Starting phenix.real_space_refine on Tue Mar 19 09:27:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1t_4168/03_2024/6f1t_4168_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1t_4168/03_2024/6f1t_4168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1t_4168/03_2024/6f1t_4168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1t_4168/03_2024/6f1t_4168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1t_4168/03_2024/6f1t_4168_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1t_4168/03_2024/6f1t_4168_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 230 5.16 5 C 57664 2.51 5 N 17027 2.21 5 O 17853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 199": "NH1" <-> "NH2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "I PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 263": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Residue "K ARG 172": "NH1" <-> "NH2" Residue "L ARG 195": "NH1" <-> "NH2" Residue "b ARG 74": "NH1" <-> "NH2" Residue "e ARG 223": "NH1" <-> "NH2" Residue "e ARG 254": "NH1" <-> "NH2" Residue "e ARG 264": "NH1" <-> "NH2" Residue "e ARG 292": "NH1" <-> "NH2" Residue "f ARG 264": "NH1" <-> "NH2" Residue "f PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 292": "NH1" <-> "NH2" Residue "f ARG 354": "NH1" <-> "NH2" Residue "f ARG 442": "NH1" <-> "NH2" Residue "f ARG 457": "NH1" <-> "NH2" Residue "f ARG 556": "NH1" <-> "NH2" Residue "f ARG 559": "NH1" <-> "NH2" Residue "f ARG 563": "NH1" <-> "NH2" Residue "f ARG 567": "NH1" <-> "NH2" Residue "f ARG 569": "NH1" <-> "NH2" Residue "f ARG 664": "NH1" <-> "NH2" Residue "f ARG 709": "NH1" <-> "NH2" Residue "f ARG 724": "NH1" <-> "NH2" Residue "f ARG 726": "NH1" <-> "NH2" Residue "f ARG 728": "NH1" <-> "NH2" Residue "f ARG 786": "NH1" <-> "NH2" Residue "f ARG 790": "NH1" <-> "NH2" Residue "f ARG 862": "NH1" <-> "NH2" Residue "f ARG 909": "NH1" <-> "NH2" Residue "f ARG 914": "NH1" <-> "NH2" Residue "h ARG 243": "NH1" <-> "NH2" Residue "h ARG 254": "NH1" <-> "NH2" Residue "h ARG 337": "NH1" <-> "NH2" Residue "h ARG 590": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "j ARG 171": "NH1" <-> "NH2" Residue "j ARG 175": "NH1" <-> "NH2" Residue "j TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 223": "NH1" <-> "NH2" Residue "m ARG 254": "NH1" <-> "NH2" Residue "m ARG 264": "NH1" <-> "NH2" Residue "m ARG 292": "NH1" <-> "NH2" Residue "m ARG 379": "NH1" <-> "NH2" Residue "m ARG 442": "NH1" <-> "NH2" Residue "m ARG 457": "NH1" <-> "NH2" Residue "m ARG 563": "NH1" <-> "NH2" Residue "m ARG 583": "NH1" <-> "NH2" Residue "m ARG 656": "NH1" <-> "NH2" Residue "m ARG 690": "NH1" <-> "NH2" Residue "n ARG 254": "NH1" <-> "NH2" Residue "n ARG 264": "NH1" <-> "NH2" Residue "n ARG 292": "NH1" <-> "NH2" Residue "n ARG 376": "NH1" <-> "NH2" Residue "n ARG 379": "NH1" <-> "NH2" Residue "n ARG 457": "NH1" <-> "NH2" Residue "n ARG 467": "NH1" <-> "NH2" Residue "n ARG 471": "NH1" <-> "NH2" Residue "n ARG 477": "NH1" <-> "NH2" Residue "n ARG 482": "NH1" <-> "NH2" Residue "n ARG 567": "NH1" <-> "NH2" Residue "n ARG 569": "NH1" <-> "NH2" Residue "o ARG 205": "NH1" <-> "NH2" Residue "o ARG 243": "NH1" <-> "NH2" Residue "o ARG 254": "NH1" <-> "NH2" Residue "o ARG 341": "NH1" <-> "NH2" Residue "o ARG 557": "NH1" <-> "NH2" Residue "o ARG 587": "NH1" <-> "NH2" Residue "o ARG 590": "NH1" <-> "NH2" Residue "p GLU 185": "OE1" <-> "OE2" Residue "p GLU 186": "OE1" <-> "OE2" Residue "p ARG 205": "NH1" <-> "NH2" Residue "p ARG 209": "NH1" <-> "NH2" Residue "s ARG 10": "NH1" <-> "NH2" Residue "s ARG 54": "NH1" <-> "NH2" Residue "s ARG 72": "NH1" <-> "NH2" Residue "t ARG 10": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92795 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "D" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "F" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "G" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "I" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "J" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2883 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2264 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 267} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2122 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 259} Chain: "M" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 2935 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 587} Link IDs: {'TRANS': 586} Chain breaks: 5 Unresolved non-hydrogen bonds: 1174 Unresolved non-hydrogen angles: 1761 Unresolved non-hydrogen dihedrals: 587 Planarities with less than four sites: {'UNK:plan-1': 587} Unresolved non-hydrogen planarities: 587 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 3080 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 616} Link IDs: {'TRANS': 615} Chain breaks: 5 Unresolved non-hydrogen bonds: 1232 Unresolved non-hydrogen angles: 1848 Unresolved non-hydrogen dihedrals: 616 Planarities with less than four sites: {'UNK:plan-1': 616} Unresolved non-hydrogen planarities: 616 Chain: "O" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 323 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 63} Link IDs: {'TRANS': 64} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 65 Chain: "P" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 323 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 63} Link IDs: {'TRANS': 64} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 65 Chain: "Q" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'TRANS': 86} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "R" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'TRANS': 86} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "U" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 843 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 11, 'TRANS': 160} Unresolved chain links: 1 Unresolved chain link angles: 14 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 486 Unresolved non-hydrogen angles: 621 Unresolved non-hydrogen dihedrals: 384 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 12, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 234 Chain: "V" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 812 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 10, 'TRANS': 154} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 4, 'PHE:plan': 9, 'GLU:plan': 6, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 228 Chain: "X" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1715 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'TRANS': 284} Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 789 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 17, 'UNK:plan-1': 64, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 352 Chain: "Y" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1315 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'TRANS': 262} Chain breaks: 11 Unresolved non-hydrogen bonds: 526 Unresolved non-hydrogen angles: 789 Unresolved non-hydrogen dihedrals: 263 Planarities with less than four sites: {'UNK:plan-1': 263} Unresolved non-hydrogen planarities: 263 Chain: "Z" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 260 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Chain: "a" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 405 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 46} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 256 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Chain: "e" Number of atoms: 5034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 5034 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 714} Link IDs: {'PTRANS': 28, 'TRANS': 897} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 2567 Unresolved non-hydrogen angles: 3288 Unresolved non-hydrogen dihedrals: 2080 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 39, 'UNK:plan-1': 49, 'ASP:plan': 39, 'TYR:plan': 20, 'ASN:plan1': 30, 'TRP:plan': 10, 'HIS:plan': 16, 'PHE:plan': 26, 'GLU:plan': 65, 'ARG:plan': 57} Unresolved non-hydrogen planarities: 1423 Chain: "f" Number of atoms: 6939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 6939 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 28, 'TRANS': 900} Chain breaks: 4 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 790 Unresolved non-hydrogen dihedrals: 464 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 7, 'UNK:plan-1': 49, 'ASP:plan': 8, 'TYR:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 298 Chain: "g" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 1961 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 345} Link IDs: {'PTRANS': 17, 'TRANS': 379} Chain breaks: 1 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1252 Unresolved non-hydrogen angles: 1630 Unresolved non-hydrogen dihedrals: 1071 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 18, 'TYR:plan': 11, 'ASN:plan1': 25, 'TRP:plan': 11, 'ASP:plan': 20, 'PHE:plan': 17, 'GLU:plan': 25, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 739 Chain: "h" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3010 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 107 Chain: "i" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1327 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 907 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 10, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 11, 'PHE:plan': 12, 'GLU:plan': 23, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 491 Chain: "j" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2284 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain breaks: 3 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "k" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "l" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "m" Number of atoms: 6260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 6260 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PTRANS': 28, 'TRANS': 897} Chain breaks: 4 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1287 Unresolved non-hydrogen angles: 1666 Unresolved non-hydrogen dihedrals: 1014 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 49, 'ASP:plan': 16, 'TYR:plan': 12, 'ASN:plan1': 15, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 12, 'GLU:plan': 36, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 673 Chain: "n" Number of atoms: 5730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 5730 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 533} Link IDs: {'PTRANS': 28, 'TRANS': 899} Chain breaks: 4 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1863 Unresolved non-hydrogen angles: 2396 Unresolved non-hydrogen dihedrals: 1505 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 29, 'UNK:plan-1': 49, 'ASP:plan': 26, 'TYR:plan': 15, 'ASN:plan1': 23, 'TRP:plan': 7, 'HIS:plan': 12, 'PHE:plan': 20, 'GLU:plan': 46, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1009 Chain: "o" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3126 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 379} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "p" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2116 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 312} Link IDs: {'PTRANS': 17, 'TRANS': 383} Chain breaks: 1 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1135 Unresolved non-hydrogen angles: 1481 Unresolved non-hydrogen dihedrals: 979 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 16, 'TYR:plan': 12, 'ASN:plan1': 22, 'TRP:plan': 11, 'ASP:plan': 20, 'PHE:plan': 14, 'GLU:plan': 18, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 664 Chain: "q" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1327 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 907 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 10, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 11, 'PHE:plan': 12, 'GLU:plan': 23, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 491 Chain: "r" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1327 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 907 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 10, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 11, 'PHE:plan': 12, 'GLU:plan': 23, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 491 Chain: "s" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 742 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "t" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 742 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "x" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 1695 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 287} Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 842 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 67, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 383 Chain: "z" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 265 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 35.96, per 1000 atoms: 0.39 Number of scatterers: 92795 At special positions: 0 Unit cell: (364.48, 276.04, 448.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 230 16.00 P 21 15.00 O 17853 8.00 N 17027 7.00 C 57664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.72 Conformation dependent library (CDL) restraints added in 12.0 seconds 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 462 helices and 98 sheets defined 58.3% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.28 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 208 through 218 removed outlier: 4.056A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.520A pdb=" N ARG A 291 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG A 292 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 294 " --> pdb=" O ARG A 291 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 295 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.707A pdb=" N SER A 339 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N THR A 340 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.137A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 255 removed outlier: 3.868A pdb=" N ARG B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.651A pdb=" N LEU B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.745A pdb=" N ARG B 291 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG B 292 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 306 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 254 through 257 No H-bonds generated for 'chain 'C' and resid 254 through 257' Processing helix chain 'C' and resid 259 through 262 Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 291 through 295 Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 336 through 348 removed outlier: 3.787A pdb=" N SER C 339 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR C 340 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP C 341 " --> pdb=" O TYR C 338 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 348 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 360 through 365 Processing helix chain 'C' and resid 368 through 374 Processing helix chain 'D' and resid 61 through 64 No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.774A pdb=" N ARG D 291 " --> pdb=" O MET D 288 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG D 292 " --> pdb=" O ASP D 289 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR D 293 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 306 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 339 through 347 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 360 through 365 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 143 through 150 Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 211 through 220 Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 265 through 268 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 292 through 296 Processing helix chain 'E' and resid 303 through 306 Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 339 through 348 Processing helix chain 'E' and resid 352 through 356 Processing helix chain 'E' and resid 360 through 365 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'F' and resid 60 through 64 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 142 through 149 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 187 through 200 Processing helix chain 'F' and resid 208 through 220 Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 252 through 260 removed outlier: 4.659A pdb=" N ALA F 258 " --> pdb=" O ARG F 255 " (cutoff:3.500A) Proline residue: F 259 - end of helix Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 291 through 295 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 310 through 321 Processing helix chain 'F' and resid 336 through 349 removed outlier: 5.222A pdb=" N THR F 340 " --> pdb=" O LEU F 337 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY F 343 " --> pdb=" O THR F 340 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 347 " --> pdb=" O GLY F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 360 through 366 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 94 Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 142 through 150 Processing helix chain 'G' and resid 187 through 201 Processing helix chain 'G' and resid 208 through 220 removed outlier: 4.010A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.903A pdb=" N ARG G 255 " --> pdb=" O GLY G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 262 removed outlier: 3.531A pdb=" N LEU G 262 " --> pdb=" O PRO G 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 259 through 262' Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 288 through 295 removed outlier: 3.702A pdb=" N ARG G 291 " --> pdb=" O MET G 288 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG G 292 " --> pdb=" O ASP G 289 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR G 293 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 294 " --> pdb=" O ARG G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 310 through 321 Processing helix chain 'G' and resid 336 through 348 removed outlier: 3.703A pdb=" N SER G 339 " --> pdb=" O ARG G 336 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR G 340 " --> pdb=" O LEU G 337 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 348 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 3.851A pdb=" N LYS G 354 " --> pdb=" O ASP G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 360 through 365 Processing helix chain 'G' and resid 368 through 374 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 79 through 92 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 removed outlier: 3.989A pdb=" N THR H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 Processing helix chain 'H' and resid 182 through 195 Processing helix chain 'H' and resid 203 through 216 removed outlier: 3.874A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 253 through 262 Proline residue: H 258 - end of helix removed outlier: 5.211A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 283 Processing helix chain 'H' and resid 287 through 295 removed outlier: 4.120A pdb=" N ARG H 290 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYS H 291 " --> pdb=" O ASP H 288 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP H 292 " --> pdb=" O ILE H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 310 through 320 Processing helix chain 'H' and resid 338 through 347 Processing helix chain 'H' and resid 352 through 355 Processing helix chain 'H' and resid 359 through 364 Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.583A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS H 371 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 55 No H-bonds generated for 'chain 'I' and resid 53 through 55' Processing helix chain 'I' and resid 60 through 63 No H-bonds generated for 'chain 'I' and resid 60 through 63' Processing helix chain 'I' and resid 83 through 94 Processing helix chain 'I' and resid 118 through 130 Processing helix chain 'I' and resid 144 through 150 Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.578A pdb=" N LYS I 200 " --> pdb=" O LEU I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 220 Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 253 through 260 removed outlier: 4.587A pdb=" N ALA I 258 " --> pdb=" O ARG I 255 " (cutoff:3.500A) Proline residue: I 259 - end of helix Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 291 through 295 Processing helix chain 'I' and resid 303 through 305 No H-bonds generated for 'chain 'I' and resid 303 through 305' Processing helix chain 'I' and resid 310 through 321 Processing helix chain 'I' and resid 339 through 348 Processing helix chain 'I' and resid 352 through 354 No H-bonds generated for 'chain 'I' and resid 352 through 354' Processing helix chain 'I' and resid 360 through 365 Processing helix chain 'I' and resid 368 through 375 Processing helix chain 'J' and resid 61 through 79 Processing helix chain 'J' and resid 99 through 111 Processing helix chain 'J' and resid 123 through 131 removed outlier: 3.997A pdb=" N LEU J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 181 Processing helix chain 'J' and resid 205 through 213 Processing helix chain 'J' and resid 220 through 230 Processing helix chain 'J' and resid 262 through 270 removed outlier: 4.998A pdb=" N VAL J 267 " --> pdb=" O ARG J 263 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU J 270 " --> pdb=" O VAL