_start: 0.8381 (t80) cc_final: 0.8079 (t80) REVERT: 2 213 GLU cc_start: 0.8277 (tp30) cc_final: 0.7785 (tm-30) REVERT: 4 249 GLU cc_start: 0.8422 (pp20) cc_final: 0.7647 (pp20) REVERT: 5 162 ASN cc_start: 0.8977 (t0) cc_final: 0.8725 (t0) REVERT: 5 182 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8466 (p) REVERT: 6 220 GLU cc_start: 0.7781 (tt0) cc_final: 0.7155 (tp30) REVERT: 7 185 ARG cc_start: 0.7857 (ptt-90) cc_final: 0.7593 (ttp-110) REVERT: 7 292 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7669 (t80) REVERT: 0 69 ASP cc_start: 0.7413 (t0) cc_final: 0.6984 (t0) REVERT: 0 158 ILE cc_start: 0.9351 (tp) cc_final: 0.9056 (tp) REVERT: 0 179 ILE cc_start: 0.8392 (tt) cc_final: 0.8136 (mm) REVERT: 0 200 TRP cc_start: 0.5290 (p90) cc_final: 0.3679 (t-100) outliers start: 147 outliers final: 103 residues processed: 600 average time/residue: 0.5052 time to fit residues: 509.4733 Evaluate side-chains 593 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 477 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 742 VAL Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 128 CYS Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain 1 residue 94 ASP Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 182 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 6 residue 129 ASN Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 176 ASP Chi-restraints excluded: chain 6 residue 328 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 99 HIS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 98 THR Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 145 VAL Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 373 optimal weight: 0.9980 chunk 289 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 508 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** H 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41767 Z= 0.357 Angle : 0.779 12.104 56878 Z= 0.393 Chirality : 0.047 0.218 6497 Planarity : 0.006 0.085 7182 Dihedral : 7.490 87.178 5901 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 16.72 % Favored : 83.07 % Rotamer: Outliers : 4.09 % Allowed : 20.27 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.11), residues: 5280 helix: -0.48 (0.11), residues: 2399 sheet: -2.54 (0.25), residues: 406 loop : -3.67 (0.11), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP 7 255 HIS 0.012 0.001 HIS F 407 PHE 0.030 0.002 PHE 9 105 TYR 0.028 0.002 TYR 9 150 ARG 0.006 0.001 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 478 time to evaluate : 4.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8844 (t60) cc_final: 0.8374 (t60) REVERT: A 146 MET cc_start: 0.7745 (ttp) cc_final: 0.7417 (ptm) REVERT: B 47 MET cc_start: 0.8371 (mtt) cc_final: 0.8102 (mtp) REVERT: B 448 LEU cc_start: 0.8984 (mm) cc_final: 0.8540 (mm) REVERT: C 98 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8362 (mm) REVERT: D 118 MET cc_start: 0.8765 (tpp) cc_final: 0.8376 (tpp) REVERT: D 271 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7688 (p-80) REVERT: D 371 MET cc_start: 0.8228 (ptp) cc_final: 0.7930 (ptp) REVERT: F 123 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7148 (p90) REVERT: F 198 MET cc_start: 0.8809 (tmm) cc_final: 0.8436 (tmm) REVERT: F 282 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8593 (tppp) REVERT: F 373 MET cc_start: 0.9149 (tpp) cc_final: 0.8663 (tpp) REVERT: G 21 LEU cc_start: 0.8506 (tp) cc_final: 0.8151 (mt) REVERT: G 66 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6900 (t80) REVERT: G 105 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8979 (mt) REVERT: G 112 MET cc_start: 0.8226 (tpp) cc_final: 0.7986 (tpp) REVERT: H 76 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6561 (tmm) REVERT: H 77 PHE cc_start: 0.5641 (m-80) cc_final: 0.5251 (m-80) REVERT: H 132 PHE cc_start: 0.8012 (m-80) cc_final: 0.7680 (m-10) REVERT: H 142 TYR