Starting phenix.real_space_refine on Mon Mar 18 03:40:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgc_38317/03_2024/8xgc_38317_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgc_38317/03_2024/8xgc_38317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgc_38317/03_2024/8xgc_38317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgc_38317/03_2024/8xgc_38317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgc_38317/03_2024/8xgc_38317_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgc_38317/03_2024/8xgc_38317_neut_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.090 sd= 1.797 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 228 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 100 5.49 5 S 319 5.16 5 C 52216 2.51 5 N 14327 2.21 5 O 15796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ASP 120": "OD1" <-> "OD2" Residue "2 ASP 130": "OD1" <-> "OD2" Residue "2 GLU 179": "OE1" <-> "OE2" Residue "2 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 280": "OE1" <-> "OE2" Residue "2 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 407": "OE1" <-> "OE2" Residue "2 ASP 413": "OD1" <-> "OD2" Residue "2 PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 557": "OE1" <-> "OE2" Residue "2 TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 690": "OE1" <-> "OE2" Residue "2 GLU 709": "OE1" <-> "OE2" Residue "2 TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 23": "OD1" <-> "OD2" Residue "3 TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 237": "OE1" <-> "OE2" Residue "3 ASP 284": "OD1" <-> "OD2" Residue "3 ASP 375": "OD1" <-> "OD2" Residue "3 PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 558": "OD1" <-> "OD2" Residue "3 PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 214": "OE1" <-> "OE2" Residue "4 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 341": "OD1" <-> "OD2" Residue "4 GLU 359": "OE1" <-> "OE2" Residue "4 ASP 361": "OD1" <-> "OD2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 408": "OD1" <-> "OD2" Residue "4 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 431": "OD1" <-> "OD2" Residue "4 TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 639": "OD1" <-> "OD2" Residue "4 GLU 647": "OE1" <-> "OE2" Residue "4 GLU 769": "OE1" <-> "OE2" Residue "4 GLU 818": "OE1" <-> "OE2" Residue "4 GLU 905": "OE1" <-> "OE2" Residue "4 GLU 913": "OE1" <-> "OE2" Residue "5 GLU 26": "OE1" <-> "OE2" Residue "5 ASP 48": "OD1" <-> "OD2" Residue "5 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 263": "OE1" <-> "OE2" Residue "5 TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 351": "OE1" <-> "OE2" Residue "5 GLU 368": "OE1" <-> "OE2" Residue "5 GLU 430": "OE1" <-> "OE2" Residue "5 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 488": "OE1" <-> "OE2" Residue "5 TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 109": "OE1" <-> "OE2" Residue "6 GLU 141": "OE1" <-> "OE2" Residue "6 GLU 260": "OE1" <-> "OE2" Residue "6 ASP 319": "OD1" <-> "OD2" Residue "6 GLU 329": "OE1" <-> "OE2" Residue "6 ASP 393": "OD1" <-> "OD2" Residue "6 PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 140": "OD1" <-> "OD2" Residue "7 GLU 287": "OE1" <-> "OE2" Residue "7 TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 377": "OE1" <-> "OE2" Residue "7 PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 1407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 1562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 1563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 1829": "OD1" <-> "OD2" Residue "8 GLU 1954": "OE1" <-> "OE2" Residue "8 TYR 2031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 2083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 2155": "OE1" <-> "OE2" Residue "8 ASP 2219": "OD1" <-> "OD2" Residue "9 GLU 86": "OE1" <-> "OE2" Residue "9 GLU 95": "OE1" <-> "OE2" Residue "9 TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 233": "OE1" <-> "OE2" Residue "9 PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 350": "OE1" <-> "OE2" Residue "9 GLU 353": "OE1" <-> "OE2" Residue "9 ASP 410": "OD1" <-> "OD2" Residue "9 PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 627": "OD1" <-> "OD2" Residue "9 ASP 650": "OD1" <-> "OD2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "E TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 426": "OE1" <-> "OE2" Residue "E ASP 486": "OD1" <-> "OD2" Residue "F TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 576": "OE1" <-> "OE2" Residue "F PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 701": "OD1" <-> "OD2" Residue "F ASP 750": "OD1" <-> "OD2" Residue "F GLU 851": "OE1" <-> "OE2" Residue "F GLU 853": "OE1" <-> "OE2" Residue "F TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 529": "OE1" <-> "OE2" Residue "G ASP 530": "OD1" <-> "OD2" Residue "G PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 714": "OE1" <-> "OE2" Residue "G GLU 715": "OE1" <-> "OE2" Residue "G ASP 723": "OD1" <-> "OD2" Residue "G GLU 765": "OE1" <-> "OE2" Residue "G GLU 824": "OE1" <-> "OE2" Residue "H PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 509": "OE1" <-> "OE2" Residue "H TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 694": "OD1" <-> "OD2" Residue "H GLU 773": "OE1" <-> "OE2" Residue "H ASP 839": "OD1" <-> "OD2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I ASP 237": "OD1" <-> "OD2" Residue "I GLU 300": "OE1" <-> "OE2" Residue "I PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I GLU 431": "OE1" <-> "OE2" Residue "I TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 522": "OD1" <-> "OD2" Residue "I GLU 635": "OE1" <-> "OE2" Residue "I GLU 680": "OE1" <-> "OE2" Residue "I ASP 714": "OD1" <-> "OD2" Residue "I PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "L GLU 489": "OE1" <-> "OE2" Residue "L PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 884": "OD1" <-> "OD2" Residue "L TYR 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 939": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "Q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "R PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 60": "OE1" <-> "OE2" Residue "R GLU 74": "OE1" <-> "OE2" Residue "R GLU 95": "OE1" <-> "OE2" Residue "R ASP 124": "OD1" <-> "OD2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 82765 Number of models: 1 Model: "" Number of chains: 36 Chain: "2" Number of atoms: 6161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6161 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 747} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "3" Number of atoms: 4795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4795 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "4" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5269 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 23, 'TRANS': 655} Chain breaks: 7 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 88 Chain: "5" Number of atoms: 5376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5376 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 652} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 4991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4991 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 610} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 4919 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 30, 'TRANS': 604} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 53 Chain: "8" Number of atoms: 6945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6945 Classifications: {'peptide': 857} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 824} Chain breaks: 3 Chain: "9" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4594 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 3 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 193} Chain breaks: 1 Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1609 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1379 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1988 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain breaks: 2 Chain: "E" Number of atoms: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4550 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 546} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3380 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3411 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 6057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6057 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 22, 'TRANS': 722} Chain breaks: 2 Chain: "J" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 788 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 163 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "L" Number of atoms: 3474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3474 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 20, 'TRANS': 472} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 526 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 331 Chain: "M" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 1876 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 11, 'TRANS': 367} Chain breaks: 7 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1321 Unresolved non-hydrogen angles: 1691 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 7, 'TYR:plan': 18, 'ASN:plan1': 24, 'TRP:plan': 4, 'ASP:plan': 26, 'PHE:plan': 24, 'GLU:plan': 25, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 791 Chain: "N" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 629 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "O" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 583 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "P" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 703 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "Q" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "R" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 741 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "S" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "X" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1041 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Y" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 796 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2248 SG CYS 2 341 128.559 113.037 143.055 1.00132.46 S ATOM 2271 SG CYS 2 344 128.807 110.861 141.425 1.00129.95 S ATOM 2429 SG CYS 2 364 125.770 110.190 143.209 1.00128.51 S ATOM 12407 SG CYS 4 349 124.683 102.092 180.842 1.00 49.43 S ATOM 12428 SG CYS 4 352 124.066 99.667 183.520 1.00 50.23 S ATOM 12575 SG CYS 4 371 126.883 102.583 183.129 1.00 67.77 S ATOM 12617 SG CYS 4 376 127.340 98.986 181.985 1.00 57.28 S ATOM 17362 SG CYS 5 183 145.997 130.856 142.940 1.00101.90 S ATOM 17387 SG CYS 5 186 148.971 129.907 141.346 1.00104.19 S ATOM 17534 SG CYS 5 211 146.152 127.067 141.657 1.00103.68 S ATOM 17562 SG CYS 5 236 148.018 128.050 144.582 1.00125.06 S ATOM 22964 SG CYS 6 311 120.669 102.360 157.779 1.00 86.15 S ATOM 22986 SG CYS 6 314 120.651 98.545 157.226 1.00 78.71 S ATOM 23143 SG CYS 6 333 121.550 99.873 160.586 1.00 73.30 S ATOM 23177 SG CYS 6 338 123.934 100.249 157.679 1.00 81.53 S ATOM 28116 SG CYS 7 262 147.079 121.214 187.433 1.00 85.46 S ATOM 28139 SG CYS 7 265 149.840 121.707 188.327 1.00 81.93 S ATOM 28326 SG CYS 7 289 149.478 119.721 184.421 1.00 91.73 S ATOM 37533 SG CYS 82108 34.602 194.770 102.214 1.00 45.55 S ATOM 37560 SG CYS 82111 32.073 194.097 103.492 1.00 47.81 S ATOM 37709 SG CYS 82130 33.729 191.310 102.180 1.00 52.18 S ATOM 37996 SG CYS 82164 76.109 185.701 123.940 1.00 67.55 S Time building chain proxies: 31.41, per 1000 atoms: 0.38 Number of scatterers: 82765 At special positions: 0 Unit cell: (237.44, 258.64, 250.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 319 16.00 P 100 15.00 O 15796 8.00 N 14327 7.00 C 52216 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=0, symmetry=0 Time building additional restraints: 24.49 Conformation dependent library (CDL) restraints added in 10.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 341 " pdb=" ZN 41000 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 376 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 211 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb=" ZN 82301 " pdb="ZN ZN 82301 " - pdb=" SG CYS 82111 " pdb="ZN ZN 82301 " - pdb=" SG CYS 82130 " pdb="ZN ZN 82301 " - pdb=" SG CYS 82108 " pdb=" ZN 82302 " pdb="ZN ZN 82302 " - pdb=" SG CYS 82164 " Number of angles added : 18 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 361 helices and 99 sheets defined 40.0% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.93 Creating SS restraints... Processing helix chain '2' and resid 60 through 67 Processing helix chain '2' and resid 77 through 79 No H-bonds generated for 'chain '2' and resid 77 through 79' Processing helix chain '2' and resid 106 through 124 Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 194 through 199 Processing helix chain '2' and resid 201 through 216 Processing helix chain '2' and resid 226 through 236 Processing helix chain '2' and resid 246 through 251 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 removed outlier: 4.368A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 478 through 489 removed outlier: 3.857A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 removed outlier: 3.688A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) Processing helix chain '2' and resid 568 through 570 No H-bonds generated for 'chain '2' and resid 568 through 570' Processing helix chain '2' and resid 597 through 599 No H-bonds generated for 'chain '2' and resid 597 through 599' Processing helix chain '2' and resid 614 through 617 No H-bonds generated for 'chain '2' and resid 614 through 617' Processing helix chain '2' and resid 621 through 625 Processing helix chain '2' and resid 653 through 655 No H-bonds generated for 'chain '2' and resid 653 through 655' Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 675 Processing helix chain '2' and resid 691 through 705 Processing helix chain '2' and resid 740 through 753 Processing helix chain '2' and resid 760 through 772 removed outlier: 3.728A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 785 through 796 Processing helix chain '2' and resid 807 through 823 Processing helix chain '2' and resid 831 through 848 Processing helix chain '2' and resid 854 through 860 Processing helix chain '2' and resid 862 through 865 No H-bonds generated for 'chain '2' and resid 862 through 865' Processing helix chain '3' and resid 19 through 34 Processing helix chain '3' and resid 37 through 53 Processing helix chain '3' and resid 100 through 104 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 122 through 136 Processing helix chain '3' and resid 144 through 148 Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 262 through 264 No H-bonds generated for 'chain '3' and resid 262 through 264' Processing helix chain '3' and resid 344 through 355 removed outlier: 3.889A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 365 Processing helix chain '3' and resid 375 through 385 Processing helix chain '3' and resid 415 through 424 Processing helix chain '3' and resid 439 through 443 removed outlier: 3.699A pdb=" N THR 3 443 " --> pdb=" O GLY 3 439 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 439 through 443' Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 492 Processing helix chain '3' and resid 537 through 542 removed outlier: 3.731A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) Processing helix chain '3' and resid 556 through 569 Processing helix chain '3' and resid 653 through 665 Processing helix chain '3' and resid 673 through 688 removed outlier: 4.378A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 716 removed outlier: 5.499A pdb=" N THR 3 710 " --> pdb=" O ARG 3 707 " (cutoff:3.500A) Processing helix chain '3' and resid 723 through 737 removed outlier: 3.505A pdb=" N VAL 3 728 " --> pdb=" O VAL 3 724 " (cutoff:3.500A) Processing helix chain '4' and resid 187 through 200 removed outlier: 3.674A pdb=" N ARG 4 195 " --> pdb=" O THR 4 191 " (cutoff:3.500A) Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 218 through 220 No H-bonds generated for 'chain '4' and resid 218 through 220' Processing helix chain '4' and resid 225 through 236 removed outlier: 3.963A pdb=" N GLN 4 229 " --> pdb=" O TYR 4 225 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG 4 234 " --> pdb=" O LEU 4 230 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 252 through 263 removed outlier: 5.091A pdb=" N ASP 4 256 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 removed outlier: 3.984A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 507 through 513 removed outlier: 3.769A pdb=" N VAL 4 512 " --> pdb=" O LYS 4 508 " (cutoff:3.500A) Processing helix chain '4' and resid 518 through 526 Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 575 through 584 Processing helix chain '4' and resid 620 through 623 No H-bonds generated for 'chain '4' and resid 620 through 623' Processing helix chain '4' and resid 634 through 636 No H-bonds generated for 'chain '4' and resid 634 through 636' Processing helix chain '4' and resid 639 through 649 removed outlier: 3.781A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 690 No H-bonds generated for 'chain '4' and resid 688 through 690' Processing helix chain '4' and resid 696 through 699 No H-bonds generated for 'chain '4' and resid 696 through 699' Processing helix chain '4' and resid 717 through 729 removed outlier: 3.847A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 757 removed outlier: 4.041A pdb=" N GLU 4 756 " --> pdb=" O SER 4 752 " (cutoff:3.500A) Processing helix chain '4' and resid 766 through 778 Processing helix chain '4' and resid 795 through 812 Processing helix chain '4' and resid 820 through 834 Processing helix chain '4' and resid 852 through 875 removed outlier: 4.081A pdb=" N ARG 4 859 " --> pdb=" O SER 4 855 " (cutoff:3.500A) Processing helix chain '4' and resid 883 through 893 Processing helix chain '4' and resid 900 through 912 removed outlier: 3.614A pdb=" N GLN 4 904 " --> pdb=" O SER 4 900 " (cutoff:3.500A) Processing helix chain '5' and resid 21 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 87 through 102 Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 262 through 264 No H-bonds generated for 'chain '5' and resid 262 through 264' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 366 through 373 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 446 through 449 No H-bonds generated for 'chain '5' and resid 446 through 449' Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 487 through 490 No H-bonds generated for 'chain '5' and resid 487 through 490' Processing helix chain '5' and resid 494 through 497 No H-bonds generated for 'chain '5' and resid 494 through 497' Processing helix chain '5' and resid 536 through 539 No H-bonds generated for 'chain '5' and resid 536 through 539' Processing helix chain '5' and resid 544 through 