J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 290 removed outlier: 4.214A pdb=" N ILE J 284 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU J 285 " --> pdb=" O ALA J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 300 Processing helix chain 'J' and resid 309 through 311 No H-bonds generated for 'chain 'J' and resid 309 through 311' Processing helix chain 'J' and resid 315 through 327 Processing helix chain 'J' and resid 333 through 336 No H-bonds generated for 'chain 'J' and resid 333 through 336' Processing helix chain 'J' and resid 350 through 362 removed outlier: 3.965A pdb=" N VAL J 353 " --> pdb=" O ALA J 350 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA J 354 " --> pdb=" O ASN J 351 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP J 355 " --> pdb=" O CYS J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 371 No H-bonds generated for 'chain 'J' and resid 368 through 371' Processing helix chain 'J' and resid 375 through 381 Processing helix chain 'K' and resid 11 through 21 removed outlier: 3.981A pdb=" N ARG K 15 " --> pdb=" O GLU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 40 removed outlier: 4.215A pdb=" N LEU K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 60 Processing helix chain 'K' and resid 91 through 93 No H-bonds generated for 'chain 'K' and resid 91 through 93' Processing helix chain 'K' and resid 118 through 135 Processing helix chain 'K' and resid 148 through 150 No H-bonds generated for 'chain 'K' and resid 148 through 150' Processing helix chain 'K' and resid 165 through 167 No H-bonds generated for 'chain 'K' and resid 165 through 167' Processing helix chain 'K' and resid 222 through 250 removed outlier: 3.772A pdb=" N MET K 250 " --> pdb=" O ASN K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 258 Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'L' and resid 3 through 14 Processing helix chain 'L' and resid 21 through 31 Processing helix chain 'L' and resid 33 through 39 removed outlier: 5.560A pdb=" N GLU L 37 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP L 38 " --> pdb=" O LEU L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 Processing helix chain 'L' and resid 209 through 243 removed outlier: 3.912A pdb=" N PHE L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 266 Processing helix chain 'M' and resid 2 through 26 removed outlier: 3.516A pdb=" N UNK M 12 " --> pdb=" O UNK M 8 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N UNK M 26 " --> pdb=" O UNK M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 43 Processing helix chain 'M' and resid 45 through 52 removed outlier: 3.691A pdb=" N UNK M 49 " --> pdb=" O UNK M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 71 removed outlier: 4.322A pdb=" N UNK M 65 " --> pdb=" O UNK M 61 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N UNK M 68 " --> pdb=" O UNK M 64 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N UNK M 69 " --> pdb=" O UNK M 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK M 71 " --> pdb=" O UNK M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 85 Processing helix chain 'M' and resid 87 through 170 removed outlier: 3.711A pdb=" N UNK M 105 " --> pdb=" O UNK M 101 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N UNK M 110 " --> pdb=" O UNK M 106 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N UNK M 111 " --> pdb=" O UNK M 107 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N UNK M 112 " --> pdb=" O UNK M 108 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N UNK M 113 " --> pdb=" O UNK M 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK M 117 " --> pdb=" O UNK M 113 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N UNK M 118 " --> pdb=" O UNK M 114 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N UNK M 122 " --> pdb=" O UNK M 118 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N UNK M 123 " --> pdb=" O UNK M 119 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N UNK M 130 " --> pdb=" O UNK M 126 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N UNK M 139 " --> pdb=" O UNK M 135 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N UNK M 163 " --> pdb=" O UNK M 159 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N UNK M 164 " --> pdb=" O UNK M 160 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N UNK M 169 " --> pdb=" O UNK M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 239 Processing helix chain 'M' and resid 241 through 264 Processing helix chain 'M' and resid 268 through 315 removed outlier: 4.166A pdb=" N UNK M 293 " --> pdb=" O UNK M 289 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N UNK M 300 " --> pdb=" O UNK M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 366 removed outlier: 4.069A pdb=" N UNK M 358 " --> pdb=" O UNK M 354 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N UNK M 359 " --> pdb=" O UNK M 355 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N UNK M 360 " --> pdb=" O UNK M 356 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N UNK M 361 " --> pdb=" O UNK M 357 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N UNK M 362 " --> pdb=" O UNK M 358 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N UNK M 363 " --> pdb=" O UNK M 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 437 removed outlier: 3.816A pdb=" N UNK M 431 " --> pdb=" O UNK M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 441 through 461 Processing helix chain 'M' and resid 469 through 558 removed outlier: 3.934A pdb=" N UNK M 488 " --> pdb=" O UNK M 484 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N UNK M 492 " --> pdb=" O UNK M 488 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N UNK M 495 " --> pdb=" O UNK M 491 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N UNK M 497 " --> pdb=" O UNK M 493 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N UNK M 498 " --> pdb=" O UNK M 494 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N UNK M 501 " --> pdb=" O UNK M 497 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N UNK M 505 " --> pdb=" O UNK M 501 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK M 508 " --> pdb=" O UNK M 504 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK M 549 " --> pdb=" O UNK M 545 " (cutoff:3.500A) Processing helix chain 'M' and resid 602 through 623 Processing helix chain 'M' and resid 702 through 740 Processing helix chain 'M' and resid 802 through 823 Processing helix chain 'N' and resid 2 through 40 removed outlier: 4.878A pdb=" N UNK N 30 " --> pdb=" O UNK N 26 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N UNK N 31 " --> pdb=" O UNK N 27 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N UNK N 32 " --> pdb=" O UNK N 28 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N UNK N 38 " --> pdb=" O UNK N 34 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N UNK N 39 " --> pdb=" O UNK N 35 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N UNK N 40 " --> pdb=" O UNK N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 58 removed outlier: 3.891A pdb=" N UNK N 49 " --> pdb=" O UNK N 45 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N UNK N 52 " --> pdb=" O UNK N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 78 removed outlier: 3.730A pdb=" N UNK N 69 " --> pdb=" O UNK N 66 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N UNK N 71 " --> pdb=" O UNK N 68 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N UNK N 76 " --> pdb=" O UNK N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 170 removed outlier: 3.749A pdb=" N UNK N 98 " --> pdb=" O UNK N 94 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N UNK N 99 " --> pdb=" O UNK N 95 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N UNK N 108 " --> pdb=" O UNK N 104 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N UNK N 109 " --> pdb=" O UNK N 105 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N UNK N 119 " --> pdb=" O UNK N 115 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N UNK N 120 " --> pdb=" O UNK N 116 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N UNK N 126 " --> pdb=" O UNK N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 242 removed outlier: 3.560A pdb=" N UNK N 238 " --> pdb=" O UNK N 234 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N UNK N 239 " --> pdb=" O UNK N 235 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK N 240 " --> pdb=" O UNK N 236 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N UNK N 242 " --> pdb=" O UNK N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 267 Processing helix chain 'N' and resid 269 through 273 removed outlier: 3.713A pdb=" N UNK N 273 " --> pdb=" O UNK N 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 269 through 273' Processing helix chain 'N' and resid 276 through 365 removed outlier: 3.740A pdb=" N UNK N 292 " --> pdb=" O UNK N 288 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N UNK N 293 " --> pdb=" O UNK N 289 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N UNK N 294 " --> pdb=" O UNK N 290 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N UNK N 296 " --> pdb=" O UNK N 292 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N UNK N 299 " --> pdb=" O UNK N 295 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N UNK N 315 " --> pdb=" O UNK N 311 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N UNK N 316 " --> pdb=" O UNK N 312 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N UNK N 358 " --> pdb=" O UNK N 354 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N UNK N 359 " --> pdb=" O UNK N 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 402 through 436 removed outlier: 4.347A pdb=" N UNK N 435 " --> pdb=" O UNK N 431 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N UNK N 436 " --> pdb=" O UNK N 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 438 through 488 removed outlier: 3.806A pdb=" N UNK N 443 " --> pdb=" O UNK N 439 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N UNK N 459 " --> pdb=" O UNK N 455 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N UNK N 467 " --> pdb=" O UNK N 463 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N UNK N 468 " --> pdb=" O UNK N 464 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N UNK N 469 " --> pdb=" O UNK N 465 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N UNK N 470 " --> pdb=" O UNK N 466 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N UNK N 471 " --> pdb=" O UNK N 467 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK N 472 " --> pdb=" O UNK N 468 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N UNK N 474 " --> pdb=" O UNK N 470 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N UNK N 475 " --> pdb=" O UNK N 471 " (cutoff:3.500A) Processing helix chain 'N' and resid 490 through 556 removed outlier: 4.652A pdb=" N UNK N 497 " --> pdb=" O UNK N 493 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N UNK N 498 " --> pdb=" O UNK N 494 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N UNK N 508 " --> pdb=" O UNK N 504 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N UNK N 509 " --> pdb=" O UNK N 505 " (cutoff:3.500A) Processing helix chain 'N' and resid 603 through 624 Processing helix chain 'N' and resid 704 through 707 removed outlier: 3.667A pdb=" N UNK N 707 " --> pdb=" O UNK N 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 704 through 707' Processing helix chain 'N' and resid 709 through 744 removed outlier: 4.345A pdb=" N UNK N 713 " --> pdb=" O UNK N 709 " (cutoff:3.500A) Processing helix chain 'N' and resid 760 through 767 removed outlier: 4.146A pdb=" N UNK N 767 " --> pdb=" O UNK N 763 " (cutoff:3.500A) Processing helix chain 'N' and resid 802 through 817 Processing helix chain 'O' and resid 81 through 93 Processing helix chain 'O' and resid 97 through 111 Processing helix chain 'P' and resid 81 through 93 Processing helix chain 'P' and resid 97 through 110 Processing helix chain 'Q' and resid 2 through 36 Processing helix chain 'Q' and resid 43 through 61 Processing helix chain 'Q' and resid 65 through 90 Processing helix chain 'R' and resid 3 through 36 Processing helix chain 'R' and resid 43 through 59 Processing helix chain 'R' and resid 66 through 89 Processing helix chain 'U' and resid 163 through 184 Proline residue: U 172 - end of helix Processing helix chain 'V' and resid 160 through 173 Processing helix chain 'X' and resid 106 through 386 Processing helix chain 'Y' and resid 443 through 471 Processing helix chain 'Z' and resid 1002 through 1026 Processing helix chain 'Z' and resid 1028 through 1037 Processing helix chain 'a' and resid 38 through 41 Processing helix chain 'a' and resid 52 through 58 Processing helix chain 'b' and resid 52 through 58 Processing helix chain 'c' and resid 3 through 8 Processing helix chain 'd' and resid 4 through 6 No H-bonds generated for 'chain 'd' and resid 4 through 6' Processing helix chain 'e' and resid 27 through 37 Processing helix chain 'e' and resid 39 through 42 No H-bonds generated for 'chain 'e' and resid 39 through 42' Processing helix chain 'e' and resid 50 through 57 Processing helix chain 'e' and resid 59 through 69 Processing helix chain 'e' and resid 145 through 165 removed outlier: 4.427A pdb=" N ALA e 158 " --> pdb=" O SER e 154 " (cutoff:3.500A) Proline residue: e 159 - end of helix Processing helix chain 'e' and resid 179 through 197 Processing helix chain 'e' and resid 211 through 222 Processing helix chain 'e' and resid 233 through 236 removed outlier: 3.642A pdb=" N VAL e 236 " --> pdb=" O GLY e 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 233 through 236' Processing helix chain 'e' and resid 239 through 260 removed outlier: 3.903A pdb=" N VAL e 259 " --> pdb=" O GLU e 255 " (cutoff:3.500A) Processing helix chain 'e' and resid 271 through 292 Processing helix chain 'e' and resid 295 through 306 Processing helix chain 'e' and resid 312 through 318 Processing helix chain 'e' and resid 322 through 336 Proline residue: e 334 - end of helix Processing helix chain 'e' and resid 340 through 345 Processing helix chain 'e' and resid 350 through 370 removed outlier: 3.965A pdb=" N ARG e 354 " --> pdb=" O LEU e 350 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN e 355 " --> pdb=" O ASP e 351 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS e 366 " --> pdb=" O THR e 362 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE e 367 " --> pdb=" O HIS e 363 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG e 368 " --> pdb=" O LEU e 364 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN e 369 " --> pdb=" O ARG e 365 " (cutoff:3.500A) Processing helix chain 'e' and resid 374 through 397 Processing helix chain 'e' and resid 406 through 443 removed outlier: 5.112A pdb=" N GLU e 443 " --> pdb=" O LYS e 439 " (cutoff:3.500A) Processing helix chain 'e' and resid 455 through 482 removed outlier: 3.695A pdb=" N LEU e 459 " --> pdb=" O ALA e 455 " (cutoff:3.500A) Processing helix chain 'e' and resid 518 through 532 removed outlier: 3.662A pdb=" N GLU e 522 " --> pdb=" O ASN e 518 " (cutoff:3.500A) Processing helix chain 'e' and resid 539 through 544 Processing helix chain 'e' and resid 546 through 570 Processing helix chain 'e' and resid 578 through 586 Processing helix chain 'e' and resid 590 through 593 No H-bonds generated for 'chain 'e' and resid 590 through 593' Processing helix chain 'e' and resid 595 through 624 removed outlier: 4.389A pdb=" N ALA e 600 " --> pdb=" O HIS e 596 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU e 603 " --> pdb=" O GLY e 599 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN e 607 " --> pdb=" O GLU e 603 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN e 610 " --> pdb=" O THR e 606 " (cutoff:3.500A) Processing helix chain 'e' and resid 631 through 638 removed outlier: 3.569A pdb=" N MET e 635 " --> pdb=" O ALA e 632 " (cutoff:3.500A) Processing helix chain 'e' and resid 643 through 668 Processing helix chain 'e' and resid 673 through 675 No H-bonds generated for 'chain 'e' and resid 673 through 675' Processing helix chain 'e' and resid 677 through 693 removed outlier: 3.864A pdb=" N GLN e 680 " --> pdb=" O VAL e 677 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER e 688 " --> pdb=" O ASP e 685 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG e 690 " --> pdb=" O ASP e 687 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N MET e 691 " --> pdb=" O SER e 688 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS e 692 " --> pdb=" O PHE e 689 " (cutoff:3.500A) Processing helix chain 'e' and resid 698 through 708 Processing helix chain 'e' and resid 711 through 714 No H-bonds generated for 'chain 'e' and resid 711 through 714' Processing helix chain 'e' and resid 729 through 731 No H-bonds generated for 'chain 'e' and resid 729 through 731' Processing helix chain 'e' and resid 738 through 740 No H-bonds generated for 'chain 'e' and resid 738 through 740' Processing helix chain 'e' and resid 743 through 754 Processing helix chain 'e' and resid 762 through 772 Processing helix chain 'e' and resid 775 through 797 removed outlier: 4.038A pdb=" N LYS e 794 " --> pdb=" O ARG e 790 " (cutoff:3.500A) Processing helix chain 'e' and resid 799 through 821 removed outlier: 5.267A pdb=" N GLY e 807 " --> pdb=" O LEU e 803 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU e 808 " --> pdb=" O LEU e 804 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU e 811 " --> pdb=" O GLY e 807 " (cutoff:3.500A) Processing helix chain 'e' and resid 829 through 863 Processing helix chain 'e' and resid 872 through 890 Processing helix chain 'e' and resid 896 through 925 Processing helix chain 'e' and resid 987 through 992 removed outlier: 3.816A pdb=" N UNK e 990 " --> pdb=" O UNK e 987 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N UNK e 992 " --> pdb=" O UNK e 989 " (cutoff:3.500A) Processing helix chain 'e' and resid 994 through 997 removed outlier: 3.625A pdb=" N UNK e 997 " --> pdb=" O UNK e 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 994 through 997' Processing helix chain 'e' and resid 999 through 1002 removed outlier: 3.762A pdb=" N UNK e1002 " --> pdb=" O UNK e 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 999 through 1002' Processing helix chain 'e' and resid 1032 through 1050 removed outlier: 4.131A pdb=" N SER e1036 " --> pdb=" O LEU e1033 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR e1037 " --> pdb=" O GLU e1034 " (cutoff:3.500A) Processing helix chain 'f' and resid 27 through 42 Proline residue: f 39 - end of helix Processing helix chain 'f' and resid 50 through 56 Processing helix chain 'f' and resid 59 through 69 Processing helix chain 'f' and resid 131 through 133 No H-bonds generated for 'chain 'f' and resid 131 through 133' Processing helix chain 'f' and resid 145 through 156 Processing helix chain 'f' and resid 158 through 166 Processing helix chain 'f' and resid 179 through 197 Processing helix chain 'f' and resid 211 through 222 removed outlier: 4.334A pdb=" N TYR f 221 " --> pdb=" O ALA f 217 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU f 222 " --> pdb=" O LYS f 218 " (cutoff:3.500A) Processing helix chain 'f' and resid 233 through 235 No H-bonds generated for 'chain 'f' and resid 233 through 235' Processing helix chain 'f' and resid 239 through 260 removed outlier: 3.587A pdb=" N VAL f 259 " --> pdb=" O GLU f 255 " (cutoff:3.500A) Processing helix chain 'f' and resid 271 through 293 Processing helix chain 'f' and resid 295 through 306 removed outlier: 3.576A pdb=" N LEU f 301 " --> pdb=" O VAL f 297 " (cutoff:3.500A) Processing helix chain 'f' and resid 310 through 318 Processing helix chain 'f' and resid 322 through 333 Processing helix chain 'f' and resid 340 through 345 Processing helix chain 'f' and resid 350 through 365 removed outlier: 3.766A pdb=" N ARG f 365 " --> pdb=" O PHE f 361 " (cutoff:3.500A) Processing helix chain 'f' and resid 374 through 398 removed outlier: 4.472A pdb=" N THR f 398 " --> pdb=" O LYS f 394 " (cutoff:3.500A) Processing helix chain 'f' and resid 406 through 440 Processing helix chain 'f' and resid 455 through 482 removed outlier: 3.920A pdb=" N ARG f 482 " --> pdb=" O ALA f 478 " (cutoff:3.500A) Processing helix chain 'f' and resid 519 through 533 Processing helix chain 'f' and resid 542 through 574 removed outlier: 4.277A pdb=" N GLU f 555 " --> pdb=" O LYS f 551 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG f 563 " --> pdb=" O ARG f 559 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU f 572 " --> pdb=" O LEU f 568 " (cutoff:3.500A) Processing helix chain 'f' and resid 578 through 587 Processing helix chain 'f' and resid 590 through 593 removed outlier: 3.642A pdb=" N VAL f 593 " --> pdb=" O ALA f 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 590 through 593' Processing helix chain 'f' and resid 597 through 624 removed outlier: 4.417A pdb=" N THR f 606 " --> pdb=" O ARG f 602 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN f 607 " --> pdb=" O GLU f 603 " (cutoff:3.500A) Processing helix chain 'f' and resid 631 through 638 Processing helix chain 'f' and resid 643 through 669 removed outlier: 3.529A pdb=" N LEU f 669 " --> pdb=" O VAL f 665 " (cutoff:3.500A) Processing helix chain 'f' and resid 679 through 692 removed outlier: 3.541A pdb=" N GLN f 684 " --> pdb=" O GLN f 680 " (cutoff:3.500A) Processing helix chain 'f' and resid 696 through 708 Processing helix chain 'f' and resid 742 through 755 Processing helix chain 'f' and resid 762 through 796 removed outlier: 3.891A pdb=" N LEU f 774 " --> pdb=" O GLN f 770 " (cutoff:3.500A) Proline residue: f 776 - end of helix Processing helix chain 'f' and resid 801 through 821 removed outlier: 5.419A pdb=" N GLY f 807 " --> pdb=" O LEU f 803 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU f 808 " --> pdb=" O LEU f 804 " (cutoff:3.500A) Processing helix chain 'f' and resid 830 through 862 Processing helix chain 'f' and resid 871 through 890 Processing helix chain 'f' and resid 896 through 925 Processing helix chain 'f' and resid 985 through 1005 removed outlier: 3.778A pdb=" N UNK f 988 " --> pdb=" O UNK f 985 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N UNK f1003 " --> pdb=" O UNK f1000 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N UNK f1005 " --> pdb=" O UNK f1002 " (cutoff:3.500A) Processing helix chain 'f' and resid 1036 through 1052 removed outlier: 4.036A pdb=" N SER f1045 " --> pdb=" O MET f1041 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU f1048 " --> pdb=" O VAL f1044 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 192 Processing helix chain 'g' and resid 194 through 209 removed outlier: 3.577A pdb=" N LEU g 197 " --> pdb=" O GLU g 194 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER g 198 " --> pdb=" O GLU g 195 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG g 205 " --> pdb=" O HIS g 202 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE g 206 " --> pdb=" O SER g 203 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL g 207 " --> pdb=" O THR g 204 " (cutoff:3.500A) Processing helix chain 'g' and resid 582 through 595 Processing helix chain 'h' and resid 194 through 210 Processing helix chain 'h' and resid 584 through 593 Processing helix chain 'i' and resid 67 through 74 removed outlier: 3.618A pdb=" N LEU i 74 " --> pdb=" O LEU i 70 " (cutoff:3.500A) Processing helix chain 'i' and resid 116 through 122 Processing helix chain 'i' and resid 128 through 130 No H-bonds generated for 'chain 'i' and resid 128 through 130' Processing helix chain 'i' and resid 142 through 163 removed outlier: 4.143A pdb=" N GLN i 150 " --> pdb=" O MET i 146 " (cutoff:3.500A) Processing helix chain 'i' and resid 169 through 185 removed outlier: 3.792A pdb=" N LYS i 176 " --> pdb=" O GLU i 172 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP i 183 " --> pdb=" O LYS i 179 " (cutoff:3.500A) Processing helix chain 'i' and resid 237 through 243 Processing helix chain 'i' and resid 248 through 264 Processing helix chain 'i' and resid 280 through 287 Processing helix chain 'i' and resid 319 through 323 Processing helix chain 'i' and resid 335 through 339 Processing helix chain 'i' and resid 363 through 372 Processing helix chain 'j' and resid 67 through 74 Processing helix chain 'j' and resid 116 through 120 Processing helix chain 'j' and resid 142 through 163 removed outlier: 3.718A pdb=" N GLU j 147 " --> pdb=" O TRP j 143 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLN j 150 " --> pdb=" O MET j 146 " (cutoff:3.500A) Processing helix chain 'j' and resid 169 through 183 removed outlier: 4.726A pdb=" N LYS j 176 " --> pdb=" O GLU j 172 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP j 183 " --> pdb=" O LYS j 179 " (cutoff:3.500A) Processing helix chain 'j' and resid 237 through 243 Processing helix chain 'j' and resid 248 through 265 removed outlier: 3.776A pdb=" N ILE j 254 " --> pdb=" O HIS j 250 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN j 255 " --> pdb=" O LEU j 251 " (cutoff:3.500A) Processing helix chain 'j' and resid 280 through 288 Processing helix chain 'j' and resid 319 through 323 Processing helix chain 'j' and resid 336 through 339 No H-bonds generated for 'chain 'j' and resid 336 through 339' Processing helix chain 'j' and resid 362 through 372 Processing helix chain 'k' and resid 5 through 12 Processing helix chain 'k' and resid 36 through 60 removed outlier: 4.060A pdb=" N TYR k 42 " --> pdb=" O THR k 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 12 Processing helix chain 'l' and resid 36 through 60 Processing helix chain 'm' and resid 27 through 40 Proline residue: m 39 - end of helix Processing helix chain 'm' and resid 50 through 56 Processing helix chain 'm' and resid 59 through 69 Processing helix chain 'm' and resid 132 through 134 No H-bonds generated for 'chain 'm' and resid 132 through 134' Processing helix chain 'm' and resid 145 through 165 removed outlier: 4.505A pdb=" N ALA m 158 " --> pdb=" O SER m 154 " (cutoff:3.500A) Proline residue: m 159 - end of helix Processing helix chain 'm' and resid 179 through 197 Processing helix chain 'm' and resid 211 through 222 Processing helix chain 'm' and resid 229 through 232 Processing helix chain 'm' and resid 239 through 260 removed outlier: 3.700A pdb=" N VAL m 259 " --> pdb=" O GLU m 255 " (cutoff:3.500A) Processing helix chain 'm' and resid 271 through 292 Processing helix chain 'm' and resid 295 through 306 Processing helix chain 'm' and resid 310 through 318 Processing helix chain 'm' and resid 322 through 336 removed outlier: 3.518A pdb=" N GLU m 327 " --> pdb=" O LYS m 323 " (cutoff:3.500A) Proline residue: m 334 - end of helix Processing helix chain 'm' and resid 341 through 343 No H-bonds generated for 'chain 'm' and resid 341 through 343' Processing helix chain 'm' and resid 350 through 369 removed outlier: 4.303A pdb=" N LYS m 366 " --> pdb=" O THR m 362 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE m 367 " --> pdb=" O HIS m 363 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG m 368 " --> pdb=" O LEU m 364 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ASN m 369 " --> pdb=" O ARG m 365 " (cutoff:3.500A) Processing helix chain 'm' and resid 374 through 399 Processing helix chain 'm' and resid 406 through 441 removed outlier: 3.856A pdb=" N ARG m 440 " --> pdb=" O ASP m 436 " (cutoff:3.500A) Processing helix chain 'm' and resid 455 through 481 removed outlier: 4.227A pdb=" N LYS m 458 " --> pdb=" O ALA m 455 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG m 471 " --> pdb=" O LYS m 468 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN m 472 " --> pdb=" O PHE m 469 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS m 473 " --> pdb=" O ARG m 470 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU m 474 " --> pdb=" O ARG m 471 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG m 477 " --> pdb=" O GLU m 474 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL m 481 " --> pdb=" O ALA m 478 " (cutoff:3.500A) Processing helix chain 'm' and resid 520 through 533 Processing helix chain 'm' and resid 540 through 573 removed outlier: 5.863A pdb=" N ALA m 548 " --> pdb=" O GLU m 544 " (cutoff:3.500A) Processing helix chain 'm' and resid 578 through 585 Processing helix chain 'm' and resid 595 through 624 removed outlier: 4.994A pdb=" N ALA m 600 " --> pdb=" O HIS m 596 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE m 601 " --> pdb=" O ILE m 597 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ARG m 602 " --> pdb=" O ARG m 598 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU m 603 " --> pdb=" O GLY m 599 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR m 604 " --> pdb=" O ALA m 600 " (cutoff:3.500A) Processing helix chain 'm' and resid 631 through 638 Processing helix chain 'm' and resid 643 through 669 Processing helix chain 'm' and resid 679 through 693 removed outlier: 3.774A pdb=" N LEU m 693 " --> pdb=" O PHE m 689 " (cutoff:3.500A) Processing helix chain 'm' and resid 695 through 710 removed outlier: 3.710A pdb=" N ASP m 701 " --> pdb=" O ILE m 698 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP m 702 " --> pdb=" O PHE m 699 " (cutoff:3.500A) Processing helix chain 'm' and resid 743 through 756 removed outlier: 4.188A pdb=" N LYS m 748 " --> pdb=" O ILE m 744 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS m 754 " --> pdb=" O VAL m 750 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP m 755 " --> pdb=" O ARG m 751 " (cutoff:3.500A) Processing helix chain 'm' and resid 762 through 772 removed outlier: 3.882A pdb=" N ALA m 771 " --> pdb=" O LYS m 767 " (cutoff:3.500A) Processing helix chain 'm' and resid 775 through 795 Processing helix chain 'm' and resid 799 through 821 removed outlier: 3.539A pdb=" N ALA m 806 " --> pdb=" O SER m 802 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY m 807 " --> pdb=" O LEU m 803 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU m 808 " --> pdb=" O LEU m 804 " (cutoff:3.500A) Processing helix chain 'm' and resid 829 through 865 removed outlier: 4.816A pdb=" N GLU m 865 " --> pdb=" O VAL m 861 " (cutoff:3.500A) Processing helix chain 'm' and resid 872 through 889 Processing helix chain 'm' and resid 896 through 925 Processing helix chain 'm' and resid 985 through 996 removed outlier: 4.032A pdb=" N UNK m 988 " --> pdb=" O UNK m 985 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N UNK m 989 " --> pdb=" O UNK m 986 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N UNK m 990 " --> pdb=" O UNK m 987 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK m 992 " --> pdb=" O UNK m 989 " (cutoff:3.500A) Processing helix chain 'm' and resid 998 through 1002 Processing helix chain 'm' and resid 1036 through 1050 removed outlier: 5.391A pdb=" N VAL m1044 " --> pdb=" O VAL m1040 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER m1045 " --> pdb=" O MET m1041 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR m1050 " --> pdb=" O GLU m1046 " (cutoff:3.500A) Processing helix chain 'n' and resid 27 through 42 Proline residue: n 39 - end of helix Processing helix chain 'n' and resid 50 through 56 Processing helix chain 'n' and resid 59 through 70 Processing helix chain 'n' and resid 131 through 134 Processing helix chain 'n' and resid 145 through 156 Processing helix chain 'n' and resid 158 through 166 Processing helix chain 'n' and resid 179 through 198 removed outlier: 3.621A pdb=" N LEU n 194 " --> pdb=" O GLU n 190 " (cutoff:3.500A) Processing helix chain 'n' and resid 211 through 221 Processing helix chain 'n' and resid 229 through 231 No H-bonds generated for 'chain 'n' and resid 229 through 231' Processing helix chain 'n' and resid 233 through 235 No H-bonds generated for 'chain 'n' and resid 233 through 235' Processing helix chain 'n' and resid 239 through 260 removed outlier: 3.941A pdb=" N VAL n 259 " --> pdb=" O GLU n 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 271 through 292 Processing helix chain 'n' and resid 295 through 306 Processing helix chain 'n' and resid 310 through 318 removed outlier: 4.056A pdb=" N ASP n 317 " --> pdb=" O THR n 313 " (cutoff:3.500A) Processing helix chain 'n' and resid 322 through 331 Processing helix chain 'n' and resid 333 through 336 No H-bonds generated for 'chain 'n' and resid 333 through 336' Processing helix chain 'n' and resid 340 through 345 Processing helix chain 'n' and resid 350 through 367 removed outlier: 4.861A pdb=" N LYS n 366 " --> pdb=" O THR n 362 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE n 367 " --> pdb=" O HIS n 363 " (cutoff:3.500A) Processing helix chain 'n' and resid 374 through 399 Processing helix chain 'n' and resid 406 through 441 Processing helix chain 'n' and resid 457 through 479 removed outlier: 4.410A pdb=" N ARG n 462 " --> pdb=" O LYS n 458 " (cutoff:3.500A) Processing helix chain 'n' and resid 519 through 531 Processing helix chain 'n' and resid 539 through 560 removed outlier: 5.768A pdb=" N ALA n 548 " --> pdb=" O GLU n 544 " (cutoff:3.500A) Processing helix chain 'n' and resid 562 through 573 removed outlier: 4.257A pdb=" N ALA n 566 " --> pdb=" O THR n 562 " (cutoff:3.500A) Processing helix chain 'n' and resid 578 through 588 removed outlier: 4.311A pdb=" N PHE n 588 " --> pdb=" O ILE n 584 " (cutoff:3.500A) Processing helix chain 'n' and resid 591 through 593 No H-bonds generated for 'chain 'n' and resid 591 through 593' Processing helix chain 'n' and resid 595 through 624 removed outlier: 5.647A pdb=" N GLU n 603 " --> pdb=" O GLY n 599 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR n 604 " --> pdb=" O ALA n 600 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN n 607 " --> pdb=" O GLU n 603 " (cutoff:3.500A) Processing helix chain 'n' and resid 631 through 638 Processing helix chain 'n' and resid 647 through 668 Processing helix chain 'n' and resid 672 through 675 No H-bonds generated for 'chain 'n' and resid 672 through 675' Processing helix chain 'n' and resid 677 through 693 removed outlier: 3.809A pdb=" N SER n 688 " --> pdb=" O GLN n 684 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE n 689 " --> pdb=" O ASP n 685 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS n 692 " --> pdb=" O SER n 688 " (cutoff:3.500A) Processing helix chain 'n' and resid 697 through 713 removed outlier: 5.550A pdb=" N LEU n 711 " --> pdb=" O GLN n 707 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY n 712 " --> pdb=" O GLN n 708 " (cutoff:3.500A) Processing helix chain 'n' and resid 742 through 755 Processing helix chain 'n' and resid 762 through 796 removed outlier: 3.846A pdb=" N GLN n 773 " --> pdb=" O HIS n 769 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU n 774 " --> pdb=" O GLN n 770 " (cutoff:3.500A) Proline residue: n 776 - end of helix Processing helix chain 'n' and resid 799 through 821 removed outlier: 3.536A pdb=" N LEU n 803 " --> pdb=" O ASN n 799 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU n 804 " --> pdb=" O THR n 800 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY n 807 " --> pdb=" O LEU n 803 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU n 808 " --> pdb=" O LEU n 804 " (cutoff:3.500A) Processing helix chain 'n' and resid 828 through 861 removed outlier: 3.528A pdb=" N TYR n 832 " --> pdb=" O LYS n 828 " (cutoff:3.500A) Processing helix chain 'n' and resid 872 through 890 Processing helix chain 'n' and resid 896 through 925 Processing helix chain 'n' and resid 985 through 998 removed outlier: 3.990A pdb=" N UNK n 988 " --> pdb=" O UNK n 985 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK n 989 " --> pdb=" O UNK n 986 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N UNK n 990 " --> pdb=" O UNK n 987 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N UNK n 993 " --> pdb=" O UNK n 990 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N UNK n 994 " --> pdb=" O UNK n 991 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N UNK n 997 " --> pdb=" O UNK n 994 " (cutoff:3.500A) Processing helix chain 'n' and resid 1001 through 1003 No H-bonds generated for 'chain 'n' and resid 1001 through 1003' Processing helix chain 'n' and resid 1032 through 1034 No H-bonds generated for 'chain 'n' and resid 1032 through 1034' Processing helix chain 'n' and resid 1036 through 1049 removed outlier: 3.878A pdb=" N VAL n1044 " --> pdb=" O VAL n1040 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER n1045 " --> pdb=" O MET n1041 " (cutoff:3.500A) Processing helix chain 'o' and resid 184 through 191 Processing helix chain 'o' and resid 196 through 211 Processing helix chain 'o' and resid 277 through 279 No H-bonds generated for 'chain 'o' and resid 277 through 279' Processing helix chain 'o' and resid 582 through 595 Processing helix chain 'p' and resid 187 through 191 removed outlier: 3.946A pdb=" N LEU p 191 " --> pdb=" O LYS p 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 187 through 191' Processing helix chain 'p' and resid 196 through 210 Processing helix chain 'p' and resid 277 through 279 No H-bonds generated for 'chain 'p' and resid 277 through 279' Processing helix chain 'p' and resid 584 through 594 Processing helix chain 'q' and resid 67 through 74 Processing helix chain 'q' and resid 116 through 120 Processing helix chain 'q' and resid 128 through 130 No H-bonds generated for 'chain 'q' and resid 128 through 130' Processing helix chain 'q' and resid 139 through 160 Proline residue: q 142 - end of helix removed outlier: 3.856A pdb=" N GLU q 147 " --> pdb=" O THR q 144 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER q 148 " --> pdb=" O VAL q 145 " (cutoff:3.500A) Processing helix chain 'q' and resid 168 through 185 removed outlier: 4.049A pdb=" N LYS q 176 " --> pdb=" O GLU q 172 " (cutoff:3.500A) Processing helix chain 'q' and resid 237 through 243 Processing helix chain 'q' and resid 248 through 264 Processing helix chain 'q' and resid 280 through 287 Processing helix chain 'q' and resid 319 through 325 removed outlier: 3.690A pdb=" N GLU q 325 " --> pdb=" O ALA q 321 " (cutoff:3.500A) Processing helix chain 'q' and resid 335 through 339 Processing helix chain 'q' and resid 362 through 372 Processing helix chain 'r' and resid 67 through 74 Processing helix chain 'r' and resid 116 through 122 Processing helix chain 'r' and resid 128 through 130 No H-bonds generated for 'chain 'r' and resid 128 through 130' Processing helix chain 'r' and resid 142 through 162 removed outlier: 3.871A pdb=" N GLN r 150 " --> pdb=" O MET r 146 " (cutoff:3.500A) Processing helix chain 'r' and resid 168 through 186 removed outlier: 4.005A pdb=" N LYS r 176 " --> pdb=" O GLU r 172 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU r 186 " --> pdb=" O GLN r 182 " (cutoff:3.500A) Processing helix chain 'r' and resid 237 through 243 Processing helix chain 'r' and resid 248 through 265 Processing helix chain 'r' and resid 280 through 287 removed outlier: 3.792A pdb=" N TYR r 284 " --> pdb=" O LEU r 280 " (cutoff:3.500A) Processing helix chain 'r' and resid 319 through 325 removed outlier: 3.549A pdb=" N GLU r 325 " --> pdb=" O ALA r 321 " (cutoff:3.500A) Processing helix chain 'r' and resid 336 through 339 No H-bonds generated for 'chain 'r' and resid 336 through 339' Processing helix chain 'r' and resid 362 through 372 removed outlier: 4.785A pdb=" N LEU r 370 " --> pdb=" O GLN r 366 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA r 371 " --> pdb=" O GLN r 367 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS r 372 " --> pdb=" O SER r 368 " (cutoff:3.500A) Processing helix chain 's' and resid 4 through 10 Processing helix chain 's' and resid 36 through 60 removed outlier: 4.395A pdb=" N TYR s 42 " --> pdb=" O THR s 38 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 12 Processing helix chain 't' and resid 36 through 60 removed outlier: 4.042A pdb=" N GLN t 41 " --> pdb=" O PRO t 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR t 42 " --> pdb=" O THR t 38 " (cutoff:3.500A) Processing helix chain 'x' and resid 106 through 389 removed outlier: 4.101A pdb=" N ALA x 256 " --> pdb=" O GLU x 252 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU x 257 " --> pdb=" O SER x 253 " (cutoff:3.500A) Processing helix chain 'z' and resid 1003 through 1040 Processing sheet with id= A, first strand: chain 'A' and resid 136 through 141 removed outlier: 6.560A pdb=" N VAL A 12 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR A 111 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE A 14 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 35 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 33 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 39 through 42 removed outlier: 3.736A pdb=" N ARG A 41 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.632A pdb=" N VAL A 156 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 165 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 183 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 240 through 242 Processing sheet with id= E, first strand: chain 'B' and resid 137 through 140 removed outlier: 6.701A pdb=" N VAL B 108 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER B 140 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 110 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL B 12 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR B 111 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE B 14 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 298 through 301 removed outlier: 6.711A pdb=" N VAL B 156 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N SER B 301 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 158 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 181 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 20 through 23 removed outlier: 4.230A pdb=" N TYR C 33 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 38 through 42 removed outlier: 3.595A pdb=" N ARG C 72 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.552A pdb=" N SER C 140 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 298 through 301 removed outlier: 6.299A pdb=" N VAL C 156 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N SER C 301 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 158 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 170 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 240 through 242 Processing sheet with id= L, first strand: chain 'D' and resid 137 through 139 removed outlier: 6.604A pdb=" N VAL D 108 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL D 12 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 39 through 42 Processing sheet with id= N, first strand: chain 'D' and resid 