Starting phenix.real_space_refine on Thu Jan 18 12:50:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/01_2024/7wz3_32903_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/01_2024/7wz3_32903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/01_2024/7wz3_32903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/01_2024/7wz3_32903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/01_2024/7wz3_32903_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz3_32903/01_2024/7wz3_32903_updated.pdb" } resolution = 4.1 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= 0.019 sd= 0.164 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 364 5.16 5 C 36697 2.51 5 N 10202 2.21 5 O 11276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ASP 42": "OD1" <-> "OD2" Residue "a GLU 68": "OE1" <-> "OE2" Residue "a GLU 77": "OE1" <-> "OE2" Residue "a GLU 99": "OE1" <-> "OE2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 174": "OD1" <-> "OD2" Residue "a TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 261": "OD1" <-> "OD2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 335": "OE1" <-> "OE2" Residue "a GLU 337": "OE1" <-> "OE2" Residue "a GLU 341": "OE1" <-> "OE2" Residue "a ASP 382": "OD1" <-> "OD2" Residue "a PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 528": "OD1" <-> "OD2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 49": "OD1" <-> "OD2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "b GLU 94": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "b PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 233": "OE1" <-> "OE2" Residue "b GLU 277": "OE1" <-> "OE2" Residue "b PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 339": "OE1" <-> "OE2" Residue "b GLU 350": "OE1" <-> "OE2" Residue "b ASP 384": "OD1" <-> "OD2" Residue "b TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 509": "OE1" <-> "OE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D ASP 332": "OD1" <-> "OD2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 26": "OD1" <-> "OD2" Residue "d PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 58": "OD1" <-> "OD2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 146": "OE1" <-> "OE2" Residue "d ASP 150": "OD1" <-> "OD2" Residue "d GLU 161": "OE1" <-> "OE2" Residue "d TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 273": "OD1" <-> "OD2" Residue "d ASP 332": "OD1" <-> "OD2" Residue "d PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 533": "OD1" <-> "OD2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ASP 156": "OD1" <-> "OD2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 349": "OE1" <-> "OE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 454": "OE1" <-> "OE2" Residue "E GLU 482": "OE1" <-> "OE2" Residue "E ASP 529": "OD1" <-> "OD2" Residue "E ASP 530": "OD1" <-> "OD2" Residue "e ASP 82": "OD1" <-> "OD2" Residue "e ASP 102": "OD1" <-> "OD2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "e ASP 156": "OD1" <-> "OD2" Residue "e PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 292": "OE1" <-> "OE2" Residue "e PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 482": "OE1" <-> "OE2" Residue "e ASP 490": "OD1" <-> "OD2" Residue "e ASP 530": "OD1" <-> "OD2" Residue "g ASP 52": "OD1" <-> "OD2" Residue "g GLU 104": "OE1" <-> "OE2" Residue "g GLU 186": "OE1" <-> "OE2" Residue "g TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 357": "OD1" <-> "OD2" Residue "g TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 521": "OD1" <-> "OD2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 340": "OE1" <-> "OE2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 368": "OD1" <-> "OD2" Residue "G GLU 473": "OE1" <-> "OE2" Residue "G GLU 483": "OE1" <-> "OE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 14": "OD1" <-> "OD2" Residue "h ASP 61": "OD1" <-> "OD2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 113": "OE1" <-> "OE2" Residue "h PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 226": "OE1" <-> "OE2" Residue "h TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 517": "OD1" <-> "OD2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 379": "OE1" <-> "OE2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 517": "OD1" <-> "OD2" Residue "H GLU 518": "OE1" <-> "OE2" Residue "Q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 357": "OD1" <-> "OD2" Residue "Q PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 405": "OD1" <-> "OD2" Residue "Q TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 485": "OE1" <-> "OE2" Residue "q GLU 38": "OE1" <-> "OE2" Residue "q ASP 68": "OD1" <-> "OD2" Residue "q GLU 75": "OE1" <-> "OE2" Residue "q GLU 77": "OE1" <-> "OE2" Residue "q GLU 94": "OE1" <-> "OE2" Residue "q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 113": "OE1" <-> "OE2" Residue "q GLU 127": "OE1" <-> "OE2" Residue "q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 342": "OE1" <-> "OE2" Residue "q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 366": "OE1" <-> "OE2" Residue "q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 85": "OD1" <-> "OD2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 136": "OE1" <-> "OE2" Residue "Z GLU 142": "OE1" <-> "OE2" Residue "Z ASP 183": "OD1" <-> "OD2" Residue "Z PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 269": "OD1" <-> "OD2" Residue "Z ASP 284": "OD1" <-> "OD2" Residue "Z PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 342": "OD1" <-> "OD2" Residue "Z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 472": "OE1" <-> "OE2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "z ASP 53": "OD1" <-> "OD2" Residue "z GLU 66": "OE1" <-> "OE2" Residue "z GLU 101": "OE1" <-> "OE2" Residue "z ASP 107": "OD1" <-> "OD2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 112": "OE1" <-> "OE2" Residue "z GLU 121": "OE1" <-> "OE2" Residue "z PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 