549 Processing helix chain '5' and resid 562 through 577 Processing helix chain '5' and resid 579 through 590 removed outlier: 3.586A pdb=" N GLU 5 589 " --> pdb=" O ASN 5 585 " (cutoff:3.500A) Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 638 removed outlier: 3.766A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 666 Processing helix chain '5' and resid 674 through 692 removed outlier: 3.726A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) Processing helix chain '5' and resid 709 through 721 Processing helix chain '5' and resid 730 through 737 Processing helix chain '5' and resid 745 through 757 removed outlier: 3.673A pdb=" N TYR 5 753 " --> pdb=" O ASP 5 749 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 120 Processing helix chain '6' and resid 135 through 146 Processing helix chain '6' and resid 155 through 160 Processing helix chain '6' and resid 165 through 172 Processing helix chain '6' and resid 174 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 197 removed outlier: 3.771A pdb=" N LEU 6 197 " --> pdb=" O PRO 6 194 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 194 through 197' Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 408 through 410 No H-bonds generated for 'chain '6' and resid 408 through 410' Processing helix chain '6' and resid 501 through 507 Processing helix chain '6' and resid 510 through 520 removed outlier: 4.127A pdb=" N ASN 6 514 " --> pdb=" O SER 6 510 " (cutoff:3.500A) Processing helix chain '6' and resid 525 through 532 Processing helix chain '6' and resid 541 through 552 Processing helix chain '6' and resid 581 through 591 Processing helix chain '6' and resid 627 through 630 No H-bonds generated for 'chain '6' and resid 627 through 630' Processing helix chain '6' and resid 646 through 655 removed outlier: 3.770A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) Processing helix chain '6' and resid 703 through 708 Processing helix chain '6' and resid 721 through 733 Processing helix chain '6' and resid 748 through 760 Processing helix chain '6' and resid 767 through 784 removed outlier: 3.579A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 787 through 789 No H-bonds generated for 'chain '6' and resid 787 through 789' Processing helix chain '6' and resid 797 through 813 Processing helix chain '6' and resid 821 through 834 Processing helix chain '7' and resid 14 through 27 removed outlier: 4.022A pdb=" N VAL 7 26 " --> pdb=" O THR 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 82 through 95 Processing helix chain '7' and resid 102 through 108 Processing helix chain '7' and resid 110 through 123 removed outlier: 3.802A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 153 Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 287 through 291 Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 363 through 368 Processing helix chain '7' and resid 397 through 407 Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 426 through 437 removed outlier: 3.595A pdb=" N LEU 7 436 " --> pdb=" O LEU 7 432 " (cutoff:3.500A) Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 531 through 542 removed outlier: 4.874A pdb=" N HIS 7 538 " --> pdb=" O ARG 7 534 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU 7 539 " --> pdb=" O THR 7 535 " (cutoff:3.500A) Processing helix chain '7' and resid 580 through 584 Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 606 through 618 removed outlier: 4.030A pdb=" N HIS 7 615 " --> pdb=" O LYS 7 611 " (cutoff:3.500A) Processing helix chain '7' and resid 638 through 648 removed outlier: 3.790A pdb=" N ALA 7 643 " --> pdb=" O ARG 7 639 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 672 Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 728 Processing helix chain '8' and resid 1404 through 1411 Processing helix chain '8' and resid 1433 through 1441 Processing helix chain '8' and resid 1455 through 1461 Processing helix chain '8' and resid 1465 through 1467 No H-bonds generated for 'chain '8' and resid 1465 through 1467' Processing helix chain '8' and resid 1525 through 1543 removed outlier: 4.250A pdb=" N GLU 81537 " --> pdb=" O LYS 81533 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS 81538 " --> pdb=" O GLN 81534 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY 81541 " --> pdb=" O GLU 81537 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS 81542 " --> pdb=" O LYS 81538 " (cutoff:3.500A) Processing helix chain '8' and resid 1567 through 1584 removed outlier: 4.087A pdb=" N ARG 81571 " --> pdb=" O SER 81567 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU 81580 " --> pdb=" O GLU 81576 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS 81581 " --> pdb=" O THR 81577 " (cutoff:3.500A) Processing helix chain '8' and resid 1598 through 1603 Processing helix chain '8' and resid 1606 through 1609 No H-bonds generated for 'chain '8' and resid 1606 through 1609' Processing helix chain '8' and resid 1628 through 1656 removed outlier: 5.218A pdb=" N GLY 81643 " --> pdb=" O VAL 81639 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER 81644 " --> pdb=" O LEU 81640 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP 81645 " --> pdb=" O SER 81641 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR 81655 " --> pdb=" O LYS 81651 " (cutoff:3.500A) Processing helix chain '8' and resid 1669 through 1682 Processing helix chain '8' and resid 1698 through 1700 No H-bonds generated for 'chain '8' and resid 1698 through 1700' Processing helix chain '8' and resid 1707 through 1714 Processing helix chain '8' and resid 1739 through 1745 Processing helix chain '8' and resid 1747 through 1750 No H-bonds generated for 'chain '8' and resid 1747 through 1750' Processing helix chain '8' and resid 1785 through 1804 removed outlier: 4.003A pdb=" N LYS 81804 " --> pdb=" O ASP 81800 " (cutoff:3.500A) Processing helix chain '8' and resid 1807 through 1821 removed outlier: 4.926A pdb=" N ALA 81817 " --> pdb=" O VAL 81813 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER 81818 " --> pdb=" O ASN 81814 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN 81821 " --> pdb=" O ALA 81817 " (cutoff:3.500A) Processing helix chain '8' and resid 1830 through 1854 removed outlier: 3.621A pdb=" N LEU 81854 " --> pdb=" O GLU 81850 " (cutoff:3.500A) Processing helix chain '8' and resid 1879 through 1890 Processing helix chain '8' and resid 1941 through 1943 No H-bonds generated for 'chain '8' and resid 1941 through 1943' Processing helix chain '8' and resid 1947 through 1976 Proline residue: 81951 - end of helix removed outlier: 3.568A pdb=" N GLU 81954 " --> pdb=" O GLN 81950 " (cutoff:3.500A) Processing helix chain '8' and resid 2003 through 2005 No H-bonds generated for 'chain '8' and resid 2003 through 2005' Processing helix chain '8' and resid 2008 through 2025 removed outlier: 3.769A pdb=" N LYS 82013 " --> pdb=" O LYS 82009 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU 82024 " --> pdb=" O LYS 82020 " (cutoff:3.500A) Processing helix chain '8' and resid 2032 through 2034 No H-bonds generated for 'chain '8' and resid 2032 through 2034' Processing helix chain '8' and resid 2050 through 2064 Processing helix chain '8' and resid 2069 through 2082 removed outlier: 4.166A pdb=" N ILE 82082 " --> pdb=" O GLU 82078 " (cutoff:3.500A) Processing helix chain '8' and resid 2139 through 2158 Processing helix chain '8' and resid 2191 through 2208 removed outlier: 4.264A pdb=" N VAL 82195 " --> pdb=" O ARG 82191 " (cutoff:3.500A) Processing helix chain '8' and resid 2211 through 2221 Processing helix chain '9' and resid 19 through 22 No H-bonds generated for 'chain '9' and resid 19 through 22' Processing helix chain '9' and resid 35 through 49 Processing helix chain '9' and resid 51 through 53 No H-bonds generated for 'chain '9' and resid 51 through 53' Processing helix chain '9' and resid 57 through 73 Processing helix chain '9' and resid 81 through 102 Processing helix chain '9' and resid 166 through 168 No H-bonds generated for 'chain '9' and resid 166 through 168' Processing helix chain '9' and resid 202 through 205 No H-bonds generated for 'chain '9' and resid 202 through 205' Processing helix chain '9' and resid 213 through 230 removed outlier: 4.530A pdb=" N PHE 9 218 " --> pdb=" O LYS 9 214 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU 9 219 " --> pdb=" O VAL 9 215 " (cutoff:3.500A) Processing helix chain '9' and resid 233 through 235 No H-bonds generated for 'chain '9' and resid 233 through 235' Processing helix chain '9' and resid 271 through 273 No H-bonds generated for 'chain '9' and resid 271 through 273' Processing helix chain '9' and resid 352 through 359 Processing helix chain '9' and resid 381 through 393 Processing helix chain '9' and resid 411 through 426 Processing helix chain '9' and resid 454 through 471 removed outlier: 3.900A pdb=" N ARG 9 471 " --> pdb=" O THR 9 467 " (cutoff:3.500A) Processing helix chain '9' and resid 473 through 478 Processing helix chain '9' and resid 493 through 496 No H-bonds generated for 'chain '9' and resid 493 through 496' Processing helix chain '9' and resid 510 through 512 No H-bonds generated for 'chain '9' and resid 510 through 512' Processing helix chain '9' and resid 514 through 517 No H-bonds generated for 'chain '9' and resid 514 through 517' Processing helix chain '9' and resid 546 through 552 Processing helix chain '9' and resid 594 through 609 Processing helix chain 'A' and resid 4 through 22 Processing helix chain 'A' and resid 34 through 60 Processing helix chain 'A' and resid 67 through 103 Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 138 through 162 removed outlier: 4.127A pdb=" N LYS B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Proline residue: B 183 - end of helix Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 48 through 54 removed outlier: 5.155A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.537A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 4.013A pdb=" N PHE C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 192 Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 56 through 72 removed outlier: 3.733A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 124 through 153 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 171 through 174 No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 177 through 197 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 279 through 287 removed outlier: 4.826A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 removed outlier: 5.053A pdb=" N SER E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 Processing helix chain 'E' and resid 64 through 72 Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 224 through 240 removed outlier: 3.840A pdb=" N GLU E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 267 through 280 removed outlier: 4.208A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 334 through 339 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 370 through 373 No H-bonds generated for 'chain 'E' and resid 370 through 373' Processing helix chain 'E' and resid 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 388 through 395 Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 421 through 433 Processing helix chain 'E' and resid 462 through 484 Processing helix chain 'E' and resid 489 through 516 removed outlier: 3.720A pdb=" N LYS E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 538 No H-bonds generated for 'chain 'E' and resid 536 through 538' Processing helix chain 'E' and resid 542 through 557 Processing helix chain 'E' and resid 605 through 615 Processing helix chain 'E' and resid 637 through 646 Processing helix chain 'F' and resid 671 through 677 removed outlier: 4.125A pdb=" N TYR F 676 " --> pdb=" O ALA F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 731 Processing helix chain 'F' and resid 783 through 789 Processing helix chain 'F' and resid 819 through 843 Processing helix chain 'F' and resid 851 through 876 removed outlier: 3.731A pdb=" N ASP F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 879 through 887 Processing helix chain 'F' and resid 895 through 905 Processing helix chain 'F' and resid 908 through 921 Processing helix chain 'G' and resid 671 through 679 Processing helix chain 'G' and resid 713 through 715 No H-bonds generated for 'chain 'G' and resid 713 through 715' Processing helix chain 'G' and resid 724 through 732 Processing helix chain 'G' and resid 783 through 789 Processing helix chain 'G' and resid 819 through 844 removed outlier: 3.866A pdb=" N ASN G 843 " --> pdb=" O ASP G 839 " (cutoff:3.500A) Processing helix chain 'G' and resid 851 through 875 removed outlier: 3.942A pdb=" N ALA G 856 " --> pdb=" O ASN G 852 " (cutoff:3.500A) Processing helix chain 'G' and resid 879 through 888 removed outlier: 3.911A pdb=" N GLU G 888 " --> pdb=" O SER G 884 " (cutoff:3.500A) Processing helix chain 'G' and resid 892 through 904 removed outlier: 3.544A pdb=" N THR G 896 " --> pdb=" O ARG G 893 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 902 " --> pdb=" O VAL G 899 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU G 903 " --> pdb=" O LYS G 900 " (cutoff:3.500A) Processing helix chain 'G' and resid 908 through 923 removed outlier: 3.906A pdb=" N LYS G 913 " --> pdb=" O SER G 909 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN G 916 " --> pdb=" O LYS G 912 " (cutoff:3.500A) Processing helix chain 'H' and resid 671 through 674 No H-bonds generated for 'chain 'H' and resid 671 through 674' Processing helix chain 'H' and resid 724 through 731 Processing helix chain 'H' and resid 783 through 788 Processing helix chain 'H' and resid 819 through 843 Processing helix chain 'H' and resid 851 through 875 removed outlier: 3.534A pdb=" N ARG H 868 " --> pdb=" O LYS H 864 " (cutoff:3.500A) Processing helix chain 'H' and resid 879 through 888 Processing helix chain 'H' and resid 892 through 904 removed outlier: 3.551A pdb=" N VAL H 899 " --> pdb=" O LEU H 895 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS H 900 " --> pdb=" O THR H 896 " (cutoff:3.500A) Processing helix chain 'H' and resid 908 through 922 removed outlier: 4.025A pdb=" N LYS H 912 " --> pdb=" O PRO H 908 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS H 913 " --> pdb=" O SER H 909 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 31 Processing helix chain 'I' and resid 52 through 64 Processing helix chain 'I' and resid 73 through 81 removed outlier: 3.878A pdb=" N TYR I 81 " --> pdb=" O ALA I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 86 No H-bonds generated for 'chain 'I' and resid 83 through 86' Processing helix chain 'I' and resid 88 through 108 Processing helix chain 'I' and resid 118 through 135 Processing helix chain 'I' and resid 147 through 172 removed outlier: 5.253A pdb=" N GLY I 154 " --> pdb=" O ILE I 150 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 187 removed outlier: 3.801A pdb=" N VAL I 186 " --> pdb=" O LEU I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 214 Processing helix chain 'I' and resid 245 through 248 No H-bonds generated for 'chain 'I' and resid 245 through 248' Processing helix chain 'I' and resid 250 through 259 Processing helix chain 'I' and resid 262 through 270 Processing helix chain 'I' and resid 279 through 294 removed outlier: 5.495A pdb=" N ILE I 284 " --> pdb=" O ASP I 280 " (cutoff:3.500A) Proline residue: I 285 - end of helix Processing helix chain 'I' and resid 299 through 302 No H-bonds generated for 'chain 'I' and resid 299 through 302' Processing helix chain 'I' and resid 330 through 352 removed outlier: 4.039A pdb=" N HIS I 352 " --> pdb=" O ASN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 385 through 394 Processing helix chain 'I' and resid 408 through 410 No H-bonds generated for 'chain 'I' and resid 408 through 410' Processing helix chain 'I' and resid 431 through 460 removed outlier: 4.015A pdb=" N PHE I 449 " --> pdb=" O ILE I 445 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASN I 450 " --> pdb=" O ASP I 446 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE I 451 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 492 Processing helix chain 'I' and resid 498 through 505 removed outlier: 5.416A pdb=" N GLU I 503 " --> pdb=" O GLN I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 522 Processing helix chain 'I' and resid 526 through 549 Processing helix chain 'I' and resid 557 through 564 Processing helix chain 'I' and resid 569 through 576 Processing helix chain 'I' and resid 585 through 605 removed outlier: 3.799A pdb=" N GLN I 604 " --> pdb=" O LYS I 600 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR I 605 " --> pdb=" O VAL I 601 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 637 Processing helix chain 'I' and resid 641 through 652 removed outlier: 3.765A pdb=" N LEU I 652 " --> pdb=" O LEU I 648 " (cutoff:3.500A) Processing helix chain 'I' and resid 659 through 666 Processing helix chain 'I' and resid 669 through 681 removed outlier: 4.237A pdb=" N ARG I 681 " --> pdb=" O ASN I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 701 Processing helix chain 'I' and resid 713 through 723 Processing helix chain 'I' and resid 734 through 755 Processing helix chain 'I' and resid 757 through 762 Processing helix chain 'I' and resid 774 through 779 Processing helix chain 'J' and resid 56 through 59 No H-bonds generated for 'chain 'J' and resid 56 through 59' Processing helix chain 'J' and resid 65 through 75 removed outlier: 5.530A pdb=" N HIS J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS J 74 " --> pdb=" O LYS J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 102 removed outlier: 3.813A pdb=" N PHE J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR J 95 " --> pdb=" O ILE J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 121 Processing helix chain 'J' and resid 123 through 138 removed outlier: 3.502A pdb=" N PHE J 133 " --> pdb=" O ARG J 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 340 Processing helix chain 'L' and resid 487 through 513 removed outlier: 3.508A pdb=" N LYS L 510 " --> pdb=" O GLU L 506 " (cutoff:3.500A) Processing helix chain 'L' and resid 613 through 616 No H-bonds generated for 'chain 'L' and resid 613 through 616' Processing helix chain 'L' and resid 636 through 660 removed outlier: 3.763A pdb=" N GLN L 642 " --> pdb=" O GLU L 638 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE L 643 " --> pdb=" O THR L 639 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS L 647 " --> pdb=" O ILE L 643 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS L 648 " --> pdb=" O ALA L 644 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU L 649 " --> pdb=" O ASP L 645 " (cutoff:3.500A) Processing helix chain 'L' and resid 789 through 818 Processing helix chain 'L' and resid 904 through 916 removed outlier: 4.769A pdb=" N ASP L 908 " --> pdb=" O GLU L 905 " (cutoff:3.500A) Processing helix chain 'L' and resid 930 through 939 Processing