cc_start: 0.5471 (m-10) cc_final: 0.5155 (m-10) REVERT: H 237 ASP cc_start: 0.7964 (t0) cc_final: 0.7561 (t0) REVERT: I 84 ARG cc_start: 0.5379 (tpp-160) cc_final: 0.4116 (ttt180) REVERT: K 28 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.4696 (mt) REVERT: K 121 TYR cc_start: 0.6378 (m-80) cc_final: 0.6033 (m-80) REVERT: K 144 ARG cc_start: 0.3883 (mpt180) cc_final: 0.3383 (mmt180) REVERT: K 205 ARG cc_start: 0.1704 (tpm170) cc_final: 0.0976 (tpt170) REVERT: M 125 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5761 (tt) REVERT: N 83 ARG cc_start: 0.7240 (tmm-80) cc_final: 0.6830 (tmt170) REVERT: 2 100 TYR cc_start: 0.8406 (t80) cc_final: 0.8021 (t80) REVERT: 2 213 GLU cc_start: 0.8363 (tp30) cc_final: 0.7822 (tm-30) REVERT: 4 249 GLU cc_start: 0.8537 (pp20) cc_final: 0.7758 (pp20) REVERT: 5 162 ASN cc_start: 0.8907 (t0) cc_final: 0.8642 (t0) REVERT: 5 182 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8440 (p) REVERT: 6 220 GLU cc_start: 0.8003 (tt0) cc_final: 0.7397 (tp30) REVERT: 6 241 MET cc_start: 0.7538 (mtm) cc_final: 0.7247 (mtt) REVERT: 6 273 GLN cc_start: 0.7142 (pp30) cc_final: 0.6938 (pp30) REVERT: 6 385 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8249 (tt) REVERT: 7 61 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: 7 185 ARG cc_start: 0.7868 (ptt-90) cc_final: 0.7566 (pmt-80) REVERT: 7 292 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7769 (t80) REVERT: 7 321 MET cc_start: 0.6961 (tmm) cc_final: 0.6719 (mmt) REVERT: 0 158 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9069 (tp) REVERT: 0 200 TRP cc_start: 0.5393 (p90) cc_final: 0.3687 (t-100) outliers start: 164 outliers final: 121 residues processed: 599 average time/residue: 0.4939 time to fit residues: 499.5552 Evaluate side-chains 593 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 458 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 735 ILE Chi-restraints excluded: chain F residue 742 VAL Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 128 CYS Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain 1 residue 94 ASP Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 138 LEU Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 182 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 6 residue 129 ASN Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 176 ASP Chi-restraints excluded: chain 6 residue 254 TYR Chi-restraints excluded: chain 6 residue 328 LEU Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 61 GLU Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 99 HIS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 229 THR Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 7 residue 338 ILE Chi-restraints excluded: chain 8 residue 135 CYS Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 129 ILE Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 145 VAL Chi-restraints excluded: chain 0 residue 158 ILE Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.0170 chunk 203 optimal weight: 0.9980 chunk 303 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 99 optimal weight: 0.0010 chunk 98 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 346 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 400 optimal weight: 10.0000 overall best weight: 0.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS N 143 HIS ** 5 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41767 Z= 0.174 Angle : 0.682 13.506 56878 Z= 0.343 Chirality : 0.044 0.192 6497 Planarity : 0.005 0.083 7182 Dihedral : 7.014 82.667 5901 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.20 % Favored : 86.69 % Rotamer: Outliers : 2.52 % Allowed : 22.42 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.19 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.12), residues: 5280 helix: -0.21 (0.11), residues: 2401 sheet: -2.14 (0.27), residues: 376 loop : -3.54 (0.11), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP 7 255 HIS 0.006 0.001 HIS F 407 PHE 0.028 0.001 PHE F 729 TYR 0.023 0.001 TYR 9 106 ARG 0.005 0.000 ARG 5 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 541 time to evaluate : 4.