298 through 301 removed outlier: 5.995A pdb=" N VAL D 156 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER D 301 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU D 158 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 240 through 242 Processing sheet with id= P, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.930A pdb=" N ARG E 41 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 108 through 111 Processing sheet with id= R, first strand: chain 'E' and resid 329 through 331 removed outlier: 5.606A pdb=" N VAL E 156 " --> pdb=" O VAL E 299 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.489A pdb=" N VAL F 108 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N SER F 140 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU F 110 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL F 12 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR F 111 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE F 14 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 39 through 42 removed outlier: 3.583A pdb=" N ARG F 41 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 298 through 301 removed outlier: 5.680A pdb=" N VAL F 156 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER F 301 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU F 158 " --> pdb=" O SER F 301 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 240 through 242 Processing sheet with id= W, first strand: chain 'G' and resid 12 through 14 Processing sheet with id= X, first strand: chain 'G' and resid 20 through 23 removed outlier: 4.062A pdb=" N PHE G 35 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR G 33 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 38 through 42 removed outlier: 3.628A pdb=" N ARG G 41 " --> pdb=" O SER G 70 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 298 through 301 removed outlier: 5.727A pdb=" N VAL G 156 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER G 301 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU G 158 " --> pdb=" O SER G 301 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 240 through 242 Processing sheet with id= AB, first strand: chain 'H' and resid 17 through 21 removed outlier: 7.595A pdb=" N VAL H 10 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU H 104 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN H 12 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N THR H 106 " --> pdb=" O ASN H 12 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 34 through 37 removed outlier: 3.525A pdb=" N VAL H 35 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 297 through 299 removed outlier: 6.184A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= AF, first strand: chain 'I' and resid 12 through 14 removed outlier: 3.869A pdb=" N THR I 111 " --> pdb=" O ILE I 14 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE I 138 " --> pdb=" O VAL I 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 20 through 23 removed outlier: 3.687A pdb=" N PHE I 35 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR I 33 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 39 through 41 Processing sheet with id= AI, first strand: chain 'I' and resid 298 through 300 removed outlier: 5.707A pdb=" N VAL I 156 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL I 157 " --> pdb=" O VAL I 168 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP I 159 " --> pdb=" O HIS I 166 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS I 166 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 240 through 242 Processing sheet with id= AK, first strand: chain 'J' and resid 88 through 92 Processing sheet with id= AL, first strand: chain 'J' and resid 303 through 307 removed outlier: 5.920A pdb=" N MET J 137 " --> pdb=" O VAL J 304 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE J 306 " --> pdb=" O MET J 137 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU J 139 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL J 138 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU J 164 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY J 162 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 87 through 89 removed outlier: 3.503A pdb=" N ILE K 94 " --> pdb=" O ASP K 89 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 97 through 99 removed outlier: 3.766A pdb=" N GLU K 104 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 140 through 148 removed outlier: 4.137A pdb=" N GLN K 152 " --> pdb=" O ILE K 181 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN K 195 " --> pdb=" O ARG K 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS K 178 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL K 189 " --> pdb=" O LYS K 178 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR K 180 " --> pdb=" O GLN K 187 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN K 187 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 192 " --> pdb=" O LYS K 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS K 210 " --> pdb=" O LEU K 192 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 71 through 73 removed outlier: 3.748A pdb=" N LYS L 78 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'L' and resid 116 through 124 removed outlier: 3.695A pdb=" N GLY L 127 " --> pdb=" O LEU L 124 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 24 through 27 Processing sheet with id= AS, first strand: chain 'P' and resid 25 through 27 removed outlier: 3.675A pdb=" N UNK P 74 " --> pdb=" O UNK P 67 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'U' and resid 33 through 35 removed outlier: 6.774A pdb=" N ASN U 54 " --> pdb=" O VAL U 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'U' and resid 61 through 63 Processing sheet with id= AV, first strand: chain 'U' and resid 105 through 107 removed outlier: 5.951A pdb=" N CYS U 123 " --> pdb=" O VAL U 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'V' and resid 102 through 104 removed outlier: 6.822A pdb=" N CYS V 120 " --> pdb=" O GLN V 103 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'V' and resid 144 through 147 removed outlier: 5.889A pdb=" N SER V 147 " --> pdb=" O PHE V 153 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE V 153 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Y' and resid 513 through 516 removed outlier: 3.571A pdb=" N UNK Y 513 " --> pdb=" O UNK Y 529 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'e' and resid 78 through 82 Processing sheet with id= BA, first strand: chain 'e' and resid 117 through 120 Processing sheet with id= BB, first strand: chain 'f' and resid 98 through 104 removed outlier: 3.615A pdb=" N LEU f 84 " --> pdb=" O PHE f 98 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN f 114 " --> pdb=" O ARG f 81 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'g' and resid 286 through 289 removed outlier: 3.789A pdb=" N TYR g 301 " --> pdb=" O VAL g 289 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'g' and resid 321 through 324 Processing sheet with id= BE, first strand: chain 'g' and resid 455 through 458 Processing sheet with id= BF, first strand: chain 'g' and resid 514 through 516 removed outlier: 4.018A pdb=" N LEU g 525 " --> pdb=" O ALA g 537 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA g 537 " --> pdb=" O LEU g 525 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'g' and resid 549 through 552 Processing sheet with id= BH, first strand: chain 'g' and resid 254 through 261 removed outlier: 7.096A pdb=" N SER g 272 " --> pdb=" O SER g 257 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU g 259 " --> pdb=" O VAL g 270 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL g 270 " --> pdb=" O LEU g 259 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'g' and resid 358 through 362 removed outlier: 6.893A pdb=" N ILE g 375 " --> pdb=" O TYR g 359 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL g 361 " --> pdb=" O ILE g 373 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE g 373 " --> pdb=" O VAL g 361 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'h' and resid 286 through 289 removed outlier: 4.036A pdb=" N TYR h 301 " --> pdb=" O VAL h 289 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'h' and resid 311 through 314 removed outlier: 3.726A pdb=" N SER h 311 " --> pdb=" O GLY h 325 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR h 313 " --> pdb=" O VAL h 323 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'h' and resid 394 through 397 removed outlier: 4.194A pdb=" N LYS h 380 " --> pdb=" O SER h 376 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N CYS h 360 " --> pdb=" O ILE h 375 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'h' and resid 421 through 423 removed outlier: 3.936A pdb=" N THR h 432 " --> pdb=" O GLU h 444 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU h 444 " --> pdb=" O THR h 432 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS h 434 " --> pdb=" O ILE h 442 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE h 442 " --> pdb=" O CYS h 434 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'h' and resid 504 through 506 removed outlier: 3.862A pdb=" N MET h 505 " --> pdb=" O ALA h 515 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA h 515 " --> pdb=" O MET h 505 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS h 516 " --> pdb=" O ASP h 524 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP h 524 " --> pdb=" O CYS h 516 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'h' and resid 549 through 552 Processing sheet with id= BP, first strand: chain 'h' and resid 453 through 457 removed outlier: 6.484A pdb=" N SER h 474 " --> pdb=" O THR h 454 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE h 456 " --> pdb=" O VAL h 472 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL h 472 " --> pdb=" O ILE h 456 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'i' and resid 56 through 61 removed outlier: 5.755A pdb=" N ASN i 105 " --> pdb=" O ILE i 57 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL i 59 " --> pdb=" O ASN i 105 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TRP i 107 " --> pdb=" O VAL i 59 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY i 61 " --> pdb=" O TRP i 107 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU i 109 " --> pdb=" O GLY i 61 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'i' and resid 134 through 138 removed outlier: 7.596A pdb=" N LEU i 228 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N ALA i 137 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL i 230 " --> pdb=" O ALA i 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'j' and resid 56 through 60 Processing sheet with id= BT, first strand: chain 'j' and resid 89 through 93 removed outlier: 3.947A pdb=" N VAL j 93 " --> pdb=" O THR j 102 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR j 102 " --> pdb=" O VAL j 93 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'k' and resid 19 through 21 removed outlier: 3.594A pdb=" N ILE k 21 " --> pdb=" O ILE k 89 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE k 89 " --> pdb=" O ILE k 21 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'l' and resid 69 through 72 Processing sheet with id= BW, first strand: chain 'm' and resid 98 through 104 Processing sheet with id= BX, first strand: chain 'n' and resid 78 through 82 Processing sheet with id= BY, first strand: chain 'n' and resid 115 through 120 Processing sheet with id= BZ, first strand: chain 'n' and resid 722 through 725 Processing sheet with id= CA, first strand: chain 'o' and resid 243 through 245 Processing sheet with id= CB, first strand: chain 'o' and resid 286 through 290 removed outlier: 3.620A pdb=" N VAL o 286 " --> pdb=" O TYR o 273 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP o 290 " --> pdb=" O LEU o 269 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU o 269 " --> pdb=" O TRP o 290 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP o 260 " --> pdb=" O VAL o 270 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER o 272 " --> pdb=" O CYS o 258 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS o 258 " --> pdb=" O SER o 272 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'o' and resid 321 through 325 Processing sheet with id= CD, first strand: chain 'o' and resid 362 through 365 removed outlier: 3.585A pdb=" N LEU o 372 " --> pdb=" O TRP o 384 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER o 374 " --> pdb=" O CYS o 382 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'o' and resid 411 through 413 Processing sheet with id= CF, first strand: chain 'o' and resid 470 through 472 Processing sheet with id= CG, first strand: chain 'o' and resid 504 through 506 Processing sheet with id= CH, first strand: chain 'o' and resid 522 through 524 Processing sheet with id= CI, first strand: chain 'p' and resid 287 through 289 removed outlier: 3.715A pdb=" N VAL p 289 " --> pdb=" O TYR p 301 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR p 301 " --> pdb=" O VAL p 289 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'p' and resid 323 through 325 Processing sheet with id= CK, first strand: chain 'p' and resid 381 through 384 Processing sheet with id= CL, first strand: chain 'p' and resid 420 through 423 Processing sheet with id= CM, first strand: chain 'p' and resid 455 through 457 Processing sheet with id= CN, first strand: chain 'p' and resid 504 through 506 Processing sheet with id= CO, first strand: chain 'p' and resid 549 through 552 removed outlier: 3.522A pdb=" N VAL p 561 " --> pdb=" O VAL p 569 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'p' and resid 255 through 258 removed outlier: 7.252A pdb=" N SER p 272 " --> pdb=" O SER p 257 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'q' and resid 269 through 271 removed outlier: 8.703A pdb=" N ILE q 270 " --> pdb=" O VAL q 227 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL q 229 " --> pdb=" O ILE q 270 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU q 228 " --> pdb=" O VAL q 133 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE q 135 " --> pdb=" O LEU q 228 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA q 137 " --> pdb=" O VAL q 230 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR q 232 " --> pdb=" O ALA q 137 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASN q 56 " --> pdb=" O LEU q 132 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ILE q 134 " --> pdb=" O ASN q 56 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU q 58 " --> pdb=" O ILE q 134 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL q 136 " --> pdb=" O LEU q 58 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE q 60 " --> pdb=" O VAL q 136 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASP q 138 " --> pdb=" O PHE q 60 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASN q 105 " --> pdb=" O ILE q 57 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL q 59 " --> pdb=" O ASN q 105 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TRP q 107 " --> pdb=" O VAL q 59 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY q 61 " --> pdb=" O TRP q 107 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU q 109 " --> pdb=" O GLY q 61 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'r' and resid 226 through 232 removed outlier: 3.533A pdb=" N ALA r 137 " --> pdb=" O VAL r 230 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN r 56 " --> pdb=" O LEU r 132 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE r 134 " --> pdb=" O ASN r 56 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU r 58 " --> pdb=" O ILE r 134 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL r 136 " --> pdb=" O LEU r 58 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE r 60 " --> pdb=" O VAL r 136 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASP r 138 " --> pdb=" O PHE r 60 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ASN r 105 " --> pdb=" O ILE r 57 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL r 59 " --> pdb=" O ASN r 105 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TRP r 107 " --> pdb=" O VAL r 59 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY r 61 " --> pdb=" O TRP r 107 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU r 109 " --> pdb=" O GLY r 61 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 's' and resid 69 through 72 Processing sheet with id= CT, first strand: chain 't' and resid 69 through 72 removed outlier: 3.780A pdb=" N VAL t 90 " --> pdb=" O MET t 79 " (cutoff:3.500A) 5357 hydrogen bonds defined for protein. 15174 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: 39.77 Time building geometry restraints manager: 32.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22985 1.33 - 1.45: 19604 1.45 - 1.57: 51006 1.57 - 1.70: 32 1.70 - 1.82: 391 Bond restraints: 94018 Sorted by residual: bond pdb=" C4 ATP H 401 " pdb=" C5 ATP H 401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.10e+01 bond pdb=" C5 ATP H 401 " pdb=" C6 ATP H 401 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.00e+01 bond pdb=" CA PRO j 343 " pdb=" C PRO j 343 " ideal model delta sigma weight residual 1.517 1.574 -0.057 9.30e-03 1.16e+04 3.71e+01 bond pdb=" CA LYS j 342 " pdb=" C LYS j 342 " ideal model delta sigma weight residual 1.524 1.596 -0.072 1.26e-02 6.30e+03 3.30e+01 bond pdb=" C4 ATP H 401 " pdb=" N9 ATP H 401 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.55e+01 ... (remaining 94013 not shown) Histogram of bond angle deviations from ideal: 93.04 - 102.92: 605 102.92 - 112.80: 51005 112.80 - 122.68: 63963 122.68 - 132.56: 12724 132.56 - 142.44: 147 Bond angle restraints: 128444 Sorted by residual: angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 123.02 16.85 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 121.43 15.40 1.00e+00 1.00e+00 2.37e+02 angle pdb=" C LYS j 342 " pdb=" N PRO j 343 " pdb=" CA PRO j 343 " ideal model delta sigma weight residual 120.38 106.58 13.80 1.03e+00 9.43e-01 1.79e+02 angle pdb=" N GLN p 188 " pdb=" CA GLN p 188 " pdb=" C GLN p 188 " ideal model delta sigma weight residual 111.28 121.15 -9.87 1.09e+00 8.42e-01 8.19e+01 angle pdb=" C PRO j 343 " pdb=" N PRO j 344 " pdb=" CA PRO j 344 " ideal model delta sigma weight residual 119.84 109.56 10.28 1.25e+00 6.40e-01 6.76e+01 ... (remaining 128439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 56129 34.41 - 68.83: 317 68.83 - 103.24: 23 103.24 - 137.66: 12 137.66 - 172.07: 11 Dihedral angle restraints: 56492 sinusoidal: 15681 harmonic: 40811 Sorted by residual: dihedral pdb=" CA UNK Z1038 " pdb=" C UNK Z1038 " pdb=" N UNK Z1039 " pdb=" CA UNK Z1039 " ideal model delta harmonic sigma weight residual 180.00 125.06 54.94 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" C5' ADP J 800 " pdb=" O5' ADP J 800 " pdb=" PA ADP J 800 " pdb=" O2A ADP J 800 " ideal model delta sinusoidal sigma weight residual -60.00 112.07 -172.07 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP D 800 " pdb=" O3A ADP D 800 " pdb=" PA ADP D 800 " pdb=" PB ADP D 800 " ideal model delta sinusoidal sigma weight residual -60.00 108.65 -168.65 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 56489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 14286 0.125 - 0.250: 1108 0.250 - 0.375: 60 0.375 - 0.500: 7 0.500 - 0.625: 4 Chirality restraints: 15465 Sorted by residual: chirality pdb=" CB VAL h 430 " pdb=" CA VAL h 430 " pdb=" CG1 VAL h 430 " pdb=" CG2 VAL h 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.00 -0.62 2.00e-01 2.50e+01 9.76e+00 chirality pdb=" CB ILE G 185 " pdb=" CA ILE G 185 " pdb=" CG1 ILE G 185 " pdb=" CG2 ILE G 185 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" CB ILE C 185 " pdb=" CA ILE C 185 " pdb=" CG1 ILE C 185 " pdb=" CG2 ILE C 185 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.27e+00 ... (remaining 15462 not shown) Planarity restraints: 17188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR n 553 " -0.116 2.00e-02 2.50e+03 6.19e-02 7.65e+01 pdb=" CG TYR n 553 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR n 553 " 0.086 2.00e-02 2.50e+03 pdb=" CD2 TYR n 553 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR n 553 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR n 553 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR n 553 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR n 553 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE o 421 " 0.038 2.00e-02 2.50e+03 5.42e-02 5.14e+01 pdb=" CG PHE o 421 " -0.118 2.00e-02 2.50e+03 pdb=" CD1 PHE o 421 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE o 421 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE o 421 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE o 421 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE o 421 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 38 " 0.037 2.00e-02 2.50e+03 5.07e-02 5.13e+01 pdb=" CG TYR I 38 " -0.118 2.00e-02 2.50e+03 pdb=" CD1 TYR I 38 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR I 38 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR I 38 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR I 38 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR I 38 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR I 38 " -0.002 2.00e-02 2.50e+03 ... (remaining 17185 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 