helix chain 'L' and resid 941 through 946 Processing helix chain 'L' and resid 972 through 974 No H-bonds generated for 'chain 'L' and resid 972 through 974' Processing helix chain 'M' and resid 86 through 89 No H-bonds generated for 'chain 'M' and resid 86 through 89' Processing helix chain 'M' and resid 162 through 165 No H-bonds generated for 'chain 'M' and resid 162 through 165' Processing helix chain 'M' and resid 336 through 340 Processing helix chain 'M' and resid 353 through 365 Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 455 through 468 Processing helix chain 'N' and resid 65 through 79 Processing helix chain 'N' and resid 87 through 114 Processing helix chain 'N' and resid 122 through 132 Processing helix chain 'O' and resid 32 through 42 Processing helix chain 'O' and resid 49 through 76 removed outlier: 3.998A pdb=" N GLU O 53 " --> pdb=" O GLY O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 94 Processing helix chain 'P' and resid 19 through 23 Processing helix chain 'P' and resid 29 through 38 Processing helix chain 'P' and resid 48 through 74 Processing helix chain 'P' and resid 82 through 91 Processing helix chain 'P' and resid 93 through 98 Processing helix chain 'Q' and resid 42 through 52 Processing helix chain 'Q' and resid 60 through 87 Processing helix chain 'Q' and resid 95 through 105 Processing helix chain 'Q' and resid 108 through 128 removed outlier: 3.882A pdb=" N HIS Q 113 " --> pdb=" O GLU Q 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 57 Processing helix chain 'R' and resid 65 through 79 removed outlier: 3.910A pdb=" N ASP R 78 " --> pdb=" O GLU R 74 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE R 79 " --> pdb=" O ILE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 115 Processing helix chain 'R' and resid 122 through 130 Processing helix chain 'S' and resid 26 through 29 removed outlier: 3.513A pdb=" N GLY S 29 " --> pdb=" O ASN S 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 26 through 29' Processing helix chain 'S' and resid 32 through 42 Processing helix chain 'S' and resid 51 through 75 Processing helix chain 'S' and resid 84 through 93 Processing sheet with id= A, first strand: chain '2' and resid 241 through 245 removed outlier: 7.026A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG 2 296 " --> pdb=" O VAL 2 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 405 through 411 removed outlier: 3.592A pdb=" N ARG 2 406 " --> pdb=" O LEU 2 390 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN 2 391 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL 2 324 " --> pdb=" O GLN 2 391 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 331 through 334 Processing sheet with id= D, first strand: chain '2' and resid 339 through 341 removed outlier: 3.867A pdb=" N ARG 2 374 " --> pdb=" O ASN 2 340 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 525 through 527 Processing sheet with id= F, first strand: chain '2' and resid 679 through 683 removed outlier: 3.600A pdb=" N GLY 2 543 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '2' and resid 578 through 582 Processing sheet with id= H, first strand: chain '2' and resid 628 through 633 Processing sheet with id= I, first strand: chain '3' and resid 95 through 99 removed outlier: 7.233A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 291 through 298 removed outlier: 3.743A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN 3 254 " --> pdb=" O LEU 3 278 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR 3 319 " --> pdb=" O ASP 3 275 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE 3 277 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE 3 321 " --> pdb=" O ILE 3 277 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS 3 318 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL 3 295 " --> pdb=" O ASN 3 324 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL 3 326 " --> pdb=" O ASN 3 293 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN 3 293 " --> pdb=" O VAL 3 326 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 208 through 213 removed outlier: 6.511A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '3' and resid 545 through 549 Processing sheet with id= M, first strand: chain '3' and resid 444 through 448 Processing sheet with id= N, first strand: chain '3' and resid 494 through 499 Processing sheet with id= O, first strand: chain '4' and resid 240 through 244 removed outlier: 7.132A pdb=" N LYS 4 302 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU 4 243 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG 4 304 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '4' and resid 432 through 439 removed outlier: 4.035A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N SER 4 414 " --> pdb=" O TYR 4 457 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR 4 459 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER 4 416 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR 4 420 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N HIS 4 465 " --> pdb=" O TYR 4 420 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL 4 466 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLU 4 434 " --> pdb=" O VAL 4 466 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 355 through 359 Processing sheet with id= R, first strand: chain '4' and resid 704 through 707 Processing sheet with id= S, first strand: chain '4' and resid 653 through 658 Processing sheet with id= T, first strand: chain '4' and resid 916 through 919 Processing sheet with id= U, first strand: chain '4' and resid 339 through 344 removed outlier: 6.924A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '5' and resid 61 through 64 Processing sheet with id= W, first strand: chain '5' and resid 274 through 279 removed outlier: 3.787A pdb=" N SER 5 168 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLN 5 259 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE 5 166 " --> pdb=" O GLN 5 259 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE 5 297 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE 5 330 " --> pdb=" O ILE 5 297 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER 5 299 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE 5 328 " --> pdb=" O SER 5 299 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 189 through 193 removed outlier: 4.305A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 552 through 556 Processing sheet with id= Z, first strand: chain '5' and resid 452 through 455 Processing sheet with id= AA, first strand: chain '5' and resid 501 through 506 Processing sheet with id= AB, first strand: chain '5' and resid 727 through 729 Processing sheet with id= AC, first strand: chain '5' and resid 172 through 178 removed outlier: 6.493A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '6' and resid 150 through 154 removed outlier: 6.831A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain '6' and resid 394 through 400 removed outlier: 6.941A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 12.955A pdb=" N THR 6 376 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE 6 452 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP 6 378 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG 6 382 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N HIS 6 458 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain '6' and resid 344 through 346 removed outlier: 6.704A pdb=" N PHE 6 309 " --> pdb=" O ASP 6 319 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASP 6 319 " --> pdb=" O PHE 6 309 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS 6 311 " --> pdb=" O ILE 6 317 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE 6 317 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 711 through 715 removed outlier: 3.983A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY 6 634 " --> pdb=" O SER 6 677 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU 6 679 " --> pdb=" O GLY 6 634 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN 6 683 " --> pdb=" O ILE 6 638 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '6' and resid 611 through 613 Processing sheet with id= AI, first strand: chain '6' and resid 660 through 665 Processing sheet with id= AJ, first strand: chain '6' and resid 301 through 306 removed outlier: 6.794A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '7' and resid 77 through 81 removed outlier: 6.226A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain '7' and resid 330 through 335 removed outlier: 3.828A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 268 through 272 removed outlier: 4.300A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 596 through 598 removed outlier: 6.292A pdb=" N GLY 7 519 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU 7 564 " --> pdb=" O GLY 7 519 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 545 through 550 Processing sheet with id= AP, first strand: chain '7' and resid 252 through 257 removed outlier: 6.477A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '8' and resid 1345 through 1352 removed outlier: 6.661A pdb=" N THR 81341 " --> pdb=" O VAL 81324 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL 81324 " --> pdb=" O THR 81341 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '8' and resid 1374 through 1378 Processing sheet with id= AS, first strand: chain '8' and resid 1445 through 1447 Processing sheet with id= AT, first strand: chain '8' and resid 1557 through 1563 removed outlier: 4.581A pdb=" N THR 81508 " --> pdb=" O LYS 81503 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU 81497 " --> pdb=" O LEU 81514 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR 81486 " --> pdb=" O PHE 81502 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU 81589 " --> pdb=" O GLY 81485 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU 81487 " --> pdb=" O LEU 81589 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU 81591 " --> pdb=" O LEU 81487 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N HIS 81489 " --> pdb=" O LEU 81591 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN 81593 " --> pdb=" O HIS 81489 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '8' and resid 1725 through 1727 removed outlier: 6.921A pdb=" N LEU 81920 " --> pdb=" O ASP 81907 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU 81909 " --> pdb=" O SER 81918 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER 81918 " --> pdb=" O LEU 81909 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '8' and resid 1899 through 1906 removed outlier: 7.100A pdb=" N ASP 81733 " --> pdb=" O LYS 81903 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR 81905 " --> pdb=" O VAL 81731 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL 81731 " --> pdb=" O TYR 81905 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS 81869 " --> pdb=" O ILE 81858 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE 81858 " --> pdb=" O LYS 81869 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '8' and resid 2162 through 2164 Processing sheet with id= AX, first strand: chain '9' and resid 171 through 173 removed outlier: 7.238A pdb=" N THR 9 638 " --> pdb=" O VAL 9 540 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N PHE 9 542 " --> pdb=" O THR 9 638 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL 9 640 " --> pdb=" O PHE 9 542 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LYS 9 657 " --> pdb=" O MET 9 639 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU 9 641 " --> pdb=" O LYS 9 657 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE 9 659 " --> pdb=" O LEU 9 641 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '9' and resid 180 through 184 removed outlier: 3.891A pdb=" N ARG 9 180 " --> pdb=" O VAL 9 193 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain '9' and resid 303 through 307 removed outlier: 4.242A pdb=" N TRP 9 296 " --> pdb=" O ILE 9 307 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN 9 280 " --> pdb=" O TYR 9 332 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR 9 332 " --> pdb=" O GLN 9 280 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE 9 331 " --> pdb=" O VAL 9 341 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL 9 341 " --> pdb=" O ILE 9 331 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR 9 333 " --> pdb=" O PHE 9 339 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE 9 339 " --> pdb=" O TYR 9 333 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '9' and resid 681 through 688 removed outlier: 6.526A pdb=" N LEU 9 431 " --> pdb=" O VAL 9 400 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU 9 402 " --> pdb=" O LEU 9 431 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE 9 433 " --> pdb=" O LEU 9 402 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR 9 480 " --> pdb=" O LEU 9 432 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TRP 9 434 " --> pdb=" O THR 9 480 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE 9 482 " --> pdb=" O TRP 9 434 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'A' and resid 162 through 166 Processing sheet with id= BC, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.140A pdb=" N GLY A 172 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 68 through 72 Processing sheet with id= BE, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.724A pdb=" N THR C 42 " --> pdb=" O PHE C 20 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'D' and resid 274 through 278 Processing sheet with id= BG, first strand: chain 'D' and resid 255 through 260 Processing sheet with id= BH, first strand: chain 'E' and resid 57 through 61 removed outlier: 6.448A pdb=" N SER E 80 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE E 30 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU E 82 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER E 32 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL E 84 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP E 119 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU E 83 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR E 121 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'E' and resid 316 through 322 Processing sheet with id= BJ, first strand: chain 'E' and resid 519 through 521 removed outlier: 7.829A pdb=" N CYS E 528 " --> pdb=" O PRO E 566 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 568 " --> pdb=" O CYS E 528 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU E 530 " --> pdb=" O VAL E 568 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA E 570 " --> pdb=" O LEU E 530 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'F' and resid 526 through 530 removed outlier: 6.146A pdb=" N THR F 504 " --> pdb=" O TYR F 493 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR F 493 " --> pdb=" O THR F 504 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS F 506 " --> pdb=" O ARG F 491 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG F 491 " --> pdb=" O LYS F 506 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'F' and resid 536 through 539 removed outlier: 3.509A pdb=" N GLN F 553 " --> pdb=" O GLN F 548 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'F' and resid 578 through 583 removed outlier: 7.234A pdb=" N GLY F 591 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL F 581 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 589 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR F 596 " --> pdb=" O THR F 592 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'F' and resid 615 through 621 removed outlier: 6.605A pdb=" N VAL F 628 " --> pdb=" O VAL F 616 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU F 618 " --> pdb=" O PHE F 626 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE F 626 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA F 620 " --> pdb=" O ARG F 624 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG F 624 " --> pdb=" O ALA F 620 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU F 642 " --> pdb=" O TYR F 650 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR F 650 " --> pdb=" O GLU F 642 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'F' and resid 686 through 689 removed outlier: 3.701A pdb=" N SER F 686 " --> pdb=" O PHE F 698 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 722 " --> pdb=" O LEU F 704 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU F 706 " --> pdb=" O PRO F 720 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER F 708 " --> pdb=" O TRP F 718 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP F 718 " --> pdb=" O SER F 708 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'F' and resid 772 through 775 removed outlier: 6.382A pdb=" N ILE F 755 " --> pdb=" O PRO F 744 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL F 757 " --> pdb=" O VAL F 742 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL F 742 " --> pdb=" O VAL F 757 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'G' and resid 526 through 530 removed outlier: 5.717A pdb=" N THR G 504 " --> pdb=" O TYR G 493 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR G 493 " --> pdb=" O THR G 504 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LYS G 506 " --> pdb=" O ARG G 491 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG G 491 " --> pdb=" O LYS G 506 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'G' and resid 536 through 539 Processing sheet with id= BS, first strand: chain 'G' and resid 578 through 583 removed outlier: 7.153A pdb=" N GLY G 591 " --> pdb=" O THR G 579 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL G 581 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE G 589 " --> pdb=" O VAL G 581 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA G 583 " --> pdb=" O ARG G 587 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG G 587 " --> pdb=" O ALA G 583 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR G 592 " --> pdb=" O TYR G 596 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR G 596 " --> pdb=" O THR G 592 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA G 608 " --> pdb=" O SER G 599 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN G 601 " --> pdb=" O PRO G 606 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'G' and resid 648 through 650 Processing sheet with id= BU, first strand: chain 'G' and resid 686 through 689 removed outlier: 6.631A pdb=" N LEU G 706 " --> pdb=" O PRO G 720 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER G 708 " --> pdb=" O TRP G 718 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TRP G 718 " --> pdb=" O SER G 708 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'G' and resid 772 through 775 removed outlier: 5.851A pdb=" N ILE G 755 " --> pdb=" O PRO G 744 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL G 757 " --> pdb=" O VAL G 742 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL G 742 " --> pdb=" O VAL G 757 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'H' and resid 491 through 493 