Starting phenix.real_space_refine on Wed Feb 14 23:02:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3u_31684/02_2024/7v3u_31684_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3u_31684/02_2024/7v3u_31684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3u_31684/02_2024/7v3u_31684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3u_31684/02_2024/7v3u_31684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3u_31684/02_2024/7v3u_31684_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3u_31684/02_2024/7v3u_31684_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 34 5.49 5 Mg 12 5.21 5 S 297 5.16 5 C 39267 2.51 5 N 10931 2.21 5 O 12095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 210": "OE1" <-> "OE2" Residue "2 GLU 217": "OE1" <-> "OE2" Residue "2 TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 236": "OE1" <-> "OE2" Residue "2 GLU 280": "OE1" <-> "OE2" Residue "2 TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 285": "OD1" <-> "OD2" Residue "2 GLU 292": "OE1" <-> "OE2" Residue "2 GLU 311": "OE1" <-> "OE2" Residue "2 GLU 357": "OE1" <-> "OE2" Residue "2 PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 378": "OE1" <-> "OE2" Residue "2 GLU 392": "OE1" <-> "OE2" Residue "2 GLU 422": "OE1" <-> "OE2" Residue "2 GLU 425": "OE1" <-> "OE2" Residue "2 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 478": "OE1" <-> "OE2" Residue "2 GLU 480": "OE1" <-> "OE2" Residue "2 ASP 510": "OD1" <-> "OD2" Residue "2 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 536": "OD1" <-> "OD2" Residue "2 GLU 588": "OE1" <-> "OE2" Residue "2 GLU 608": "OE1" <-> "OE2" Residue "2 TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 671": "OE1" <-> "OE2" Residue "2 GLU 689": "OE1" <-> "OE2" Residue "2 GLU 690": "OE1" <-> "OE2" Residue "2 ASP 701": "OD1" <-> "OD2" Residue "2 GLU 761": "OE1" <-> "OE2" Residue "2 TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 811": "OE1" <-> "OE2" Residue "2 GLU 818": "OE1" <-> "OE2" Residue "2 ASP 833": "OD1" <-> "OD2" Residue "2 ASP 835": "OD1" <-> "OD2" Residue "3 ASP 23": "OD1" <-> "OD2" Residue "3 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 105": "OE1" <-> "OE2" Residue "3 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 235": "OD1" <-> "OD2" Residue "3 ASP 252": "OD1" <-> "OD2" Residue "3 ASP 280": "OD1" <-> "OD2" Residue "3 PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 458": "OE1" <-> "OE2" Residue "3 GLU 474": "OE1" <-> "OE2" Residue "3 GLU 488": "OE1" <-> "OE2" Residue "3 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 524": "OD1" <-> "OD2" Residue "3 TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 665": "OE1" <-> "OE2" Residue "4 ASP 210": "OD1" <-> "OD2" Residue "4 GLU 222": "OE1" <-> "OE2" Residue "4 GLU 235": "OE1" <-> "OE2" Residue "4 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 316": "OE1" <-> "OE2" Residue "4 ASP 341": "OD1" <-> "OD2" Residue "4 GLU 367": "OE1" <-> "OE2" Residue "4 ASP 375": "OD1" <-> "OD2" Residue "4 ASP 477": "OD1" <-> "OD2" Residue "4 GLU 494": "OE1" <-> "OE2" Residue "4 GLU 497": "OE1" <-> "OE2" Residue "4 ASP 505": "OD1" <-> "OD2" Residue "4 GLU 532": "OE1" <-> "OE2" Residue "4 TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 632": "OD1" <-> "OD2" Residue "4 GLU 633": "OE1" <-> "OE2" Residue "4 GLU 647": "OE1" <-> "OE2" Residue "4 ASP 710": "OD1" <-> "OD2" Residue "4 GLU 818": "OE1" <-> "OE2" Residue "5 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 26": "OE1" <-> "OE2" Residue "5 ASP 41": "OD1" <-> "OD2" Residue "5 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 82": "OE1" <-> "OE2" Residue "5 GLU 91": "OE1" <-> "OE2" Residue "5 ASP 150": "OD1" <-> "OD2" Residue "5 GLU 154": "OE1" <-> "OE2" Residue "5 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 260": "OE1" <-> "OE2" Residue "5 GLU 263": "OE1" <-> "OE2" Residue "5 ASP 279": "OD1" <-> "OD2" Residue "5 GLU 351": "OE1" <-> "OE2" Residue "5 GLU 356": "OE1" <-> "OE2" Residue "5 GLU 430": "OE1" <-> "OE2" Residue "5 TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 481": "OE1" <-> "OE2" Residue "5 GLU 488": "OE1" <-> "OE2" Residue "5 GLU 495": "OE1" <-> "OE2" Residue "5 GLU 498": "OE1" <-> "OE2" Residue "5 ASP 558": "OD1" <-> "OD2" Residue "5 GLU 562": "OE1" <-> "OE2" Residue "5 GLU 597": "OE1" <-> "OE2" Residue "5 GLU 654": "OE1" <-> "OE2" Residue "5 GLU 661": "OE1" <-> "OE2" Residue "5 GLU 667": "OE1" <-> "OE2" Residue "5 ASP 695": "OD1" <-> "OD2" Residue "6 ASP 105": "OD1" <-> "OD2" Residue "6 GLU 133": "OE1" <-> "OE2" Residue "6 GLU 141": "OE1" <-> "OE2" Residue "6 GLU 195": "OE1" <-> "OE2" Residue "6 GLU 260": "OE1" <-> "OE2" Residue "6 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 322": "OE1" <-> "OE2" Residue "6 PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 355": "OD1" <-> "OD2" Residue "6 ASP 511": "OD1" <-> "OD2" Residue "6 GLU 523": "OE1" <-> "OE2" Residue "6 GLU 624": "OE1" <-> "OE2" Residue "6 ASP 632": "OD1" <-> "OD2" Residue "6 ASP 642": "OD1" <-> "OD2" Residue "6 ASP 645": "OD1" <-> "OD2" Residue "6 ASP 718": "OD1" <-> "OD2" Residue "6 GLU 726": "OE1" <-> "OE2" Residue "6 GLU 740": "OE1" <-> "OE2" Residue "6 GLU 743": "OE1" <-> "OE2" Residue "6 TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 775": "OE1" <-> "OE2" Residue "6 TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 839": "OD1" <-> "OD2" Residue "7 ASP 23": "OD1" <-> "OD2" Residue "7 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 115": "OE1" <-> "OE2" Residue "7 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 137": "OD1" <-> "OD2" Residue "7 GLU 183": "OE1" <-> "OE2" Residue "7 TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 250": "OD1" <-> "OD2" Residue "7 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 272": "OE1" <-> "OE2" Residue "7 GLU 312": "OE1" <-> "OE2" Residue "7 ASP 347": "OD1" <-> "OD2" Residue "7 PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 373": "OE1" <-> "OE2" Residue "7 GLU 398": "OE1" <-> "OE2" Residue "7 GLU 403": "OE1" <-> "OE2" Residue "7 GLU 421": "OE1" <-> "OE2" Residue "7 ASP 446": "OD1" <-> "OD2" Residue "7 GLU 539": "OE1" <-> "OE2" Residue "7 GLU 674": "OE1" <-> "OE2" Residue "7 PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 709": "OD1" <-> "OD2" Residue "7 ASP 711": "OD1" <-> "OD2" Residue "7 GLU 714": "OE1" <-> "OE2" Residue "7 GLU 715": "OE1" <-> "OE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B ASP 616": "OD1" <-> "OD2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B ASP 701": "OD1" <-> "OD2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B ASP 792": "OD1" <-> "OD2" Residue "B GLU 811": "OE1" <-> "OE2" Residue "B GLU 818": "OE1" <-> "OE2" Residue "B ASP 847": "OD1" <-> "OD2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C ASP 544": "OD1" <-> "OD2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C ASP 558": "OD1" <-> "OD2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "C TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 689": "OD1" <-> "OD2" Residue "C GLU 703": "OE1" <-> "OE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 491": "OD1" <-> "OD2" Residue "D GLU 496": "OE1" <-> "OE2" Residue "D ASP 561": "OD1" <-> "OD2" Residue "D ASP 569": "OD1" <-> "OD2" Residue "D TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 617": "OE1" <-> "OE2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D ASP 713": "OD1" <-> "OD2" Residue "D GLU 719": "OE1" <-> "OE2" Residue "D ASP 731": "OD1" <-> "OD2" Residue "D GLU 769": "OE1" <-> "OE2" Residue "D GLU 806": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D ASP 835": "OD1" <-> "OD2" Residue "D TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 355": "OE1" <-> "OE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E ASP 456": "OD1" <-> "OD2" Residue "E ASP 473": "OD1" <-> "OD2" Residue "E GLU 481": "OE1" <-> "OE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "E TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 562": "OE1" <-> "OE2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "E ASP 565": "OD1" <-> "OD2" Residue "E ASP 695": "OD1" <-> "OD2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 378": "OD1" <-> "OD2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F GLU 518": "OE1" <-> "OE2" Residue "F ASP 568": "OD1" <-> "OD2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "F GLU 721": "OE1" <-> "OE2" Residue "F GLU 726": "OE1" <-> "OE2" Residue "F GLU 749": "OE1" <-> "OE2" Residue "F GLU 801": "OE1" <-> "OE2" Residue "F GLU 818": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "G ASP 250": "OD1" <-> "OD2" Residue "G TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 272": "OE1" <-> "OE2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "G GLU 312": "OE1" <-> "OE2" Residue "G ASP 347": "OD1" <-> "OD2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G GLU 398": "OE1" <-> "OE2" Residue "G GLU 403": "OE1" <-> "OE2" Residue "G GLU 421": "OE1" <-> "OE2" Residue "G ASP 453": "OD1" <-> "OD2" Residue "G ASP 461": "OD1" <-> "OD2" Residue "G GLU 542": "OE1" <-> "OE2" Residue "G GLU 614": "OE1" <-> "OE2" Residue "G GLU 634": "OE1" <-> "OE2" Residue "G PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 714": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62646 Number of models: 1 Model: "" Number of chains: 24 Chain: "2" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "3" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "4" Number of atoms: 5509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5509 Classifications: {'peptide': 692} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5143 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "7" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "B" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "C" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "D" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5323 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5143 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "G" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1302 SG CYS 2 341 93.746 112.830 65.295 1.00 75.28 S ATOM 1325 SG CYS 2 344 97.167 111.084 65.438 1.00 79.22 S ATOM 1483 SG CYS 2 364 95.332 111.588 62.120 1.00 80.80 S ATOM 1504 SG CYS 2 367 94.094 109.062 64.601 1.00 85.84 S ATOM 11586 SG CYS 4 349 52.482 121.748 46.875 1.00 43.84 S ATOM 11607 SG CYS 4 352 50.162 121.050 44.115 1.00 51.06 S ATOM 11754 SG CYS 4 371 48.817 120.506 47.562 1.00 56.66 S ATOM 11796 SG CYS 4 376 51.522 118.155 46.114 1.00 69.30 S ATOM 16779 SG CYS 5 183 85.614 110.847 87.974 1.00 30.85 S ATOM 16804 SG CYS 5 186 87.123 107.147 88.741 1.00 36.10 S ATOM 16991 SG CYS 5 211 88.084 108.984 85.828 1.00 38.53 S ATOM 17109 SG CYS 5 236 84.456 107.895 86.025 1.00 46.83 S ATOM 21857 SG CYS 6 311 71.291 116.989 48.554 1.00 97.48 S ATOM 21879 SG CYS 6 314 71.790 114.417 45.781 1.00101.92 S ATOM 22036 SG CYS 6 333 68.194 115.837 46.355 1.00 99.76 S ATOM 22070 SG CYS 6 338 69.922 113.554 48.776 1.00110.45 S ATOM 27590 SG CYS 7 262 41.029 122.804 73.074 1.00 26.56 S ATOM 27613 SG CYS 7 265 39.123 120.839 75.708 1.00 27.28 S ATOM 27767 SG CYS 7 284 42.872 121.540 76.110 1.00 25.62 S ATOM 27804 SG CYS 7 289 41.632 119.031 73.598 1.00 32.45 S ATOM 32525 SG CYS B 341 61.549 112.483 65.607 1.00 68.84 S ATOM 32548 SG CYS B 344 58.248 114.399 65.440 1.00 72.50 S ATOM 32706 SG CYS B 364 60.199 113.631 62.225 1.00 74.77 S ATOM 32727 SG CYS B 367 61.587 116.129 64.645 1.00 75.83 S ATOM 42623 SG CYS D 349 103.142 103.282 46.814 1.00 61.68 S ATOM 42644 SG CYS D 352 105.361 104.052 43.944 1.00 67.72 S ATOM 42791 SG CYS D 371 106.593 104.585 47.537 1.00 73.61 S ATOM 42833 SG CYS D 376 