19 2.15 - 2.83: 31584 2.83 - 3.52: 133685 3.52 - 4.21: 210221 4.21 - 4.90: 354030 Nonbonded interactions: 729539 Sorted by model distance: nonbonded pdb=" CA ASP n 558 " pdb=" OE2 GLU n 561 " model vdw 1.456 3.470 nonbonded pdb=" C ASP n 558 " pdb=" OE2 GLU n 561 " model vdw 1.790 3.270 nonbonded pdb=" O ASP n 558 " pdb=" OE2 GLU n 561 " model vdw 1.874 3.040 nonbonded pdb=" O GLU o 208 " pdb=" OH TYR o 294 " model vdw 1.917 2.440 nonbonded pdb=" O ARG n 556 " pdb=" CG2 VAL n 560 " model vdw 1.928 3.460 ... (remaining 729534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'M' selection = (chain 'N' and resid 30 through 818) } ncs_group { reference = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'X' and ((resid 105 through 133 and (name N or name CA or name C or name \ O or name CB )) or resid 134 through 201 or (resid 202 through 283 and (name N o \ r name CA or name C or name O or name CB )) or resid 284 through 389)) selection = (chain 'x' and resid 105 through 389) } ncs_group { reference = chain 'Z' selection = (chain 'z' and resid 1002 through 1053) } ncs_group { reference = (chain 'e' and (resid 21 through 168 or resid 177 through 482 or resid 517 throu \ gh 1053)) selection = (chain 'f' and (resid 21 through 86 or resid 98 through 337 or (resid 338 throug \ h 396 and (name N or name CA or name C or name O or name CB )) or resid 397 or ( \ resid 398 through 482 and (name N or name CA or name C or name O or name CB )) o \ r (resid 517 through 534 and (name N or name CA or name C or name O or name CB ) \ ) or resid 535 or (resid 536 through 541 and (name N or name CA or name C or nam \ e O or name CB )) or resid 542 or (resid 543 through 572 and (name N or name CA \ or name C or name O or name CB )) or resid 573 or (resid 574 through 598 and (na \ me N or name CA or name C or name O or name CB )) or (resid 599 through 645 and \ (name N or name CA or name C or name O or name CB )) or resid 646 or (resid 647 \ through 669 and (name N or name CA or name C or name O or name CB )) or resid 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 or (resid 673 through 678 and (name N or name CA or name C or name O or na \ me CB )) or resid 679 or (resid 680 through 685 and (name N or name CA or name C \ or name O or name CB )) or resid 686 or (resid 687 through 711 and (name N or n \ ame CA or name C or name O or name CB )) or resid 712 or (resid 713 through 714 \ and (name N or name CA or name C or name O or name CB )) or resid 715 or (resid \ 716 through 726 and (name N or name CA or name C or name O or name CB )) or resi \ d 727 or (resid 728 through 729 and (name N or name CA or name C or name O or na \ me CB )) or resid 730 or (resid 731 through 756 and (name N or name CA or name C \ or name O or name CB )) or resid 757 or (resid 758 through 806 and (name N or n \ ame CA or name C or name O or name CB )) or resid 807 or (resid 808 through 818 \ and (name N or name CA or name C or name O or name CB )) or resid 819 or (resid \ 820 through 911 and (name N or name CA or name C or name O or name CB )) or resi \ d 912 or (resid 913 through 917 and (name N or name CA or name C or name O or na \ me CB )) or resid 918 or (resid 919 through 1041 and (name N or name CA or name \ C or name O or name CB )) or resid 1042 or (resid 1043 through 1053 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'm' and (resid 21 through 168 or resid 177 through 337 or (resid 338 thro \ ugh 396 and (name N or name CA or name C or name O or name CB )) or resid 397 or \ (resid 398 through 482 and (name N or name CA or name C or name O or name CB )) \ or (resid 517 through 534 and (name N or name CA or name C or name O or name CB \ )) or resid 535 or (resid 536 through 541 and (name N or name CA or name C or n \ ame O or name CB )) or resid 542 or (resid 543 through 572 and (name N or name C \ A or name C or name O or name CB )) or resid 573 or (resid 574 through 598 and ( \ name N or name CA or name C or name O or name CB )) or (resid 599 through 645 an \ d (name N or name CA or name C or name O or name CB )) or resid 646 or (resid 64 \ 7 through 669 and (name N or name CA or name C or name O or name CB )) or resid \ 670 or (resid 671 and (name N or name CA or name C or name O or name CB )) or re \ sid 672 or (resid 673 through 678 and (name N or name CA or name C or name O or \ name CB )) or resid 679 or (resid 680 through 685 and (name N or name CA or name \ C or name O or name CB )) or resid 686 or (resid 687 through 711 and (name N or \ name CA or name C or name O or name CB )) or (resid 712 through 756 and (name N \ or name CA or name C or name O or name CB )) or resid 757 or (resid 758 through \ 806 and (name N or name CA or name C or name O or name CB )) or resid 807 throu \ gh 1053)) selection = (chain 'n' and (resid 21 through 86 or resid 98 through 337 or (resid 338 throug \ h 396 and (name N or name CA or name C or name O or name CB )) or resid 397 or ( \ resid 398 through 534 and (name N or name CA or name C or name O or name CB )) o \ r resid 535 or (resid 536 through 541 and (name N or name CA or name C or name O \ or name CB )) or resid 542 or (resid 543 through 572 and (name N or name CA or \ name C or name O or name CB )) or resid 573 or (resid 574 through 598 and (name \ N or name CA or name C or name O or name CB )) or resid 599 through 1053)) } ncs_group { reference = (chain 'g' and (resid 182 through 185 or resid 187 through 595)) selection = (chain 'h' and (resid 182 through 217 or (resid 238 through 284 and (name N or n \ ame CA or name C or name O or name CB )) or resid 285 or (resid 286 through 323 \ and (name N or name CA or name C or name O or name CB )) or resid 324 through 32 \ 5 or (resid 326 through 328 and (name N or name CA or name C or name O or name C \ B )) or resid 329 or (resid 330 through 364 and (name N or name CA or name C or \ name O or name CB )) or resid 365 or (resid 366 through 378 and (name N or name \ CA or name C or name O or name CB )) or resid 379 or (resid 380 through 415 and \ (name N or name CA or name C or name O or name CB )) or resid 416 or (resid 417 \ through 423 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 4 or (resid 425 through 427 and (name N or name CA or name C or name O or name C \ B )) or resid 428 or (resid 429 through 436 and (name N or name CA or name C or \ name O or name CB )) or resid 437 or (resid 438 through 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 or (resid 442 through 447 and \ (name N or name CA or name C or name O or name CB )) or resid 448 or (resid 449 \ through 450 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 1 or (resid 452 through 454 and (name N or name CA or name C or name O or name C \ B )) or resid 455 or (resid 456 through 462 and (name N or name CA or name C or \ name O or name CB )) or (resid 463 through 498 and (name N or name CA or name C \ or name O or name CB )) or resid 499 or (resid 500 through 518 and (name N or na \ me CA or name C or name O or name CB )) or resid 519 or (resid 520 and (name N o \ r name CA or name C or name O or name CB )) or resid 521 or (resid 522 through 5 \ 42 and (name N or name CA or name C or name O or name CB )) or resid 543 or (res \ id 544 through 555 and (name N or name CA or name C or name O or name CB )) or r \ esid 556 or (resid 557 through 561 and (name N or name CA or name C or name O or \ name CB )) or resid 562 or (resid 563 through 565 and (name N or name CA or nam \ e C or name O or name CB )) or resid 566 or (resid 567 through 573 and (name N o \ r name CA or name C or name O or name CB )) or resid 574 or (resid 575 through 5 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 589 or (res \ id 590 through 595 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'o' and ((resid 182 through 185 and (name N or name CA or name C or name \ O or name CB )) or (resid 187 through 284 and (name N or name CA or name C or na \ me O or name CB )) or resid 285 or (resid 286 through 323 and (name N or name CA \ or name C or name O or name CB )) or resid 324 through 325 or (resid 326 throug \ h 328 and (name N or name CA or name C or name O or name CB )) or resid 329 or ( \ resid 330 through 364 and (name N or name CA or name C or name O or name CB )) o \ r resid 365 or (resid 366 through 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 or (resid 380 through 415 and (name N or name CA or \ name C or name O or name CB )) or resid 416 or (resid 417 through 423 and (name \ N or name CA or name C or name O or name CB )) or resid 424 or (resid 425 throug \ h 427 and (name N or name CA or name C or name O or name CB )) or resid 428 or ( \ resid 429 through 436 and (name N or name CA or name C or name O or name CB )) o \ r resid 437 or (resid 438 through 440 and (name N or name CA or name C or name O \ or name CB )) or resid 441 or (resid 442 through 447 and (name N or name CA or \ name C or name O or name CB )) or resid 448 or (resid 449 through 450 and (name \ N or name CA or name C or name O or name CB )) or resid 451 or (resid 452 throug \ h 454 and (name N or name CA or name C or name O or name CB )) or resid 455 or ( \ resid 456 through 462 and (name N or name CA or name C or name O or name CB )) o \ r (resid 463 through 498 and (name N or name CA or name C or name O or name CB ) \ ) or resid 499 or (resid 500 through 518 and (name N or name CA or name C or nam \ e O or name CB )) or resid 519 or (resid 520 and (name N or name CA or name C or \ name O or name CB )) or resid 521 or (resid 522 through 542 and (name N or name \ CA or name C or name O or name CB )) or resid 543 or (resid 544 through 555 and \ (name N or name CA or name C or name O or name CB )) or resid 556 or (resid 557 \ through 561 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 62 or (resid 563 through 565 and (name N or name CA or name C or name O or name \ CB )) or resid 566 or (resid 567 through 573 and (name N or name CA or name C or \ name O or name CB )) or resid 574 or (resid 575 through 588 and (name N or name \ CA or name C or name O or name CB )) or resid 589 or (resid 590 through 595 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'p' and ((resid 182 through 185 and (name N or name CA or name C or name \ O or name CB )) or (resid 187 through 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 238 through 595)) } ncs_group { reference = chain 'i' selection = (chain 'j' and ((resid 52 through 53 and (name N or name CA or name C or name O \ or name CB )) or resid 54 or (resid 55 through 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 or (resid 62 through 63 and (name N or na \ me CA or name C or name O or name CB )) or resid 64 or (resid 65 and (name N or \ name CA or name C or name O or name CB )) or resid 66 or (resid 67 through 79 an \ d (name N or name CA or name C or name O or name CB )) or (resid 80 through 110 \ and (name N or name CA or name C or name O or name CB )) or resid 111 or (resid \ 112 through 116 and (name N or name CA or name C or name O or name CB )) or resi \ d 117 or (resid 118 through 189 and (name N or name CA or name C or name O or na \ me CB )) or resid 190 or (resid 216 through 223 and (name N or name CA or name C \ or name O or name CB )) or resid 224 or (resid 225 through 265 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 266 through 312 and (name N o \ r name CA or name C or name O or name CB )) or resid 313 or (resid 314 through 3 \ 41 and (name N or name CA or name C or name O or name CB )) or (resid 362 throug \ h 373 and (name N or name CA or name C or name O or name CB )))) selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'k' selection = chain 'l' selection = (chain 's' and ((resid 3 through 15 and (name N or name CA or name C or name O o \ r name CB )) or resid 16 or (resid 17 through 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 26 and (name N or nam \ e CA or name C or name O or name CB )) or resid 27 or (resid 28 through 95 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 't' and ((resid 3 through 15 and (name N or name CA or name C or name O o \ r name CB )) or resid 16 or (resid 17 through 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 26 and (name N or nam \ e CA or name C or name O or name CB )) or resid 27 or (resid 28 through 95 and ( \ name N or name CA or name C or name O or name CB )))) } 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: 15.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 43.500 Check model and map are aligned: 1.010 Set scattering table: 0.650 Process input model: 194.080 Find NCS groups from input model: 5.890 Set up NCS constraints: 0.900 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 263.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 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 : 0.011 0.151 94018 Z= 0.743 Angle : 1.430 22.936 128444 Z= 0.818 Chirality : 0.070 0.625 15465 Planarity : 0.007 0.125 17188 Dihedral : 10.006 172.071 29798 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.79 % Favored : 89.05 % Rotamer: Outliers : 0.44 % Allowed : 4.02 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.06), residues: 11630 helix: -2.04 (0.05), residues: 5425 sheet: -3.20 (0.12), residues: 1327 loop : -3.19 (0.08), residues: 4878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.007 TRP C 357 HIS 0.040 0.005 HIS h 469 PHE 0.118 0.005 PHE o 421 TYR 0.118 0.006 TYR I 38 ARG 0.026 0.002 ARG m 563 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1317 time to evaluate : 7.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 94 TYR cc_start: 0.8016 (m-80) cc_final: 0.7515 (m-80) REVERT: B 181 MET cc_start: 0.7931 (mmm) cc_final: 0.7717 (mmm) REVERT: B 227 ASN cc_start: 0.8387 (m-40) cc_final: 0.8176 (m-40) REVERT: E 256 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8156 (p90) REVERT: E 289 ASP cc_start: 0.6391 (m-30) cc_final: 0.6016 (m-30) REVERT: G 47 VAL cc_start: 0.7704 (t) cc_final: 0.7335 (m) REVERT: G 75 MET cc_start: 0.8071 (ttm) cc_final: 0.7388 (ttm) REVERT: I 75 MET cc_start: 0.5985 (ttm) cc_final: 0.5754 (ttm) REVERT: I 115 LEU cc_start: 0.7018 (mt) cc_final: 0.6723 (mp) REVERT: I 273 GLU cc_start: 0.6126 (mp0) cc_final: 0.5712 (mt-10) REVERT: I 325 ASP cc_start: 0.8895 (m-30) cc_final: 0.8373 (t0) REVERT: I 351 ASP cc_start: 0.8568 (m-30) cc_final: 0.8302 (t0) REVERT: J 120 LEU cc_start: 0.6981 (mt) cc_final: 0.6760 (mt) REVERT: J 225 LYS cc_start: 0.7916 (mttt) cc_final: 0.7694 (tppt) REVERT: J 387 TRP cc_start: 0.5495 (p-90) cc_final: 0.5186 (p-90) REVERT: K 277 TYR cc_start: 0.7111 (p90) cc_final: 0.6737 (p90) REVERT: X 133 GLN cc_start: 0.7567 (mt0) cc_final: 0.7275 (pp30) REVERT: X 139 LYS cc_start: 0.8113 (mttp) cc_final: 0.7884 (mmtt) REVERT: X 147 HIS cc_start: 0.8377 (m-70) cc_final: 0.8045 (m-70) REVERT: X 161 ASN cc_start: 0.7356 (m-40) cc_final: 0.7082 (t0) REVERT: X 178 LYS cc_start: 0.8139 (mttp) cc_final: 0.7735 (ttpp) REVERT: a 5 LYS cc_start: 0.7642 (mptp) cc_final: 0.7416 (pttm) REVERT: a 38 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7702 (tm-30) REVERT: a 49 ILE cc_start: 0.9079 (mp) cc_final: 0.8875 (tp) REVERT: a 58 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8525 (tttt) REVERT: b 48 ILE cc_start: 0.8817 (mt) cc_final: 0.8209 (pt) REVERT: c 1 MET cc_start: 0.5871 (mtt) cc_final: 0.4807 (mmm) REVERT: e 234 ASP cc_start: 0.7441 (m-30) cc_final: 0.7215 (m-30) REVERT: e 238 ASP cc_start: 0.7519 (m-30) cc_final: 0.7238 (t0) REVERT: f 355 GLN cc_start: 0.8224 (mt0) cc_final: 0.7452 (mm110) REVERT: f 635 MET cc_start: 0.6719 (mmm) cc_final: 0.6315 (mmp) REVERT: f 649 ILE cc_start: 0.7754 (mt) cc_final: 0.7457 (pt) REVERT: h 292 MET cc_start: 0.6781 (mmm) cc_final: 0.6179 (tpp) REVERT: j 104 CYS cc_start: 0.4475 (t) cc_final: 0.4268 (m) REVERT: j 158 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7334 (tp30) REVERT: j 164 LYS cc_start: 0.1592 (tmtm) cc_final: 0.1352 (mttp) REVERT: j 176 LYS cc_start: 0.6709 (mmmm) cc_final: 0.6487 (ptpt) REVERT: j 180 ASP cc_start: 0.4492 (m-30) cc_final: 0.4105 (t70) REVERT: m 206 SER cc_start: 0.7975 (m) cc_final: 0.7765 (t) REVERT: m 437 ILE cc_start: 0.8708 (mt) cc_final: 0.8309 (tp) REVERT: m 760 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.6653 (t) REVERT: n 329 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7035 (t) REVERT: p 205 ARG cc_start: 0.2629 (tpm170) cc_final: 0.2225 (mtm180) REVERT: s 34 MET cc_start: 0.1722 (mmt) cc_final: 0.1430 (mpp) REVERT: s 74 LYS cc_start: 0.6864 (ttpt) cc_final: 0.6609 (mmtm) REVERT: s 78 ILE cc_start: 0.5090 (mt) cc_final: 0.4719 (mt) REVERT: t 85 ASP cc_start: 0.4099 (p0) cc_final: 0.3723 (m-30) REVERT: x 149 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6766 (tp30) REVERT: x 190 HIS cc_start: 0.7083 (m90) cc_final: 0.6754 (m-70) outliers start: 29 outliers final: 6 residues processed: 1343 average time/residue: 0.9061 time to fit residues: 2032.9986 Evaluate side-chains 612 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 603 time to evaluate : 7.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain m residue 658 LEU Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain n residue 329 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 1117 optimal weight: 0.8980 chunk 1002 optimal weight: 0.5980 chunk 556 optimal weight: 9.9990 chunk 342 optimal weight: 0.7980 chunk 676 optimal weight: 0.5980 chunk 535 optimal weight: 3.9990 chunk 1036 optimal weight: 0.8980 chunk 401 optimal weight: 0.8980 chunk 630 optimal weight: 5.9990 chunk 771 optimal weight: 0.9990 chunk 1201 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 120 ASN ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 133 ASN C 120 ASN C 133 ASN C 297 ASN D 240 GLN E 98 GLN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS F 98 GLN F 297 ASN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN G 297 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS H 161 HIS I 98 GLN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 ASN I 372 HIS J 178 GLN J 273 GLN J 317 HIS ** K 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 24 ASN L 229 ASN ** X 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 311 HIS ** f 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 596 HIS f 653 GLN f 684 GLN f 731 ASN ** f 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 291 ASN h 320 ASN h 367 GLN h 393 GLN h 567 GLN j 105 ASN j 115 HIS j 221 HIS ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN m 311 HIS m 391 GLN m 589 ASN ** m 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 772 ASN n 472 GLN ** n 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 475 GLN ** o 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 436 HIS ** o 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 189 GLN s 24 ASN s 36 ASN s 93 ASN t 12 GLN t 14 GLN t 36 ASN x 161 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 94018 Z= 0.225 Angle : 0.657 12.795 128444 Z= 0.341 Chirality : 0.043 0.384 15465 Planarity : 0.005 0.088 17188 Dihedral : 7.189 177.541 14750 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.34 % Favored : 93.65 % Rotamer: Outliers : 2.29 % Allowed : 10.09 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.07), residues: 11630 helix: -0.45 (0.06), residues: 5467 sheet: -2.79 (0.12), residues: 1535 loop : -2.67 (0.08), residues: 4628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP o 585 HIS 0.011 0.001 HIS h 469 PHE 0.033 0.002 PHE A 193 TYR 0.067 0.002 TYR n 553 ARG 0.013 0.001 ARG f 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 728 time to evaluate : 7.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.7928 (m-80) cc_final: 0.7479 (m-80) REVERT: A 356 MET cc_start: 0.7624 (mtm) cc_final: 0.7013 (mpp) REVERT: C 105 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7062 (tt0) REVERT: F 48 MET cc_start: 0.8222 (ttm) cc_final: 0.7744 (mtp) REVERT: G 197 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7490 (t80) REVERT: G 231 ASP cc_start: 0.6608 (m-30) cc_final: 0.5809 (t0) REVERT: G 237 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7771 (mp0) REVERT: H 222 ASP cc_start: 0.8013 (t0) cc_final: 0.7628 (p0) REVERT: I 273 GLU cc_start: 0.5997 (mp0) cc_final: 0.5724 (mt-10) REVERT: I 325 ASP cc_start: 0.8765 (m-30) cc_final: 0.8260 (t0) REVERT: J 225 LYS cc_start: 0.8017 (mttt) cc_final: 0.7741 (tppt) REVERT: X 139 LYS cc_start: 0.8155 (mttp) cc_final: 0.7946 (mmtt) REVERT: X 158 ARG cc_start: 0.8996 (mtt180) cc_final: 0.8753 (mtm110) REVERT: X 178 LYS cc_start: 0.7898 (mttp) cc_final: 0.7627 (ttpp) REVERT: X 184 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7156 (mt) REVERT: a 38 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7668 (tm-30) REVERT: a 46 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7270 (tm-30) REVERT: c 1 MET cc_start: 0.5424 (mtt) cc_final: 0.4565 (mmm) REVERT: e 238 ASP cc_start: 0.7549 (m-30) cc_final: 0.7244 (t0) REVERT: e 249 VAL cc_start: 0.8925 (t) cc_final: 0.8702 (t) REVERT: f 355 GLN cc_start: 0.8263 (mt0) cc_final: 0.7441 (mm110) REVERT: f 564 ILE cc_start: 0.6653 (mt) cc_final: 0.6442 (mm) REVERT: f 576 LYS cc_start: 0.5668 (mmtt) cc_final: 0.4541 (mmtm) REVERT: f 635 MET cc_start: 0.6713 (mmm) cc_final: 0.6334 (mmp) REVERT: f 649 ILE cc_start: 0.7867 (mt) cc_final: 0.6796 (pt) REVERT: f 662 MET cc_start: 0.7798 (tpp) cc_final: 0.7565 (tpp) REVERT: f 733 LEU cc_start: 0.3322 (OUTLIER) cc_final: 0.2971 (pp) REVERT: h 388 MET cc_start: 0.7224 (tmm) cc_final: 0.6851 (ttt) REVERT: h 408 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.7034 (t) REVERT: j 176 LYS cc_start: 0.6655 (mmmm) cc_final: 0.6394 (pttt) REVERT: j 243 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7351 (mm-30) REVERT: j 314 TRP cc_start: 0.1474 (t60) cc_final: 0.0814 (t60) REVERT: m 437 ILE cc_start: 0.8632 (mt) cc_final: 0.8360 (tp) REVERT: o 310 MET cc_start: 0.5968 (mmm) cc_final: 0.5623 (tpt) REVERT: p 205 ARG cc_start: 0.2635 (tpm170) cc_final: 0.2243 (tpp80) REVERT: s 34 MET cc_start: 0.2157 (mmt) cc_final: 0.1783 (mpp) REVERT: t 38 THR cc_start: 0.3314 (m) cc_final: 0.3102 (m) REVERT: t 85 ASP cc_start: 0.3812 (p0) cc_final: 0.3599 (m-30) REVERT: x 149 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6763 (tp30) REVERT: x 156 ARG cc_start: 0.8507 (ptm-80) cc_final: 0.8304 (ptt90) REVERT: x 179 GLN cc_start: 0.8170 (mm110) cc_final: 0.7865 (mp10) REVERT: x 190 HIS cc_start: 0.7050 (m90) cc_final: 0.6705 (m-70) REVERT: x 196 ARG cc_start: 0.5194 (mmm160) cc_final: 0.4427 (ptm160) outliers start: 151 outliers final: 63 residues processed: 843 average time/residue: 0.8373 time to fit residues: 1228.5246 Evaluate side-chains 604 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 537 time to evaluate : 7.