Processing sheet with id= BX, first strand: chain 'H' and resid 536 through 539 Processing sheet with id= BY, first strand: chain 'H' and resid 578 through 583 removed outlier: 7.390A pdb=" N GLY H 591 " --> pdb=" O THR H 579 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL H 581 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE H 589 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA H 583 " --> pdb=" O ARG H 587 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG H 587 " --> pdb=" O ALA H 583 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR H 596 " --> pdb=" O THR H 592 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN H 601 " --> pdb=" O PRO H 606 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'H' and resid 615 through 621 removed outlier: 6.677A pdb=" N VAL H 628 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU H 618 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE H 626 " --> pdb=" O LEU H 618 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA H 620 " --> pdb=" O ARG H 624 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG H 624 " --> pdb=" O ALA H 620 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU H 642 " --> pdb=" O TYR H 650 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR H 650 " --> pdb=" O GLU H 642 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'H' and resid 686 through 689 removed outlier: 3.997A pdb=" N LEU H 722 " --> pdb=" O LEU H 704 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU H 706 " --> pdb=" O PRO H 720 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER H 708 " --> pdb=" O TRP H 718 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TRP H 718 " --> pdb=" O SER H 708 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'H' and resid 772 through 775 removed outlier: 3.626A pdb=" N ALA H 746 " --> pdb=" O ASN H 753 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE H 755 " --> pdb=" O PRO H 744 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL H 757 " --> pdb=" O VAL H 742 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL H 742 " --> pdb=" O VAL H 757 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'I' and resid 363 through 366 Processing sheet with id= CD, first strand: chain 'I' and resid 612 through 614 Processing sheet with id= CE, first strand: chain 'L' and resid 561 through 565 Processing sheet with id= CF, first strand: chain 'L' and resid 625 through 629 Processing sheet with id= CG, first strand: chain 'L' and resid 704 through 708 Processing sheet with id= CH, first strand: chain 'L' and resid 757 through 763 removed outlier: 3.682A pdb=" N VAL L 739 " --> pdb=" O GLN L 730 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'L' and resid 834 through 838 Processing sheet with id= CJ, first strand: chain 'L' and resid 851 through 854 Processing sheet with id= CK, first strand: chain 'L' and resid 897 through 899 Processing sheet with id= CL, first strand: chain 'M' and resid 18 through 21 Processing sheet with id= CM, first strand: chain 'M' and resid 75 through 77 removed outlier: 3.793A pdb=" N THR M 54 " --> pdb=" O ASN M 69 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'M' and resid 115 through 118 Processing sheet with id= CO, first strand: chain 'M' and resid 142 through 145 Processing sheet with id= CP, first strand: chain 'M' and resid 243 through 245 removed outlier: 3.924A pdb=" N VAL M 243 " --> pdb=" O ILE M 261 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE M 259 " --> pdb=" O PHE M 245 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'M' and resid 248 through 250 Processing sheet with id= CR, first strand: chain 'M' and resid 315 through 321 Processing sheet with id= CS, first strand: chain 'M' and resid 325 through 329 removed outlier: 4.413A pdb=" N ALA M 351 " --> pdb=" O THR M 326 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL M 328 " --> pdb=" O TYR M 349 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR M 349 " --> pdb=" O VAL M 328 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'M' and resid 384 through 388 Processing sheet with id= CU, first strand: chain 'M' and resid 419 through 423 3430 hydrogen bonds defined for protein. 9843 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: 44.83 Time building geometry restraints manager: 27.05 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: 21197 1.33 - 1.46: 16874 1.46 - 1.58: 45613 1.58 - 1.70: 198 1.70 - 1.82: 521 Bond restraints: 84403 Sorted by residual: bond pdb=" CG PRO 5 208 " pdb=" CD PRO 5 208 " ideal model delta sigma weight residual 1.503 1.266 0.237 3.40e-02 8.65e+02 4.85e+01 bond pdb=" CA LEU 81368 " pdb=" CB LEU 81368 " ideal model delta sigma weight residual 1.527 1.629 -0.102 2.48e-02 1.63e+03 1.69e+01 bond pdb=" C PRO I 240 " pdb=" N PRO I 241 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" CB PRO 5 208 " pdb=" CG PRO 5 208 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.93e+00 bond pdb=" C3' DT X 37 " pdb=" O3' DT X 37 " ideal model delta sigma weight residual 1.422 1.506 -0.084 3.00e-02 1.11e+03 7.76e+00 ... (remaining 84398 not shown) Histogram of bond angle deviations from ideal: 89.21 - 98.66: 16 98.66 - 108.11: 4104 108.11 - 117.57: 58249 117.57 - 127.02: 51229 127.02 - 136.47: 976 Bond angle restraints: 114574 Sorted by residual: angle pdb=" N PRO 5 208 " pdb=" CD PRO 5 208 " pdb=" CG PRO 5 208 " ideal model delta sigma weight residual 103.20 89.21 13.99 1.50e+00 4.44e-01 8.70e+01 angle pdb=" CA PRO 5 208 " pdb=" N PRO 5 208 " pdb=" CD PRO 5 208 " ideal model delta sigma weight residual 112.00 102.42 9.58 1.40e+00 5.10e-01 4.68e+01 angle pdb=" N GLU L 797 " pdb=" CA GLU L 797 " pdb=" CB GLU L 797 " ideal model delta sigma weight residual 110.40 120.78 -10.38 1.63e+00 3.76e-01 4.05e+01 angle pdb=" N ILE E 524 " pdb=" CA ILE E 524 " pdb=" C ILE E 524 " ideal model delta sigma weight residual 113.71 107.98 5.73 9.50e-01 1.11e+00 3.64e+01 angle pdb=" C ALA I 704 " pdb=" N LYS I 705 " pdb=" CA LYS I 705 " ideal model delta sigma weight residual 125.02 135.47 -10.45 1.76e+00 3.23e-01 3.53e+01 ... (remaining 114569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 49864 35.92 - 71.84: 1310 71.84 - 107.76: 69 107.76 - 143.68: 6 143.68 - 179.60: 3 Dihedral angle restraints: 51252 sinusoidal: 21012 harmonic: 30240 Sorted by residual: dihedral pdb=" O2A ADP 61102 " pdb=" O3A ADP 61102 " pdb=" PA ADP 61102 " pdb=" PB ADP 61102 " ideal model delta sinusoidal sigma weight residual -60.00 73.13 -133.13 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" C5' ADP 7 902 " pdb=" O5' ADP 7 902 " pdb=" PA ADP 7 902 " pdb=" O2A ADP 7 902 " ideal model delta sinusoidal sigma weight residual -60.00 66.87 -126.87 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" O2A ADP 7 902 " pdb=" O3A ADP 7 902 " pdb=" PA ADP 7 902 " pdb=" PB ADP 7 902 " ideal model delta sinusoidal sigma weight residual -60.00 64.25 -124.25 1 2.00e+01 2.50e-03 3.75e+01 ... (remaining 51249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 12633 0.120 - 0.241: 466 0.241 - 0.361: 16 0.361 - 0.481: 4 0.481 - 0.601: 1 Chirality restraints: 13120 Sorted by residual: chirality pdb=" CB ILE 81509 " pdb=" CA ILE 81509 " pdb=" CG1 ILE 81509 " pdb=" CG2 ILE 81509 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.60 2.00e-01 2.50e+01 9.04e+00 chirality pdb=" CB ILE 2 207 " pdb=" CA ILE 2 207 " pdb=" CG1 ILE 2 207 " pdb=" CG2 ILE 2 207 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CB ILE 3 497 " pdb=" CA ILE 3 497 " pdb=" CG1 ILE 3 497 " pdb=" CG2 ILE 3 497 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 13117 not shown) Planarity restraints: 14405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 473 " -0.050 2.00e-02 2.50e+03 4.30e-02 4.62e+01 pdb=" CG TRP E 473 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 TRP E 473 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP E 473 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 473 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 473 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 473 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 473 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 473 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 473 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR 9 269 " -0.092 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PRO 9 270 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO 9 270 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO 9 270 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU 81332 " -0.075 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO 81333 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO 81333 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO 81333 " -0.060 5.00e-02 4.00e+02 ... (remaining 14402 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 13366 2.77 - 3.30: 76341 3.30 - 3.83: 139100 3.83 - 4.37: 158194 4.37 - 4.90: 270761 Nonbonded interactions: 657762 Sorted by model distance: nonbonded pdb=" OG1 THR 3 447 " pdb=" OE2 GLU 3 458 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR 3 433 " pdb=" OG SER 5 503 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR 81432 " pdb=" OE1 GLN 81435 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASP 2 113 " pdb=" OH TYR S 73 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR I 368 " pdb=" O ASP I 370 " model vdw 2.252 2.440 ... (remaining 657757 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 'F' and (resid 474 through 663 or resid 670 through 789 or (resid 790 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 892 o \ r (resid 893 through 894 and (name N or name CA or name C or name O or name CB ) \ ) or resid 895 through 901 or (resid 902 and (name N or name CA or name C or nam \ e O or name CB )) or resid 903 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 923)) selection = (chain 'G' and (resid 474 through 789 or (resid 790 and (name N or name CA or na \ me C or name O or name CB )) or resid 814 through 901 or (resid 902 and (name N \ or name CA or name C or name O or name CB )) or resid 903 through 909 or (resid \ 910 and (name N or name CA or name C or name O or name CB )) or resid 911 throug \ h 923)) selection = (chain 'H' and (resid 474 through 663 or resid 670 through 892 or (resid 893 thr \ ough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 t \ hrough 909 or (resid 910 and (name N or name CA or name C or name O or name CB ) \ ) or resid 911 or (resid 912 and (name N or name CA or name C or name O or name \ CB )) or resid 913 through 923)) } ncs_group { reference = chain 'N' selection = (chain 'R' and resid 59 through 135) } ncs_group { reference = chain 'O' selection = (chain 'S' and resid 25 through 97) } 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.370 Construct map_model_manager: 0.060 Extract box with map and model: 15.420 Check model and map are aligned: 0.900 Set scattering table: 0.550 Process input model: 192.170 Find NCS groups from input model: 3.940 Set up NCS constraints: 0.430 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 219.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.004 0.237 84403 Z= 0.298 Angle : 0.926 16.476 114574 Z= 0.486 Chirality : 0.054 0.601 13120 Planarity : 0.007 0.137 14405 Dihedral : 15.909 179.600 31580 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.02 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.07), residues: 10135 helix: -1.12 (0.07), residues: 4251 sheet: -0.27 (0.13), residues: 1663 loop : -1.14 (0.09), residues: 4221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.002 TRP E 473 HIS 0.020 0.001 HIS B 139 PHE 0.049 0.002 PHE 3 475 TYR 0.049 0.002 TYR A 32 ARG 0.033 0.001 ARG 2 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1520 time to evaluate : 8.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 78 MET cc_start: 0.8213 (ppp) cc_final: 0.7970 (ppp) REVERT: 2 710 ASN cc_start: 0.6645 (t0) cc_final: 0.6442 (p0) REVERT: 2 783 MET cc_start: 0.7672 (mmp) cc_final: 0.7428 (mmm) REVERT: 3 676 ILE cc_start: 0.8708 (mm) cc_final: 0.8419 (mm) REVERT: 5 103 ILE cc_start: 0.8423 (mm) cc_final: 0.8112 (mt) REVERT: 5 258 LEU cc_start: 0.8953 (tp) cc_final: 0.8631 (tp) REVERT: 5 552 MET cc_start: 0.8478 (mmt) cc_final: 0.8147 (mpp) REVERT: 5 638 LEU cc_start: 0.8092 (mt) cc_final: 0.7849 (mt) REVERT: 5 714 PHE cc_start: 0.6400 (t80) cc_final: 0.5970 (t80) REVERT: 5 746 LEU cc_start: 0.8191 (tp) cc_final: 0.7801 (tt) REVERT: 5 756 GLU cc_start: 0.6358 (tp30) cc_final: 0.6121 (tp30) REVERT: 6 174 TYR cc_start: 0.8485 (t80) cc_final: 0.8154 (t80) REVERT: 6 178 LEU cc_start: 0.8875 (tp) cc_final: 0.8626 (tp) REVERT: 6 394 ARG cc_start: 0.6215 (mmm-85) cc_final: 0.5762 (mpp80) REVERT: 6 505 LEU cc_start: 0.7646 (pp) cc_final: 0.7336 (mt) REVERT: 7 363 PHE cc_start: 0.4922 (t80) cc_final: 0.4537 (t80) REVERT: 7 403 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6409 (pt0) REVERT: 7 459 MET cc_start: 0.6280 (ttt) cc_final: 0.5892 (ttt) REVERT: 8 1366 MET cc_start: 0.7006 (tpp) cc_final: 0.6783 (tpp) REVERT: 9 384 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7356 (tttp) REVERT: A 32 TYR cc_start: 0.8530 (t80) cc_final: 0.8114 (t80) REVERT: A 95 ASP cc_start: 0.8479 (m-30) cc_final: 0.8097 (t0) REVERT: A 136 ASP cc_start: 0.8042 (m-30) cc_final: 0.7407 (t0) REVERT: B 124 ARG cc_start: 0.8729 (tmt170) cc_final: 0.8111 (tmt170) REVERT: B 178 ILE cc_start: 0.8398 (mm) cc_final: 0.8096 (mm) REVERT: C 22 TYR cc_start: 0.7622 (m-10) cc_final: 0.7290 (m-10) REVERT: C 134 GLU cc_start: 0.8130 (tp30) cc_final: 0.7373 (tp30) REVERT: E 44 MET cc_start: 0.8550 (mtm) cc_final: 0.8318 (mtm) REVERT: E 573 ASP cc_start: 0.7560 (t0) cc_final: 0.7269 (t0) REVERT: E 576 THR cc_start: 0.8743 (m) cc_final: 0.7824 (m) REVERT: F 637 SER cc_start: 0.9209 (p) cc_final: 0.8950 (p) REVERT: H 915 ASN cc_start: 0.6976 (m110) cc_final: 0.6457 (m110) REVERT: H 916 ASN cc_start: 0.7364 (m110) cc_final: 0.6973 (m-40) REVERT: I 66 ASP cc_start: 0.7467 (m-30) cc_final: 0.7173 (m-30) REVERT: I 337 LYS cc_start: 0.8647 (mptt) cc_final: 0.8120 (mppt) REVERT: J 116 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7388 (mt0) REVERT: J 136 GLU cc_start: 0.6940 (pp20) cc_final: 0.6573 (pp20) REVERT: L 489 GLU cc_start: 0.6981 (pm20) cc_final: 0.6532 (pm20) REVERT: L 668 LYS cc_start: 0.6255 (pptt) cc_final: 0.5754 (mtpp) REVERT: L 790 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6915 (pm20) REVERT: L 882 ASN cc_start: 0.7279 (p0) cc_final: 0.6964 (p0) REVERT: O 72 THR cc_start: 0.8429 (p) cc_final: 0.8167 (p) REVERT: P 96 ASN cc_start: 0.7981 (t0) cc_final: 0.7724 (m110) REVERT: Q 51 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7588 (tt0) REVERT: Q 80 GLU cc_start: 0.8139 (tp30) cc_final: 0.7931 (tp30) REVERT: Q 97 GLU cc_start: 0.7435 (pt0) cc_final: 0.7039 (pt0) REVERT: Q 103 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7752 (ttp80) REVERT: R 122 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7275 (tppt) REVERT: S 83 THR cc_start: 0.8111 (m) cc_final: 0.7868 (m) outliers start: 2 outliers final: 0 residues processed: 1521 average time/residue: 0.7405 time to fit residues: 1955.0820 Evaluate side-chains 1091 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1091 time to evaluate : 7.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 868 optimal weight: 3.9990 chunk 779 optimal weight: 3.9990 chunk 432 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 526 optimal weight: 2.9990 chunk 416 optimal weight: 8.9990 chunk 806 optimal weight: 4.9990 chunk 312 optimal weight: 0.2980 chunk 490 optimal weight: 0.9980 chunk 600 optimal weight: 0.9990 chunk 934 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 688 ASN 4 240 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 58 ASN ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 698 ASN 7 112 HIS ** 7 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 81434 HIS ** 81708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 628 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 135 HIS C 103 HIS ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 843 ASN H 555 GLN H 843 ASN H 891 GLN I 211 ASN I 340 GLN I 658 ASN J 90 ASN ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN Q 60 GLN Q 67 ASN ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 84403 Z= 0.201 Angle : 0.562 15.996 114574 Z= 0.289 Chirality : 0.041 0.247 13120 Planarity : 0.004 0.075 14405 Dihedral : 11.347 179.562 12216 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.37 % Allowed : 8.91 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.08), residues: 10135 helix: 0.22 (0.08), residues: 4253 sheet: -0.19 (0.13), residues: 1617 loop : -0.85 (0.09), residues: 4265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP E 473 HIS 0.010 0.001 HIS I 357 PHE 0.030 0.001 PHE I 293 TYR 0.024 0.001 TYR 9 223 ARG 0.008 0.000 ARG 6 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1146 time to evaluate : 7.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 479 GLU cc_start: 0.7072 (tp30) cc_final: 0.6851 (tp30) REVERT: 2 567 THR cc_start: 0.8472 (t) cc_final: 0.8262 (t) REVERT: 2 710 ASN cc_start: 0.6772 (t0) cc_final: 0.6440 (p0) REVERT: 2 783 MET cc_start: 0.7555 (mmp) cc_final: 0.7169 (mmm) REVERT: 3 478 MET cc_start: 0.7375 (mmm) cc_final: 0.7132 (mmt) REVERT: 3 676 ILE cc_start: 0.8693 (mm) cc_final: 0.8461 (mm) REVERT: 4 296 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8245 (pt) REVERT: 4 359 GLU cc_start: 0.7075 (pt0) cc_final: 0.6770 (pt0) REVERT: 4 636 LYS cc_start: 0.8419 (tppt) cc_final: 0.8001 (tppp) REVERT: 4 639 ASP cc_start: 0.7854 (p0) cc_final: 0.7613 (t0) REVERT: 5 103 ILE cc_start: 0.8523 (mm) cc_final: 0.8194 (mt) REVERT: 5 258 LEU cc_start: 0.9016 (tp) cc_final: 0.8712 (tp) REVERT: 5 487 ASP cc_start: 0.7443 (m-30) cc_final: 0.7006 (t70) REVERT: 5 552 MET cc_start: 0.8626 (mmt) cc_final: 0.8395 (mmm) REVERT: 5 714 PHE cc_start: 0.6685 (t80) cc_final: 0.6287 (t80) REVERT: 5 746 LEU cc_start: 0.8269 (tp) cc_final: 0.7881 (tt) REVERT: 6 394 ARG cc_start: 0.6629 (mmm-85) cc_final: 0.6051 (mpp80) REVERT: 7 403 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6518 (pt0) REVERT: 8 1366 MET cc_start: 0.7032 (tpp) cc_final: 0.6750 (tpt) REVERT: 8 1419 ASN cc_start: 0.5040 (t160) cc_final: 0.4632 (t0) REVERT: 8 2175 MET cc_start: 0.7815 (ppp) cc_final: 0.7478 (ptm) REVERT: 9 384 LYS cc_start: 0.7704 (tmtt) cc_final: 0.7346 (tptt) REVERT: 9 689 ILE cc_start: 0.6959 (mt) cc_final: 0.6683 (tt) REVERT: A 8 LYS cc_start: 0.7925 (mmpt) cc_final: 0.7465 (mmtt) REVERT: A 95 ASP cc_start: 0.8542 (m-30) cc_final: 0.8220 (t0) REVERT: A 136 ASP cc_start: 0.8263 (m-30) cc_final: 0.7517 (t0) REVERT: B 50 TRP cc_start: 0.7264 (m100) cc_final: 0.5818 (m100) REVERT: B 118 ASN cc_start: 0.7671 (p0) cc_final: 0.7308 (p0) REVERT: C 22 TYR cc_start: 0.7739 (m-10) cc_final: 0.7455 (m-10) REVERT: D 96 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7872 (mm-40) REVERT: E 1 MET cc_start: 0.6774 (tpt) cc_final: 0.6483 (tpp) REVERT: E 44 MET cc_start: 0.8601 (mtm) cc_final: 0.8264 (mtm) REVERT: E 469 LEU cc_start: 0.8310 (tp) cc_final: 0.7760 (tp) REVERT: E 473 TRP cc_start: 0.8162 (m-90) cc_final: 0.7310 (m-90) REVERT: E 573 ASP cc_start: 0.7694 (t0) cc_final: 0.7323 (t0) REVERT: F 675 ASP cc_start: 0.7781 (t0) cc_final: 0.7548 (t0) REVERT: G 477 MET cc_start: 0.7150 (mmp) cc_final: 0.6883 (mmp) REVERT: G 726 MET cc_start: 0.8254 (mmm) cc_final: 0.7956 (mmm) REVERT: G 851 GLU cc_start: 0.8062 (mp0) cc_final: 0.7355 (pm20) REVERT: H 912 LYS cc_start: 0.8115 (tppt) cc_final: 0.7424 (tppt) REVERT: H 916 ASN cc_start: 0.7674 (m110) cc_final: 0.7197 (m-40) REVERT: J 116 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7449 (mt0) REVERT: J 136 GLU cc_start: 0.7128 (pp20) cc_final: 0.6731 (pp20) REVERT: L 489 GLU cc_start: 0.6915 (pm20) cc_final: 0.6625 (pm20) REVERT: L 668 LYS cc_start: 0.6411 (pptt) cc_final: 0.5775 (mtpp) REVERT: L 790 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6998 (pm20) REVERT: L 869 GLU cc_start: 0.6902 (tt0) cc_final: 0.6449 (tt0) REVERT: N 131 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9040 (mm) REVERT: O 60 LYS cc_start: 0.8413 (tptp) cc_final: 0.7769 (tptt) REVERT: Q 80 GLU cc_start: 0.8181 (tp30) cc_final: 0.7930 (tp30) REVERT: Q 97 GLU cc_start: 0.7820 (pt0) cc_final: 0.7284 (pt0) REVERT: Q 103 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.8087 (ttp80) REVERT: R 60 GLU cc_start: 0.7508 (pp20) cc_final: 0.7149 (pp20) REVERT: R 82 ASP cc_start: 0.7191 (p0) cc_final: 0.6532 (p0) REVERT: S 54 GLU cc_start: 0.7427 (tp30) cc_final: 0.6893 (tp30) outliers start: 119 outliers final: 82 residues processed: 1224 average time/residue: 0.7290 time to fit residues: 1554.9450 Evaluate side-chains 1104 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1020 time to evaluate : 7.