243": "OE1" <-> "OE2" Residue "z PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 254": "OE1" <-> "OE2" Residue "z PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 337": "OD1" <-> "OD2" Residue "z ASP 338": "OD1" <-> "OD2" Residue "z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 519": "OD1" <-> "OD2" Residue "z GLU 520": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 58551 Number of models: 1 Model: "" Number of chains: 22 Chain: "a" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3949 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 12, 'TRANS': 507} Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3590 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 11, 'TRANS': 464} Chain breaks: 1 Chain: "b" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3580 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 9, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2426 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 1 Chain: "D" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3259 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 421} Chain breaks: 4 Chain: "d" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3902 Classifications: {'peptide': 516} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 500} Chain: "E" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3936 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain: "e" Number of atoms: 3921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3921 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 17, 'TRANS': 492} Chain: "g" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3724 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 16, 'TRANS': 464} Chain breaks: 1 Chain: "G" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3165 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "h" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3927 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 14, 'TRANS': 496} Chain: "H" Number of atoms: 3898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3898 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 14, 'TRANS': 492} Chain: "Q" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3602 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 12, 'TRANS': 459} Chain breaks: 1 Chain: "q" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3688 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "Z" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3907 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 13, 'TRANS': 495} Chain: "z" Number of atoms: 3915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3915 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 13, 'TRANS': 496} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.21, per 1000 atoms: 0.38 Number of scatterers: 58551 At special positions: 0 Unit cell: (188.474, 196.382, 183.202, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 364 16.00 P 12 15.00 O 11276 8.00 N 10202 7.00 C 36697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.93 Conformation dependent library (CDL) restraints added in 8.8 seconds 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 277 helices and 79 sheets defined 50.6% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.91 Creating SS restraints... Processing helix chain 'a' and resid 15 through 31 Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 removed outlier: 3.646A pdb=" N VAL a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS a 76 " --> pdb=" O ALA a 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU a 77 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.693A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE a 95 " --> pdb=" O THR a 91 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 removed outlier: 3.649A pdb=" N LEU a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 153 Processing helix chain 'a' and resid 155 through 158 removed outlier: 4.426A pdb=" N SER a 158 " --> pdb=" O SER a 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 155 through 158' Processing helix chain 'a' and resid 160 through 178 removed outlier: 3.662A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN a 164 " --> pdb=" O ILE a 161 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY a 165 " --> pdb=" O GLY a 162 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE a 167 " --> pdb=" O ASN a 164 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN a 170 " --> pdb=" O PHE a 167 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET a 171 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP a 174 " --> pdb=" O MET a 171 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU a 177 " --> pdb=" O ASP a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 281 removed outlier: 3.565A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU a 273 " --> pdb=" O ASP a 269 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN a 276 " --> pdb=" O LYS a 272 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR a 281 " --> pdb=" O LYS a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 removed outlier: 3.508A pdb=" N LYS a 298 " --> pdb=" O ASP a 294 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE a 300 " --> pdb=" O CYS a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 323 removed outlier: 3.590A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 382 through 402 removed outlier: 3.632A pdb=" N GLU a 387 " --> pdb=" O PHE a 383 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG a 390 " --> pdb=" O ASP a 386 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER a 391 " --> pdb=" O GLU a 387 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS a 397 " --> pdb=" O HIS a 393 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 430 removed outlier: 4.062A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 455 removed outlier: 3.658A pdb=" N LEU a 445 " --> pdb=" O