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain X residue 163 GLU Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain b residue 21 GLU Chi-restraints excluded: chain b residue 41 THR Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain f residue 277 PHE Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 733 LEU Chi-restraints excluded: chain h residue 350 SER Chi-restraints excluded: chain h residue 408 VAL Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 454 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 569 VAL Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 106 VAL Chi-restraints excluded: chain m residue 533 VAL Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain n residue 311 HIS Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain n residue 469 PHE Chi-restraints excluded: chain n residue 562 THR Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 395 SER Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 472 VAL Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain p residue 191 LEU Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain x residue 177 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 667 optimal weight: 0.5980 chunk 372 optimal weight: 6.9990 chunk 999 optimal weight: 10.0000 chunk 818 optimal weight: 0.8980 chunk 331 optimal weight: 0.7980 chunk 1203 optimal weight: 0.9990 chunk 1300 optimal weight: 0.0870 chunk 1071 optimal weight: 10.0000 chunk 1193 optimal weight: 0.5980 chunk 410 optimal weight: 2.9990 chunk 965 optimal weight: 6.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 HIS F 91 GLN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 ASN L 5 GLN ** X 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 181 GLN e 280 ASN f 250 ASN f 473 HIS f 571 GLN ** f 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 882 GLN j 150 GLN ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS n 473 HIS ** o 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 47 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 94018 Z= 0.180 Angle : 0.576 10.986 128444 Z= 0.295 Chirality : 0.041 0.368 15465 Planarity : 0.004 0.075 17188 Dihedral : 6.744 177.861 14739 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.63 % Allowed : 11.56 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.08), residues: 11630 helix: 0.41 (0.07), residues: 5516 sheet: -2.51 (0.12), residues: 1554 loop : -2.41 (0.09), residues: 4560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP h 526 HIS 0.018 0.001 HIS X 138 PHE 0.027 0.001 PHE j 327 TYR 0.064 0.002 TYR n 553 ARG 0.011 0.001 ARG o 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 618 time to evaluate : 7.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8029 (m-80) cc_final: 0.7558 (m-80) REVERT: B 94 TYR cc_start: 0.8231 (m-80) cc_final: 0.8012 (m-80) REVERT: C 105 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7094 (tt0) REVERT: G 197 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7465 (t80) REVERT: G 231 ASP cc_start: 0.6766 (m-30) cc_final: 0.5967 (t0) REVERT: G 237 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7771 (mp0) REVERT: H 222 ASP cc_start: 0.8012 (t0) cc_final: 0.7606 (p0) REVERT: H 277 THR cc_start: 0.8032 (m) cc_final: 0.7759 (m) REVERT: I 273 GLU cc_start: 0.5889 (mp0) cc_final: 0.5433 (mt-10) REVERT: I 325 ASP cc_start: 0.8847 (m-30) cc_final: 0.8333 (t0) REVERT: J 225 LYS cc_start: 0.8117 (mttt) cc_final: 0.7848 (tppt) REVERT: X 153 HIS cc_start: 0.6908 (t-170) cc_final: 0.6682 (t-170) REVERT: X 158 ARG cc_start: 0.9119 (mtt180) cc_final: 0.8768 (mtm110) REVERT: X 178 LYS cc_start: 0.7920 (mttp) cc_final: 0.7719 (ttpp) REVERT: a 38 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7804 (tm-30) REVERT: a 46 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7140 (tm-30) REVERT: d 12 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7771 (mt) REVERT: e 238 ASP cc_start: 0.7533 (m-30) cc_final: 0.7189 (t0) REVERT: e 249 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8643 (t) REVERT: f 369 ASN cc_start: 0.5794 (OUTLIER) cc_final: 0.5044 (p0) REVERT: f 407 GLU cc_start: 0.6622 (pm20) cc_final: 0.6092 (pm20) REVERT: f 576 LYS cc_start: 0.5173 (mmtt) cc_final: 0.4000 (mmtm) REVERT: f 635 MET cc_start: 0.6819 (mmm) cc_final: 0.6450 (mmp) REVERT: f 662 MET cc_start: 0.7894 (tpp) cc_final: 0.7677 (tpp) REVERT: f 733 LEU cc_start: 0.3500 (OUTLIER) cc_final: 0.3263 (pp) REVERT: f 1041 MET cc_start: 0.6337 (mmt) cc_final: 0.5961 (mmt) REVERT: h 292 MET cc_start: 0.5711 (tpt) cc_final: 0.5216 (tpp) REVERT: h 388 MET cc_start: 0.7086 (tmm) cc_final: 0.6828 (tmm) REVERT: h 396 MET cc_start: 0.6292 (pmm) cc_final: 0.6063 (pmm) REVERT: h 408 VAL cc_start: 0.7219 (OUTLIER) cc_final: 0.6995 (t) REVERT: j 157 ARG cc_start: 0.4056 (mmm-85) cc_final: 0.3802 (tpt170) REVERT: j 163 MET cc_start: 0.5067 (ppp) cc_final: 0.3329 (tpt) REVERT: j 176 LYS cc_start: 0.6725 (mmmm) cc_final: 0.6281 (pttt) REVERT: m 581 MET cc_start: 0.7459 (ttt) cc_final: 0.7171 (ttm) REVERT: n 559 ARG cc_start: 0.7709 (tmm160) cc_final: 0.7410 (ttp80) REVERT: o 520 MET cc_start: 0.6350 (mmt) cc_final: 0.6002 (mpp) REVERT: s 34 MET cc_start: 0.2130 (mmt) cc_final: 0.1629 (mpp) REVERT: t 85 ASP cc_start: 0.3912 (p0) cc_final: 0.3666 (m-30) REVERT: x 149 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6803 (tp30) REVERT: x 182 ASP cc_start: 0.9021 (m-30) cc_final: 0.8798 (p0) REVERT: x 190 HIS cc_start: 0.7418 (m90) cc_final: 0.7058 (m-70) REVERT: x 196 ARG cc_start: 0.4402 (mmm160) cc_final: 0.4076 (ptm160) outliers start: 173 outliers final: 86 residues processed: 748 average time/residue: 0.7988 time to fit residues: 1052.8488 Evaluate side-chains 610 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 518 time to evaluate : 7.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain X residue 163 GLU Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain a residue 18 ASP Chi-restraints excluded: chain b residue 21 GLU Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain d residue 12 ILE Chi-restraints excluded: chain e residue 249 VAL Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 318 THR Chi-restraints excluded: chain f residue 229 VAL Chi-restraints excluded: chain f residue 369 ASN Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 733 LEU Chi-restraints excluded: chain f residue 830 ASP Chi-restraints excluded: chain h residue 361 VAL Chi-restraints excluded: chain h residue 408 VAL Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 454 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 534 VAL Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 180 ASP Chi-restraints excluded: chain j residue 181 PHE Chi-restraints excluded: chain j residue 225 ILE Chi-restraints excluded: chain j residue 333 GLU Chi-restraints excluded: chain j residue 354 LEU Chi-restraints excluded: chain m residue 293 GLU Chi-restraints excluded: chain m residue 525 LEU Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 658 LEU Chi-restraints excluded: chain m residue 662 MET Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain n residue 311 HIS Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain n residue 466 MET Chi-restraints excluded: chain n residue 469 PHE Chi-restraints excluded: chain o residue 183 THR Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 377 THR Chi-restraints excluded: chain o residue 395 SER Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 472 VAL Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain p residue 219 PHE Chi-restraints excluded: chain s residue 25 THR Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain t residue 88 LEU Chi-restraints excluded: chain x residue 177 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 1189 optimal weight: 5.9990 chunk 904 optimal weight: 6.9990 chunk 624 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 574 optimal weight: 10.0000 chunk 808 optimal weight: 7.9990 chunk 1207 optimal weight: 0.4980 chunk 1278 optimal weight: 0.3980 chunk 631 optimal weight: 5.9990 chunk 1144 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 ASN C 98 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN E 91 GLN E 166 HIS ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS G 116 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS H 246 GLN ** H 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN I 178 HIS ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** J 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN K 30 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN K 220 ASN L 212 ASN ** X 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 147 HIS ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 203 GLN ** X 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 311 HIS e 330 ASN f 421 GLN f 694 ASN ** f 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 871 HIS f 891 HIS ** h 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 150 GLN ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 465 GLN ** m 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 324 GLN n 375 GLN ** n 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 24 ASN t 14 GLN ** x 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.133 94018 Z= 0.578 Angle : 0.905 12.152 128444 Z= 0.467 Chirality : 0.051 0.864 15465 Planarity : 0.006 0.080 17188 Dihedral : 7.726 166.279 14739 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.50 % Favored : 90.45 % Rotamer: Outliers : 4.39 % Allowed : 12.81 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.07), residues: 11630 helix: -0.10 (0.07), residues: 5384 sheet: -2.63 (0.12), residues: 1447 loop : -2.53 (0.08), residues: 4799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 357 HIS 0.032 0.003 HIS x 138 PHE 0.043 0.003 PHE h 246 TYR 0.049 0.003 TYR n 553 ARG 0.039 0.001 ARG m 462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 500 time to evaluate : 7.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.7255 (mtm) cc_final: 0.6680 (mpp) REVERT: B 118 ARG cc_start: 0.6975 (mmm160) cc_final: 0.6664 (mmp80) REVERT: C 197 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7234 (m-10) REVERT: C 227 ASN cc_start: 0.7927 (t0) cc_final: 0.7550 (t0) REVERT: D 120 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8606 (t0) REVERT: F 30 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8782 (tt) REVERT: F 48 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7716 (mtp) REVERT: F 181 MET cc_start: 0.8053 (mmm) cc_final: 0.7787 (mmm) REVERT: F 197 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.8077 (m-10) REVERT: G 197 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.7503 (t80) REVERT: G 237 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7585 (mp0) REVERT: G 288 MET cc_start: 0.7315 (tpp) cc_final: 0.6886 (tpp) REVERT: H 47 MET cc_start: 0.4773 (mmt) cc_final: 0.4548 (mmt) REVERT: H 95 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6714 (mtp85) REVERT: H 277 THR cc_start: 0.8171 (m) cc_final: 0.7875 (m) REVERT: I 325 ASP cc_start: 0.8825 (m-30) cc_final: 0.8357 (t0) REVERT: J 225 LYS cc_start: 0.7893 (mttt) cc_final: 0.7593 (tppt) REVERT: X 158 ARG cc_start: 0.9179 (mtt180) cc_final: 0.8686 (mtm-85) REVERT: X 178 LYS cc_start: 0.8182 (mttp) cc_final: 0.7775 (ttpp) REVERT: a 46 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7229 (tm-30) REVERT: b 46 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7254 (tm-30) REVERT: b 75 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7686 (mt) REVERT: c 1 MET cc_start: 0.3966 (mtt) cc_final: 0.3302 (mmt) REVERT: e 212 MET cc_start: 0.5751 (tpp) cc_final: 0.5521 (tpp) REVERT: e 249 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8934 (t) REVERT: f 369 ASN cc_start: 0.5395 (OUTLIER) cc_final: 0.4919 (p0) REVERT: f 402 MET cc_start: 0.5846 (tpp) cc_final: 0.5563 (tpp) REVERT: f 635 MET cc_start: 0.6566 (mmm) cc_final: 0.6336 (mmp) REVERT: f 662 MET cc_start: 0.7661 (tpp) cc_final: 0.7385 (tpp) REVERT: f 1041 MET cc_start: 0.6561 (mmt) cc_final: 0.6336 (mmt) REVERT: h 292 MET cc_start: 0.6852 (tpt) cc_final: 0.6176 (tpp) REVERT: h 388 MET cc_start: 0.7446 (tmm) cc_final: 0.7076 (tmm) REVERT: j 157 ARG cc_start: 0.4131 (mmm-85) cc_final: 0.3741 (tpt170) REVERT: j 163 MET cc_start: 0.5721 (ppp) cc_final: 0.4400 (tpt) REVERT: j 222 ASN cc_start: 0.5012 (m-40) cc_final: 0.4793 (p0) REVERT: m 212 MET cc_start: 0.6515 (tpp) cc_final: 0.6128 (tpp) REVERT: m 581 MET cc_start: 0.7708 (ttt) cc_final: 0.7488 (ttm) REVERT: m 690 ARG cc_start: 0.7285 (ttm170) cc_final: 0.7081 (ttm110) REVERT: n 559 ARG cc_start: 0.8052 (tmm160) cc_final: 0.7354 (tmm-80) REVERT: n 563 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.6027 (mtp-110) REVERT: o 267 GLU cc_start: 0.5223 (mp0) cc_final: 0.4813 (mp0) REVERT: o 449 HIS cc_start: 0.4456 (OUTLIER) cc_final: 0.3900 (t70) REVERT: p 188 GLN cc_start: 0.0276 (mt0) cc_final: -0.0301 (mm-40) REVERT: p 205 ARG cc_start: 0.3589 (tpt-90) cc_final: 0.2109 (tpp80) REVERT: s 72 ARG cc_start: 0.3537 (OUTLIER) cc_final: 0.1603 (ptp90) REVERT: t 31 LYS cc_start: 0.4633 (mttt) cc_final: 0.4275 (mptt) REVERT: t 85 ASP cc_start: 0.4302 (p0) cc_final: 0.3964 (m-30) REVERT: t 86 TYR cc_start: 0.2759 (OUTLIER) cc_final: 0.1329 (m-10) REVERT: x 149 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6433 (tp30) REVERT: x 190 HIS cc_start: 0.7304 (m90) cc_final: 0.6957 (m-70) REVERT: x 196 ARG cc_start: 0.4366 (mmm160) cc_final: 0.4053 (ptm160) outliers start: 289 outliers final: 168 residues processed: 746 average time/residue: 0.7964 time to fit residues: 1048.8311 Evaluate side-chains 623 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 441 time to evaluate : 7.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 132 PHE Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 44 HIS Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain L residue 251 ASP Chi-restraints excluded: chain L residue 264 GLU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain X residue 157 ARG Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain a residue 18 ASP Chi-restraints excluded: chain b residue 21 GLU Chi-restraints excluded: chain b residue 41 THR Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain e residue 249 VAL Chi-restraints excluded: chain e residue 270 THR Chi-restraints excluded: chain e residue 288 ILE Chi-restraints excluded: chain f residue 369 ASN Chi-restraints excluded: chain f residue 433 LEU Chi-restraints excluded: chain f residue 436 ASP Chi-restraints excluded: chain f residue 446 LEU Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 729 THR Chi-restraints excluded: chain f residue 737 VAL Chi-restraints excluded: chain f residue 762 LEU Chi-restraints excluded: chain f residue 830 ASP Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain f residue 886 ASP Chi-restraints excluded: chain h residue 269 LEU Chi-restraints excluded: chain h residue 270 VAL Chi-restraints excluded: chain h residue 361 VAL Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 454 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 500 TYR Chi-restraints excluded: chain h residue 529 ASN Chi-restraints excluded: chain h residue 534 VAL Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain h residue 569 VAL Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 174 GLU Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 181 PHE Chi-restraints excluded: chain j residue 183 ASP Chi-restraints excluded: chain j residue 219 LEU Chi-restraints excluded: chain j residue 225 ILE Chi-restraints excluded: chain j residue 314 TRP Chi-restraints excluded: chain j residue 333 GLU Chi-restraints excluded: chain j residue 354 LEU Chi-restraints excluded: chain m residue 275 ILE Chi-restraints excluded: chain m residue 303 ILE Chi-restraints excluded: chain m residue 364 LEU Chi-restraints excluded: chain m residue 525 LEU Chi-restraints excluded: chain m residue 533 VAL Chi-restraints excluded: chain m residue 584 ILE Chi-restraints excluded: chain m residue 658 LEU Chi-restraints excluded: chain m residue 662 MET Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain m residue 765 VAL Chi-restraints excluded: chain n residue 219 GLN Chi-restraints excluded: chain n residue 311 HIS Chi-restraints excluded: chain n residue 324 GLN Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 355 GLN Chi-restraints excluded: chain n residue 408 GLU Chi-restraints excluded: chain n residue 432 VAL Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain n residue 466 MET Chi-restraints excluded: chain n residue 469 PHE Chi-restraints excluded: chain n residue 528 GLU Chi-restraints excluded: chain n residue 531 LYS Chi-restraints excluded: chain n residue 560 VAL Chi-restraints excluded: chain n residue 563 ARG Chi-restraints excluded: chain o residue 183 THR Chi-restraints excluded: chain o residue 212 SER Chi-restraints excluded: chain o residue 242 ASN Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 367 GLN Chi-restraints excluded: chain o residue 377 THR Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 449 HIS Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 472 VAL Chi-restraints excluded: chain o residue 493 SER Chi-restraints excluded: chain o residue 525 LEU Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain o residue 579 VAL Chi-restraints excluded: chain p residue 191 LEU Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain s residue 20 ILE Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain s residue 88 LEU Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 69 LEU Chi-restraints excluded: chain t residue 76 ASN Chi-restraints excluded: chain t residue 86 TYR Chi-restraints excluded: chain t residue 88 LEU Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain x residue 177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 1065 optimal weight: 9.9990 chunk 725 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 952 optimal weight: 6.9990 chunk 527 optimal weight: 0.9990 chunk 1091 optimal weight: 0.0370 chunk 883 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 653 optimal weight: 0.9990 chunk 1147 optimal weight: 0.9980 chunk 322 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 HIS D 29 GLN D 142 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN ** J 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN K 220 ASN L 5 GLN ** X 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 203 GLN X 209 ASN d 15 ASN ** f 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 354 HIS ** o 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 457 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 94018 Z= 0.175 Angle : 0.581 10.722 128444 Z= 0.294 Chirality : 0.041 0.300 15465 Planarity : 0.003 0.070 17188 Dihedral : 6.783 169.634 14739 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.28 % Allowed : 15.39 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.08), residues: 11630 helix: 0.80 (0.07), residues: 5437 sheet: -2.39 (0.12), residues: 1488 loop : -2.22 (0.09), residues: 4705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP h 384 HIS 0.008 0.001 HIS X 147 PHE 0.019 0.001 PHE n 469 TYR 0.040 0.001 TYR o 294 ARG 0.016 0.001 ARG K 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 540 time to evaluate : 7.