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 624 MET Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 4 residue 219 THR Chi-restraints excluded: chain 4 residue 240 ASN Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 368 GLU Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 690 ASP Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 286 SER Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 409 ASP Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 709 ASP Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1527 SER Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1728 ASP Chi-restraints excluded: chain 8 residue 1858 ILE Chi-restraints excluded: chain 8 residue 1999 SER Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 217 MET Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain 9 residue 682 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain G residue 580 SER Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 700 SER Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 673 ASN Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 612 VAL Chi-restraints excluded: chain I residue 658 ASN Chi-restraints excluded: chain I residue 662 VAL Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 519 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 777 optimal weight: 0.4980 chunk 636 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 936 optimal weight: 1.9990 chunk 1011 optimal weight: 7.9990 chunk 833 optimal weight: 10.0000 chunk 928 optimal weight: 0.9980 chunk 319 optimal weight: 9.9990 chunk 750 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 188 ASN 4 350 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS 7 622 HIS ** 81386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 81422 ASN ** 81702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 HIS ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 843 ASN L 500 ASN ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS S 76 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 84403 Z= 0.281 Angle : 0.583 13.765 114574 Z= 0.300 Chirality : 0.042 0.283 13120 Planarity : 0.004 0.062 14405 Dihedral : 11.154 178.628 12216 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.16 % Allowed : 11.69 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.08), residues: 10135 helix: 0.72 (0.08), residues: 4268 sheet: -0.17 (0.13), residues: 1560 loop : -0.69 (0.09), residues: 4307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 473 HIS 0.007 0.001 HIS E 382 PHE 0.044 0.002 PHE G 766 TYR 0.025 0.001 TYR 9 223 ARG 0.005 0.000 ARG I 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1077 time to evaluate : 7.332 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: 2 45 MET cc_start: 0.5931 (tmm) cc_final: 0.5695 (tmm) REVERT: 2 188 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7432 (t0) REVERT: 2 479 GLU cc_start: 0.7146 (tp30) cc_final: 0.6939 (tp30) REVERT: 2 567 THR cc_start: 0.8530 (t) cc_final: 0.8300 (t) REVERT: 2 710 ASN cc_start: 0.6920 (t0) cc_final: 0.6510 (p0) REVERT: 2 815 ARG cc_start: 0.7948 (mpp-170) cc_final: 0.7427 (mtm-85) REVERT: 3 478 MET cc_start: 0.7642 (mmm) cc_final: 0.7368 (mmt) REVERT: 4 296 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8400 (pt) REVERT: 4 636 LYS cc_start: 0.8553 (tppt) cc_final: 0.8132 (tppp) REVERT: 4 639 ASP cc_start: 0.7838 (p0) cc_final: 0.7602 (t0) REVERT: 4 847 MET cc_start: 0.6413 (tpp) cc_final: 0.6087 (tpp) REVERT: 5 31 PHE cc_start: 0.8078 (t80) cc_final: 0.7681 (t80) REVERT: 5 258 LEU cc_start: 0.9127 (tp) cc_final: 0.8917 (tp) REVERT: 5 487 ASP cc_start: 0.7561 (m-30) cc_final: 0.7097 (t70) REVERT: 5 552 MET cc_start: 0.8729 (mmt) cc_final: 0.8491 (mmt) REVERT: 5 565 ASP cc_start: 0.7096 (m-30) cc_final: 0.6816 (m-30) REVERT: 5 638 LEU cc_start: 0.8143 (mt) cc_final: 0.7891 (mt) REVERT: 5 676 HIS cc_start: 0.8539 (m170) cc_final: 0.8323 (m90) REVERT: 5 714 PHE cc_start: 0.6829 (t80) cc_final: 0.6443 (t80) REVERT: 5 746 LEU cc_start: 0.8343 (tp) cc_final: 0.7855 (tt) REVERT: 6 394 ARG cc_start: 0.6920 (mmm-85) cc_final: 0.6193 (mpp80) REVERT: 7 403 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6541 (pt0) REVERT: 8 1419 ASN cc_start: 0.5361 (t160) cc_final: 0.4978 (t160) REVERT: 8 1668 MET cc_start: 0.8135 (tpp) cc_final: 0.7935 (tpp) REVERT: 8 2175 MET cc_start: 0.8322 (ppp) cc_final: 0.7778 (ptt) REVERT: 9 188 MET cc_start: 0.7782 (mpp) cc_final: 0.7191 (tpt) REVERT: 9 689 ILE cc_start: 0.7182 (mt) cc_final: 0.6825 (tt) REVERT: A 1 MET cc_start: 0.8195 (tmm) cc_final: 0.7870 (tmm) REVERT: A 95 ASP cc_start: 0.8535 (m-30) cc_final: 0.8244 (t0) REVERT: B 50 TRP cc_start: 0.7319 (m100) cc_final: 0.6009 (m100) REVERT: B 118 ASN cc_start: 0.7992 (p0) cc_final: 0.7462 (p0) REVERT: C 22 TYR cc_start: 0.7746 (m-10) cc_final: 0.7428 (m-10) REVERT: C 126 GLU cc_start: 0.7671 (tp30) cc_final: 0.7123 (tp30) REVERT: C 134 GLU cc_start: 0.8349 (tp30) cc_final: 0.7692 (tp30) REVERT: C 186 ASP cc_start: 0.8671 (t70) cc_final: 0.8054 (t0) REVERT: D 83 LEU cc_start: 0.9558 (tp) cc_final: 0.9331 (tt) REVERT: D 185 THR cc_start: 0.9141 (p) cc_final: 0.8941 (t) REVERT: E 248 VAL cc_start: 0.7315 (m) cc_final: 0.7084 (p) REVERT: E 573 ASP cc_start: 0.7725 (t0) cc_final: 0.7409 (t70) REVERT: E 615 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7524 (mp0) REVERT: F 675 ASP cc_start: 0.7787 (t0) cc_final: 0.7584 (t0) REVERT: G 851 GLU cc_start: 0.8288 (mp0) cc_final: 0.7101 (mp0) REVERT: H 851 GLU cc_start: 0.7879 (mp0) cc_final: 0.7432 (mp0) REVERT: H 914 ILE cc_start: 0.8706 (mm) cc_final: 0.8501 (mm) REVERT: I 248 ILE cc_start: 0.8761 (mm) cc_final: 0.8544 (mt) REVERT: I 337 LYS cc_start: 0.8496 (mptt) cc_final: 0.8151 (mptt) REVERT: J 116 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7526 (mt0) REVERT: J 136 GLU cc_start: 0.7091 (pp20) cc_final: 0.6756 (pp20) REVERT: L 489 GLU cc_start: 0.7002 (pm20) cc_final: 0.6629 (pm20) REVERT: L 668 LYS cc_start: 0.6638 (pptt) cc_final: 0.5884 (mtpp) REVERT: L 790 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6827 (pm20) REVERT: L 898 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7560 (p90) REVERT: N 85 PHE cc_start: 0.3701 (OUTLIER) cc_final: 0.2192 (m-80) REVERT: N 131 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9120 (mm) REVERT: O 60 LYS cc_start: 0.8392 (tptp) cc_final: 0.7833 (tptt) REVERT: Q 103 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.8063 (ttp80) REVERT: R 60 GLU cc_start: 0.7566 (pp20) cc_final: 0.7314 (pp20) REVERT: R 82 ASP cc_start: 0.6976 (p0) cc_final: 0.6255 (p0) REVERT: R 88 SER cc_start: 0.8659 (p) cc_final: 0.8333 (p) outliers start: 187 outliers final: 127 residues processed: 1197 average time/residue: 0.7487 time to fit residues: 1567.4006 Evaluate side-chains 1132 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1000 time to evaluate : 7.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 488 SER Chi-restraints excluded: chain 2 residue 612 MET Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 3 residue 155 LEU Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 544 ASP Chi-restraints excluded: chain 4 residue 219 THR Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 562 ILE Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 368 GLU Chi-restraints excluded: chain 5 residue 389 VAL Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 596 ILE Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 286 SER Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 435 SER Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 714 VAL Chi-restraints excluded: chain 7 residue 62 LYS Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 300 MET Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 409 ASP Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 633 VAL Chi-restraints excluded: chain 8 residue 1356 THR Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1527 SER Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1728 ASP Chi-restraints excluded: chain 8 residue 1884 TYR Chi-restraints excluded: chain 8 residue 1999 SER Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2173 ASP Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 269 THR Chi-restraints excluded: chain 9 residue 309 ILE Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 523 VAL Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain 9 residue 659 ILE Chi-restraints excluded: chain 9 residue 682 THR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 682 MET Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 565 ASN Chi-restraints excluded: chain G residue 580 SER Chi-restraints excluded: chain G residue 586 VAL Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 700 SER Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 838 THR Chi-restraints excluded: chain G residue 841 LEU Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 840 THR Chi-restraints excluded: chain H residue 911 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 662 VAL Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain L residue 811 PHE Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 888 VAL Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 70 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 924 optimal weight: 0.7980 chunk 703 optimal weight: 0.0980 chunk 485 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 446 optimal weight: 0.8980 chunk 628 optimal weight: 5.9990 chunk 939 optimal weight: 30.0000 chunk 994 optimal weight: 3.9990 chunk 490 optimal weight: 1.9990 chunk 890 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 508 HIS 4 350 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 425 ASN 7 622 HIS ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 139 HIS C 159 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 HIS ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 887 HIS H 843 ASN I 130 GLN I 433 ASN I 658 ASN ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 84403 Z= 0.226 Angle : 0.553 12.543 114574 Z= 0.282 Chirality : 0.041 0.311 13120 Planarity : 0.004 0.058 14405 Dihedral : 11.021 178.723 12216 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.40 % Allowed : 13.18 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.08), residues: 10135 helix: 1.01 (0.08), residues: 4269 sheet: -0.16 (0.13), residues: 1574 loop : -0.61 (0.09), residues: 4292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP 9 70 HIS 0.008 0.001 HIS E 382 PHE 0.025 0.001 PHE 9 181 TYR 0.025 0.001 TYR 9 223 ARG 0.005 0.000 ARG 81475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1068 time to evaluate : 7.239 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: 2 45 MET cc_start: 0.6027 (tmm) cc_final: 0.5754 (tmm) REVERT: 2 49 GLU cc_start: 0.8109 (tt0) cc_final: 0.7770 (tt0) REVERT: 2 272 ASP cc_start: 0.7197 (p0) cc_final: 0.6944 (p0) REVERT: 2 434 TYR cc_start: 0.8910 (t80) cc_final: 0.8509 (t80) REVERT: 2 479 GLU cc_start: 0.7111 (tp30) cc_final: 0.6895 (tp30) REVERT: 2 567 THR cc_start: 0.8548 (t) cc_final: 0.8295 (t) REVERT: 2 710 ASN cc_start: 0.6947 (t0) cc_final: 0.6514 (p0) REVERT: 2 815 ARG cc_start: 0.7966 (mpp-170) cc_final: 0.7714 (mtm-85) REVERT: 3 478 MET cc_start: 0.7779 (mmm) cc_final: 0.7550 (mmt) REVERT: 3 546 LEU cc_start: 0.9153 (tp) cc_final: 0.8940 (tt) REVERT: 4 296 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8392 (pt) REVERT: 4 636 LYS cc_start: 0.8586 (tppt) cc_final: 0.8171 (tppp) REVERT: 4 639 ASP cc_start: 0.7800 (p0) cc_final: 0.7591 (t0) REVERT: 5 31 PHE cc_start: 0.8090 (t80) cc_final: 0.7612 (t80) REVERT: 5 258 LEU cc_start: 0.9151 (tp) cc_final: 0.8925 (tp) REVERT: 5 487 ASP cc_start: 0.7570 (m-30) cc_final: 0.7086 (t70) REVERT: 5 565 ASP cc_start: 0.7118 (m-30) cc_final: 0.6798 (m-30) REVERT: 5 638 LEU cc_start: 0.8168 (mt) cc_final: 0.7920 (mt) REVERT: 5 676 HIS cc_start: 0.8588 (m170) cc_final: 0.8387 (m90) REVERT: 5 714 PHE cc_start: 0.6764 (t80) cc_final: 0.6408 (t80) REVERT: 5 746 LEU cc_start: 0.8352 (tp) cc_final: 0.7873 (tt) REVERT: 6 394 ARG cc_start: 0.7057 (mmm-85) cc_final: 0.6337 (mpp80) REVERT: 7 403 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6708 (tm-30) REVERT: 8 1366 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6810 (tpt) REVERT: 8 1419 ASN cc_start: 0.5367 (t160) cc_final: 0.4961 (t160) REVERT: 8 2175 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8114 (ptt) REVERT: 9 689 ILE cc_start: 0.7153 (mt) cc_final: 0.6838 (tt) REVERT: A 1 MET cc_start: 0.8130 (tmm) cc_final: 0.7833 (tmm) REVERT: A 95 ASP cc_start: 0.8538 (m-30) cc_final: 0.8226 (t0) REVERT: B 50 TRP cc_start: 0.7149 (m100) cc_final: 0.6063 (m100) REVERT: B 118 ASN cc_start: 0.7934 (p0) cc_final: 0.7294 (p0) REVERT: C 22 TYR cc_start: 0.7755 (m-10) cc_final: 0.7414 (m-10) REVERT: C 134 GLU cc_start: 0.8320 (tp30) cc_final: 0.7664 (tp30) REVERT: C 186 ASP cc_start: 0.8613 (t70) cc_final: 0.8112 (t0) REVERT: D 83 LEU cc_start: 0.9558 (tp) cc_final: 0.9311 (tt) REVERT: D 96 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7943 (mm-40) REVERT: E 573 ASP cc_start: 0.7753 (t0) cc_final: 0.7425 (t70) REVERT: E 615 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7546 (mp0) REVERT: F 675 ASP cc_start: 0.7754 (t0) cc_final: 0.7552 (t0) REVERT: F 887 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7076 (t-90) REVERT: G 477 MET cc_start: 0.7115 (mmp) cc_final: 0.6854 (mmp) REVERT: G 726 MET cc_start: 0.8277 (tpp) cc_final: 0.7954 (mmm) REVERT: G 851 GLU cc_start: 0.8289 (mp0) cc_final: 0.7617 (mp0) REVERT: H 851 GLU cc_start: 0.7869 (mp0) cc_final: 0.7515 (mp0) REVERT: H 914 ILE cc_start: 0.8735 (mm) cc_final: 0.8523 (mm) REVERT: I 248 ILE cc_start: 0.8821 (mm) cc_final: 0.8615 (mt) REVERT: J 116 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7468 (mt0) REVERT: J 136 GLU cc_start: 0.7090 (pp20) cc_final: 0.6759 (pp20) REVERT: L 489 GLU cc_start: 0.6991 (pm20) cc_final: 0.6563 (pm20) REVERT: L 668 LYS cc_start: 0.6646 (pptt) cc_final: 0.5841 (mtpp) REVERT: L 790 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6864 (pm20) REVERT: L 898 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7511 (p90) REVERT: N 85 PHE cc_start: 0.3972 (OUTLIER) cc_final: 0.2478 (m-80) REVERT: N 131 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9152 (mm) REVERT: O 60 LYS cc_start: 0.8364 (tptp) cc_final: 0.7746 (tptt) REVERT: Q 97 GLU cc_start: 0.7920 (pt0) cc_final: 0.7391 (pt0) REVERT: Q 103 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.8024 (ttp80) REVERT: R 82 ASP cc_start: 0.7028 (p0) cc_final: 0.6197 (p0) REVERT: R 88 SER cc_start: 0.8628 (p) cc_final: 0.8290 (p) REVERT: R 130 ARG cc_start: 0.8361 (tmm-80) cc_final: 0.8137 (ttp80) outliers start: 208 outliers final: 140 residues processed: 1202 average time/residue: 0.7214 time to fit residues: 1515.7391 Evaluate side-chains 1151 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1004 time to evaluate : 7.