PHE a 441 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix removed outlier: 3.951A pdb=" N VAL a 454 " --> pdb=" O ASN a 450 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 476 removed outlier: 3.976A pdb=" N VAL a 464 " --> pdb=" O SER a 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'A' and resid 15 through 31 removed outlier: 3.586A pdb=" N SER A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.501A pdb=" N LYS A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.876A pdb=" N VAL A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.665A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.781A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 165 through 177 removed outlier: 3.660A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.595A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 382 through 404 removed outlier: 3.901A pdb=" N MET A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.911A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.684A pdb=" N ALA A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix removed outlier: 3.709A pdb=" N VAL A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 removed outlier: 3.576A pdb=" N PHE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 526 removed outlier: 3.613A pdb=" N LYS A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 42 removed outlier: 3.999A pdb=" N LEU b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE b 35 " --> pdb=" O GLY b 31 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N SER b 41 " --> pdb=" O ASP b 37 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR b 42 " --> pdb=" O LEU b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 73 removed outlier: 3.526A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 94 removed outlier: 3.602A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL b 85 " --> pdb=" O ALA b 81 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL b 90 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN b 91 " --> pdb=" O MET b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 119 removed outlier: 3.569A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU b 110 " --> pdb=" O ALA b 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA b 118 " --> pdb=" O GLU b 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 143 removed outlier: 3.583A pdb=" N GLY b 129 " --> pdb=" O THR b 125 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU b 132 " --> pdb=" O ALA b 128 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS b 135 " --> pdb=" O ARG b 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 152 through 166 removed outlier: 3.513A pdb=" N MET b 160 " --> pdb=" O ARG b 156 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN b 161 " --> pdb=" O GLN b 157 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 173 No H-bonds generated for 'chain 'b' and resid 171 through 173' Processing helix chain 'b' and resid 176 through 190 removed outlier: 4.042A pdb=" N LYS b 181 " --> pdb=" O ASP b 177 " (cutoff:3.500A) Processing helix chain 'b' and resid 271 through 285 removed outlier: 3.699A pdb=" N LYS b 276 " --> pdb=" O LYS b 272 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE b 282 " --> pdb=" O LYS b 278 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS b 284 " --> pdb=" O GLU b 280 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 307 removed outlier: 3.731A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE b 304 " --> pdb=" O PRO b 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY b 305 " --> pdb=" O GLU b 301 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA b 306 " --> pdb=" O GLN b 302 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA b 307 " --> pdb=" O LEU b 303 " (cutoff:3.500A) Processing helix chain 'b' and resid 317 through 326 removed outlier: 3.946A pdb=" N LEU b 323 " --> pdb=" O GLY b 319 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU b 325 " --> pdb=" O GLU b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 402 removed outlier: 3.584A pdb=" N SER b 389 " --> pdb=" O GLU b 385 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL b 396 " --> pdb=" O ASP b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 412 through 426 removed outlier: 4.092A pdb=" N ASN b 426 " --> pdb=" O THR b 422 " (cutoff:3.500A) Processing helix chain 'b' and resid 430 through 453 removed outlier: 3.883A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA b 435 " --> pdb=" O LYS b 431 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU b 446 " --> pdb=" O ALA b 442 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 458 through 470 removed outlier: 3.652A pdb=" N VAL b 462 " --> pdb=" O SER b 458 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA b 463 " --> pdb=" O ALA b 459 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU b 465 " --> pdb=" O LEU b 461 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG b 466 " --> pdb=" O VAL b 462 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA b 467 " --> pdb=" O ALA b 463 " (cutoff:3.500A) Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 removed outlier: 3.801A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.727A pdb=" N LEU B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 67 through 73 removed outlier: 3.526A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 73' Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.981A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.658A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 removed outlier: 3.514A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.557A pdb=" N MET B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.897A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 182 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 402 removed outlier: 3.618A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 399 " --> pdb=" O CYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 426 removed outlier: 4.148A pdb=" N ASN B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 removed outlier: 3.700A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.779A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.738A pdb=" N LEU B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.641A pdb=" N VAL B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.503A pdb=" N ILE D 33 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 34 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE D 35 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN D 37 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 38 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 40 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 43 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 46 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 50 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 removed outlier: 3.510A pdb=" N LYS D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.823A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 removed outlier: 4.178A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 removed outlier: 3.513A pdb=" N LYS D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 removed outlier: 3.952A pdb=" N SER D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 188 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 312 through 319 removed outlier: 3.659A pdb=" N ASN D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 340 removed outlier: 3.769A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 336 " --> pdb=" O ILE D 333 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS D 337 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE D 340 " --> pdb=" O CYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 removed outlier: 3.583A pdb=" N VAL D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.925A pdb=" N GLU D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 441 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 468 removed outlier: 3.937A pdb=" N MET D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.050A pdb=" N VAL D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 530 removed outlier: 3.543A pdb=" N LEU D 519 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 51 removed outlier: 3.501A pdb=" N SER d 36 " --> pdb=" O GLN d 32 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA d 45 " --> pdb=" O ALA d 41 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR d 50 " --> pdb=" O ASP d 46 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER d 51 " --> pdb=" O ALA d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 79 removed outlier: 4.132A pdb=" N LEU d 78 " --> pdb=" O GLY d 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 74 through 79' Processing helix chain 'd' and resid 86 through 101 removed outlier: 3.585A pdb=" N MET d 90 " --> pdb=" O PRO d 86 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL d 92 " --> pdb=" O ALA d 88 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU d 93 " --> pdb=" O ARG d 89 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE d 100 " --> pdb=" O LYS d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 126 removed outlier: 4.036A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE d 111 " --> pdb=" O THR d 107 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS d 126 " --> pdb=" O LYS d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 151 removed outlier: 3.644A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET d 151 " --> pdb=" O ILE d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 172 removed outlier: 3.641A pdb=" N SER d 170 " --> pdb=" O SER d 166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU d 171 " --> pdb=" O ALA d 167 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 194 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 269 through 293 removed outlier: 3.704A pdb=" N ARG d 280 " --> pdb=" O LEU d 276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU d 286 " --> pdb=" O TYR d 282 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS d 292 " --> pdb=" O LYS d 288 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 319 removed outlier: 3.859A pdb=" N ASN d 318 " --> pdb=" O LEU d 314 " (cutoff:3.500A) Processing helix chain 'd' and resid 330 through 340 removed outlier: 3.808A pdb=" N GLU d 334 " --> pdb=" O ARG d 330 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE d 335 " --> pdb=" O GLU d 331 " (cutoff:3.500A) Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 417 removed outlier: 3.666A pdb=" N VAL d 411 " --> pdb=" O ASP d 407 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS d 417 " --> pdb=" O ARG d 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 427 through 442 removed outlier: 3.521A pdb=" N GLU d 431 " --> pdb=" O ALA d 427 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU d 438 " --> pdb=" O LEU d 434 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG d 441 " --> pdb=" O THR d 437 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 468 removed outlier: 4.059A pdb=" N SER d 448 " --> pdb=" O GLY d 445 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR d 449 " --> pdb=" O MET d 446 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS d 450 " --> pdb=" O GLU d 447 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG d 452 " --> pdb=" O TYR d 449 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA d 453 " --> pdb=" O CYS d 450 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP d 456 " --> pdb=" O ALA d 453 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA d 457 " --> pdb=" O PHE d 454 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL d 460 " --> pdb=" O ALA d 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE d 461 " --> pdb=" O MET d 458 " (cutoff:3.500A) Proline residue: d 462 - end of