103.945 106.927 45.940 1.00 81.75 S ATOM 47816 SG CYS E 183 69.948 114.462 88.060 1.00 28.23 S ATOM 47841 SG CYS E 186 68.574 118.240 88.751 1.00 34.13 S ATOM 48028 SG CYS E 211 67.581 116.295 85.862 1.00 38.03 S ATOM 48146 SG CYS E 236 71.213 117.325 86.041 1.00 44.54 S ATOM 52894 SG CYS F 311 84.141 108.278 48.548 1.00 98.82 S ATOM 52916 SG CYS F 314 83.846 110.793 45.627 1.00101.13 S ATOM 53073 SG CYS F 333 87.199 108.853 46.155 1.00100.75 S ATOM 53107 SG CYS F 338 85.882 111.489 48.504 1.00109.55 S ATOM 58627 SG CYS G 262 114.614 102.338 72.963 1.00 27.94 S ATOM 58650 SG CYS G 265 116.503 104.282 75.611 1.00 28.40 S ATOM 58804 SG CYS G 284 112.725 103.591 75.985 1.00 29.52 S ATOM 58841 SG CYS G 289 113.979 106.117 73.530 1.00 36.28 S Time building chain proxies: 24.45, per 1000 atoms: 0.39 Number of scatterers: 62646 At special positions: 0 Unit cell: (156.748, 226.18, 148.332, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 297 16.00 P 34 15.00 Mg 12 11.99 O 12095 8.00 N 10931 7.00 C 39267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.25 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 22003 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 341 " pdb=" ZN 42003 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 371 " pdb=" ZN 52003 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 186 " pdb=" ZN 62003 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 333 " pdb=" ZN 72003 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 262 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 367 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 364 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 341 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 344 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 349 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 352 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 371 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 376 " pdb=" ZN E2003 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 211 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 236 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 183 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 186 " pdb=" ZN F2003 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 338 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 314 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 311 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 333 " pdb=" ZN G2003 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 284 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 265 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 289 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 262 " Number of angles added : 60 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14996 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 300 helices and 90 sheets defined 38.4% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.64 Creating SS restraints... 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 217 Processing helix chain '2' and resid 226 through 237 Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 removed outlier: 3.559A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 289 No H-bonds generated for 'chain '2' and resid 286 through 289' Processing helix chain '2' and resid 306 through 308 No H-bonds generated for 'chain '2' and resid 306 through 308' 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 478 through 488 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 Processing helix chain '2' and resid 594 through 598 Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 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 671 through 674 No H-bonds generated for 'chain '2' and resid 671 through 674' Processing helix chain '2' and resid 689 through 705 Processing helix chain '2' and resid 760 through 773 removed outlier: 3.687A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 780 through 800 removed outlier: 4.385A pdb=" N ASP 2 784 " --> pdb=" O MET 2 781 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS 2 785 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL 2 786 " --> pdb=" O MET 2 783 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER 2 787 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR 2 790 " --> pdb=" O SER 2 787 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG 2 795 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR 2 800 " --> pdb=" O SER 2 797 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 823 removed outlier: 3.714A pdb=" N MET 2 823 " --> pdb=" O SER 2 819 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 848 removed outlier: 3.953A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) Processing helix chain '2' and resid 851 through 860 removed outlier: 3.585A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG 2 859 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) 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 36 through 58 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 135 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' 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 344 through 355 removed outlier: 3.618A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 365 removed outlier: 3.561A pdb=" N SER 3 364 " --> pdb=" O PHE 3 360 " (cutoff:3.500A) Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 425 Processing helix chain '3' and resid 439 through 442 No H-bonds generated for 'chain '3' and resid 439 through 442' 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 removed outlier: 3.963A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 529 through 533 Processing helix chain '3' and resid 537 through 542 Processing helix chain '3' and resid 555 through 568 Processing helix chain '3' and resid 653 through 665 removed outlier: 3.551A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 687 removed outlier: 3.987A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 715 removed outlier: 3.591A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 723 through 737 removed outlier: 3.595A pdb=" N PHE 3 735 " --> pdb=" O ASN 3 731 " (cutoff:3.500A) Processing helix chain '4' and resid 187 through 200 Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 218 through 221 No H-bonds generated for 'chain '4' and resid 218 through 221' Processing helix chain '4' and resid 225 through 235 Processing helix chain '4' and resid 245 through 250 removed outlier: 3.658A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 263 removed outlier: 3.552A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 285 removed outlier: 3.937A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (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 478 through 480 No H-bonds generated for 'chain '4' and resid 478 through 480' Processing helix chain '4' and resid 482 through 491 Processing helix chain '4' and resid 503 through 514 Processing helix chain '4' and resid 518 through 524 Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 574 through 584 Processing helix chain '4' and resid 598 through 602 removed outlier: 3.739A pdb=" N THR 4 602 " --> pdb=" O ALA 4 598 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 598 through 602' 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 639 through 650 removed outlier: 3.967A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 701 removed outlier: 3.863A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 729 removed outlier: 3.771A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU 4 729 " --> pdb=" O THR 4 725 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 757 Processing helix chain '4' and resid 764 through 782 removed outlier: 3.555A pdb=" N ASP 4 782 " --> pdb=" O ARG 4 778 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 811 Processing helix chain '4' and resid 819 through 832 Processing helix chain '5' and resid 24 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 83 through 106 Proline residue: 5 88 - end of helix removed outlier: 3.664A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 5 104 " --> pdb=" O ARG 5 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG 5 106 " --> pdb=" O SER 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 150 No H-bonds generated for 'chain '5' and resid 148 through 150' 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 213 through 216 No H-bonds generated for 'chain '5' and resid 213 through 216' Processing helix chain '5' and resid 245 through 247 No H-bonds generated for 'chain '5' and resid 245 through 247' 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 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 487 through 498 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 removed outlier: 3.596A pdb=" N SER 5 548 " --> pdb=" O THR 5 544 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 577 removed outlier: 3.663A pdb=" N SER 5 567 " --> pdb=" O GLU 5 563 " (cutoff:3.500A) Processing helix chain '5' and resid 579 through 590 Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 640 removed outlier: 4.396A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG 5 630 " --> pdb=" O PHE 5 626 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 667 removed outlier: 4.185A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 694 removed outlier: 3.624A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 121 removed outlier: 3.689A pdb=" N GLU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 146 removed outlier: 3.631A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 159 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 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 505 Processing helix chain '6' and resid 510 through 521 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 removed outlier: 3.838A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 605 through 608 No H-bonds generated for 'chain '6' and resid 605 through 608' 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 658 removed outlier: 4.052A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 708 removed outlier: 3.877A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 741 removed outlier: 7.827A pdb=" N ASP 6 739 " --> pdb=" O HIS 6 735 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU 6 740 " --> pdb=" O MET 6 736 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA 6 741 " --> pdb=" O LYS 6 737 " (cutoff:3.500A) Processing helix chain '6' and resid 748 through 760 removed outlier: 3.894A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 790 removed outlier: 3.715A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER 6 789 " --> pdb=" O ALA 6 785 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG 6 790 " --> pdb=" O GLN 6 786 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 Processing helix chain '6' and resid 821 through 834 Processing helix chain '7' and resid 16 through 27 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: 3.906A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 164 Processing helix chain '7' and resid 174 through 188 Processing helix chain '7' and resid 194 through 197 Processing helix chain '7' and resid 209 through 214 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 395 through 407 removed outlier: 3.906A pdb=" N GLU 7 399 " --> pdb=" O SER 7 395 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 416 Processing helix chain '7' and resid 426 through 437 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 526 through 528 No H-bonds generated for 'chain '7' and resid 526 through 528' Processing helix chain '7' and resid 531 through 543 removed outlier: 4.261A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 