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 145 MET Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 488 SER Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 3 residue 155 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 491 GLU Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 544 ASP Chi-restraints excluded: chain 4 residue 219 THR Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 562 ILE Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 4 residue 848 ASN Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 368 GLU Chi-restraints excluded: chain 5 residue 389 VAL Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 596 ILE Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 286 SER Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 435 SER Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 445 VAL Chi-restraints excluded: chain 7 residue 62 LYS Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 409 ASP Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 709 ASP Chi-restraints excluded: chain 8 residue 1356 THR Chi-restraints excluded: chain 8 residue 1366 MET Chi-restraints excluded: chain 8 residue 1460 GLN Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1527 SER Chi-restraints excluded: chain 8 residue 1547 SER Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1728 ASP Chi-restraints excluded: chain 8 residue 1858 ILE Chi-restraints excluded: chain 8 residue 1884 TYR Chi-restraints excluded: chain 8 residue 1999 SER Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2173 ASP Chi-restraints excluded: chain 8 residue 2175 MET Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 174 ASN Chi-restraints excluded: chain 9 residue 309 ILE Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain 9 residue 659 ILE Chi-restraints excluded: chain 9 residue 682 THR Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 382 HIS Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 782 VAL Chi-restraints excluded: chain F residue 887 HIS Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 565 ASN Chi-restraints excluded: chain G residue 580 SER Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 700 SER Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 766 PHE Chi-restraints excluded: chain G residue 788 GLU Chi-restraints excluded: chain G residue 817 ILE Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 838 THR Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain H residue 515 VAL Chi-restraints excluded: chain H residue 637 SER Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 840 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 612 VAL Chi-restraints excluded: chain I residue 662 VAL Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 850 ASP Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain L residue 909 PHE Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 70 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 828 optimal weight: 1.9990 chunk 564 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 740 optimal weight: 0.9980 chunk 410 optimal weight: 3.9990 chunk 848 optimal weight: 0.8980 chunk 687 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 507 optimal weight: 4.9990 chunk 892 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 188 ASN ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 531 GLN 4 350 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 81396 GLN 81702 GLN ** 81708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 HIS ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 629 HIS H 843 ASN ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 84403 Z= 0.211 Angle : 0.542 12.572 114574 Z= 0.276 Chirality : 0.041 0.309 13120 Planarity : 0.004 0.057 14405 Dihedral : 10.904 178.945 12216 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.71 % Allowed : 14.09 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.08), residues: 10135 helix: 1.17 (0.08), residues: 4275 sheet: -0.10 (0.13), residues: 1584 loop : -0.56 (0.09), residues: 4276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP 9 70 HIS 0.013 0.001 HIS F 887 PHE 0.025 0.001 PHE 9 181 TYR 0.025 0.001 TYR 9 223 ARG 0.012 0.000 ARG 5 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1075 time to evaluate : 7.206 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: 2 45 MET cc_start: 0.6152 (tmm) cc_final: 0.5807 (tmm) REVERT: 2 78 MET cc_start: 0.8326 (ppp) cc_final: 0.8108 (ppp) REVERT: 2 272 ASP cc_start: 0.7212 (p0) cc_final: 0.6948 (p0) REVERT: 2 479 GLU cc_start: 0.7090 (tp30) cc_final: 0.6872 (tp30) REVERT: 2 567 THR cc_start: 0.8560 (t) cc_final: 0.8304 (t) REVERT: 2 812 SER cc_start: 0.8460 (p) cc_final: 0.8158 (m) REVERT: 3 478 MET cc_start: 0.7837 (mmm) cc_final: 0.7580 (mmt) REVERT: 3 546 LEU cc_start: 0.9154 (tp) cc_final: 0.8951 (tt) REVERT: 4 296 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8350 (pt) REVERT: 4 639 ASP cc_start: 0.7872 (p0) cc_final: 0.7612 (t0) REVERT: 5 31 PHE cc_start: 0.8107 (t80) cc_final: 0.7590 (t80) REVERT: 5 77 LYS cc_start: 0.7676 (mttm) cc_final: 0.7118 (mttm) REVERT: 5 487 ASP cc_start: 0.7548 (m-30) cc_final: 0.7061 (t0) REVERT: 5 565 ASP cc_start: 0.7142 (m-30) cc_final: 0.6790 (m-30) REVERT: 5 638 LEU cc_start: 0.8117 (mt) cc_final: 0.7870 (mt) REVERT: 5 714 PHE cc_start: 0.6773 (t80) cc_final: 0.6415 (t80) REVERT: 5 746 LEU cc_start: 0.8368 (tp) cc_final: 0.7887 (tt) REVERT: 6 394 ARG cc_start: 0.6954 (mmm-85) cc_final: 0.6365 (mpp80) REVERT: 7 403 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6775 (tm-30) REVERT: 8 1366 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6689 (tpt) REVERT: 8 1419 ASN cc_start: 0.5381 (t160) cc_final: 0.4931 (t0) REVERT: 8 1638 HIS cc_start: 0.6608 (OUTLIER) cc_final: 0.5540 (m-70) REVERT: 8 2175 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8182 (ptt) REVERT: 9 689 ILE cc_start: 0.7127 (mt) cc_final: 0.6819 (tt) REVERT: A 1 MET cc_start: 0.8145 (tmm) cc_final: 0.7871 (tmm) REVERT: A 8 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7846 (mttp) REVERT: A 95 ASP cc_start: 0.8573 (m-30) cc_final: 0.8225 (t0) REVERT: B 50 TRP cc_start: 0.7007 (m100) cc_final: 0.6051 (m100) REVERT: B 118 ASN cc_start: 0.7853 (p0) cc_final: 0.7114 (p0) REVERT: C 22 TYR cc_start: 0.7758 (m-10) cc_final: 0.7408 (m-10) REVERT: C 134 GLU cc_start: 0.8323 (tp30) cc_final: 0.7669 (tp30) REVERT: C 186 ASP cc_start: 0.8628 (t70) cc_final: 0.8117 (t0) REVERT: D 83 LEU cc_start: 0.9557 (tp) cc_final: 0.9309 (tt) REVERT: D 96 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8094 (mm-40) REVERT: E 1 MET cc_start: 0.7279 (tpp) cc_final: 0.6845 (tpp) REVERT: E 573 ASP cc_start: 0.7805 (t0) cc_final: 0.7414 (t70) REVERT: E 615 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7592 (mp0) REVERT: F 675 ASP cc_start: 0.7756 (t0) cc_final: 0.7555 (t0) REVERT: F 887 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7455 (t-170) REVERT: G 726 MET cc_start: 0.8293 (tpp) cc_final: 0.8045 (mmm) REVERT: G 851 GLU cc_start: 0.8224 (mp0) cc_final: 0.7530 (mp0) REVERT: H 851 GLU cc_start: 0.7870 (mp0) cc_final: 0.7515 (mp0) REVERT: I 248 ILE cc_start: 0.8832 (mm) cc_final: 0.8607 (mt) REVERT: I 337 LYS cc_start: 0.8440 (mptt) cc_final: 0.8136 (mptt) REVERT: J 116 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7434 (mt0) REVERT: J 136 GLU cc_start: 0.7116 (pp20) cc_final: 0.6772 (pp20) REVERT: L 489 GLU cc_start: 0.6930 (pm20) cc_final: 0.6623 (pm20) REVERT: L 790 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6911 (pm20) REVERT: L 869 GLU cc_start: 0.6896 (tt0) cc_final: 0.6395 (tt0) REVERT: L 898 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7451 (p90) REVERT: N 85 PHE cc_start: 0.4108 (OUTLIER) cc_final: 0.2701 (m-80) REVERT: N 131 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9148 (mm) REVERT: O 60 LYS cc_start: 0.8341 (tptp) cc_final: 0.7724 (tptt) REVERT: O 89 TYR cc_start: 0.6280 (m-10) cc_final: 0.6047 (m-10) REVERT: P 59 TYR cc_start: 0.7536 (t80) cc_final: 0.7080 (t80) REVERT: Q 97 GLU cc_start: 0.7920 (pt0) cc_final: 0.7375 (pt0) REVERT: Q 103 ARG cc_start: 0.8537 (ttp-170) cc_final: 0.8106 (ttp80) REVERT: R 82 ASP cc_start: 0.7009 (p0) cc_final: 0.6247 (p0) REVERT: R 88 SER cc_start: 0.8610 (p) cc_final: 0.8281 (p) outliers start: 235 outliers final: 166 residues processed: 1230 average time/residue: 0.7151 time to fit residues: 1540.4455 Evaluate side-chains 1184 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1010 time to evaluate : 7.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 145 MET Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 488 SER Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 3 residue 155 LEU Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 3 residue 491 GLU Chi-restraints excluded: chain 3 residue 544 ASP Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 562 ILE Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 4 residue 819 LEU Chi-restraints excluded: chain 4 residue 848 ASN Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 350 THR Chi-restraints excluded: chain 5 residue 368 GLU Chi-restraints excluded: chain 5 residue 389 VAL Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 469 MET Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 596 ILE Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 286 SER Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 435 SER Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 445 VAL Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 646 ILE Chi-restraints excluded: chain 6 residue 715 ILE Chi-restraints excluded: chain 7 residue 62 LYS Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 348 ILE Chi-restraints excluded: chain 7 residue 409 ASP Chi-restraints excluded: chain 7 residue 581 LEU Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 614 GLU Chi-restraints excluded: chain 7 residue 709 ASP Chi-restraints excluded: chain 8 residue 1356 THR Chi-restraints excluded: chain 8 residue 1366 MET Chi-restraints excluded: chain 8 residue 1460 GLN Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1527 SER Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1638 HIS Chi-restraints excluded: chain 8 residue 1685 ILE Chi-restraints excluded: chain 8 residue 1728 ASP Chi-restraints excluded: chain 8 residue 1884 TYR Chi-restraints excluded: chain 8 residue 1999 SER Chi-restraints excluded: chain 8 residue 2091 VAL Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2158 LEU Chi-restraints excluded: chain 8 residue 2175 MET Chi-restraints excluded: chain 8 residue 2195 VAL Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 72 GLN Chi-restraints excluded: chain 9 residue 174 ASN Chi-restraints excluded: chain 9 residue 269 THR Chi-restraints excluded: chain 9 residue 309 ILE Chi-restraints excluded: chain 9 residue 325 MET Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 513 THR Chi-restraints excluded: chain 9 residue 523 VAL Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain 9 residue 659 ILE Chi-restraints excluded: chain 9 residue 682 THR Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 682 MET Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 782 VAL Chi-restraints excluded: chain F residue 887 HIS Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 565 ASN Chi-restraints excluded: chain G residue 580 SER Chi-restraints excluded: chain G residue 586 VAL Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 700 SER Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 766 PHE Chi-restraints excluded: chain G residue 788 GLU Chi-restraints excluded: chain G residue 817 ILE Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 838 THR Chi-restraints excluded: chain G residue 855 LEU Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain H residue 515 VAL Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 840 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 646 ASP Chi-restraints excluded: chain I residue 662 VAL Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 746 ASN Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 850 ASP Chi-restraints excluded: chain L residue 853 VAL Chi-restraints excluded: chain L residue 888 VAL Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain L residue 909 PHE Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 70 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 334 optimal weight: 0.9990 chunk 895 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 chunk 583 optimal weight: 0.0670 chunk 245 optimal weight: 7.9990 chunk 995 optimal weight: 6.9990 chunk 826 optimal weight: 0.9990 chunk 460 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 329 optimal weight: 4.9990 chunk 522 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 188 ASN 2 439 ASN ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 350 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 81702 GLN 9 103 HIS ** 9 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 843 ASN ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 84403 Z= 0.154 Angle : 0.524 12.697 114574 Z= 0.265 Chirality : 0.041 0.332 13120 Planarity : 0.003 0.057 14405 Dihedral : 10.774 179.443 12216 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.19 % Allowed : 15.18 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.08), residues: 10135 helix: 1.34 (0.08), residues: 4268 sheet: -0.08 (0.13), residues: 1617 loop : -0.48 (0.09), residues: 4250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP 9 70 HIS 0.005 0.001 HIS B 139 PHE 0.025 0.001 PHE 9 181 TYR 0.035 0.001 TYR J 128 ARG 0.010 0.000 ARG 5 630 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1097 time to evaluate : 7.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 MET cc_start: 0.6169 (tmm) cc_final: 0.5875 (tmm) REVERT: 2 272 ASP cc_start: 0.7253 (p0) cc_final: 0.6986 (p0) REVERT: 2 434 TYR cc_start: 0.8934 (t80) cc_final: 0.8523 (t80) REVERT: 2 567 THR cc_start: 0.8578 (t) cc_final: 0.8354 (t) REVERT: 2 710 ASN cc_start: 0.7060 (t0) cc_final: 0.6523 (p0) REVERT: 2 812 SER cc_start: 0.8835 (p) cc_final: 0.8469 (m) REVERT: 3 478 MET cc_start: 0.7815 (mmm) cc_final: 0.7585 (mmt) REVERT: 3 546 LEU cc_start: 0.9156 (tp) cc_final: 0.8920 (tt) REVERT: 4 296 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8316 (pt) REVERT: 4 639 ASP cc_start: 0.7845 (p0) cc_final: 0.7586 (t0) REVERT: 5 31 PHE cc_start: 0.8164 (t80) cc_final: 0.7586 (t80) REVERT: 5 565 ASP cc_start: 0.7250 (m-30) cc_final: 0.6907 (m-30) REVERT: 5 638 LEU cc_start: 0.8034 (mt) cc_final: 0.7818 (mt) REVERT: 5 714 PHE cc_start: 0.6685 (t80) cc_final: 0.6384 (t80) REVERT: 5 746 LEU cc_start: 0.8357 (tp) cc_final: 0.7957 (tt) REVERT: 6 394 ARG cc_start: 0.6964 (mmm-85) cc_final: 0.6070 (mpp80) REVERT: 7 403 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6693 (tm-30) REVERT: 8 1366 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6541 (tpt) REVERT: 8 1419 ASN cc_start: 0.5301 (t160) cc_final: 0.4877 (t0) REVERT: 8 1638 HIS cc_start: 0.6578 (OUTLIER) cc_final: 0.5503 (m-70) REVERT: 8 1827 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8313 (mp) REVERT: 8 2175 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8090 (ptt) REVERT: 9 689 ILE cc_start: 0.6958 (mt) cc_final: 0.6679 (tt) REVERT: A 8 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7645 (mmtt) REVERT: A 95 ASP cc_start: 0.8594 (m-30) cc_final: 0.7998 (t0) REVERT: A 98 ASP cc_start: 0.7815 (m-30) cc_final: 0.6931 (m-30) REVERT: B 50 TRP cc_start: 0.6827 (m100) cc_final: 0.5927 (m100) REVERT: B 118 ASN cc_start: 0.7688 (p0) cc_final: 0.7401 (p0) REVERT: C 22 TYR cc_start: 0.7778 (m-10) cc_final: 0.7381 (m-10) REVERT: C 134 GLU cc_start: 0.8299 (tp30) cc_final: 0.7654 (tp30) REVERT: C 186 ASP cc_start: 0.8602 (t70) cc_final: 0.8112 (t0) REVERT: D 83 LEU cc_start: 0.9547 (tp) cc_final: 0.9280 (tt) REVERT: D 96 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8174 (mm-40) REVERT: E 44 MET cc_start: 0.8567 (mtm) cc_final: 0.8267 (mtm) REVERT: E 248 VAL cc_start: 0.7401 (m) cc_final: 0.7149 (p) REVERT: E 473 TRP cc_start: 0.8051 (m-10) cc_final: 0.7576 (m-90) REVERT: E 573 ASP cc_start: 0.7607 (t0) cc_final: 0.7374 (t70) REVERT: E 615 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7574 (mp0) REVERT: F 610 GLU cc_start: 0.7702 (tt0) cc_final: 0.7458 (tt0) REVERT: F 675 ASP cc_start: 0.7806 (t0) cc_final: 0.7605 (t0) REVERT: F 887 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.6748 (t-170) REVERT: G 726 MET cc_start: 0.8321 (tpp) cc_final: 0.8060 (mmm) REVERT: G 851 GLU cc_start: 0.8206 (mp0) cc_final: 0.7455 (mp0) REVERT: I 248 ILE cc_start: 0.8812 (mm) cc_final: 0.8612 (mt) REVERT: I 667 MET cc_start: 0.8691 (mmt) cc_final: 0.8384 (mmt) REVERT: J 116 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7358 (mt0) REVERT: J 136 GLU cc_start: 0.7053 (pp20) cc_final: 0.6783 (pp20) REVERT: L 489 GLU cc_start: 0.6987 (pm20) cc_final: 0.6702 (pm20) REVERT: L 790 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6890 (pm20) REVERT: L 869 GLU cc_start: 0.6842 (tt0) cc_final: 0.6393 (tt0) REVERT: L 898 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7430 (p90) REVERT: N 85 PHE cc_start: 0.4091 (OUTLIER) cc_final: 0.2776 (m-80) REVERT: N 131 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9110 (mm) REVERT: O 60 LYS cc_start: 0.8289 (tptp) cc_final: 0.7667 (tptt) REVERT: P 59 TYR cc_start: 0.7583 (t80) cc_final: 0.7070 (t80) REVERT: Q 97 GLU cc_start: 0.7875 (pt0) cc_final: 0.7331 (pt0) REVERT: Q 103 ARG cc_start: 0.8497 (ttp-170) cc_final: 0.8250 (mtm110) REVERT: R 82 ASP cc_start: 0.7069 (p0) cc_final: 0.6145 (p0) REVERT: R 88 SER cc_start: 0.8616 (p) cc_final: 0.8307 (p) outliers start: 190 outliers final: 130 residues processed: 1217 average time/residue: 0.7405 time to fit residues: 1581.2112 Evaluate side-chains 1160 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1021 time to evaluate : 7.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 145 MET Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 3 residue 155 LEU Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 562 ILE Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 4 residue 848 ASN Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 350 THR Chi-restraints excluded: chain 5 residue 368 GLU Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 596 ILE Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 286 SER Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 435 SER Chi-restraints excluded: chain 7 residue 62 LYS Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 348 ILE Chi-restraints excluded: chain 7 residue 581 LEU Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 614 GLU Chi-restraints excluded: chain 7 residue 709 ASP Chi-restraints excluded: chain 8 residue 1366 MET Chi-restraints excluded: chain 8 residue 1460 GLN Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1638 HIS Chi-restraints excluded: chain 8 residue 1685 ILE Chi-restraints excluded: chain 8 residue 1827 LEU Chi-restraints excluded: chain 8 residue 1884 TYR Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2158 LEU Chi-restraints excluded: chain 8 residue 2175 MET Chi-restraints excluded: chain 8 residue 2195 VAL Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 72 GLN Chi-restraints excluded: chain 9 residue 269 THR Chi-restraints excluded: chain 9 residue 309 ILE Chi-restraints excluded: chain 9 residue 325 MET Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 513 THR Chi-restraints excluded: chain 9 residue 523 VAL Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain 9 residue 659 ILE Chi-restraints excluded: chain 9 residue 682 THR Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 887 HIS Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 565 ASN Chi-restraints excluded: chain G residue 580 SER Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 766 PHE Chi-restraints excluded: chain G residue 817 ILE Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 612 VAL Chi-restraints excluded: chain I residue 646 ASP Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 746 ASN Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 853 VAL Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain L residue 909 PHE Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 70 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 959 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 567 optimal weight: 2.9990 chunk 727 optimal weight: 0.9990 chunk 563 optimal weight: 8.9990 chunk 838 optimal weight: 0.0970 chunk 555 optimal weight: 4.9990 chunk 991 optimal weight: 0.9990 chunk 620 optimal weight: 7.9990 chunk 604 optimal weight: 1.9990 chunk 457 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 350 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 58 ASN ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 81702 GLN ** 81708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 280 GLN ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 850 ASN H 843 ASN I 211 ASN ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 84403 Z= 0.214 Angle : 0.551 12.646 114574 Z= 0.278 Chirality : 0.041 0.314 13120 Planarity : 0.004 0.057 14405 Dihedral : 10.723 179.303 12216 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.77 % Allowed : 15.56 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.08), residues: 