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8805 (t60) cc_final: 0.8456 (t60) REVERT: A 146 MET cc_start: 0.7760 (ttp) cc_final: 0.7491 (ptm) REVERT: B 47 MET cc_start: 0.8380 (mtt) cc_final: 0.7866 (ppp) REVERT: B 329 ILE cc_start: 0.8285 (mp) cc_final: 0.8038 (mp) REVERT: B 448 LEU cc_start: 0.8899 (mm) cc_final: 0.8427 (mm) REVERT: C 73 ASP cc_start: 0.8215 (t0) cc_final: 0.8000 (t0) REVERT: C 98 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8365 (mm) REVERT: D 118 MET cc_start: 0.8616 (tpp) cc_final: 0.8270 (tpp) REVERT: D 196 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6980 (t0) REVERT: D 371 MET cc_start: 0.7993 (ptp) cc_final: 0.7647 (ptp) REVERT: F 71 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9028 (tp) REVERT: F 174 ASN cc_start: 0.8870 (t0) cc_final: 0.8646 (t0) REVERT: F 198 MET cc_start: 0.8834 (tmm) cc_final: 0.8531 (tmm) REVERT: F 373 MET cc_start: 0.8911 (tpp) cc_final: 0.8449 (tpp) REVERT: G 21 LEU cc_start: 0.8381 (tp) cc_final: 0.8042 (mt) REVERT: G 66 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6882 (t80) REVERT: G 105 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8918 (mt) REVERT: G 112 MET cc_start: 0.8072 (tpp) cc_final: 0.7747 (tpp) REVERT: H 77 PHE cc_start: 0.5749 (m-80) cc_final: 0.5424 (m-80) REVERT: H 132 PHE cc_start: 0.8034 (m-80) cc_final: 0.7683 (m-10) REVERT: H 142 TYR cc_start: 0.5755 (m-10) cc_final: 0.5345 (m-80) REVERT: H 237 ASP cc_start: 0.8109 (t0) cc_final: 0.7676 (t0) REVERT: I 84 ARG cc_start: 0.5375 (tpp-160) cc_final: 0.4170 (ttt180) REVERT: I 114 CYS cc_start: 0.0913 (OUTLIER) cc_final: 0.0458 (m) REVERT: J 51 TYR cc_start: 0.5090 (t80) cc_final: 0.4741 (t80) REVERT: K 28 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4633 (mt) REVERT: K 121 TYR cc_start: 0.6207 (m-80) cc_final: 0.5833 (m-80) REVERT: K 144 ARG cc_start: 0.3759 (mpt180) cc_final: 0.3457 (mmt180) REVERT: K 205 ARG cc_start: 0.1411 (tpm170) cc_final: 0.0811 (tpt170) REVERT: N 83 ARG cc_start: 0.7229 (tmm-80) cc_final: 0.6834 (tmt170) REVERT: 2 100 TYR cc_start: 0.8162 (t80) cc_final: 0.7843 (t80) REVERT: 2 213 GLU cc_start: 0.8226 (tp30) cc_final: 0.7704 (tm-30) REVERT: 4 249 GLU cc_start: 0.8325 (pp20) cc_final: 0.7983 (pt0) REVERT: 5 162 ASN cc_start: 0.8934 (t0) cc_final: 0.8668 (t0) REVERT: 6 220 GLU cc_start: 0.7770 (tt0) cc_final: 0.7121 (tp30) REVERT: 6 354 MET cc_start: 0.8181 (tpp) cc_final: 0.7098 (tpp) REVERT: 6 385 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7790 (tt) REVERT: 7 292 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.7162 (t80) REVERT: 8 113 ILE cc_start: 0.8562 (pt) cc_final: 0.8303 (pt) REVERT: 9 157 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6767 (tt0) REVERT: 0 69 ASP cc_start: 0.7177 (t0) cc_final: 0.6772 (t0) REVERT: 0 158 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8996 (tp) REVERT: 0 179 ILE cc_start: 0.8283 (tt) cc_final: 0.8008 (mm) REVERT: 0 200 TRP cc_start: 0.5167 (p90) cc_final: 0.3666 (t-100) outliers start: 101 outliers final: 70 residues processed: 612 average time/residue: 0.4859 time to fit residues: 500.1405 Evaluate side-chains 568 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 488 time to evaluate : 4.