580 through 583 No H-bonds generated for 'chain '7' and resid 580 through 583' Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 606 through 622 removed outlier: 3.704A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 647 Processing helix chain '7' and resid 654 through 673 Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 729 removed outlier: 3.754A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 614 through 625 Processing helix chain 'B' and resid 653 through 655 No H-bonds generated for 'chain 'B' and resid 653 through 655' Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 671 through 675 Processing helix chain 'B' and resid 689 through 705 Processing helix chain 'B' and resid 760 through 773 removed outlier: 4.024A pdb=" N LYS B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 800 removed outlier: 4.534A pdb=" N ASP B 784 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL B 786 " --> pdb=" O MET B 783 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 790 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 794 " --> pdb=" O ALA B 791 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 795 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 800 " --> pdb=" O SER B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 823 Processing helix chain 'B' and resid 831 through 847 Processing helix chain 'B' and resid 851 through 860 removed outlier: 3.743A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 865 No H-bonds generated for 'chain 'B' and resid 862 through 865' Processing helix chain 'C' and resid 19 through 34 Processing helix chain 'C' and resid 36 through 58 Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 118 through 136 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.535A pdb=" N LYS C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.635A pdb=" N GLN C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 386 Processing helix chain 'C' and resid 415 through 425 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 461 through 464 No H-bonds generated for 'chain 'C' and resid 461 through 464' Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 480 through 491 removed outlier: 3.890A pdb=" N GLU C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 555 through 570 Processing helix chain 'C' and resid 653 through 665 Processing helix chain 'C' and resid 673 through 688 removed outlier: 3.810A pdb=" N VAL C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 688 " --> pdb=" O THR C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 715 Processing helix chain 'C' and resid 723 through 737 removed outlier: 3.529A pdb=" N PHE C 735 " --> pdb=" O ASN C 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 255 through 263 removed outlier: 4.025A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.607A pdb=" N SER D 270 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 284 " --> pdb=" O MET D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 482 through 491 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.625A pdb=" N ALA D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 524 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 620 through 623 No H-bonds generated for 'chain 'D' and resid 620 through 623' Processing helix chain 'D' and resid 634 through 636 No H-bonds generated for 'chain 'D' and resid 634 through 636' Processing helix chain 'D' and resid 639 through 651 removed outlier: 3.823A pdb=" N VAL D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS D 646 " --> pdb=" O ARG D 642 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 692 Processing helix chain 'D' and resid 696 through 701 removed outlier: 4.026A pdb=" N ARG D 701 " --> pdb=" O PRO D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 729 removed outlier: 3.870A pdb=" N LEU D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR D 728 " --> pdb=" O LEU D 724 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 729 " --> pdb=" O THR D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 757 Processing helix chain 'D' and resid 764 through 782 removed outlier: 3.736A pdb=" N ASP D 782 " --> pdb=" O ARG D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 811 Processing helix chain 'D' and resid 819 through 832 Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 83 through 106 Proline residue: E 88 - end of helix removed outlier: 3.685A pdb=" N ARG E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 213 through 216 No H-bonds generated for 'chain 'E' and resid 213 through 216' Processing helix chain 'E' and resid 245 through 247 No H-bonds generated for 'chain 'E' and resid 245 through 247' Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 351 through 361 Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 422 through 432 Processing helix chain 'E' and resid 468 through 471 No H-bonds generated for 'chain 'E' and resid 468 through 471' Processing helix chain 'E' and resid 487 through 498 Processing helix chain 'E' and resid 536 through 539 No H-bonds generated for 'chain 'E' and resid 536 through 539' Processing helix chain 'E' and resid 544 through 549 removed outlier: 3.604A pdb=" N SER E 548 " --> pdb=" O THR E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 577 removed outlier: 3.814A pdb=" N SER E 567 " --> pdb=" O GLU E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 590 Processing helix chain 'E' and resid 596 through 609 Processing helix chain 'E' and resid 616 through 640 removed outlier: 4.347A pdb=" N GLU E 620 " --> pdb=" O PRO E 616 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS E 621 " --> pdb=" O GLN E 617 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 622 " --> pdb=" O ALA E 618 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE E 629 " --> pdb=" O ASN E 625 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG E 630 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 666 Processing helix chain 'E' and resid 674 through 694 removed outlier: 3.822A pdb=" N MET E 689 " --> pdb=" O GLN E 685 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP E 690 " --> pdb=" O ALA E 686 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.659A pdb=" N GLU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 146 Processing helix chain 'F' and resid 155 through 159 Processing helix chain 'F' and resid 165 through 172 Processing helix chain 'F' and resid 174 through 192 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 408 through 410 No H-bonds generated for 'chain 'F' and resid 408 through 410' Processing helix chain 'F' and resid 501 through 505 Processing helix chain 'F' and resid 510 through 521 Processing helix chain 'F' and resid 525 through 532 Processing helix chain 'F' and resid 541 through 552 Processing helix chain 'F' and resid 581 through 591 removed outlier: 3.767A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 627 through 630 No H-bonds generated for 'chain 'F' and resid 627 through 630' Processing helix chain 'F' and resid 646 through 658 removed outlier: 3.788A pdb=" N ALA F 655 " --> pdb=" O ALA F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 698 No H-bonds generated for 'chain 'F' and resid 695 through 698' Processing helix chain 'F' and resid 703 through 708 removed outlier: 3.759A pdb=" N ARG F 708 " --> pdb=" O PRO F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 737 Processing helix chain 'F' and resid 748 through 760 removed outlier: 3.885A pdb=" N THR F 760 " --> pdb=" O LYS F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 767 through 790 removed outlier: 3.836A pdb=" N SER F 771 " --> pdb=" O LYS F 767 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER F 789 " --> pdb=" O ALA F 785 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG F 790 " --> pdb=" O GLN F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 813 Processing helix chain 'F' and resid 821 through 834 Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 14 through 27 removed outlier: 3.519A pdb=" N VAL G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 82 through 95 Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 110 through 123 removed outlier: 3.923A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 164 Processing helix chain 'G' and resid 174 through 188 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 209 through 214 Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 337 through 339 No H-bonds generated for 'chain 'G' and resid 337 through 339' Processing helix chain 'G' and resid 395 through 407 removed outlier: 3.741A pdb=" N GLU G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG G 400 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 466 through 476 Processing helix chain 'G' and resid 512 through 515 No H-bonds generated for 'chain 'G' and resid 512 through 515' Processing helix chain 'G' and resid 526 through 528 No H-bonds generated for 'chain 'G' and resid 526 through 528' Processing helix chain 'G' and resid 531 through 543 removed outlier: 4.379A pdb=" N GLU G 542 " --> pdb=" O HIS G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 583 No H-bonds generated for 'chain 'G' and resid 580 through 583' Processing helix chain 'G' and resid 588 through 593 Processing helix chain 'G' and resid 606 through 622 removed outlier: 3.536A pdb=" N GLU G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS G 611 " --> pdb=" O ASP G 607 " (cutoff:3.500A) Processing helix chain 'G' and resid 635 through 647 removed outlier: 3.633A pdb=" N THR G 647 " --> pdb=" O ALA G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 654 through 675 Processing helix chain 'G' and resid 686 through 702 Processing helix chain 'G' and resid 710 through 729 removed outlier: 3.997A pdb=" N LYS G 724 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER G 726 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU G 727 " --> pdb=" O SER G 723 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 241 through 245 removed outlier: 6.320A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 6.030A 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 410 removed outlier: 3.973A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN 2 391 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL 2 324 " --> pdb=" O GLN 2 391 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 339 through 341 Processing sheet with id= D, first strand: chain '2' and resid 525 through 527 Processing sheet with id= E, first strand: chain '2' and resid 679 through 683 removed outlier: 6.681A pdb=" N GLY 2 602 " --> pdb=" O SER 2 645 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE 2 647 " --> pdb=" O GLY 2 602 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 579 through 582 Processing sheet with id= G, first strand: chain '2' and resid 628 through 633 Processing sheet with id= H, first strand: chain '2' and resid 331 through 336 removed outlier: 6.716A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 95 through 99 removed outlier: 7.044A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.279A 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 165 through 167 removed outlier: 8.111A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG 3 291 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 208 through 213 Processing sheet with id= L, first strand: chain '3' and resid 273 through 278 removed outlier: 3.829A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 545 through 549 removed outlier: 3.750A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY 3 468 " --> pdb=" O SER 3 511 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE 3 513 " --> pdb=" O GLY 3 468 