10135 helix: 1.38 (0.08), residues: 4277 sheet: -0.08 (0.13), residues: 1616 loop : -0.43 (0.10), residues: 4242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP 9 70 HIS 0.009 0.001 HIS 7 615 PHE 0.024 0.001 PHE 9 181 TYR 0.029 0.001 TYR 9 223 ARG 0.007 0.000 ARG 5 630 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1034 time to evaluate : 7.388 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: 2 45 MET cc_start: 0.6280 (tmm) cc_final: 0.6004 (tmm) REVERT: 2 49 GLU cc_start: 0.7930 (tt0) cc_final: 0.7633 (tt0) REVERT: 2 272 ASP cc_start: 0.7284 (p0) cc_final: 0.7004 (p0) REVERT: 2 501 MET cc_start: 0.8132 (ttm) cc_final: 0.7895 (tpp) REVERT: 3 478 MET cc_start: 0.7899 (mmm) cc_final: 0.7678 (mmt) REVERT: 3 546 LEU cc_start: 0.9163 (tp) cc_final: 0.8941 (tt) REVERT: 4 296 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8314 (pt) REVERT: 4 639 ASP cc_start: 0.7971 (p0) cc_final: 0.7731 (t0) REVERT: 5 565 ASP cc_start: 0.7251 (m-30) cc_final: 0.6892 (m-30) REVERT: 5 638 LEU cc_start: 0.8084 (mt) cc_final: 0.7844 (mt) REVERT: 5 714 PHE cc_start: 0.6753 (t80) cc_final: 0.6360 (t80) REVERT: 5 746 LEU cc_start: 0.8400 (tp) cc_final: 0.7931 (tt) REVERT: 6 394 ARG cc_start: 0.7121 (mmm-85) cc_final: 0.6180 (mpp80) REVERT: 7 403 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6770 (tm-30) REVERT: 8 1366 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6768 (tpt) REVERT: 8 1419 ASN cc_start: 0.5441 (t160) cc_final: 0.5014 (t0) REVERT: 8 1482 MET cc_start: 0.4478 (tmm) cc_final: 0.4172 (tpt) REVERT: 8 1582 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5780 (mm-30) REVERT: 8 1638 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.5534 (m-70) REVERT: 8 1827 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8372 (mp) REVERT: 8 2175 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (ptt) REVERT: 9 70 TRP cc_start: 0.6439 (t60) cc_final: 0.6213 (t60) REVERT: 9 689 ILE cc_start: 0.7109 (mt) cc_final: 0.6787 (tt) REVERT: A 95 ASP cc_start: 0.8581 (m-30) cc_final: 0.7992 (t0) REVERT: A 98 ASP cc_start: 0.7793 (m-30) cc_final: 0.6980 (m-30) REVERT: B 50 TRP cc_start: 0.6836 (m100) cc_final: 0.5990 (m100) REVERT: B 118 ASN cc_start: 0.7755 (p0) cc_final: 0.7163 (p0) REVERT: C 22 TYR cc_start: 0.7839 (m-10) cc_final: 0.7466 (m-10) REVERT: C 134 GLU cc_start: 0.8340 (tp30) cc_final: 0.7650 (tp30) REVERT: C 186 ASP cc_start: 0.8699 (t70) cc_final: 0.8157 (t0) REVERT: D 83 LEU cc_start: 0.9559 (tp) cc_final: 0.9298 (tt) REVERT: E 44 MET cc_start: 0.8624 (mtm) cc_final: 0.8341 (mtm) REVERT: E 473 TRP cc_start: 0.7954 (m-10) cc_final: 0.7561 (m-90) REVERT: E 573 ASP cc_start: 0.7630 (t0) cc_final: 0.7389 (t70) REVERT: E 615 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7602 (mp0) REVERT: F 887 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.6970 (t-170) REVERT: G 477 MET cc_start: 0.7102 (mmp) cc_final: 0.6848 (mmp) REVERT: G 851 GLU cc_start: 0.8174 (mp0) cc_final: 0.7249 (mp0) REVERT: H 844 ASP cc_start: 0.6602 (t0) cc_final: 0.6385 (t0) REVERT: I 337 LYS cc_start: 0.8412 (mptt) cc_final: 0.8151 (mptt) REVERT: J 116 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7405 (mt0) REVERT: J 136 GLU cc_start: 0.7101 (pp20) cc_final: 0.6811 (pp20) REVERT: L 489 GLU cc_start: 0.6993 (pm20) cc_final: 0.6706 (pm20) REVERT: L 668 LYS cc_start: 0.6624 (pptt) cc_final: 0.5842 (mtpp) REVERT: L 790 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6901 (pm20) REVERT: L 869 GLU cc_start: 0.6858 (tt0) cc_final: 0.6359 (tt0) REVERT: L 898 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7380 (p90) REVERT: N 85 PHE cc_start: 0.4053 (OUTLIER) cc_final: 0.2713 (m-80) REVERT: N 131 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9138 (mm) REVERT: O 59 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8695 (mm) REVERT: O 60 LYS cc_start: 0.8461 (tptp) cc_final: 0.7949 (tptt) REVERT: P 59 TYR cc_start: 0.7628 (t80) cc_final: 0.7124 (t80) REVERT: Q 97 GLU cc_start: 0.7777 (pt0) cc_final: 0.7206 (pt0) REVERT: Q 103 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8331 (mtm110) REVERT: R 82 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6201 (p0) REVERT: R 88 SER cc_start: 0.8810 (p) cc_final: 0.8437 (p) REVERT: R 130 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.7846 (ttp-110) outliers start: 240 outliers final: 166 residues processed: 1189 average time/residue: 0.7274 time to fit residues: 1510.5169 Evaluate side-chains 1172 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 994 time to evaluate : 7.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 145 MET Chi-restraints excluded: chain 2 residue 181 LEU Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 488 SER Chi-restraints excluded: chain 2 residue 616 ASP Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 764 MET Chi-restraints excluded: chain 3 residue 155 LEU Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 651 VAL Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 562 ILE Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 4 residue 819 LEU Chi-restraints excluded: chain 4 residue 848 ASN Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 346 VAL Chi-restraints excluded: chain 5 residue 350 THR Chi-restraints excluded: chain 5 residue 368 GLU Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 469 MET Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 286 SER Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 435 SER Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 445 VAL Chi-restraints excluded: chain 6 residue 715 ILE Chi-restraints excluded: chain 7 residue 62 LYS Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 348 ILE Chi-restraints excluded: chain 7 residue 581 LEU Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 614 GLU Chi-restraints excluded: chain 7 residue 709 ASP Chi-restraints excluded: chain 8 residue 1350 THR Chi-restraints excluded: chain 8 residue 1356 THR Chi-restraints excluded: chain 8 residue 1366 MET Chi-restraints excluded: chain 8 residue 1460 GLN Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1527 SER Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1582 GLU Chi-restraints excluded: chain 8 residue 1638 HIS Chi-restraints excluded: chain 8 residue 1685 ILE Chi-restraints excluded: chain 8 residue 1728 ASP Chi-restraints excluded: chain 8 residue 1827 LEU Chi-restraints excluded: chain 8 residue 1858 ILE Chi-restraints excluded: chain 8 residue 1884 TYR Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2158 LEU Chi-restraints excluded: chain 8 residue 2175 MET Chi-restraints excluded: chain 8 residue 2195 VAL Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 72 GLN Chi-restraints excluded: chain 9 residue 269 THR Chi-restraints excluded: chain 9 residue 309 ILE Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 513 THR Chi-restraints excluded: chain 9 residue 523 VAL Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain 9 residue 659 ILE Chi-restraints excluded: chain 9 residue 682 THR Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 382 HIS Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 782 VAL Chi-restraints excluded: chain F residue 887 HIS Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 565 ASN Chi-restraints excluded: chain G residue 580 SER Chi-restraints excluded: chain G residue 586 VAL Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 700 SER Chi-restraints excluded: chain G residue 817 ILE Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 855 LEU Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 727 GLU Chi-restraints excluded: chain H residue 840 THR Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 612 VAL Chi-restraints excluded: chain I residue 627 GLU Chi-restraints excluded: chain I residue 646 ASP Chi-restraints excluded: chain I residue 662 VAL Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 746 ASN Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 850 ASP Chi-restraints excluded: chain L residue 853 VAL Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain L residue 909 PHE Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 613 optimal weight: 0.7980 chunk 396 optimal weight: 5.9990 chunk 592 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 630 optimal weight: 10.0000 chunk 675 optimal weight: 0.8980 chunk 490 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 779 optimal weight: 2.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 188 ASN ** 2 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 58 ASN 5 500 GLN ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 412 ASN 7 622 HIS ** 81789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 82022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 139 HIS B 196 HIS E 345 ASN ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 753 ASN F 887 HIS G 629 HIS H 843 ASN ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 84403 Z= 0.283 Angle : 0.595 16.896 114574 Z= 0.300 Chirality : 0.043 0.318 13120 Planarity : 0.004 0.057 14405 Dihedral : 10.765 178.733 12216 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.89 % Allowed : 16.08 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.08), residues: 10135 helix: 1.29 (0.08), residues: 4290 sheet: -0.17 (0.13), residues: 1595 loop : -0.50 (0.10), residues: 4250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP 9 70 HIS 0.007 0.001 HIS G 629 PHE 0.027 0.002 PHE 3 655 TYR 0.035 0.002 TYR 9 223 ARG 0.007 0.000 ARG 5 630 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1018 time to evaluate : 7.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 MET cc_start: 0.6412 (tmm) cc_final: 0.6091 (tmm) REVERT: 2 272 ASP cc_start: 0.7275 (p0) cc_final: 0.6980 (p0) REVERT: 2 812 SER cc_start: 0.8920 (p) cc_final: 0.8532 (m) REVERT: 3 384 MET cc_start: 0.9008 (tpp) cc_final: 0.8758 (tpp) REVERT: 3 478 MET cc_start: 0.7984 (mmm) cc_final: 0.7721 (mmt) REVERT: 4 342 MET cc_start: 0.8718 (mmt) cc_final: 0.8404 (mmt) REVERT: 4 639 ASP cc_start: 0.7990 (p0) cc_final: 0.7668 (t0) REVERT: 4 847 MET cc_start: 0.6408 (tpp) cc_final: 0.6186 (tpp) REVERT: 5 565 ASP cc_start: 0.7337 (m-30) cc_final: 0.6979 (m-30) REVERT: 5 638 LEU cc_start: 0.8092 (mt) cc_final: 0.7891 (mt) REVERT: 5 714 PHE cc_start: 0.6887 (t80) cc_final: 0.6484 (t80) REVERT: 5 746 LEU cc_start: 0.8459 (tp) cc_final: 0.7971 (tt) REVERT: 6 168 MET cc_start: 0.8081 (mmm) cc_final: 0.7828 (mmp) REVERT: 6 394 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6451 (mtm180) REVERT: 6 551 MET cc_start: 0.8461 (mtp) cc_final: 0.8211 (mtp) REVERT: 7 403 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6482 (pt0) REVERT: 8 1366 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6837 (tpp) REVERT: 8 1419 ASN cc_start: 0.5667 (t160) cc_final: 0.5219 (t0) REVERT: 8 1638 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.5662 (m-70) REVERT: 8 1827 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8432 (mp) REVERT: 8 1885 MET cc_start: 0.7901 (ttm) cc_final: 0.7680 (ttp) REVERT: 8 2048 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8123 (mmtt) REVERT: 9 689 ILE cc_start: 0.7259 (mt) cc_final: 0.7010 (tt) REVERT: A 95 ASP cc_start: 0.8497 (m-30) cc_final: 0.8005 (t0) REVERT: A 98 ASP cc_start: 0.7871 (m-30) cc_final: 0.7187 (m-30) REVERT: B 50 TRP cc_start: 0.6928 (m100) cc_final: 0.6094 (m100) REVERT: B 118 ASN cc_start: 0.7719 (p0) cc_final: 0.7294 (p0) REVERT: C 22 TYR cc_start: 0.7876 (m-10) cc_final: 0.7485 (m-10) REVERT: D 83 LEU cc_start: 0.9569 (tp) cc_final: 0.9328 (tt) REVERT: D 157 TYR cc_start: 0.8626 (t80) cc_final: 0.8189 (t80) REVERT: D 255 CYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7183 (p) REVERT: E 1 MET cc_start: 0.7291 (tpp) cc_final: 0.6894 (tpp) REVERT: E 44 MET cc_start: 0.8683 (mtm) cc_final: 0.8420 (mtm) REVERT: E 473 TRP cc_start: 0.7905 (m-10) cc_final: 0.7563 (m-90) REVERT: E 573 ASP cc_start: 0.7595 (t0) cc_final: 0.7356 (t70) REVERT: E 612 ILE cc_start: 0.8442 (mt) cc_final: 0.7976 (mt) REVERT: E 615 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7551 (mp0) REVERT: F 684 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8665 (mm) REVERT: F 887 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7048 (t-90) REVERT: G 851 GLU cc_start: 0.8167 (mp0) cc_final: 0.7215 (mp0) REVERT: H 903 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: I 337 LYS cc_start: 0.8371 (mptt) cc_final: 0.8105 (mptt) REVERT: J 116 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7513 (mt0) REVERT: J 136 GLU cc_start: 0.7052 (pp20) cc_final: 0.6767 (pp20) REVERT: L 489 GLU cc_start: 0.6975 (pm20) cc_final: 0.6677 (pm20) REVERT: L 790 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6827 (pm20) REVERT: L 869 GLU cc_start: 0.6988 (tt0) cc_final: 0.6478 (tt0) REVERT: L 898 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7471 (p90) REVERT: N 85 PHE cc_start: 0.4161 (OUTLIER) cc_final: 0.2671 (m-80) REVERT: N 131 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9195 (mm) REVERT: O 60 LYS cc_start: 0.8491 (tptp) cc_final: 0.8033 (tptt) REVERT: P 59 TYR cc_start: 0.7636 (t80) cc_final: 0.7176 (t80) REVERT: Q 103 ARG cc_start: 0.8629 (ttp-170) cc_final: 0.8403 (mtm110) REVERT: Q 106 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8205 (mm) REVERT: R 82 ASP cc_start: 0.7068 (p0) cc_final: 0.6114 (p0) REVERT: R 88 SER cc_start: 0.8904 (p) cc_final: 0.8489 (p) outliers start: 250 outliers final: 187 residues processed: 1183 average time/residue: 0.7463 time to fit residues: 1547.6559 Evaluate side-chains 1172 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 974 time to evaluate : 7.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 145 MET Chi-restraints excluded: chain 2 residue 181 LEU Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 488 SER Chi-restraints excluded: chain 2 residue 577 THR Chi-restraints excluded: chain 2 residue 612 MET Chi-restraints excluded: chain 2 residue 616 ASP Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 660 THR Chi-restraints excluded: chain 2 residue 764 MET Chi-restraints excluded: chain 3 residue 155 LEU Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 531 GLN Chi-restraints excluded: chain 3 residue 544 ASP Chi-restraints excluded: chain 3 residue 651 VAL Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 376 CYS Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 562 ILE Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 4 residue 819 LEU Chi-restraints excluded: chain 4 residue 848 ASN Chi-restraints excluded: chain 5 residue 58 ASN Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 260 GLU Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 337 VAL Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 346 VAL Chi-restraints excluded: chain 5 residue 350 THR Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 469 MET Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 596 ILE Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 286 SER Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 435 SER Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 445 VAL Chi-restraints excluded: chain 6 residue 715 ILE Chi-restraints excluded: chain 7 residue 62 LYS Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 348 ILE Chi-restraints excluded: chain 7 residue 581 LEU Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 614 GLU Chi-restraints excluded: chain 7 residue 633 VAL Chi-restraints excluded: chain 7 residue 709 ASP Chi-restraints excluded: chain 8 residue 1350 THR Chi-restraints excluded: chain 8 residue 1356 THR Chi-restraints excluded: chain 8 residue 1366 MET Chi-restraints excluded: chain 8 residue 1460 GLN Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1527 SER Chi-restraints excluded: chain 8 residue 1547 SER Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1638 HIS Chi-restraints excluded: chain 8 residue 1685 ILE Chi-restraints excluded: chain 8 residue 1728 ASP Chi-restraints excluded: chain 8 residue 1827 LEU Chi-restraints excluded: chain 8 residue 1858 ILE Chi-restraints excluded: chain 8 residue 1884 TYR Chi-restraints excluded: chain 8 residue 1999 SER Chi-restraints excluded: chain 8 residue 2091 VAL Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2158 LEU Chi-restraints excluded: chain 8 residue 2195 VAL Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 72 GLN Chi-restraints excluded: chain 9 residue 269 THR Chi-restraints excluded: chain 9 residue 309 ILE Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 513 THR Chi-restraints excluded: chain 9 residue 523 VAL Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain 9 residue 659 ILE Chi-restraints excluded: chain 9 residue 682 THR Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 255 CYS Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 782 VAL Chi-restraints excluded: chain F residue 887 HIS Chi-restraints excluded: chain F residue 899 VAL Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 565 ASN Chi-restraints excluded: chain G residue 580 SER Chi-restraints excluded: chain G residue 586 VAL Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 700 SER Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 788 GLU Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 855 LEU Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain H residue 515 VAL Chi-restraints excluded: chain H residue 530 ASP Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 840 THR Chi-restraints excluded: chain H residue 903 GLU Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 612 VAL Chi-restraints excluded: chain I residue 646 ASP Chi-restraints excluded: chain I residue 662 VAL Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 706 GLU Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain L residue 680 LEU Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 746 ASN Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 850 ASP Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain L residue 909 PHE Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain O residue 73 TYR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 70 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 902 optimal weight: 6.9990 chunk 950 optimal weight: 0.0060 chunk 866 optimal weight: 1.9990 chunk 924 optimal weight: 0.7980 chunk 949 optimal weight: 0.0170 chunk 556 optimal weight: 6.9990 chunk 402 optimal weight: 5.9990 chunk 725 optimal weight: 0.1980 chunk 283 optimal weight: 3.9990 chunk 835 optimal weight: 1.9990 chunk 874 optimal weight: 0.0000 overall best weight: 0.