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain 1 residue 94 ASP Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 4 residue 216 MET Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 254 TYR Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 99 HIS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 229 THR Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 106 TYR Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 158 ILE Chi-restraints excluded: chain 0 residue 197 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 7.9990 chunk 487 optimal weight: 5.9990 chunk 444 optimal weight: 0.7980 chunk 474 optimal weight: 0.0870 chunk 285 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 372 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 428 optimal weight: 1.9990 chunk 448 optimal weight: 6.9990 chunk 472 optimal weight: 10.0000 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 ASN ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS 5 86 ASN ** 5 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41767 Z= 0.204 Angle : 0.696 13.607 56878 Z= 0.349 Chirality : 0.044 0.203 6497 Planarity : 0.005 0.078 7182 Dihedral : 6.943 82.089 5901 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.28 % Favored : 85.57 % Rotamer: Outliers : 2.82 % Allowed : 22.59 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.19 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.12), residues: 5280 helix: -0.11 (0.11), residues: 2396 sheet: -2.01 (0.27), residues: 359 loop : -3.51 (0.11), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP H 217 HIS 0.008 0.001 HIS F 407 PHE 0.034 0.001 PHE F 504 TYR 0.022 0.001 TYR A 314 ARG 0.007 0.000 ARG 7 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 510 time to evaluate : 4.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8832 (t60) cc_final: 0.8511 (t60) REVERT: A 146 MET cc_start: 0.7759 (ttp) cc_final: 0.7454 (ptm) REVERT: A 302 MET cc_start: 0.2450 (ppp) cc_final: 0.2148 (tmm) REVERT: B 47 MET cc_start: 0.8410 (mtt) cc_final: 0.7892 (ppp) REVERT: B 323 MET cc_start: 0.8072 (ttp) cc_final: 0.7811 (ttp) REVERT: B 329 ILE cc_start: 0.8300 (mp) cc_final: 0.8056 (mp) REVERT: B 448 LEU cc_start: 0.8989 (mm) cc_final: 0.8470 (mm) REVERT: C 98 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8370 (mm) REVERT: D 118 MET cc_start: 0.8690 (tpp) cc_final: 0.8302 (tpp) REVERT: D 196 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7083 (t0) REVERT: D 271 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7469 (p-80) REVERT: E 39 ASN cc_start: 0.9250 (OUTLIER) cc_final: 0.9009 (m-40) REVERT: F 71 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9023 (tp) REVERT: F 198 MET cc_start: 0.8814 (tmm) cc_final: 0.8478 (tmm) REVERT: F 282 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.6975 (tptt) REVERT: F 373 MET cc_start: 0.8816 (tpp) cc_final: 0.8462 (tpp) REVERT: G 21 LEU cc_start: 0.8385 (tp) cc_final: 0.8061 (mt) REVERT: G 66 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7212 (t80) REVERT: G 105 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8866 (mt) REVERT: G 112 MET cc_start: 0.8065 (tpp) cc_final: 0.7672 (tpp) REVERT: H 132 PHE cc_start: 0.8023 (m-80) cc_final: 0.7721 (m-10) REVERT: H 142 TYR cc_start: 0.5767 (m-10) cc_final: 0.5361 (m-80) REVERT: H 237 ASP cc_start: 0.8095 (t0) cc_final: 0.7722 (t0) REVERT: I 84 ARG cc_start: 0.4847 (tpp-160) cc_final: 0.3886 (ttt180) REVERT: J 51 TYR cc_start: 0.5108 (t80) cc_final: 0.4757 (t80) REVERT: K 28 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.4711 (mt) REVERT: K 121 TYR cc_start: 0.6180 (m-80) cc_final: 0.5796 (m-80) REVERT: K 144 ARG cc_start: 0.3774 (mpt180) cc_final: 0.3465 (mmt180) REVERT: K 205 ARG cc_start: 0.1566 (tpm170) cc_final: 0.0929 (tpt170) REVERT: N 83 ARG cc_start: 0.7217 (tmm-80) cc_final: 0.6827 (tmt170) REVERT: 2 100 TYR cc_start: 0.8315 (t80) cc_final: 0.7989 (t80) REVERT: 2 213 GLU cc_start: 0.8213 (tp30) cc_final: 0.7675 (tm-30) REVERT: 4 249 GLU cc_start: 0.8354 (pp20) cc_final: 0.8029 (pt0) REVERT: 5 86 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7404 (t0) REVERT: 5 182 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8472 (p) REVERT: 6 220 GLU cc_start: 0.7771 (tt0) cc_final: 0.7148 (tp30) REVERT: 6 354 MET cc_start: 0.8155 (tpp) cc_final: 