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '3' and resid 444 through 448 Processing sheet with id= O, first strand: chain '3' and resid 494 through 498 Processing sheet with id= P, first strand: chain '3' and resid 193 through 198 removed outlier: 6.759A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 149 through 151 Processing sheet with id= R, first strand: chain '4' and resid 240 through 244 removed outlier: 6.903A pdb=" N LYS 4 302 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU 4 243 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG 4 304 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain '4' and resid 414 through 420 removed outlier: 3.731A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '4' and resid 339 through 342 Processing sheet with id= U, first strand: chain '4' and resid 355 through 359 Processing sheet with id= V, first strand: chain '4' and resid 704 through 708 Processing sheet with id= W, first strand: chain '4' and resid 603 through 607 Processing sheet with id= X, first strand: chain '4' and resid 653 through 657 Processing sheet with id= Y, first strand: chain '5' and resid 60 through 64 removed outlier: 6.574A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain '5' and resid 291 through 298 removed outlier: 3.884A pdb=" N LYS 5 158 " --> pdb=" O TYR 5 298 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR 5 275 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N GLY 5 332 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '5' and resid 189 through 193 removed outlier: 4.600A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '5' and resid 552 through 556 removed outlier: 6.636A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '5' and resid 501 through 505 Processing sheet with id= AD, first strand: chain '5' and resid 173 through 178 removed outlier: 6.632A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '5' and resid 452 through 455 removed outlier: 3.677A pdb=" N GLY 5 466 " --> pdb=" O SER 5 452 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN 5 454 " --> pdb=" O LEU 5 464 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU 5 464 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain '6' and resid 150 through 154 removed outlier: 6.424A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain '6' and resid 394 through 400 removed outlier: 6.739A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) removed outlier: 14.459A pdb=" N TYR 6 450 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 12.343A pdb=" N ASP 6 378 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE 6 452 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ILE 6 380 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 380 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ARG 6 382 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA 6 456 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '6' and resid 308 through 311 removed outlier: 4.720A pdb=" N SER 6 308 " --> pdb=" O ASN 6 347 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '6' and resid 418 through 420 Processing sheet with id= AJ, first strand: chain '6' and resid 711 through 715 removed outlier: 3.938A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '6' and resid 610 through 614 Processing sheet with id= AL, first strand: chain '6' and resid 660 through 663 Processing sheet with id= AM, first strand: chain '6' and resid 301 through 306 removed outlier: 6.736A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 77 through 81 removed outlier: 6.195A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain '7' and resid 330 through 336 removed outlier: 3.807A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '7' and resid 268 through 272 Processing sheet with id= AQ, first strand: chain '7' and resid 596 through 600 Processing sheet with id= AR, first strand: chain '7' and resid 495 through 500 Processing sheet with id= AS, first strand: chain '7' and resid 545 through 549 Processing sheet with id= AT, first strand: chain '7' and resid 252 through 257 removed outlier: 6.815A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.458A pdb=" N HIS B 294 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL B 244 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG B 296 " --> pdb=" O VAL B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'B' and resid 423 through 430 removed outlier: 3.896A pdb=" N SER B 316 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR B 389 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG B 327 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ARG B 387 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR B 449 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU B 407 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 448 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR B 427 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE B 456 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU B 425 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= AX, first strand: chain 'B' and resid 525 through 527 Processing sheet with id= AY, first strand: chain 'B' and resid 679 through 683 removed outlier: 6.567A pdb=" N GLY B 602 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE B 647 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 604 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA B 649 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 606 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'B' and resid 579 through 582 Processing sheet with id= BA, first strand: chain 'B' and resid 628 through 633 Processing sheet with id= BB, first strand: chain 'B' and resid 331 through 336 removed outlier: 6.670A pdb=" N VAL B 381 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'C' and resid 95 through 99 removed outlier: 7.018A pdb=" N LYS C 154 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE C 98 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER C 156 " --> pdb=" O ILE C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= BC Processing sheet with id= BD, first strand: chain 'C' and resid 165 through 167 removed outlier: 8.039A pdb=" N LEU C 166 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 181 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 178 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG C 291 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 297 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLY C 323 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS C 299 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILE C 321 " --> pdb=" O LYS C 299 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU C 301 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR C 319 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'C' and resid 208 through 213 Processing sheet with id= BF, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.690A pdb=" N LYS C 188 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN C 259 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL C 186 " --> pdb=" O GLN C 259 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'C' and resid 545 through 549 removed outlier: 3.801A pdb=" N GLY C 409 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 468 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE C 513 " --> pdb=" O GLY C 468 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL C 470 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA C 515 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE C 472 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'C' and resid 444 through 448 Processing sheet with id= BI, first strand: chain 'C' and resid 494 through 498 Processing sheet with id= BJ, first strand: chain 'C' and resid 193 through 198 removed outlier: 6.607A pdb=" N THR C 249 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.997A pdb=" N LYS D 302 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 243 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG D 304 " --> pdb=" O LEU D 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= BK Processing sheet with id= BL, first strand: chain 'D' and resid 414 through 420 removed outlier: 3.746A pdb=" N ARG D 334 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN D 400 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL D 332 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR D 438 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL D 463 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG D 440 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL D 461 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE D 442 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR D 459 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'D' and resid 339 through 342 Processing sheet with id= BN, first strand: chain 'D' and resid 355 through 359 Processing sheet with id= BO, first strand: chain 'D' and resid 704 through 708 removed outlier: 6.235A pdb=" N VAL D 589 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP D 632 " --> pdb=" O VAL D 589 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR D 591 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'D' and resid 603 through 607 Processing sheet with id= BQ, first strand: chain 'D' and resid 653 through 657 Processing sheet with id= BR, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.466A pdb=" N GLN E 136 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL E 63 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE E 138 " --> pdb=" O VAL E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'E' and resid 291 through 298 removed outlier: 4.056A pdb=" N LYS E 158 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR E 275 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP E 279 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLY E 332 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL E 295 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE E 333 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 293 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'E' and resid 189 through 193 removed outlier: 4.579A pdb=" N SER E 180 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'E' and resid 552 through 556 removed outlier: 6.511A pdb=" N GLY E 475 " --> pdb=" O SER E 518 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU E 520 " --> pdb=" O GLY E 475 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL E 477 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA E 522 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE E 479 " --> pdb=" O ALA E 522 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'E' and resid 501 through 505 Processing sheet with id= BW, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.583A pdb=" N LYS E 249 " --> pdb=" O THR E 177 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'E' and resid 452 through 455 removed outlier: 3.707A pdb=" N GLY E 466 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN E 454 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU E 464 " --> pdb=" O GLN E 454 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.482A pdb=" N GLN F 264 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE F 153 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N SER F 266 " --> pdb=" O ILE F 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'F' and resid 394 through 400 removed outlier: 6.711A pdb=" N ARG F 360 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 12.381A pdb=" N ASP F 378 " --> pdb=" O TYR F 450 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE F 452 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N ILE F 380 