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.7870 (m-80) cc_final: 0.7388 (m-80) REVERT: A 356 MET cc_start: 0.7572 (mtm) cc_final: 0.6984 (mpp) REVERT: C 94 TYR cc_start: 0.9125 (m-80) cc_final: 0.8919 (m-80) REVERT: C 197 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.7017 (m-10) REVERT: F 48 MET cc_start: 0.7538 (mtp) cc_final: 0.7281 (mtp) REVERT: G 237 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7655 (mp0) REVERT: H 283 MET cc_start: 0.8270 (mmm) cc_final: 0.7987 (mmm) REVERT: I 325 ASP cc_start: 0.8887 (m-30) cc_final: 0.8286 (t0) REVERT: J 126 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.5336 (mmm) REVERT: X 158 ARG cc_start: 0.9200 (mtt180) cc_final: 0.8805 (mtm110) REVERT: X 178 LYS cc_start: 0.7892 (mttp) cc_final: 0.7517 (ttpp) REVERT: a 46 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7237 (tm-30) REVERT: e 212 MET cc_start: 0.5495 (tpp) cc_final: 0.5217 (tpp) REVERT: e 238 ASP cc_start: 0.7268 (m-30) cc_final: 0.6956 (t70) REVERT: e 249 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8761 (t) REVERT: f 369 ASN cc_start: 0.5359 (OUTLIER) cc_final: 0.4774 (p0) REVERT: f 407 GLU cc_start: 0.6603 (pm20) cc_final: 0.6267 (pm20) REVERT: f 635 MET cc_start: 0.6578 (mmm) cc_final: 0.6343 (mmp) REVERT: f 662 MET cc_start: 0.7632 (tpp) cc_final: 0.7231 (tpp) REVERT: h 292 MET cc_start: 0.6238 (tpt) cc_final: 0.5674 (tpp) REVERT: h 388 MET cc_start: 0.7234 (tmm) cc_final: 0.6651 (tmm) REVERT: h 396 MET cc_start: 0.6722 (pmm) cc_final: 0.6362 (pmm) REVERT: j 157 ARG cc_start: 0.4450 (mmm-85) cc_final: 0.4084 (tpt170) REVERT: j 163 MET cc_start: 0.6361 (ppp) cc_final: 0.4917 (tpt) REVERT: m 581 MET cc_start: 0.7327 (ttt) cc_final: 0.7110 (ttm) REVERT: m 690 ARG cc_start: 0.7105 (ttm170) cc_final: 0.6900 (ttm110) REVERT: n 393 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7009 (tp) REVERT: n 559 ARG cc_start: 0.7825 (tmm160) cc_final: 0.7226 (tmm-80) REVERT: n 563 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5807 (mtp-110) REVERT: o 402 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.6128 (tm-30) REVERT: p 188 GLN cc_start: 0.0325 (mt0) cc_final: -0.0163 (mm-40) REVERT: p 205 ARG cc_start: 0.3472 (tpt-90) cc_final: 0.1817 (mtm180) REVERT: s 34 MET cc_start: 0.0795 (mmm) cc_final: 0.0223 (mpp) REVERT: t 31 LYS cc_start: 0.3696 (mttt) cc_final: 0.3473 (mptt) REVERT: t 85 ASP cc_start: 0.3860 (p0) cc_final: 0.3151 (m-30) REVERT: t 86 TYR cc_start: 0.2695 (m-10) cc_final: 0.1365 (m-10) REVERT: x 136 GLN cc_start: 0.7175 (mt0) cc_final: 0.6932 (pp30) REVERT: x 137 MET cc_start: 0.8246 (ptt) cc_final: 0.7935 (ptt) REVERT: x 149 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6843 (tp30) REVERT: x 190 HIS cc_start: 0.7404 (m90) cc_final: 0.7053 (m-70) outliers start: 150 outliers final: 91 residues processed: 660 average time/residue: 0.8207 time to fit residues: 963.7495 Evaluate side-chains 581 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 483 time to evaluate : 7.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain X residue 157 ARG Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 203 GLN Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain e residue 249 VAL Chi-restraints excluded: chain f residue 369 ASN Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 762 LEU Chi-restraints excluded: chain f residue 830 ASP Chi-restraints excluded: chain h residue 270 VAL Chi-restraints excluded: chain h residue 350 SER Chi-restraints excluded: chain h residue 361 VAL Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 569 VAL Chi-restraints excluded: chain h residue 572 ASP Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 180 ASP Chi-restraints excluded: chain j residue 181 PHE Chi-restraints excluded: chain j residue 219 LEU Chi-restraints excluded: chain j residue 314 TRP Chi-restraints excluded: chain j residue 354 LEU Chi-restraints excluded: chain m residue 520 ILE Chi-restraints excluded: chain m residue 525 LEU Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 658 LEU Chi-restraints excluded: chain m residue 662 MET Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain n residue 311 HIS Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 393 LEU Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain n residue 469 PHE Chi-restraints excluded: chain n residue 563 ARG Chi-restraints excluded: chain o residue 183 THR Chi-restraints excluded: chain o residue 289 VAL Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 402 GLN Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 472 VAL Chi-restraints excluded: chain o residue 525 LEU Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain p residue 191 LEU Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain t residue 88 LEU Chi-restraints excluded: chain t residue 89 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 430 optimal weight: 9.9990 chunk 1151 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 750 optimal weight: 0.0970 chunk 315 optimal weight: 3.9990 chunk 1280 optimal weight: 9.9990 chunk 1062 optimal weight: 9.9990 chunk 592 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 423 optimal weight: 5.9990 chunk 672 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN D 142 GLN G 44 HIS ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN ** J 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 150 GLN ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 675 ASN f 680 GLN ** f 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 360 GLN ** m 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 431 GLN ** m 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 400 HIS ** o 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 188 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 94018 Z= 0.308 Angle : 0.640 10.480 128444 Z= 0.325 Chirality : 0.043 0.252 15465 Planarity : 0.004 0.067 17188 Dihedral : 6.782 168.027 14739 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.94 % Favored : 92.05 % Rotamer: Outliers : 3.19 % Allowed : 15.94 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.08), residues: 11630 helix: 0.85 (0.07), residues: 5419 sheet: -2.42 (0.12), residues: 1532 loop : -2.17 (0.09), residues: 4679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP h 384 HIS 0.008 0.002 HIS I 206 PHE 0.025 0.002 PHE t 49 TYR 0.040 0.002 TYR o 294 ARG 0.011 0.001 ARG e 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 486 time to evaluate : 7.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.7866 (m-80) cc_final: 0.7460 (m-80) REVERT: A 356 MET cc_start: 0.7461 (mtm) cc_final: 0.6873 (mpp) REVERT: B 197 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: C 197 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: F 273 GLU cc_start: 0.7569 (mp0) cc_final: 0.7223 (mt-10) REVERT: G 204 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8139 (t0) REVERT: G 237 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7656 (mp0) REVERT: H 153 MET cc_start: 0.7900 (tpp) cc_final: 0.7516 (tpp) REVERT: I 325 ASP cc_start: 0.8792 (m-30) cc_final: 0.8201 (t0) REVERT: L 176 TRP cc_start: 0.6746 (t-100) cc_final: 0.6177 (t-100) REVERT: X 150 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6766 (mm110) REVERT: X 158 ARG cc_start: 0.9202 (mtt180) cc_final: 0.8771 (mtm110) REVERT: X 178 LYS cc_start: 0.7867 (mttp) cc_final: 0.7464 (ttpp) REVERT: X 200 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5864 (mtm-85) REVERT: a 46 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7133 (tm-30) REVERT: e 212 MET cc_start: 0.5646 (tpp) cc_final: 0.5385 (tpp) REVERT: e 238 ASP cc_start: 0.7304 (m-30) cc_final: 0.6983 (t70) REVERT: e 249 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8849 (t) REVERT: f 369 ASN cc_start: 0.5481 (OUTLIER) cc_final: 0.4917 (p0) REVERT: f 402 MET cc_start: 0.5573 (tpp) cc_final: 0.5372 (tpp) REVERT: f 635 MET cc_start: 0.6769 (mmm) cc_final: 0.6506 (mmp) REVERT: h 291 ASN cc_start: 0.6523 (OUTLIER) cc_final: 0.6313 (p0) REVERT: h 292 MET cc_start: 0.6472 (tpt) cc_final: 0.6093 (tpp) REVERT: h 388 MET cc_start: 0.7304 (tmm) cc_final: 0.6741 (tmm) REVERT: j 163 MET cc_start: 0.6409 (ppp) cc_final: 0.5047 (tpt) REVERT: j 185 MET cc_start: 0.1857 (ppp) cc_final: 0.1646 (ptm) REVERT: m 581 MET cc_start: 0.7207 (ttt) cc_final: 0.7007 (ttm) REVERT: m 690 ARG cc_start: 0.7234 (ttm170) cc_final: 0.6999 (ttm110) REVERT: n 393 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7063 (tp) REVERT: o 402 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: p 205 ARG cc_start: 0.3032 (tpt-90) cc_final: 0.1708 (mtm180) REVERT: t 85 ASP cc_start: 0.4172 (p0) cc_final: 0.3122 (m-30) REVERT: x 149 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6826 (tp30) REVERT: x 190 HIS cc_start: 0.7266 (m90) cc_final: 0.7021 (m90) outliers start: 210 outliers final: 127 residues processed: 657 average time/residue: 0.8248 time to fit residues: 959.8052 Evaluate side-chains 599 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 462 time to evaluate : 8.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 356 MET Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 251 ASP Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain X residue 150 GLN Chi-restraints excluded: chain X residue 157 ARG Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 200 ARG Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain b residue 21 GLU Chi-restraints excluded: chain b residue 41 THR Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 75 ILE Chi-restraints excluded: chain e residue 249 VAL Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain f residue 229 VAL Chi-restraints excluded: chain f residue 369 ASN Chi-restraints excluded: chain f residue 574 THR Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 751 ARG Chi-restraints excluded: chain f residue 762 LEU Chi-restraints excluded: chain f residue 822 LEU Chi-restraints excluded: chain f residue 830 ASP Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain h residue 270 VAL Chi-restraints excluded: chain h residue 291 ASN Chi-restraints excluded: chain h residue 361 VAL Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 422 VAL Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 534 VAL Chi-restraints excluded: chain h residue 569 VAL Chi-restraints excluded: chain h residue 572 ASP Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 180 ASP Chi-restraints excluded: chain j residue 181 PHE Chi-restraints excluded: chain j residue 219 LEU Chi-restraints excluded: chain j residue 314 TRP Chi-restraints excluded: chain j residue 325 GLU Chi-restraints excluded: chain j residue 333 GLU Chi-restraints excluded: chain j residue 354 LEU Chi-restraints excluded: chain m residue 520 ILE Chi-restraints excluded: chain m residue 525 LEU Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 658 LEU Chi-restraints excluded: chain m residue 662 MET Chi-restraints excluded: chain m residue 685 ASP Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain m residue 745 THR Chi-restraints excluded: chain n residue 311 HIS Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 393 LEU Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain n residue 469 PHE Chi-restraints excluded: chain o residue 183 THR Chi-restraints excluded: chain o residue 255 VAL Chi-restraints excluded: chain o residue 289 VAL Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 402 GLN Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 472 VAL Chi-restraints excluded: chain o residue 525 LEU Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain o residue 568 ILE Chi-restraints excluded: chain p residue 191 LEU Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain s residue 88 LEU Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain x residue 177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 1234 optimal weight: 20.0000 chunk 144 optimal weight: 0.5980 chunk 729 optimal weight: 9.9990 chunk 934 optimal weight: 40.0000 chunk 724 optimal weight: 7.9990 chunk 1077 optimal weight: 9.9990 chunk 714 optimal weight: 9.9990 chunk 1275 optimal weight: 20.0000 chunk 798 optimal weight: 3.9990 chunk 777 optimal weight: 6.9990 chunk 588 optimal weight: 9.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 HIS ** J 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN ** K 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 HIS ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 229 ASN ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 529 ASN f 675 ASN f 708 GLN ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 367 GLN ** h 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 436 HIS ** h 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 431 GLN ** m 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 280 ASN ** n 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 216 ASN x 150 GLN ** x 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.198 94018 Z= 0.963 Angle : 1.213 16.623 128444 Z= 0.624 Chirality : 0.058 0.331 15465 Planarity : 0.008 0.088 17188 Dihedral : 8.578 174.220 14739 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 27.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.32 % Favored : 87.60 % Rotamer: Outliers : 4.67 % Allowed : 15.89 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.07), residues: 11630 helix: -0.97 (0.06), residues: 5334 sheet: -2.70 (0.12), residues: 1399 loop : -2.82 (0.08), residues: 4897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP h 506 HIS 0.020 0.004 HIS f 769 PHE 0.054 0.005 PHE f 588 TYR 0.050 0.004 TYR o 294 ARG 0.014 0.002 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 420 time to evaluate : 7.835 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 356 MET cc_start: 0.7182 (mtm) cc_final: 0.6554 (mpp) REVERT: C 158 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8825 (tm) REVERT: C 197 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: D 120 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8793 (t0) REVERT: E 197 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7381 (t80) REVERT: F 197 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: G 197 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.7523 (t80) REVERT: G 237 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7637 (mp0) REVERT: H 95 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6725 (mtp85) REVERT: I 325 ASP cc_start: 0.8783 (m-30) cc_final: 0.8305 (t0) REVERT: L 176 TRP cc_start: 0.6853 (t-100) cc_final: 0.6361 (t-100) REVERT: X 158 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8508 (mtm-85) REVERT: X 178 LYS cc_start: 0.8263 (mttp) cc_final: 0.7915 (ttpp) REVERT: a 46 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7403 (tm-30) REVERT: c 1 MET cc_start: 0.4938 (mtt) cc_final: 0.4266 (mmm) REVERT: d 14 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.6016 (mpp80) REVERT: e 249 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8937 (t) REVERT: f 261 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8874 (pttm) REVERT: f 402 MET cc_start: 0.4950 (tpp) cc_final: 0.4556 (tpp) REVERT: f 635 MET cc_start: 0.6963 (mmm) cc_final: 0.6689 (mmp) REVERT: h 291 ASN cc_start: 0.7229 (OUTLIER) cc_final: 0.6876 (p0) REVERT: h 292 MET cc_start: 0.7025 (tpt) cc_final: 0.6621 (tpp) REVERT: h 388 MET cc_start: 0.7563 (tmm) cc_final: 0.6995 (tmm) REVERT: h 529 ASN cc_start: 0.3965 (OUTLIER) cc_final: 0.3048 (p0) REVERT: j 163 MET cc_start: 0.5343 (ppp) cc_final: 0.4697 (tpt) REVERT: j 171 ARG cc_start: 0.2646 (mmt90) cc_final: 0.2372 (tpp-160) REVERT: m 212 MET cc_start: 0.7328 (tpp) cc_final: 0.6714 (tpp) REVERT: m 309 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7915 (mtm110) REVERT: m 581 MET cc_start: 0.7475 (ttt) cc_final: 0.7261 (ttm) REVERT: m 690 ARG cc_start: 0.7500 (ttm170) cc_final: 0.7268 (ttm110) REVERT: n 477 ARG cc_start: 0.5306 (OUTLIER) cc_final: 0.4871 (tmm160) REVERT: o 391 HIS cc_start: 0.6284 (OUTLIER) cc_final: 0.4693 (t70) REVERT: o 445 MET cc_start: 0.7090 (tpt) cc_final: 0.6578 (tpt) REVERT: o 449 HIS cc_start: 0.5056 (OUTLIER) cc_final: 0.4335 (t70) REVERT: p 205 ARG cc_start: 0.3461 (tpt-90) cc_final: 0.2928 (tpp80) REVERT: s 85 ASP cc_start: 0.5865 (t0) cc_final: 0.5176 (t0) REVERT: x 149 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6217 (tp30) outliers start: 308 outliers final: 209 residues processed: 691 average time/residue: 0.8194 time to fit residues: 1009.6866 Evaluate side-chains 622 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 397 time to evaluate : 7.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 351 ASP Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 132 PHE Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 44 HIS Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 206 HIS Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 355 LYS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 272 ASN Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 230 GLU Chi-restraints excluded: chain L residue 251 ASP Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain X residue 157 ARG Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 200 ARG Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain a residue 18 ASP Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain b residue 41 THR Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain e residue 249 VAL Chi-restraints excluded: chain e residue 270 THR Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain f residue 229 VAL Chi-restraints excluded: chain f residue 261 LYS Chi-restraints excluded: chain f residue 303 ILE Chi-restraints excluded: chain f residue 338 ASP Chi-restraints excluded: chain f residue 369 ASN Chi-restraints excluded: chain f residue 388 LEU Chi-restraints excluded: chain f residue 436 ASP Chi-restraints excluded: chain f residue 540 LYS Chi-restraints excluded: chain f residue 574 THR Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 718 PHE Chi-restraints excluded: chain f residue 729 THR Chi-restraints excluded: chain f residue 737 VAL Chi-restraints excluded: chain f residue 738 ASN Chi-restraints excluded: chain f residue 751 ARG Chi-restraints excluded: chain f residue 762 LEU Chi-restraints excluded: chain f residue 830 ASP Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain h residue 269 LEU Chi-restraints excluded: chain h residue 270 VAL Chi-restraints excluded: chain h residue 291 ASN Chi-restraints excluded: chain h residue 350 SER Chi-restraints excluded: chain h residue 361 VAL Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 422 VAL Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 474 SER Chi-restraints excluded: chain h residue 529 ASN Chi-restraints excluded: chain h residue 534 VAL Chi-restraints excluded: chain h residue 539 ILE Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain h residue 569 VAL Chi-restraints excluded: chain h residue 572 ASP Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 180 ASP Chi-restraints excluded: chain j residue 181 PHE Chi-restraints excluded: chain j residue 314 TRP Chi-restraints excluded: chain j residue 325 GLU Chi-restraints excluded: chain j residue 333 GLU Chi-restraints excluded: chain j residue 354 LEU Chi-restraints excluded: chain m residue 275 ILE Chi-restraints excluded: chain m residue 309 ARG Chi-restraints excluded: chain m residue 360 ILE Chi-restraints excluded: chain m residue 408 GLU Chi-restraints excluded: chain m residue 520 ILE Chi-restraints excluded: chain m residue 525 LEU Chi-restraints excluded: chain m residue 530 VAL Chi-restraints excluded: chain m residue 533 VAL Chi-restraints excluded: chain m residue 538 VAL Chi-restraints excluded: chain m residue 584 ILE Chi-restraints excluded: chain m residue 658 LEU Chi-restraints excluded: chain m residue 662 MET Chi-restraints excluded: chain m residue 685 ASP Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain m residue 745 THR Chi-restraints excluded: chain m residue 765 VAL Chi-restraints excluded: chain n residue 311 HIS Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 355 GLN Chi-restraints excluded: chain n residue 367 ILE Chi-restraints excluded: chain n residue 393 LEU Chi-restraints excluded: chain n residue 408 GLU Chi-restraints excluded: chain n residue 432 VAL Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain n residue 477 ARG Chi-restraints excluded: chain n residue 528 GLU Chi-restraints excluded: chain n residue 567 ARG Chi-restraints excluded: chain o residue 183 THR Chi-restraints excluded: chain o residue 255 VAL Chi-restraints excluded: chain o residue 289 VAL Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 367 GLN Chi-restraints excluded: chain o residue 391 HIS Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 449 HIS Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 472 VAL Chi-restraints excluded: chain o residue 525 LEU Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain o residue 568 ILE Chi-restraints excluded: chain p residue 191 LEU Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain s residue 20 ILE Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain s residue 88 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 76 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain x residue 156 ARG Chi-restraints excluded: chain x residue 177 VAL Chi-restraints excluded: chain x residue 184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 788 optimal weight: 5.9990 chunk 509 optimal weight: 0.6980 chunk 761 optimal weight: 0.6980 chunk 384 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 247 optimal weight: 0.5980 chunk 810 optimal weight: 0.9990 chunk 868 optimal weight: 8.9990 chunk 630 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 1002 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN J 172 HIS ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 ASN K 234 HIS L 229 ASN X 150 GLN ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 320 ASN h 497 ASN j 101 HIS ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 244 HIS ** m 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 190 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 94018 Z= 0.211 Angle : 0.643 12.686 128444 Z= 0.325 Chirality : 0.043 0.266 15465 Planarity : 0.004 0.065 17188 Dihedral : 7.044 179.061 14739 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.57 % Favored : 93.42 % Rotamer: Outliers : 2.50 % Allowed : 17.89 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.08), residues: 11630 helix: 0.42 (0.07), residues: 5360 sheet: -2.53 (0.12), residues: 1459 loop : -2.28 (0.09), residues: 4811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP h 506 HIS 0.018 0.001 HIS K 234 PHE 0.032 0.002 PHE t 49 TYR 0.045 0.002 TYR o 294 ARG 0.020 0.001 ARG h 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 488 time to evaluate : 7.