0.6996 (tpp) REVERT: 6 385 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7790 (tt) REVERT: 7 232 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6482 (tt0) REVERT: 7 292 PHE cc_start: 0.7609 (t80) cc_final: 0.7367 (t80) REVERT: 0 69 ASP cc_start: 0.7323 (t0) cc_final: 0.6845 (t0) REVERT: 0 158 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9015 (tp) REVERT: 0 179 ILE cc_start: 0.8234 (tt) cc_final: 0.7999 (mm) REVERT: 0 200 TRP cc_start: 0.5227 (p90) cc_final: 0.3713 (t-100) outliers start: 113 outliers final: 85 residues processed: 595 average time/residue: 0.5008 time to fit residues: 504.8129 Evaluate side-chains 585 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 486 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain 1 residue 94 ASP Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 4 residue 216 MET Chi-restraints excluded: chain 5 residue 86 ASN Chi-restraints excluded: chain 5 residue 182 THR Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 176 ASP Chi-restraints excluded: chain 6 residue 254 TYR Chi-restraints excluded: chain 6 residue 328 LEU Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 99 HIS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 215 TYR Chi-restraints excluded: chain 7 residue 229 THR Chi-restraints excluded: chain 7 residue 232 GLU Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 114 VAL Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 158 ILE Chi-restraints excluded: chain 0 residue 197 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 10.0000 chunk 501 optimal weight: 9.9990 chunk 306 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 chunk 526 optimal weight: 0.7980 chunk 484 optimal weight: 3.9990 chunk 418 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 323 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN H 93 GLN I 58 HIS I 136 ASN ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS 5 86 ASN ** 7 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 41767 Z= 0.411 Angle : 0.825 12.454 56878 Z= 0.417 Chirality : 0.049 0.227 6497 Planarity : 0.006 0.089 7182 Dihedral : 7.390 79.995 5901 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.23 % Favored : 83.60 % Rotamer: Outliers : 2.99 % Allowed : 22.77 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.11), residues: 5280 helix: -0.35 (0.11), residues: 2390 sheet: -2.30 (0.27), residues: 361 loop : -3.54 (0.11), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP 7 255 HIS 0.012 0.002 HIS F 407 PHE 0.048 0.002 PHE F 504 TYR 0.055 0.002 TYR I 137 ARG 0.008 0.001 ARG K 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 465 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8854 (t60) cc_final: 0.8492 (t60) REVERT: A 146 MET cc_start: 0.7743 (ttp) cc_final: 0.7336 (tmm) REVERT: A 302 MET cc_start: 0.2995 (ppp) cc_final: 0.2375 (tmm) REVERT: B 323 MET cc_start: 0.8102 (ttp) cc_final: 0.7886 (ttp) REVERT: B 448 LEU cc_start: 0.8966 (mm) cc_final: 0.8517 (mm) REVERT: C 98 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8370 (mm) REVERT: D 118 MET cc_start: 0.8782 (tpp) cc_final: 0.8396 (tpp) REVERT: D 271 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7762 (p-80) REVERT: E 39 ASN cc_start: 0.9435 (OUTLIER) cc_final: 0.9083 (m-40) REVERT: F 198 MET cc_start: 0.8814 (tmm) cc_final: 0.8472 (tmm) REVERT: F 282 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8618 (tppp) REVERT: F 373 MET cc_start: 0.8957 (tpp) cc_final: 0.8611 (tpp) REVERT: G 21 LEU cc_start: 0.8495 (tp) cc_final: 0.8160 (mt) REVERT: G 66 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7681 (t80) REVERT: G 105 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8917 (mt) REVERT: G 112 MET cc_start: 0.8242 (tpp) cc_final: 0.7972 (tpp) REVERT: H 76 MET cc_start: 0.7123 (tpp) cc_final: 0.6741 (tpp) REVERT: H 132 PHE cc_start: 0.8048 (m-80) cc_final: 0.7758 (m-10) REVERT: H 142 TYR cc_start: 0.5400 (m-10) cc_final: 0.5022 (m-80) REVERT: H 237 ASP cc_start: 0.8056 (t0) cc_final: 0.7664 (t0) REVERT: I 84 ARG cc_start: 0.5016 (tpp-160) cc_final: 0.3965 (ttt180) REVERT: K 28 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.4898 (mt) REVERT: K 121 TYR cc_start: 0.6356 (m-80) cc_final: 0.6029 (m-80) REVERT: K 144 ARG cc_start: 0.3790 (mpt180) cc_final: 0.3373 (mmt180) REVERT: K 205 ARG cc_start: 0.1857 (tpm170) cc_final: 0.1181 (tpt170) REVERT: N 83 ARG cc_start: 0.7322 (tmm-80) cc_final: 0.6870 (tmt170) REVERT: 2 100 TYR cc_start: 0.8374 (t80) cc_final: 0.7966 (t80) REVERT: 2 213 GLU cc_start: 0.8332 (tp30) cc_final: 0.7798 (tm-30) REVERT: 4 249 GLU cc_start: 0.8536 (pp20) cc_final: 0.7709 (pp20) REVERT: 5 182 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8453 (p) REVERT: 6 220 GLU cc_start: 0.7989 (tt0) cc_final: 0.7420 (tp30) REVERT: 6 385 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8219 (tt) REVERT: 7 215 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8146 (t80) REVERT: 7 232 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: 7 292 PHE cc_start: 0.8007 (t80) cc_final: 0.7796 (t80) REVERT: 0 158 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9082 (tp) REVERT: 0 200 TRP cc_start: 0.5263 (p90) cc_final: 0.3676 (t-100) outliers start: 120 outliers final: 88 residues processed: 551 average time/residue: 0.4859 time to fit residues: 453.6993 Evaluate side-chains 556 residues out of total 4600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 456 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 504 PHE Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain 1 residue 94 ASP Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 182 THR Chi-restraints excluded: chain 6 residue 176 ASP Chi-restraints excluded: chain 6 residue 242 PHE Chi-restraints excluded: chain 6 residue 254 TYR Chi-restraints excluded: chain 6 residue 328 LEU Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 99 HIS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 215 TYR Chi-restraints excluded: chain 7 residue 229 THR Chi-restraints excluded: chain 7 residue 232 GLU Chi-restraints excluded: chain 7 residue 295 ILE Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 129 ILE Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 158 ILE Chi-restraints excluded: chain 0 residue 197 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 6.9990 chunk 446 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 386 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 419 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 430 optimal weight: 6.9990 chunk 53 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS 5 86 ASN 9 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.134900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.105994 restraints weight = 98941.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105515 restraints weight = 68982.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.106074 restraints weight = 50973.314| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41767 Z= 0.188 Angle : 0.714 23.413 56878 Z= 0.357 Chirality : 0.044 0.202 6497 Planarity : 0.005 0.074 7182 Dihedral : 7.037 80.010 5901 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.31 % Favored : 86.57 % Rotamer: Outliers : 2.47 % Allowed : 23.49 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.19 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.12), residues: 5280 helix: -0.11 (0.11), residues: 2400 sheet: -2.15 (0.27), residues: 360 loop : -3.44 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP H 217 HIS 0.007 0.001 HIS F 407 PHE 0.045 0.001 PHE F 504 TYR 0.046 0.001 TYR I 137 ARG 0.007 0.000 ARG 7 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9177.11 seconds wall clock time: 166 minutes 54.50 seconds (10014.50 seconds total)