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE F 454 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ARG F 382 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA F 456 " --> pdb=" O ARG F 382 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR F 398 " --> pdb=" O CYS F 457 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL F 459 " --> pdb=" O LYS F 396 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS F 396 " --> pdb=" O VAL F 459 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'F' and resid 309 through 311 Processing sheet with id= CB, first strand: chain 'F' and resid 711 through 715 removed outlier: 3.850A pdb=" N GLY F 575 " --> pdb=" O ALA F 682 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL F 596 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASP F 639 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR F 598 " --> pdb=" O ASP F 639 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'F' and resid 610 through 614 Processing sheet with id= CD, first strand: chain 'F' and resid 660 through 663 Processing sheet with id= CE, first strand: chain 'F' and resid 301 through 306 removed outlier: 6.733A pdb=" N ARG F 352 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.121A pdb=" N PHE G 201 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE G 80 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR G 203 " --> pdb=" O ILE G 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= CF Processing sheet with id= CG, first strand: chain 'G' and resid 330 through 336 removed outlier: 3.737A pdb=" N ARG G 247 " --> pdb=" O LYS G 314 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN G 316 " --> pdb=" O ILE G 245 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE G 245 " --> pdb=" O GLN G 316 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE G 354 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ALA G 378 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU G 356 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU G 376 " --> pdb=" O LEU G 356 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA G 358 " --> pdb=" O THR G 374 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N THR G 374 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'G' and resid 268 through 272 removed outlier: 4.497A pdb=" N ALA G 259 " --> pdb=" O SER G 301 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'G' and resid 596 through 600 removed outlier: 6.168A pdb=" N VAL G 481 " --> pdb=" O CYS G 522 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP G 524 " --> pdb=" O VAL G 481 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR G 483 " --> pdb=" O ASP G 524 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'G' and resid 495 through 500 Processing sheet with id= CK, first strand: chain 'G' and resid 545 through 549 Processing sheet with id= CL, first strand: chain 'G' and resid 252 through 257 removed outlier: 6.995A pdb=" N LYS G 306 " --> pdb=" O GLU G 256 " (cutoff:3.500A) 2364 hydrogen bonds defined for protein. 6879 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: 24.18 Time building geometry restraints manager: 21.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 21235 1.37 - 1.51: 18196 1.51 - 1.66: 23726 1.66 - 1.80: 374 1.80 - 1.95: 100 Bond restraints: 63631 Sorted by residual: bond pdb=" CB PRO E 647 " pdb=" CG PRO E 647 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.99e+00 bond pdb=" CB PRO 2 524 " pdb=" CG PRO 2 524 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.23e+00 bond pdb=" CG GLU 3 563 " pdb=" CD GLU 3 563 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.15e+00 bond pdb=" CG1 ILE E 251 " pdb=" CD1 ILE E 251 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.91e+00 bond pdb=" C PRO D 696 " pdb=" N PRO D 697 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.22e+00 ... (remaining 63626 not shown) Histogram of bond angle deviations from ideal: 97.58 - 105.26: 1146 105.26 - 112.94: 35279 112.94 - 120.62: 26993 120.62 - 128.30: 22434 128.30 - 135.98: 257 Bond angle restraints: 86109 Sorted by residual: angle pdb=" CA PRO E 647 " pdb=" N PRO E 647 " pdb=" CD PRO E 647 " ideal model delta sigma weight residual 112.00 103.77 8.23 1.40e+00 5.10e-01 3.46e+01 angle pdb=" CA GLU 3 563 " pdb=" CB GLU 3 563 " pdb=" CG GLU 3 563 " ideal model delta sigma weight residual 114.10 125.04 -10.94 2.00e+00 2.50e-01 2.99e+01 angle pdb=" N GLU 3 563 " pdb=" CA GLU 3 563 " pdb=" CB GLU 3 563 " ideal model delta sigma weight residual 110.28 118.54 -8.26 1.55e+00 4.16e-01 2.84e+01 angle pdb=" C ILE 6 819 " pdb=" N THR 6 820 " pdb=" CA THR 6 820 " ideal model delta sigma weight residual 120.69 135.55 -14.86 2.95e+00 1.15e-01 2.54e+01 angle pdb=" C ILE F 819 " pdb=" N THR F 820 " pdb=" CA THR F 820 " ideal model delta sigma weight residual 120.69 134.36 -13.67 2.95e+00 1.15e-01 2.15e+01 ... (remaining 86104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.51: 37898 30.51 - 61.03: 1254 61.03 - 91.54: 119 91.54 - 122.05: 2 122.05 - 152.56: 4 Dihedral angle restraints: 39277 sinusoidal: 16176 harmonic: 23101 Sorted by residual: dihedral pdb=" O2A ADP C2001 " pdb=" O3A ADP C2001 " pdb=" PA ADP C2001 " pdb=" PB ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 68.57 -128.57 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O2A ADP 32001 " pdb=" O3A ADP 32001 " pdb=" PA ADP 32001 " pdb=" PB ADP 32001 " ideal model delta sinusoidal sigma weight residual -60.00 65.66 -125.65 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" O1B ADP C2001 " pdb=" O3A ADP C2001 " pdb=" PB ADP C2001 " pdb=" PA ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 -168.52 108.52 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 39274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 8512 0.067 - 0.133: 1405 0.133 - 0.200: 66 0.200 - 0.267: 5 0.267 - 0.333: 3 Chirality restraints: 9991 Sorted by residual: chirality pdb=" CB ILE E 646 " pdb=" CA ILE E 646 " pdb=" CG1 ILE E 646 " pdb=" CG2 ILE E 646 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE 5 646 " pdb=" CA ILE 5 646 " pdb=" CG1 ILE 5 646 " pdb=" CG2 ILE 5 646 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB VAL 6 403 " pdb=" CA VAL 6 403 " pdb=" CG1 VAL 6 403 " pdb=" CG2 VAL 6 403 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 9988 not shown) Planarity restraints: 11074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU 4 378 " -0.067 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO 4 379 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO 4 379 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO 4 379 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 5 535 " -0.048 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO 5 536 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO 5 536 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO 5 536 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG 3 559 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ARG 3 559 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG 3 559 " -0.017 2.00e-02 2.50e+03 pdb=" N SER 3 560 " -0.015 2.00e-02 2.50e+03 ... (remaining 11071 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 519 2.59 - 3.17: 49822 3.17 - 3.74: 97353 3.74 - 4.32: 137635 4.32 - 4.90: 228587 Nonbonded interactions: 513916 Sorted by model distance: nonbonded pdb=" O2G AGS 62001 " pdb="MG MG 62002 " model vdw 2.009 2.170 nonbonded pdb=" OG SER 6 582 " pdb="MG MG 62002 " model vdw 2.025 2.170 nonbonded pdb=" OG SER 4 575 " pdb="MG MG 42002 " model vdw 2.033 2.170 nonbonded pdb=" O2G AGS 72001 " pdb="MG MG 72002 " model vdw 2.053 2.170 nonbonded pdb=" OG SER 7 467 " pdb="MG MG 72002 " model vdw 2.057 2.170 ... (remaining 513911 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 '2' selection = chain 'B' } ncs_group { reference = chain '3' selection = chain 'C' } ncs_group { reference = (chain '4' and (resid 176 through 853 or resid 2001 through 2003)) selection = chain 'D' } ncs_group { reference = chain '5' selection = chain 'E' } ncs_group { reference = chain '6' selection = chain 'F' } ncs_group { reference = chain '7' selection = chain 'G' } 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 individual isotropic 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 11.560 Check model and map are aligned: 0.710 Set scattering table: 0.450 Process input model: 140.840 Find NCS groups from input model: 5.280 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 0.141 63631 Z= 0.252 Angle : 0.694 14.862 86109 Z= 0.370 Chirality : 0.047 0.333 9991 Planarity : 0.006 0.099 11074 Dihedral : 14.709 152.564 24278 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.63 % 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: -0.34 (0.09), residues: 7808 helix: 0.07 (0.09), residues: 3128 sheet: -0.09 (0.13), residues: 1493 loop : -0.41 (0.10), residues: 3187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 343 HIS 0.018 0.001 HIS 7 538 PHE 0.040 0.002 PHE E 197 TYR 0.042 0.001 TYR 6 828 ARG 0.017 0.001 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 971 time to evaluate : 5.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 788 ARG cc_start: 0.7384 (mmm160) cc_final: 0.7099 (mmm160) REVERT: 2 847 ASP cc_start: 0.7148 (m-30) cc_final: 0.6858 (m-30) REVERT: 3 346 ASP cc_start: 0.7213 (m-30) cc_final: 0.6939 (m-30) REVERT: 3 576 TYR cc_start: 0.7713 (m-80) cc_final: 0.7425 (m-80) REVERT: 5 572 VAL cc_start: 0.9390 (t) cc_final: 0.9184 (t) REVERT: 6 521 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7945 (mmtm) REVERT: 6 561 GLU cc_start: 0.7808 (mp0) cc_final: 0.7384 (mm-30) REVERT: 6 658 GLN cc_start: 0.8224 (mp10) cc_final: 0.7972 (mm-40) REVERT: 6 829 ASP cc_start: 0.7944 (m-30) cc_final: 0.7534 (m-30) REVERT: 7 177 MET cc_start: 0.6257 (tpt) cc_final: 0.5894 (tpt) REVERT: B 272 ASP cc_start: 0.7133 (m-30) cc_final: 0.6732 (m-30) REVERT: B 671 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6260 (mm-30) REVERT: B 681 CYS cc_start: 0.7800 (m) cc_final: 0.7550 (m) REVERT: B 843 ASP cc_start: 0.7048 (m-30) cc_final: 0.6735 (m-30) REVERT: C 55 ASN cc_start: 0.5539 (m-40) cc_final: 0.4959 (t0) REVERT: E 5 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7500 (ttm170) REVERT: E 267 VAL cc_start: 0.7873 (m) cc_final: 0.7642 (t) REVERT: G 27 THR cc_start: 0.8127 (m) cc_final: 0.7909 (m) REVERT: G 670 ASP cc_start: 0.7670 (m-30) cc_final: 0.7068 (m-30) outliers start: 2 outliers final: 2 residues processed: 973 average time/residue: 0.6523 time to fit residues: 1071.7230 Evaluate side-chains 720 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 718 time to evaluate : 5.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain E residue 339 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 660 optimal weight: 0.0370 chunk 592 optimal weight: 0.0070 chunk 328 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 399 optimal weight: 0.9980 chunk 316 optimal weight: 0.7980 chunk 612 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 372 optimal weight: 0.9980 chunk 456 optimal weight: 1.9990 chunk 710 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 290 HIS 2 653 ASN 2 779 HIS 3 52 ASN 3 151 HIS 3 324 ASN 3 417 GLN 4 240 ASN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 90 ASN 7 297 GLN D 386 HIS D 579 GLN ** E 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN F 347 ASN F 501 GLN F 506 ASN ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 63631 Z= 0.141 Angle : 0.468 9.627 86109 Z= 0.241 Chirality : 0.041 0.159 9991 Planarity : 0.004 0.059 11074 Dihedral : 6.998 155.166 8855 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.80 % Allowed : 6.42 % Favored : 92.78 % 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: 0.31 (0.09), residues: 7808 helix: 0.90 (0.09), residues: 3128 sheet: -0.09 (0.13), residues: 1496 loop : -0.20 (0.10), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 344 HIS 0.011 0.001 HIS F 653 PHE 0.016 0.001 PHE C 421 TYR 0.022 0.001 TYR G 618 ARG 0.007 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 784 time to evaluate : 5.