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.7810 (m-80) cc_final: 0.7387 (m-80) REVERT: A 356 MET cc_start: 0.7398 (mtm) cc_final: 0.6727 (mpp) REVERT: B 197 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: C 217 ILE cc_start: 0.9217 (mt) cc_final: 0.9015 (tt) REVERT: G 197 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7282 (t80) REVERT: I 325 ASP cc_start: 0.8811 (m-30) cc_final: 0.8328 (t0) REVERT: X 150 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7334 (mm110) REVERT: X 158 ARG cc_start: 0.9169 (mtt180) cc_final: 0.8705 (mtm110) REVERT: a 46 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7245 (tm-30) REVERT: c 1 MET cc_start: 0.4612 (mtt) cc_final: 0.4107 (mmm) REVERT: d 3 ASP cc_start: 0.5086 (OUTLIER) cc_final: 0.4748 (p0) REVERT: e 238 ASP cc_start: 0.7170 (m-30) cc_final: 0.6656 (t70) REVERT: f 277 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6656 (p90) REVERT: f 369 ASN cc_start: 0.5040 (OUTLIER) cc_final: 0.4494 (p0) REVERT: f 402 MET cc_start: 0.5619 (tpp) cc_final: 0.5358 (tpp) REVERT: f 635 MET cc_start: 0.6728 (mmm) cc_final: 0.6414 (mmp) REVERT: f 751 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8154 (mmt-90) REVERT: h 292 MET cc_start: 0.6522 (tpt) cc_final: 0.6272 (tpp) REVERT: j 114 TYR cc_start: 0.6493 (t80) cc_final: 0.6140 (t80) REVERT: j 163 MET cc_start: 0.5392 (ppp) cc_final: 0.4832 (tpt) REVERT: n 550 MET cc_start: 0.5933 (mmp) cc_final: 0.5724 (mmm) REVERT: o 449 HIS cc_start: 0.5017 (OUTLIER) cc_final: 0.4551 (t70) REVERT: p 201 ASP cc_start: 0.2697 (t0) cc_final: 0.2337 (t0) REVERT: p 205 ARG cc_start: 0.3242 (tpt-90) cc_final: 0.2196 (mtm180) REVERT: s 72 ARG cc_start: 0.3807 (OUTLIER) cc_final: 0.2282 (ptp90) REVERT: x 149 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6500 (tp30) outliers start: 165 outliers final: 113 residues processed: 617 average time/residue: 0.8278 time to fit residues: 914.8764 Evaluate side-chains 565 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 443 time to evaluate : 7.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 230 GLU Chi-restraints excluded: chain X residue 150 GLN Chi-restraints excluded: chain X residue 157 ARG Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain b residue 21 GLU Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain d residue 3 ASP Chi-restraints excluded: chain e residue 249 VAL Chi-restraints excluded: chain e residue 270 THR Chi-restraints excluded: chain f residue 277 PHE Chi-restraints excluded: chain f residue 303 ILE Chi-restraints excluded: chain f residue 338 ASP Chi-restraints excluded: chain f residue 369 ASN Chi-restraints excluded: chain f residue 574 THR Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 689 PHE Chi-restraints excluded: chain f residue 751 ARG Chi-restraints excluded: chain f residue 762 LEU Chi-restraints excluded: chain f residue 830 ASP Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain h residue 350 SER Chi-restraints excluded: chain h residue 361 VAL Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 474 SER Chi-restraints excluded: chain h residue 500 TYR Chi-restraints excluded: chain h residue 534 VAL Chi-restraints excluded: chain h residue 539 ILE Chi-restraints excluded: chain h residue 569 VAL Chi-restraints excluded: chain h residue 572 ASP Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 174 GLU Chi-restraints excluded: chain j residue 180 ASP Chi-restraints excluded: chain j residue 181 PHE Chi-restraints excluded: chain j residue 314 TRP Chi-restraints excluded: chain j residue 325 GLU Chi-restraints excluded: chain j residue 354 LEU Chi-restraints excluded: chain m residue 520 ILE Chi-restraints excluded: chain m residue 525 LEU Chi-restraints excluded: chain m residue 609 ILE Chi-restraints excluded: chain m residue 685 ASP Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain m residue 745 THR Chi-restraints excluded: chain m residue 765 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain o residue 183 THR Chi-restraints excluded: chain o residue 289 VAL Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 449 HIS Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 525 LEU Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain s residue 88 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain x residue 177 VAL Chi-restraints excluded: chain x residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 1159 optimal weight: 10.0000 chunk 1221 optimal weight: 30.0000 chunk 1114 optimal weight: 0.9990 chunk 1188 optimal weight: 1.9990 chunk 715 optimal weight: 20.0000 chunk 517 optimal weight: 9.9990 chunk 933 optimal weight: 30.0000 chunk 364 optimal weight: 4.9990 chunk 1073 optimal weight: 9.9990 chunk 1123 optimal weight: 6.9990 chunk 1184 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN ** K 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 HIS ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 ASN ** x 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 188 GLN x 190 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.161 94018 Z= 0.782 Angle : 1.030 14.869 128444 Z= 0.526 Chirality : 0.053 0.372 15465 Planarity : 0.007 0.089 17188 Dihedral : 8.014 179.603 14739 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.28 % Favored : 87.64 % Rotamer: Outliers : 3.37 % Allowed : 17.76 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.07), residues: 11630 helix: -0.58 (0.07), residues: 5324 sheet: -2.69 (0.12), residues: 1413 loop : -2.73 (0.08), residues: 4893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP L 176 HIS 0.019 0.003 HIS X 147 PHE 0.036 0.004 PHE F 263 TYR 0.045 0.003 TYR o 294 ARG 0.014 0.001 ARG e 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 406 time to evaluate : 7.582 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 356 MET cc_start: 0.7199 (mtm) cc_final: 0.6584 (mpp) REVERT: C 197 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: E 197 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7539 (t80) REVERT: G 197 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.7550 (t80) REVERT: I 325 ASP cc_start: 0.8668 (m-30) cc_final: 0.8167 (t0) REVERT: K 255 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: X 150 GLN cc_start: 0.7923 (tp40) cc_final: 0.7529 (mm110) REVERT: X 158 ARG cc_start: 0.9065 (mtt180) cc_final: 0.8551 (mtm-85) REVERT: a 46 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7417 (tm-30) REVERT: c 1 MET cc_start: 0.5215 (mtt) cc_final: 0.4511 (mmm) REVERT: d 3 ASP cc_start: 0.5700 (OUTLIER) cc_final: 0.5357 (p0) REVERT: d 14 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.5818 (mpp80) REVERT: e 249 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8950 (t) REVERT: f 344 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7829 (tp) REVERT: f 369 ASN cc_start: 0.5314 (OUTLIER) cc_final: 0.4863 (p0) REVERT: f 402 MET cc_start: 0.5324 (tpp) cc_final: 0.4940 (tpp) REVERT: f 635 MET cc_start: 0.6893 (mmm) cc_final: 0.6589 (mmp) REVERT: f 751 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7743 (mmt-90) REVERT: h 292 MET cc_start: 0.6758 (tpt) cc_final: 0.6247 (tpp) REVERT: h 388 MET cc_start: 0.7343 (tmm) cc_final: 0.6950 (tmm) REVERT: j 163 MET cc_start: 0.4893 (ppp) cc_final: 0.4414 (tpt) REVERT: j 169 LYS cc_start: 0.3559 (OUTLIER) cc_final: 0.2991 (mtmt) REVERT: n 550 MET cc_start: 0.6579 (mmp) cc_final: 0.6275 (mmm) REVERT: o 449 HIS cc_start: 0.5305 (OUTLIER) cc_final: 0.4516 (t70) REVERT: p 205 ARG cc_start: 0.3726 (tpt-90) cc_final: 0.3140 (tpp80) REVERT: s 46 MET cc_start: 0.3611 (ptm) cc_final: 0.3397 (ptm) REVERT: x 149 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6201 (tp30) outliers start: 222 outliers final: 173 residues processed: 595 average time/residue: 0.7987 time to fit residues: 847.9823 Evaluate side-chains 580 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 395 time to evaluate : 7.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 217 CYS Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 44 HIS Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 206 HIS Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 230 GLU Chi-restraints excluded: chain L residue 251 ASP Chi-restraints excluded: chain X residue 157 ARG Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain b residue 41 THR Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain d residue 3 ASP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain e residue 249 VAL Chi-restraints excluded: chain e residue 270 THR Chi-restraints excluded: chain e residue 302 ASP Chi-restraints excluded: chain f residue 229 VAL Chi-restraints excluded: chain f residue 303 ILE Chi-restraints excluded: chain f residue 338 ASP Chi-restraints excluded: chain f residue 344 LEU Chi-restraints excluded: chain f residue 369 ASN Chi-restraints excluded: chain f residue 388 LEU Chi-restraints excluded: chain f residue 436 ASP Chi-restraints excluded: chain f residue 536 LEU Chi-restraints excluded: chain f residue 544 GLU Chi-restraints excluded: chain f residue 574 THR Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 738 ASN Chi-restraints excluded: chain f residue 751 ARG Chi-restraints excluded: chain f residue 762 LEU Chi-restraints excluded: chain f residue 830 ASP Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain h residue 337 ARG Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 422 VAL Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 474 SER Chi-restraints excluded: chain h residue 534 VAL Chi-restraints excluded: chain h residue 539 ILE Chi-restraints excluded: chain h residue 544 ASN Chi-restraints excluded: chain h residue 569 VAL Chi-restraints excluded: chain h residue 572 ASP Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 169 LYS Chi-restraints excluded: chain j residue 174 GLU Chi-restraints excluded: chain j residue 180 ASP Chi-restraints excluded: chain j residue 181 PHE Chi-restraints excluded: chain j residue 231 CYS Chi-restraints excluded: chain j residue 314 TRP Chi-restraints excluded: chain j residue 325 GLU Chi-restraints excluded: chain j residue 354 LEU Chi-restraints excluded: chain m residue 408 GLU Chi-restraints excluded: chain m residue 520 ILE Chi-restraints excluded: chain m residue 525 LEU Chi-restraints excluded: chain m residue 530 VAL Chi-restraints excluded: chain m residue 609 ILE Chi-restraints excluded: chain m residue 658 LEU Chi-restraints excluded: chain m residue 662 MET Chi-restraints excluded: chain m residue 685 ASP Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain m residue 745 THR Chi-restraints excluded: chain m residue 765 VAL Chi-restraints excluded: chain n residue 311 HIS Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 393 LEU Chi-restraints excluded: chain n residue 448 MET Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain n residue 528 GLU Chi-restraints excluded: chain o residue 183 THR Chi-restraints excluded: chain o residue 255 VAL Chi-restraints excluded: chain o residue 289 VAL Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 449 HIS Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 525 LEU Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain o residue 568 ILE Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain s residue 88 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 76 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain x residue 156 ARG Chi-restraints excluded: chain x residue 177 VAL Chi-restraints excluded: chain x residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 780 optimal weight: 0.9980 chunk 1256 optimal weight: 20.0000 chunk 766 optimal weight: 0.7980 chunk 596 optimal weight: 9.9990 chunk 873 optimal weight: 10.0000 chunk 1318 optimal weight: 6.9990 chunk 1213 optimal weight: 10.0000 chunk 1049 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 810 optimal weight: 4.9990 chunk 643 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 HIS ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN ** K 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 HIS ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 150 GLN ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 391 HIS ** o 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 ASN ** x 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 190 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 94018 Z= 0.390 Angle : 0.733 13.026 128444 Z= 0.371 Chirality : 0.045 0.264 15465 Planarity : 0.005 0.079 17188 Dihedral : 7.295 177.982 14739 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.98 % Favored : 91.01 % Rotamer: Outliers : 2.78 % Allowed : 18.23 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.08), residues: 11630 helix: 0.00 (0.07), residues: 5348 sheet: -2.62 (0.12), residues: 1444 loop : -2.50 (0.09), residues: 4838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 176 HIS 0.016 0.002 HIS X 147 PHE 0.029 0.002 PHE t 49 TYR 0.040 0.002 TYR o 294 ARG 0.014 0.001 ARG e 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23260 Ramachandran restraints generated. 11630 Oldfield, 0 Emsley, 11630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 428 time to evaluate : 7.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.7268 (mtm) cc_final: 0.6604 (mpp) REVERT: B 181 MET cc_start: 0.8339 (mmm) cc_final: 0.8045 (mmm) REVERT: B 197 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: C 197 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.7199 (m-10) REVERT: D 197 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7731 (t80) REVERT: E 197 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.7501 (t80) REVERT: G 197 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.7424 (t80) REVERT: I 325 ASP cc_start: 0.8633 (m-30) cc_final: 0.8129 (t0) REVERT: X 158 ARG cc_start: 0.9055 (mtt180) cc_final: 0.8559 (mtm-85) REVERT: a 46 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7296 (tm-30) REVERT: c 1 MET cc_start: 0.5130 (mtt) cc_final: 0.4673 (mmm) REVERT: d 3 ASP cc_start: 0.5278 (OUTLIER) cc_final: 0.4922 (p0) REVERT: e 249 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8838 (t) REVERT: f 369 ASN cc_start: 0.5597 (OUTLIER) cc_final: 0.5089 (p0) REVERT: f 402 MET cc_start: 0.5391 (tpp) cc_final: 0.4989 (tpp) REVERT: f 751 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7875 (mmt-90) REVERT: h 292 MET cc_start: 0.6614 (tpt) cc_final: 0.6271 (tpp) REVERT: h 388 MET cc_start: 0.7242 (tmm) cc_final: 0.6925 (tmm) REVERT: j 139 MET cc_start: 0.2156 (mmt) cc_final: 0.1926 (mmt) REVERT: j 163 MET cc_start: 0.5733 (ppp) cc_final: 0.5123 (tpt) REVERT: j 364 MET cc_start: 0.6752 (tmm) cc_final: 0.6494 (tmm) REVERT: m 402 MET cc_start: 0.7170 (mmm) cc_final: 0.6959 (mmm) REVERT: m 481 VAL cc_start: 0.7013 (t) cc_final: 0.6679 (t) REVERT: n 550 MET cc_start: 0.6660 (mmp) cc_final: 0.6298 (mmm) REVERT: o 449 HIS cc_start: 0.5058 (OUTLIER) cc_final: 0.4387 (t70) REVERT: p 205 ARG cc_start: 0.3645 (tpt-90) cc_final: 0.3097 (tpp80) REVERT: s 46 MET cc_start: 0.3497 (ptm) cc_final: 0.3242 (ptm) REVERT: t 25 THR cc_start: 0.3870 (t) cc_final: 0.3656 (t) REVERT: x 149 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6318 (tp30) outliers start: 183 outliers final: 150 residues processed: 583 average time/residue: 0.7912 time to fit residues: 825.7045 Evaluate side-chains 577 residues out of total 10426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 417 time to evaluate : 7.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 230 GLU Chi-restraints excluded: chain X residue 144 LYS Chi-restraints excluded: chain X residue 157 ARG Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 200 ARG Chi-restraints excluded: chain a residue 8 ASP Chi-restraints excluded: chain b residue 47 HIS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain d residue 3 ASP Chi-restraints excluded: chain e residue 249 VAL Chi-restraints excluded: chain e residue 270 THR Chi-restraints excluded: chain e residue 302 ASP Chi-restraints excluded: chain f residue 229 VAL Chi-restraints excluded: chain f residue 277 PHE Chi-restraints excluded: chain f residue 285 LEU Chi-restraints excluded: chain f residue 338 ASP Chi-restraints excluded: chain f residue 369 ASN Chi-restraints excluded: chain f residue 388 LEU Chi-restraints excluded: chain f residue 544 GLU Chi-restraints excluded: chain f residue 574 THR Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 738 ASN Chi-restraints excluded: chain f residue 751 ARG Chi-restraints excluded: chain f residue 762 LEU Chi-restraints excluded: chain f residue 830 ASP Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain h residue 269 LEU Chi-restraints excluded: chain h residue 270 VAL Chi-restraints excluded: chain h residue 337 ARG Chi-restraints excluded: chain h residue 409 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 474 SER Chi-restraints excluded: chain h residue 534 VAL Chi-restraints excluded: chain h residue 539 ILE Chi-restraints excluded: chain h residue 569 VAL Chi-restraints excluded: chain h residue 572 ASP Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 174 GLU Chi-restraints excluded: chain j residue 180 ASP Chi-restraints excluded: chain j residue 181 PHE Chi-restraints excluded: chain j residue 314 TRP Chi-restraints excluded: chain j residue 325 GLU Chi-restraints excluded: chain j residue 354 LEU Chi-restraints excluded: chain m residue 520 ILE Chi-restraints excluded: chain m residue 525 LEU Chi-restraints excluded: chain m residue 658 LEU Chi-restraints excluded: chain m residue 662 MET Chi-restraints excluded: chain m residue 685 ASP Chi-restraints excluded: chain m residue 697 GLU Chi-restraints excluded: chain m residue 745 THR Chi-restraints excluded: chain m residue 765 VAL Chi-restraints excluded: chain n residue 311 HIS Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 367 ILE Chi-restraints excluded: chain n residue 393 LEU Chi-restraints excluded: chain n residue 448 MET Chi-restraints excluded: chain n residue 453 ASN Chi-restraints excluded: chain o residue 183 THR Chi-restraints excluded: chain o residue 255 VAL Chi-restraints excluded: chain o residue 361 VAL Chi-restraints excluded: chain o residue 364 VAL Chi-restraints excluded: chain o residue 412 SER Chi-restraints excluded: chain o residue 432 THR Chi-restraints excluded: chain o residue 449 HIS Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 525 LEU Chi-restraints excluded: chain o residue 550 VAL Chi-restraints excluded: chain p residue 202 HIS Chi-restraints excluded: chain p residue 206 ILE Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 79 MET Chi-restraints excluded: chain s residue 88 LEU Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 76 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain x residue 156 ARG Chi-restraints excluded: chain x residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1323 random chunks: chunk 833 optimal weight: 4.9990 chunk 1118 optimal weight: 0.0370 chunk 321 optimal weight: 0.4980 chunk 967 optimal weight: 10.0000 chunk 154 optimal weight: 0.3980 chunk 291 optimal weight: 0.6980 chunk 1051 optimal weight: 6.9990 chunk 439 optimal weight: 3.9990 chunk 1079 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 193 optimal weight: 0.0980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN D 142 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 HIS ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 529 ASN ** f 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 475 GLN ** o 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.105447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.082642 restraints weight = 505379.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.083946 restraints weight = 253958.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.083936 restraints weight = 132902.666| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 94018 Z= 0.167 Angle : 0.595 12.072 128444 Z= 0.299 Chirality : 0.042 0.284 15465 Planarity : 0.004 0.067 17188 Dihedral : 6.455 177.294 14739 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.63 % Favored : 93.36 % Rotamer: Outliers : 1.75 % Allowed : 19.30 % Favored : 78.95 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.08), residues: 11630 helix: 0.89 (0.07), residues: 5374 sheet: -2.48 (0.12), residues: 1492 loop : -2.11 (0.09), residues: 4764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 357 HIS 0.023 0.001 HIS K 234 PHE 0.030 0.001 PHE t 49 TYR 0.027 0.001 TYR o 294 ARG 0.014 0.001 ARG e 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19647.67 seconds wall clock time: 346 minutes 47.53 seconds (20807.53 seconds total)