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 188 ASN ** 2 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 350 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 259 GLN ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS 81419 ASN 81702 GLN 82022 GLN 9 177 GLN 9 199 ASN ** 9 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS B 62 ASN B 139 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 ASN ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 887 HIS H 843 ASN ** I 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 84403 Z= 0.146 Angle : 0.552 13.551 114574 Z= 0.276 Chirality : 0.041 0.338 13120 Planarity : 0.003 0.058 14405 Dihedral : 10.625 179.790 12216 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.87 % Allowed : 17.39 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.08), residues: 10135 helix: 1.47 (0.08), residues: 4270 sheet: -0.07 (0.13), residues: 1648 loop : -0.38 (0.10), residues: 4217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP 9 70 HIS 0.034 0.001 HIS F 887 PHE 0.025 0.001 PHE 9 181 TYR 0.040 0.001 TYR 5 59 ARG 0.009 0.000 ARG 9 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1089 time to evaluate : 7.173 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: 2 45 MET cc_start: 0.6229 (tmm) cc_final: 0.5956 (tmm) REVERT: 2 272 ASP cc_start: 0.7245 (p0) cc_final: 0.6945 (p0) REVERT: 2 434 TYR cc_start: 0.8969 (t80) cc_final: 0.8649 (t80) REVERT: 2 812 SER cc_start: 0.8841 (p) cc_final: 0.8415 (m) REVERT: 3 270 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7672 (mm) REVERT: 3 384 MET cc_start: 0.8928 (tpp) cc_final: 0.8643 (tpp) REVERT: 3 475 PHE cc_start: 0.8410 (t80) cc_final: 0.8209 (t80) REVERT: 3 490 MET cc_start: 0.8435 (mmm) cc_final: 0.8232 (mmm) REVERT: 4 296 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8377 (pt) REVERT: 4 342 MET cc_start: 0.8628 (mmt) cc_final: 0.8255 (mmt) REVERT: 4 639 ASP cc_start: 0.7941 (p0) cc_final: 0.7650 (t0) REVERT: 4 847 MET cc_start: 0.6466 (tpp) cc_final: 0.6207 (tpp) REVERT: 5 565 ASP cc_start: 0.7331 (m-30) cc_final: 0.6978 (m-30) REVERT: 5 638 LEU cc_start: 0.8034 (mt) cc_final: 0.7809 (mt) REVERT: 5 714 PHE cc_start: 0.6812 (t80) cc_final: 0.6484 (t80) REVERT: 5 746 LEU cc_start: 0.8328 (tp) cc_final: 0.7948 (tt) REVERT: 5 756 GLU cc_start: 0.6622 (tp30) cc_final: 0.5725 (tp30) REVERT: 6 394 ARG cc_start: 0.6998 (mmm-85) cc_final: 0.6229 (mtm180) REVERT: 7 403 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6918 (tm-30) REVERT: 8 1366 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6596 (tpt) REVERT: 8 1419 ASN cc_start: 0.5067 (t0) cc_final: 0.4784 (t0) REVERT: 8 1638 HIS cc_start: 0.6536 (OUTLIER) cc_final: 0.5496 (m-70) REVERT: 8 1827 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8017 (mp) REVERT: 8 2048 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8073 (mmtt) REVERT: 9 188 MET cc_start: 0.7583 (mpp) cc_final: 0.7193 (tpt) REVERT: 9 689 ILE cc_start: 0.6950 (mt) cc_final: 0.6672 (tt) REVERT: A 32 TYR cc_start: 0.8485 (t80) cc_final: 0.8237 (t80) REVERT: A 95 ASP cc_start: 0.8601 (m-30) cc_final: 0.8032 (t0) REVERT: A 98 ASP cc_start: 0.7786 (m-30) cc_final: 0.7135 (m-30) REVERT: A 136 ASP cc_start: 0.8092 (m-30) cc_final: 0.7376 (t0) REVERT: B 50 TRP cc_start: 0.6616 (m100) cc_final: 0.5784 (m100) REVERT: B 118 ASN cc_start: 0.7392 (p0) cc_final: 0.6929 (p0) REVERT: C 22 TYR cc_start: 0.7833 (m-10) cc_final: 0.7472 (m-10) REVERT: C 126 GLU cc_start: 0.7652 (tp30) cc_final: 0.7229 (tp30) REVERT: C 134 GLU cc_start: 0.8287 (tp30) cc_final: 0.7599 (tp30) REVERT: C 186 ASP cc_start: 0.8558 (t70) cc_final: 0.8088 (t0) REVERT: D 83 LEU cc_start: 0.9545 (tp) cc_final: 0.9233 (tt) REVERT: D 157 TYR cc_start: 0.8513 (t80) cc_final: 0.8076 (t80) REVERT: D 255 CYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6998 (p) REVERT: E 44 MET cc_start: 0.8593 (mtm) cc_final: 0.8343 (mtm) REVERT: E 248 VAL cc_start: 0.7392 (m) cc_final: 0.7127 (p) REVERT: E 473 TRP cc_start: 0.7861 (m-10) cc_final: 0.7604 (m-90) REVERT: E 498 LEU cc_start: 0.9281 (mt) cc_final: 0.9055 (mp) REVERT: E 573 ASP cc_start: 0.7539 (t0) cc_final: 0.7314 (t70) REVERT: E 612 ILE cc_start: 0.8443 (mt) cc_final: 0.8152 (mm) REVERT: E 615 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7747 (mp0) REVERT: F 610 GLU cc_start: 0.7681 (tt0) cc_final: 0.7419 (tt0) REVERT: G 477 MET cc_start: 0.6996 (mmp) cc_final: 0.6734 (mmp) REVERT: G 851 GLU cc_start: 0.7984 (mp0) cc_final: 0.7424 (mp0) REVERT: H 903 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: H 912 LYS cc_start: 0.8113 (tppt) cc_final: 0.7887 (tppt) REVERT: I 96 GLU cc_start: 0.8484 (tp30) cc_final: 0.8274 (tp30) REVERT: I 337 LYS cc_start: 0.8433 (mptt) cc_final: 0.8121 (mptt) REVERT: J 116 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7312 (mt0) REVERT: J 136 GLU cc_start: 0.6986 (pp20) cc_final: 0.6741 (pp20) REVERT: L 489 GLU cc_start: 0.7037 (pm20) cc_final: 0.6755 (pm20) REVERT: L 668 LYS cc_start: 0.6626 (pptt) cc_final: 0.5861 (mtpp) REVERT: L 790 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6904 (pm20) REVERT: L 898 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7288 (p90) REVERT: N 131 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9130 (mm) REVERT: O 60 LYS cc_start: 0.8458 (tptp) cc_final: 0.8009 (tptt) REVERT: P 59 TYR cc_start: 0.7597 (t80) cc_final: 0.7126 (t80) REVERT: Q 51 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7277 (mt0) REVERT: Q 97 GLU cc_start: 0.7683 (pt0) cc_final: 0.7115 (pt0) REVERT: Q 103 ARG cc_start: 0.8575 (ttp-170) cc_final: 0.8345 (mtm110) REVERT: R 82 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6140 (p0) REVERT: R 88 SER cc_start: 0.8675 (p) cc_final: 0.8279 (p) outliers start: 162 outliers final: 121 residues processed: 1193 average time/residue: 0.7837 time to fit residues: 1643.7313 Evaluate side-chains 1142 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1011 time to evaluate : 7.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 145 MET Chi-restraints excluded: chain 2 residue 181 LEU Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 427 THR Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 616 ASP Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 3 residue 155 LEU Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 270 LEU Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 376 CYS Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 4 residue 819 LEU Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 260 GLU Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 337 VAL Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 350 THR Chi-restraints excluded: chain 5 residue 368 GLU Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 641 THR Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 445 VAL Chi-restraints excluded: chain 6 residue 715 ILE Chi-restraints excluded: chain 7 residue 62 LYS Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 348 ILE Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 614 GLU Chi-restraints excluded: chain 7 residue 622 HIS Chi-restraints excluded: chain 7 residue 709 ASP Chi-restraints excluded: chain 8 residue 1350 THR Chi-restraints excluded: chain 8 residue 1366 MET Chi-restraints excluded: chain 8 residue 1460 GLN Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1638 HIS Chi-restraints excluded: chain 8 residue 1685 ILE Chi-restraints excluded: chain 8 residue 1827 LEU Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2195 VAL Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 72 GLN Chi-restraints excluded: chain 9 residue 284 LEU Chi-restraints excluded: chain 9 residue 309 ILE Chi-restraints excluded: chain 9 residue 321 VAL Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 523 VAL Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain 9 residue 659 ILE Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 255 CYS Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 382 HIS Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 782 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 607 PHE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 600 PHE Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 903 GLU Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 627 GLU Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 706 GLU Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain L residue 680 LEU Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 746 ASN Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain L residue 909 PHE Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain S residue 26 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 920 optimal weight: 0.3980 chunk 606 optimal weight: 6.9990 chunk 977 optimal weight: 2.9990 chunk 596 optimal weight: 9.9990 chunk 463 optimal weight: 5.9990 chunk 679 optimal weight: 3.9990 chunk 1025 optimal weight: 9.9990 chunk 943 optimal weight: 30.0000 chunk 816 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 630 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 350 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 500 GLN ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS 7 622 HIS 81419 ASN ** 81702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 81789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 82060 HIS 9 280 GLN ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 843 ASN ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 84403 Z= 0.251 Angle : 0.589 14.133 114574 Z= 0.294 Chirality : 0.042 0.335 13120 Planarity : 0.004 0.056 14405 Dihedral : 10.639 179.565 12216 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.78 % Allowed : 17.82 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.08), residues: 10135 helix: 1.45 (0.08), residues: 4284 sheet: -0.10 (0.13), residues: 1607 loop : -0.41 (0.10), residues: 4244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 9 70 HIS 0.006 0.001 HIS I 357 PHE 0.030 0.002 PHE 3 655 TYR 0.039 0.001 TYR 9 223 ARG 0.008 0.000 ARG 5 630 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20270 Ramachandran restraints generated. 10135 Oldfield, 0 Emsley, 10135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1015 time to evaluate : 7.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 MET cc_start: 0.6373 (tmm) cc_final: 0.6111 (tmm) REVERT: 2 272 ASP cc_start: 0.7272 (p0) cc_final: 0.6978 (p0) REVERT: 2 434 TYR cc_start: 0.8988 (t80) cc_final: 0.8589 (t80) REVERT: 3 270 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7747 (mm) REVERT: 4 342 MET cc_start: 0.8718 (mmt) cc_final: 0.8300 (mmt) REVERT: 4 639 ASP cc_start: 0.7997 (p0) cc_final: 0.7672 (t0) REVERT: 4 847 MET cc_start: 0.6480 (tpp) cc_final: 0.6197 (tpp) REVERT: 5 565 ASP cc_start: 0.7344 (m-30) cc_final: 0.6980 (m-30) REVERT: 5 638 LEU cc_start: 0.8085 (mt) cc_final: 0.7852 (mt) REVERT: 5 714 PHE cc_start: 0.6849 (t80) cc_final: 0.6478 (t80) REVERT: 5 746 LEU cc_start: 0.8344 (tp) cc_final: 0.7868 (tt) REVERT: 6 394 ARG cc_start: 0.7067 (mmm-85) cc_final: 0.6407 (mtm180) REVERT: 6 551 MET cc_start: 0.8465 (mtp) cc_final: 0.8214 (mtp) REVERT: 7 403 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6495 (pt0) REVERT: 7 621 MET cc_start: 0.7276 (mmm) cc_final: 0.6157 (ttt) REVERT: 8 1366 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6795 (tpp) REVERT: 8 1419 ASN cc_start: 0.5718 (t160) cc_final: 0.5256 (t0) REVERT: 8 1482 MET cc_start: 0.4538 (tmm) cc_final: 0.4182 (tpt) REVERT: 8 1638 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.5566 (m-70) REVERT: 8 1827 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8226 (mp) REVERT: 8 2048 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8098 (mmtt) REVERT: 9 689 ILE cc_start: 0.7154 (mt) cc_final: 0.6838 (tt) REVERT: A 95 ASP cc_start: 0.8563 (m-30) cc_final: 0.8082 (t0) REVERT: A 98 ASP cc_start: 0.7883 (m-30) cc_final: 0.7213 (m-30) REVERT: A 198 ARG cc_start: 0.7028 (ttp-170) cc_final: 0.6729 (ptt180) REVERT: B 50 TRP cc_start: 0.6768 (m100) cc_final: 0.5985 (m100) REVERT: B 118 ASN cc_start: 0.7625 (p0) cc_final: 0.7185 (p0) REVERT: C 22 TYR cc_start: 0.7888 (m-10) cc_final: 0.7483 (m-10) REVERT: C 134 GLU cc_start: 0.8343 (tp30) cc_final: 0.7662 (tp30) REVERT: D 83 LEU cc_start: 0.9561 (tp) cc_final: 0.9302 (tt) REVERT: D 157 TYR cc_start: 0.8585 (t80) cc_final: 0.8148 (t80) REVERT: D 255 CYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7217 (p) REVERT: E 1 MET cc_start: 0.7230 (tpp) cc_final: 0.6771 (tpp) REVERT: E 44 MET cc_start: 0.8656 (mtm) cc_final: 0.8391 (mtm) REVERT: E 473 TRP cc_start: 0.7871 (m-10) cc_final: 0.7538 (m-90) REVERT: E 573 ASP cc_start: 0.7573 (t0) cc_final: 0.7335 (t70) REVERT: E 612 ILE cc_start: 0.8457 (mt) cc_final: 0.8176 (mm) REVERT: E 615 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7714 (mp0) REVERT: G 851 GLU cc_start: 0.8010 (mp0) cc_final: 0.7089 (mp0) REVERT: H 903 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: I 337 LYS cc_start: 0.8456 (mptt) cc_final: 0.8166 (mptt) REVERT: I 533 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8386 (ttp) REVERT: J 116 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7420 (mt0) REVERT: J 136 GLU cc_start: 0.7042 (pp20) cc_final: 0.6800 (pp20) REVERT: L 489 GLU cc_start: 0.7001 (pm20) cc_final: 0.6710 (pm20) REVERT: L 668 LYS cc_start: 0.6419 (pptt) cc_final: 0.5759 (mtpp) REVERT: L 790 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6867 (pm20) REVERT: L 869 GLU cc_start: 0.6828 (tt0) cc_final: 0.6312 (tt0) REVERT: L 898 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7508 (p90) REVERT: N 131 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9158 (mm) REVERT: O 60 LYS cc_start: 0.8437 (tptp) cc_final: 0.8040 (tptt) REVERT: P 59 TYR cc_start: 0.7611 (t80) cc_final: 0.7164 (t80) REVERT: Q 51 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7232 (mt0) REVERT: Q 103 ARG cc_start: 0.8649 (ttp-170) cc_final: 0.8414 (mtm110) REVERT: R 82 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6187 (p0) REVERT: R 88 SER cc_start: 0.8826 (p) cc_final: 0.8439 (p) outliers start: 154 outliers final: 130 residues processed: 1117 average time/residue: 0.7550 time to fit residues: 1475.4344 Evaluate side-chains 1131 residues out of total 9258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 991 time to evaluate : 7.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 145 MET Chi-restraints excluded: chain 2 residue 181 LEU Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 427 THR Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 577 THR Chi-restraints excluded: chain 2 residue 616 ASP Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 3 residue 155 LEU Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 270 LEU Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 376 CYS Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 664 THR Chi-restraints excluded: chain 4 residue 666 ASN Chi-restraints excluded: chain 4 residue 819 LEU Chi-restraints excluded: chain 5 residue 159 ILE Chi-restraints excluded: chain 5 residue 260 GLU Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 337 VAL Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 350 THR Chi-restraints excluded: chain 5 residue 414 LEU Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 641 THR Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 319 ASP Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 445 VAL Chi-restraints excluded: chain 6 residue 715 ILE Chi-restraints excluded: chain 7 residue 62 LYS Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 348 ILE Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 607 ASP Chi-restraints excluded: chain 7 residue 614 GLU Chi-restraints excluded: chain 7 residue 622 HIS Chi-restraints excluded: chain 7 residue 709 ASP Chi-restraints excluded: chain 8 residue 1350 THR Chi-restraints excluded: chain 8 residue 1366 MET Chi-restraints excluded: chain 8 residue 1460 GLN Chi-restraints excluded: chain 8 residue 1509 ILE Chi-restraints excluded: chain 8 residue 1560 PHE Chi-restraints excluded: chain 8 residue 1606 LEU Chi-restraints excluded: chain 8 residue 1638 HIS Chi-restraints excluded: chain 8 residue 1685 ILE Chi-restraints excluded: chain 8 residue 1827 LEU Chi-restraints excluded: chain 8 residue 1858 ILE Chi-restraints excluded: chain 8 residue 2102 VAL Chi-restraints excluded: chain 8 residue 2195 VAL Chi-restraints excluded: chain 8 residue 2198 LEU Chi-restraints excluded: chain 9 residue 72 GLN Chi-restraints excluded: chain 9 residue 284 LEU Chi-restraints excluded: chain 9 residue 309 ILE Chi-restraints excluded: chain 9 residue 356 LEU Chi-restraints excluded: chain 9 residue 491 TRP Chi-restraints excluded: chain 9 residue 523 VAL Chi-restraints excluded: chain 9 residue 633 CYS Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 255 CYS Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 782 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 835 GLU Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 600 PHE Chi-restraints excluded: chain H residue 627 SER Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 903 GLU Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 533 MET Chi-restraints excluded: chain I residue 557 ILE Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 693 VAL Chi-restraints excluded: chain I residue 706 GLU Chi-restraints excluded: chain I residue 768 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain L residue 680 LEU Chi-restraints excluded: chain L residue 738 VAL Chi-restraints excluded: chain L residue 746 ASN Chi-restraints excluded: chain L residue 813 ASP Chi-restraints excluded: chain L residue 843 VAL Chi-restraints excluded: chain L residue 898 HIS Chi-restraints excluded: chain L residue 909 PHE Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain O residue 73 TYR Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 26 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 500 optimal weight: 5.9990 chunk 648 optimal weight: 3.9990 chunk 869 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 752 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 817 optimal weight: 1.9990 chunk 342 optimal weight: 9.9990 chunk 839 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 350 ASN ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS 81702 GLN ** 81789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 189 GLN ** 9 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 843 ASN ** I 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125167 restraints weight = 168087.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122962 restraints weight = 224678.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121008 restraints weight = 147411.662| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 84403 Z= 0.179 Angle : 0.560 13.517 114574 Z= 0.280 Chirality : 0.041 0.334 13120 Planarity : 0.003 0.057 14405 Dihedral : 10.586 179.767 12216 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.91 % Allowed : 17.82 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.08), residues: 10135 helix: 1.51 (0.08), residues: 4278 sheet: -0.07 (0.13), residues: 1625 loop : -0.38 (0.10), residues: 4232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 9 70 HIS 0.017 0.001 HIS 7 622 PHE 0.030 0.001 PHE 3 655 TYR 0.025 0.001 TYR O 89 ARG 0.007 0.000 ARG 5 630 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22161.48 seconds wall clock time: 389 minutes 6.91 seconds (23346.91 seconds total)