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 779 HIS cc_start: 0.6272 (OUTLIER) cc_final: 0.6011 (p-80) REVERT: 2 847 ASP cc_start: 0.7025 (m-30) cc_final: 0.6664 (m-30) REVERT: 3 346 ASP cc_start: 0.7235 (m-30) cc_final: 0.6942 (m-30) REVERT: 4 772 ARG cc_start: 0.7948 (tmm-80) cc_final: 0.7353 (ttm-80) REVERT: 6 561 GLU cc_start: 0.7765 (mp0) cc_final: 0.7515 (mm-30) REVERT: 6 829 ASP cc_start: 0.7980 (m-30) cc_final: 0.7575 (m-30) REVERT: 7 215 TYR cc_start: 0.5252 (m-10) cc_final: 0.4597 (m-10) REVERT: 7 582 ASP cc_start: 0.7868 (m-30) cc_final: 0.7604 (m-30) REVERT: B 272 ASP cc_start: 0.7102 (m-30) cc_final: 0.6699 (m-30) REVERT: B 671 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6227 (mm-30) REVERT: B 681 CYS cc_start: 0.7857 (m) cc_final: 0.7607 (m) REVERT: C 55 ASN cc_start: 0.5329 (m-40) cc_final: 0.4719 (t0) REVERT: E 69 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7936 (mm) REVERT: F 501 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7344 (pt0) REVERT: G 167 MET cc_start: 0.4419 (mtp) cc_final: 0.4176 (mtt) REVERT: G 543 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: G 670 ASP cc_start: 0.7641 (m-30) cc_final: 0.7243 (m-30) outliers start: 56 outliers final: 40 residues processed: 814 average time/residue: 0.5970 time to fit residues: 815.6167 Evaluate side-chains 756 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 712 time to evaluate : 5.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 653 ASN Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 731 ASP Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 108 GLN Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 111 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 394 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 591 optimal weight: 4.9990 chunk 483 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 711 optimal weight: 0.5980 chunk 768 optimal weight: 0.6980 chunk 633 optimal weight: 5.9990 chunk 705 optimal weight: 3.9990 chunk 242 optimal weight: 8.9990 chunk 570 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 405 HIS 3 351 ASN 3 417 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 499 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 673 ASN 7 89 GLN 7 264 GLN 7 669 GLN E 130 ASN E 334 GLN E 560 HIS ** E 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 GLN F 750 GLN G 19 ASN G 95 GLN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 63631 Z= 0.237 Angle : 0.493 9.440 86109 Z= 0.252 Chirality : 0.042 0.167 9991 Planarity : 0.004 0.055 11074 Dihedral : 6.812 152.086 8853 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.36 % Allowed : 8.70 % Favored : 89.94 % 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 (0.09), residues: 7808 helix: 1.17 (0.09), residues: 3141 sheet: -0.11 (0.13), residues: 1452 loop : -0.15 (0.10), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 356 HIS 0.013 0.001 HIS 2 779 PHE 0.016 0.001 PHE C 421 TYR 0.019 0.001 TYR 2 769 ARG 0.005 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 747 time to evaluate : 5.711 Fit side-chains revert: symmetry clash REVERT: 2 779 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.6093 (p90) REVERT: 2 847 ASP cc_start: 0.7087 (m-30) cc_final: 0.6761 (m-30) REVERT: 3 346 ASP cc_start: 0.7249 (m-30) cc_final: 0.6951 (m-30) REVERT: 3 386 MET cc_start: 0.9079 (mmt) cc_final: 0.8746 (mmp) REVERT: 3 576 TYR cc_start: 0.7809 (m-80) cc_final: 0.7482 (m-80) REVERT: 4 772 ARG cc_start: 0.7932 (tmm-80) cc_final: 0.7365 (ttm-80) REVERT: 5 7 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7357 (mm-30) REVERT: 5 368 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7448 (mm-30) REVERT: 6 521 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7718 (mmtm) REVERT: 6 561 GLU cc_start: 0.7794 (mp0) cc_final: 0.7550 (mm-30) REVERT: 6 829 ASP cc_start: 0.7999 (m-30) cc_final: 0.7563 (m-30) REVERT: 7 215 TYR cc_start: 0.5502 (m-10) cc_final: 0.4970 (m-10) REVERT: B 272 ASP cc_start: 0.7135 (m-30) cc_final: 0.6745 (m-30) REVERT: B 671 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6292 (mm-30) REVERT: B 681 CYS cc_start: 0.7935 (m) cc_final: 0.7681 (m) REVERT: D 273 ASP cc_start: 0.7510 (m-30) cc_final: 0.7281 (m-30) REVERT: D 417 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8856 (pp) REVERT: E 69 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8155 (mm) REVERT: E 82 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7352 (mm-30) REVERT: F 313 MET cc_start: 0.7242 (ptp) cc_final: 0.6838 (ptm) REVERT: F 501 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7375 (pt0) REVERT: F 506 ASN cc_start: 0.7462 (m-40) cc_final: 0.7202 (m-40) REVERT: G 543 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: G 670 ASP cc_start: 0.7584 (m-30) cc_final: 0.7327 (m-30) outliers start: 95 outliers final: 68 residues processed: 801 average time/residue: 0.6004 time to fit residues: 808.8654 Evaluate side-chains 782 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 709 time to evaluate : 5.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 223 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 651 VAL Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 685 ASN Chi-restraints excluded: chain 4 residue 731 ASP Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 560 HIS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 702 optimal weight: 6.9990 chunk 534 optimal weight: 7.9990 chunk 369 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 339 optimal weight: 0.7980 chunk 477 optimal weight: 1.9990 chunk 713 optimal weight: 1.9990 chunk 755 optimal weight: 1.9990 chunk 373 optimal weight: 0.7980 chunk 676 optimal weight: 0.0970 chunk 203 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 856 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 159 ASN 7 669 GLN E 130 ASN ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 63631 Z= 0.177 Angle : 0.464 9.832 86109 Z= 0.237 Chirality : 0.041 0.273 9991 Planarity : 0.004 0.053 11074 Dihedral : 6.637 151.338 8853 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.49 % Allowed : 10.06 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.09), residues: 7808 helix: 1.35 (0.09), residues: 3153 sheet: -0.09 (0.13), residues: 1438 loop : -0.11 (0.10), residues: 3217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 356 HIS 0.011 0.001 HIS F 653 PHE 0.014 0.001 PHE C 735 TYR 0.016 0.001 TYR 2 769 ARG 0.006 0.000 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 755 time to evaluate : 5.701 Fit side-chains revert: symmetry clash REVERT: 2 783 MET cc_start: 0.7940 (tmm) cc_final: 0.7654 (tmm) REVERT: 2 847 ASP cc_start: 0.7119 (m-30) cc_final: 0.6788 (m-30) REVERT: 3 346 ASP cc_start: 0.7154 (m-30) cc_final: 0.6867 (m-30) REVERT: 3 576 TYR cc_start: 0.7795 (m-80) cc_final: 0.7456 (m-80) REVERT: 4 199 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7876 (mmp) REVERT: 4 200 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8593 (p) REVERT: 4 690 GLU cc_start: 0.6933 (tp30) cc_final: 0.6701 (tp30) REVERT: 4 772 ARG cc_start: 0.7934 (tmm-80) cc_final: 0.7386 (ttm-80) REVERT: 5 7 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7349 (mm-30) REVERT: 5 368 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7336 (mm-30) REVERT: 5 404 MET cc_start: 0.6708 (ptm) cc_final: 0.6372 (ptm) REVERT: 6 319 ASP cc_start: 0.7913 (m-30) cc_final: 0.7393 (m-30) REVERT: 6 521 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7805 (mmtm) REVERT: 6 561 GLU cc_start: 0.7759 (mp0) cc_final: 0.7521 (mm-30) REVERT: 6 733 ASP cc_start: 0.7428 (m-30) cc_final: 0.7225 (m-30) REVERT: 6 829 ASP cc_start: 0.8006 (m-30) cc_final: 0.7566 (m-30) REVERT: 7 177 MET cc_start: 0.6141 (tpt) cc_final: 0.5775 (tpt) REVERT: 7 215 TYR cc_start: 0.5635 (m-10) cc_final: 0.5045 (m-10) REVERT: B 272 ASP cc_start: 0.6947 (m-30) cc_final: 0.6487 (m-30) REVERT: B 671 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6290 (mm-30) REVERT: C 55 ASN cc_start: 0.5366 (m-40) cc_final: 0.4719 (t0) REVERT: C 320 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8804 (pp) REVERT: D 273 ASP cc_start: 0.7511 (m-30) cc_final: 0.7285 (m-30) REVERT: D 417 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8847 (pp) REVERT: D 777 MET cc_start: 0.7637 (ptp) cc_final: 0.7242 (ptm) REVERT: D 806 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7651 (mt-10) REVERT: E 69 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8224 (mm) REVERT: E 82 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7348 (mm-30) REVERT: E 661 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7528 (mt-10) REVERT: F 313 MET cc_start: 0.7244 (ptp) cc_final: 0.6673 (ptm) REVERT: F 506 ASN cc_start: 0.7451 (m-40) cc_final: 0.7178 (m-40) REVERT: G 94 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7633 (mp) REVERT: G 543 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: G 670 ASP cc_start: 0.7564 (m-30) cc_final: 0.7265 (m-30) outliers start: 104 outliers final: 77 residues processed: 813 average time/residue: 0.6008 time to fit residues: 825.0864 Evaluate side-chains 793 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 709 time to evaluate : 5.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 205 LYS Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 223 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 685 ASN Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 108 GLN Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 636 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 629 optimal weight: 7.9990 chunk 429 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 562 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 645 optimal weight: 0.7980 chunk 522 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 678 optimal weight: 6.9990 chunk 190 optimal weight: 0.0980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 391 GLN 2 703 HIS 2 856 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 543 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 112 HIS 7 669 GLN C 210 HIS C 731 ASN E 344 ASN E 560 HIS E 636 ASN ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN G 264 GLN G 334 HIS ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 63631 Z= 0.366 Angle : 0.568 10.732 86109 Z= 0.288 Chirality : 0.045 0.209 9991 Planarity : 0.004 0.083 11074 Dihedral : 6.793 146.897 8853 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.32 % Allowed : 11.00 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.09), residues: 7808 helix: 1.16 (0.09), residues: 3181 sheet: -0.28 (0.13), residues: 1458 loop : -0.22 (0.10), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 153 HIS 0.013 0.001 HIS 7 622 PHE 0.020 0.002 PHE 5 90 TYR 0.018 0.002 TYR 6 136 ARG 0.007 0.000 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 720 time to evaluate : 5.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 847 ASP cc_start: 0.7266 (m-30) cc_final: 0.6943 (m-30) REVERT: 3 43 ARG cc_start: 0.8372 (tpt170) cc_final: 0.8101 (tpm170) REVERT: 3 320 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8822 (pp) REVERT: 3 346 ASP cc_start: 0.7186 (m-30) cc_final: 0.6907 (m-30) REVERT: 3 576 TYR cc_start: 0.7938 (m-80) cc_final: 0.7689 (m-80) REVERT: 4 199 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7829 (mmp) REVERT: 4 690 GLU cc_start: 0.7103 (tp30) cc_final: 0.6891 (tp30) REVERT: 4 772 ARG cc_start: 0.7937 (tmm-80) cc_final: 0.7393 (ttm-80) REVERT: 5 368 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7395 (mm-30) REVERT: 6 521 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7578 (mmtm) REVERT: 6 615 ASP cc_start: 0.5097 (OUTLIER) cc_final: 0.3994 (t70) REVERT: 6 658 GLN cc_start: 0.8189 (mp10) cc_final: 0.7914 (mp10) REVERT: 7 297 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: B 272 ASP cc_start: 0.7007 (m-30) cc_final: 0.6521 (m-30) REVERT: C 320 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8767 (pp) REVERT: D 273 ASP cc_start: 0.7531 (m-30) cc_final: 0.7269 (m-30) REVERT: D 417 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9021 (pp) REVERT: D 806 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7745 (mt-10) REVERT: E 82 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7431 (mm-30) REVERT: F 313 MET cc_start: 0.7054 (ptp) cc_final: 0.6626 (ptm) REVERT: F 795 ILE cc_start: 0.9186 (mp) cc_final: 0.8877 (mp) REVERT: G 543 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: G 670 ASP cc_start: 0.7593 (m-30) cc_final: 0.7342 (m-30) REVERT: G 683 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7349 (tm-30) outliers start: 162 outliers final: 112 residues processed: 827 average time/residue: 0.6043 time to fit residues: 842.1084 Evaluate side-chains 796 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 676 time to evaluate : 5.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 577 THR Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 2 residue 811 GLU Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 223 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 3 residue 641 ASN Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 380 ASN Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 445 VAL Chi-restraints excluded: chain 6 residue 513 ILE Chi-restraints excluded: chain 6 residue 615 ASP Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 811 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 560 HIS Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 802 SER Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 671 SER Chi-restraints excluded: chain G residue 683 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 254 optimal weight: 0.3980 chunk 680 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 443 optimal weight: 0.7980 chunk 186 optimal weight: 0.9980 chunk 756 optimal weight: 2.9990 chunk 628 optimal weight: 2.9990 chunk 350 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 397 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 340 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 487 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 ASN ** B 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN G 89 GLN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 662 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 63631 Z= 0.158 Angle : 0.470 10.364 86109 Z= 0.241 Chirality : 0.041 0.207 9991 Planarity : 0.004 0.059 11074 Dihedral : 6.555 147.671 8853 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.72 % Allowed : 12.08 % Favored : 86.20 % 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: 0.65 (0.09), residues: 7808 helix: 1.40 (0.09), residues: 3181 sheet: -0.27 (0.13), residues: 1406 loop : -0.10 (0.11), residues: 3221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 356 HIS 0.022 0.001 HIS E 560 PHE 0.018 0.001 PHE C 735 TYR 0.019 0.001 TYR 2 769 ARG 0.007 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 720 time to evaluate : 5.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 781 MET cc_start: 0.7388 (ppp) cc_final: 0.6506 (ppp) REVERT: 2 783 MET cc_start: 0.8096 (tmm) cc_final: 0.7763 (tmm) REVERT: 2 847 ASP cc_start: 0.7191 (m-30) cc_final: 0.6900 (m-30) REVERT: 3 43 ARG cc_start: 0.8441 (tpt170) cc_final: 0.8231 (tpm170) REVERT: 3 346 ASP cc_start: 0.7096 (m-30) cc_final: 0.6851 (m-30) REVERT: 3 576 TYR cc_start: 0.7878 (m-80) cc_final: 0.7581 (m-80) REVERT: 4 199 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7768 (mmp) REVERT: 4 200 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8725 (p) REVERT: 4 690 GLU cc_start: 0.7099 (tp30) cc_final: 0.6881 (tp30) REVERT: 4 772 ARG cc_start: 0.7979 (tmm-80) cc_final: 0.7444 (ttm-80) REVERT: 6 521 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7579 (mmtm) REVERT: 7 177 MET cc_start: 0.6175 (tpt) cc_final: 0.5800 (tpt) REVERT: B 272 ASP cc_start: 0.6903 (m-30) cc_final: 0.6412 (m-30) REVERT: B 276 MET cc_start: 0.9002 (tpt) cc_final: 0.8768 (tpt) REVERT: B 357 GLU cc_start: 0.6850 (tp30) cc_final: 0.6536 (tm-30) REVERT: C 134 ASP cc_start: 0.7104 (m-30) cc_final: 0.6898 (m-30) REVERT: C 320 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8839 (pp) REVERT: C 386 MET cc_start: 0.8729 (mmt) cc_final: 0.8239 (mmt) REVERT: D 273 ASP cc_start: 0.7509 (m-30) cc_final: 0.7272 (m-30) REVERT: D 417 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8874 (pp) REVERT: D 806 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7678 (mt-10) REVERT: E 82 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7408 (mm-30) REVERT: F 313 MET cc_start: 0.7031 (ptp) cc_final: 0.6688 (ptm) REVERT: G 543 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: G 670 ASP cc_start: 0.7626 (m-30) cc_final: 0.7395 (m-30) outliers start: 120 outliers final: 85 residues processed: 788 average time/residue: 0.5971 time to fit residues: 796.4414 Evaluate side-chains 778 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 688 time to evaluate : 5.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 685 ASN Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 459 MET Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 586 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 729 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 431 optimal weight: 4.9990 chunk 552 optimal weight: 2.9990 chunk 428 optimal weight: 4.9990 chunk 636 optimal weight: 4.9990 chunk 422 optimal weight: 6.9990 chunk 753 optimal weight: 2.9990 chunk 471 optimal weight: 0.2980 chunk 459 optimal weight: 0.8980 chunk 347 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 340 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 63631 Z= 0.196 Angle : 0.479 10.196 86109 Z= 0.244 Chirality : 0.041 0.199 9991 Planarity : 0.004 0.057 11074 Dihedral : 6.505 147.204 8853 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.86 % Allowed : 12.38 % Favored : 85.76 % 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: 0.70 (0.09), residues: 7808 helix: 1.47 (0.09), residues: 3180 sheet: -0.27 (0.13), residues: 1416 loop : -0.07 (0.11), residues: 3212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 356 HIS 0.012 0.001 HIS 6 653 PHE 0.023 0.001 PHE C 735 TYR 0.017 0.001 TYR 2 769 ARG 0.006 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 706 time to evaluate : 5.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 779 HIS cc_start: 0.6279 (OUTLIER) cc_final: 0.5922 (p90) REVERT: 2 781 MET cc_start: 0.7478 (ppp) cc_final: 0.6848 (ppp) REVERT: 2 847 ASP cc_start: 0.7196 (m-30) cc_final: 0.6903 (m-30) REVERT: 3 43 ARG cc_start: 0.8445 (tpt170) cc_final: 0.8224 (tpm170) REVERT: 3 320 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8740 (pp) REVERT: 3 346 ASP cc_start: 0.7093 (m-30) cc_final: 0.6851 (m-30) REVERT: 3 576 TYR cc_start: 0.7895 (m-80) cc_final: 0.7586 (m-80) REVERT: 4 199 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7791 (mmp) REVERT: 4 200 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8758 (p) REVERT: 4 690 GLU cc_start: 0.7120 (tp30) cc_final: 0.6896 (tp30) REVERT: 4 772 ARG cc_start: 0.7979 (tmm-80) cc_final: 0.7468 (ttm-80) REVERT: 6 313 MET cc_start: 0.6210 (mtm) cc_final: 0.4932 (ptp) REVERT: 6 521 LYS cc_start: 0.7969 (mmtm) cc_final: 0.7576 (mmtm) REVERT: 7 177 MET cc_start: 0.6125 (tpt) cc_final: 0.5770 (tpt) REVERT: B 272 ASP cc_start: 0.6876 (m-30) cc_final: 0.6388 (m-30) REVERT: B 276 MET cc_start: 0.8997 (tpt) cc_final: 0.8790 (tpt) REVERT: C 320 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8826 (pp) REVERT: D 417 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8894 (pp) REVERT: D 724 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8825 (mp) REVERT: D 806 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7719 (mt-10) REVERT: D 816 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8595 (p) REVERT: E 82 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7419 (mm-30) REVERT: F 313 MET cc_start: 0.7020 (ptp) cc_final: 0.6666 (ptm) REVERT: F 672 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8744 (mt) REVERT: G 95 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6967 (mt0) REVERT: G 543 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: G 670 ASP cc_start: 0.7619 (m-30) cc_final: 0.7385 (m-30) outliers start: 130 outliers final: 94 residues processed: 789 average time/residue: 0.6053 time to fit residues: 805.7900 Evaluate side-chains 786 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 682 time to evaluate : 5.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 2 residue 811 GLU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 636 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 466 optimal weight: 0.0970 chunk 300 optimal weight: 8.9990 chunk 450 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 479 optimal weight: 0.7980 chunk 513 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 592 optimal weight: 0.5980 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 340 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 613 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 669 GLN ** B 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 63631 Z= 0.191 Angle : 0.476 10.964 86109 Z= 0.242 Chirality : 0.041 0.203 9991 Planarity : 0.004 0.057 11074 Dihedral : 6.453 146.363 8853 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.91 % Allowed : 12.71 % Favored : 85.39 % 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: 0.73 (0.09), residues: 7808 helix: 1.51 (0.09), residues: 3185 sheet: -0.36 (0.13), residues: 1454 loop : -0.02 (0.11), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 356 HIS 0.012 0.001 HIS 6 653 PHE 0.025 0.001 PHE C 421 TYR 0.019 0.001 TYR 2 769 ARG 0.006 0.000 ARG G 593 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 700 time to evaluate : 5.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 779 HIS cc_start: 0.6271 (OUTLIER) cc_final: 0.5917 (p90) REVERT: 2 781 MET cc_start: 0.7480 (ppp) cc_final: 0.6861 (ppp) REVERT: 2 847 ASP cc_start: 0.7193 (m-30) cc_final: 0.6917 (m-30) REVERT: 3 43 ARG cc_start: 0.8455 (tpt170) cc_final: 0.8229 (tpm170) REVERT: 3 320 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8769 (pp) REVERT: 3 346 ASP cc_start: 0.7087 (m-30) cc_final: 0.6849 (m-30) REVERT: 3 576 TYR cc_start: 0.7895 (m-80) cc_final: 0.7577 (m-80) REVERT: 4 199 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7767 (mmp) REVERT: 4 200 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8778 (p) REVERT: 4 690 GLU cc_start: 0.7138 (tp30) cc_final: 0.6921 (tp30) REVERT: 4 772 ARG cc_start: 0.7964 (tmm-80) cc_final: 0.7456 (ttm-80) REVERT: 5 139 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8562 (pp) REVERT: 6 313 MET cc_start: 0.6219 (mtm) cc_final: 0.5022 (ptp) REVERT: 6 521 LYS cc_start: 0.7977 (mmtm) cc_final: 0.7580 (mmtm) REVERT: 7 177 MET cc_start: 0.6192 (tpt) cc_final: 0.5794 (tpt) REVERT: B 272 ASP cc_start: 0.6927 (m-30) cc_final: 0.6446 (m-30) REVERT: C 320 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8824 (pp) REVERT: D 273 ASP cc_start: 0.7453 (m-30) cc_final: 0.7162 (m-30) REVERT: D 417 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8887 (pp) REVERT: D 724 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8835 (mp) REVERT: D 806 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7814 (mt-10) REVERT: D 816 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8599 (p) REVERT: E 82 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7400 (mm-30) REVERT: E 625 ASN cc_start: 0.8147 (t0) cc_final: 0.7826 (t0) REVERT: F 102 LYS cc_start: 0.7792 (mttt) cc_final: 0.7205 (mmtm) REVERT: F 313 MET cc_start: 0.7007 (ptp) cc_final: 0.6667 (ptm) REVERT: F 506 ASN cc_start: 0.7475 (m-40) cc_final: 0.7245 (m-40) REVERT: F 672 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8742 (mt) REVERT: G 95 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6845 (mt0) REVERT: G 543 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: G 670 ASP cc_start: 0.7617 (m-30) cc_final: 0.7385 (m-30) REVERT: G 683 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7487 (tm-30) outliers start: 133 outliers final: 104 residues processed: 785 average time/residue: 0.5984 time to fit residues: 797.0630 Evaluate side-chains 799 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 683 time to evaluate : 5.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 3 residue 641 ASN Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 200 SER Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 524 ASN Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 366 LEU Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 673 ARG Chi-restraints excluded: chain G residue 683 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 685 optimal weight: 9.9990 chunk 722 optimal weight: 2.9990 chunk 658 optimal weight: 0.0470 chunk 702 optimal weight: 6.9990 chunk 721 optimal weight: 0.6980 chunk 422 optimal weight: 8.9990 chunk 305 optimal weight: 4.9990 chunk 551 optimal weight: 0.8980 chunk 215 optimal weight: 0.0870 chunk 634 optimal weight: 0.9980 chunk 664 optimal weight: 6.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 340 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 145 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 669 GLN B 780 GLN C 682 ASN ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 63631 Z= 0.139 Angle : 0.457 11.744 86109 Z= 0.233 Chirality : 0.041 0.255 9991 Planarity : 0.003 0.056 11074 Dihedral : 6.342 146.840 8853 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.65 % Allowed : 13.14 % Favored : 85.21 % 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: 0.84 (0.10), residues: 7808 helix: 1.62 (0.09), residues: 3179 sheet: -0.31 (0.13), residues: 1458 loop : 0.02 (0.11), residues: 3171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 356 HIS 0.013 0.001 HIS 6 653 PHE 0.031 0.001 PHE C 735 TYR 0.018 0.001 TYR 2 769 ARG 0.007 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 730 time to evaluate : 6.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 779 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5885 (p90) REVERT: 2 781 MET cc_start: 0.7476 (ppp) cc_final: 0.6874 (ppp) REVERT: 2 783 MET cc_start: 0.8139 (tmm) cc_final: 0.7752 (tmm) REVERT: 2 847 ASP cc_start: 0.7153 (m-30) cc_final: 0.6882 (m-30) REVERT: 3 43 ARG cc_start: 0.8363 (tpt170) cc_final: 0.8133 (tpm170) REVERT: 3 320 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8683 (pp) REVERT: 3 346 ASP cc_start: 0.7058 (m-30) cc_final: 0.6820 (m-30) REVERT: 3 576 TYR cc_start: 0.7862 (m-80) cc_final: 0.7530 (m-80) REVERT: 4 199 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7801 (mmp) REVERT: 4 690 GLU cc_start: 0.7136 (tp30) cc_final: 0.6920 (tp30) REVERT: 4 772 ARG cc_start: 0.7939 (tmm-80) cc_final: 0.7439 (ttm-80) REVERT: 5 139 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8525 (pp) REVERT: 6 313 MET cc_start: 0.6204 (mtm) cc_final: 0.5006 (ptp) REVERT: B 272 ASP cc_start: 0.6898 (m-30) cc_final: 0.6423 (m-30) REVERT: C 55 ASN cc_start: 0.5395 (m-40) cc_final: 0.4853 (t0) REVERT: C 320 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8771 (pp) REVERT: C 719 LYS cc_start: 0.8448 (tppt) cc_final: 0.8244 (tppt) REVERT: D 417 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8863 (pp) REVERT: D 504 GLN cc_start: 0.8074 (mp10) cc_final: 0.7852 (tt0) REVERT: D 724 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8827 (mp) REVERT: D 816 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8600 (p) REVERT: E 82 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7364 (mm-30) REVERT: E 625 ASN cc_start: 0.8169 (t0) cc_final: 0.7868 (t0) REVERT: F 102 LYS cc_start: 0.7827 (mttt) cc_final: 0.7334 (mmtm) REVERT: F 313 MET cc_start: 0.7022 (ptp) cc_final: 0.6687 (ptm) REVERT: F 672 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8736 (mt) REVERT: G 95 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6707 (mt0) REVERT: G 543 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: G 637 LYS cc_start: 0.8265 (mmtt) cc_final: 0.8034 (ttmt) REVERT: G 670 ASP cc_start: 0.7571 (m-30) cc_final: 0.7268 (m-30) outliers start: 115 outliers final: 89 residues processed: 802 average time/residue: 0.6003 time to fit residues: 812.2028 Evaluate side-chains 802 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 703 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 760 GLN Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 793 LEU Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 552 MET Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 673 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 699 optimal weight: 0.0980 chunk 461 optimal weight: 0.5980 chunk 742 optimal weight: 1.9990 chunk 453 optimal weight: 4.9990 chunk 352 optimal weight: 0.8980 chunk 516 optimal weight: 1.9990 chunk 779 optimal weight: 4.9990 chunk 717 optimal weight: 2.9990 chunk 620 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 479 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 52 ASN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 669 GLN B 282 HIS B 780 GLN D 380 ASN ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 63631 Z= 0.127 Angle : 0.454 12.136 86109 Z= 0.231 Chirality : 0.040 0.187 9991 Planarity : 0.003 0.055 11074 Dihedral : 6.274 146.878 8853 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.50 % Allowed : 13.47 % Favored : 85.03 % 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: 0.91 (0.10), residues: 7808 helix: 1.70 (0.09), residues: 3179 sheet: -0.29 (0.13), residues: 1454 loop : 0.05 (0.11), residues: 3175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 344 HIS 0.013 0.001 HIS 6 653 PHE 0.041 0.001 PHE C 735 TYR 0.018 0.001 TYR F 192 ARG 0.006 0.000 ARG G 593 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15616 Ramachandran restraints generated. 7808 Oldfield, 0 Emsley, 7808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 725 time to evaluate : 5.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 779 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5869 (p90) REVERT: 2 781 MET cc_start: 0.7470 (ppp) cc_final: 0.6865 (ppp) REVERT: 2 783 MET cc_start: 0.8017 (tmm) cc_final: 0.7697 (tmm) REVERT: 2 847 ASP cc_start: 0.7145 (m-30) cc_final: 0.6873 (m-30) REVERT: 3 320 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8664 (pp) REVERT: 3 346 ASP cc_start: 0.7045 (m-30) cc_final: 0.6747 (m-30) REVERT: 4 199 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7816 (mmp) REVERT: 4 690 GLU cc_start: 0.7101 (tp30) cc_final: 0.6885 (tp30) REVERT: 4 772 ARG cc_start: 0.7900 (tmm-80) cc_final: 0.7414 (ttm-80) REVERT: 5 139 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8532 (pp) REVERT: 6 313 MET cc_start: 0.6269 (mtm) cc_final: 0.4971 (ptp) REVERT: B 272 ASP cc_start: 0.6925 (m-30) cc_final: 0.6455 (m-30) REVERT: C 55 ASN cc_start: 0.5392 (m-40) cc_final: 0.4851 (t0) REVERT: C 320 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8763 (pp) REVERT: D 417 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8864 (pp) REVERT: D 504 GLN cc_start: 0.8068 (mp10) cc_final: 0.7862 (tt0) REVERT: D 724 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8835 (mp) REVERT: D 816 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8587 (p) REVERT: E 82 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7332 (mm-30) REVERT: E 209 ARG cc_start: 0.7612 (mpt180) cc_final: 0.7400 (mmp80) REVERT: E 625 ASN cc_start: 0.8149 (t0) cc_final: 0.7866 (t0) REVERT: F 102 LYS cc_start: 0.7795 (mttt) cc_final: 0.7395 (mptt) REVERT: F 313 MET cc_start: 0.7095 (ptp) cc_final: 0.6749 (ptm) REVERT: F 672 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8726 (mt) REVERT: G 95 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6693 (mt0) REVERT: G 543 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: G 637 LYS cc_start: 0.8279 (mmtt) cc_final: 0.8050 (ttmt) REVERT: G 670 ASP cc_start: 0.7573 (m-30) cc_final: 0.7266 (m-30) outliers start: 105 outliers final: 82 residues processed: 792 average time/residue: 0.6045 time to fit residues: 810.9132 Evaluate side-chains 791 residues out of total 6986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 699 time to evaluate : 5.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 628 SER Chi-restraints excluded: chain 2 residue 631 ILE Chi-restraints excluded: chain 2 residue 682 VAL Chi-restraints excluded: chain 2 residue 683 VAL Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 563 GLU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 5 residue 599 MET Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 384 ASP Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 407 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 764 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 155 SER Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 300 PHE Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 749 MET Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 831 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 617 THR Chi-restraints excluded: chain G residue 673 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 380 optimal weight: 4.9990 chunk 492 optimal weight: 9.9990 chunk 660 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 572 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 621 optimal weight: 7.9990 chunk 260 optimal weight: 3.9990 chunk 638 optimal weight: 5.9990 chunk 78 optimal weight: 0.0470 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 856 GLN 3 340 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 468 GLN 7 669 GLN B 192 ASN B 282 HIS ** B 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 GLN ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN ** G 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110354 restraints weight = 81592.508| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.90 r_work: 0.3009 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 63631 Z= 0.280 Angle : 0.522 13.177 86109 Z= 0.265 Chirality : 0.043 0.192 9991 Planarity : 0.004 0.066 11074 Dihedral : 6.430 145.499 8853 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.65 % Allowed : 13.27 % Favored : 85.09 % 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: 0.76 (0.09), residues: 7808 helix: 1.54 (0.09), residues: 3182 sheet: -0.25 (0.13), residues: 1455 loop : -0.07 (0.11), residues: 3171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 344 HIS 0.013 0.001 HIS 6 653 PHE 0.046 0.001 PHE C 735 TYR 0.021 0.001 TYR F 192 ARG 0.012 0.000 ARG F 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14279.68 seconds wall clock time: 254 minutes 14.19 seconds (15254.19 seconds total)