helix removed outlier: 3.521A pdb=" N ALA d 466 " --> pdb=" O SER d 463 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 486 removed outlier: 4.127A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU d 479 " --> pdb=" O SER d 475 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 506 No H-bonds generated for 'chain 'd' and resid 503 through 506' Processing helix chain 'd' and resid 512 through 531 removed outlier: 3.701A pdb=" N ALA d 522 " --> pdb=" O ALA d 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 46 removed outlier: 4.272A pdb=" N VAL E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 99 removed outlier: 3.985A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU E 91 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 93 " --> pdb=" O MET E 89 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 123 removed outlier: 4.235A pdb=" N VAL E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 148 removed outlier: 3.549A pdb=" N ARG E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 173 removed outlier: 3.666A pdb=" N GLN E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER E 173 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 removed outlier: 3.758A pdb=" N HIS E 180 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG E 181 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET E 183 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 184 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 187 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN E 189 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 190 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 191 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU E 192 " --> pdb=" O ASN E 189 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL E 194 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 206 No H-bonds generated for 'chain 'E' and resid 204 through 206' Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 269 through 292 removed outlier: 3.607A pdb=" N ALA E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU E 292 " --> pdb=" O GLN E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.781A pdb=" N GLN E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 removed outlier: 3.512A pdb=" N GLU E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 412 removed outlier: 3.739A pdb=" N ARG E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 437 removed outlier: 3.599A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LYS E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 463 removed outlier: 3.752A pdb=" N TYR E 444 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E 447 " --> pdb=" O TYR E 444 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 451 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 452 " --> pdb=" O PHE E 449 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 456 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 457 - end of helix Processing helix chain 'E' and resid 470 through 478 removed outlier: 3.645A pdb=" N GLU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG E 476 " --> pdb=" O MET E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 508 through 526 removed outlier: 3.782A pdb=" N ILE E 515 " --> pdb=" O LYS E 511 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 519 " --> pdb=" O ILE E 515 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 46 removed outlier: 4.205A pdb=" N LEU e 32 " --> pdb=" O LEU e 29 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS e 33 " --> pdb=" O GLU e 30 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER e 34 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET e 37 " --> pdb=" O SER e 34 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS e 40 " --> pdb=" O MET e 37 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA e 41 " --> pdb=" O ALA e 38 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN e 44 " --> pdb=" O ALA e 41 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR e 45 " --> pdb=" O VAL e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 78 Processing helix chain 'e' and resid 84 through 96 removed outlier: 3.515A pdb=" N LEU e 88 " --> pdb=" O GLN e 84 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET e 89 " --> pdb=" O ILE e 85 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL e 90 " --> pdb=" O ALA e 86 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU e 91 " --> pdb=" O LYS e 87 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU e 92 " --> pdb=" O LEU e 88 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER e 93 " --> pdb=" O MET e 89 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS e 94 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 122 removed outlier: 4.074A pdb=" N VAL e 108 " --> pdb=" O THR e 104 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 148 removed outlier: 3.520A pdb=" N ARG e 140 " --> pdb=" O GLU e 136 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL e 141 " --> pdb=" O GLN e 137 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.551A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR e 170 " --> pdb=" O THR e 166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY e 172 " --> pdb=" O LYS e 168 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER e 173 " --> pdb=" O THR e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 194 removed outlier: 4.304A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS e 180 " --> pdb=" O ASN e 177 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG e 181 " --> pdb=" O SER e 178 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN e 182 " --> pdb=" O CYS e 179 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU e 185 " --> pdb=" O GLN e 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE e 186 " --> pdb=" O MET e 183 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL e 188 " --> pdb=" O GLU e 185 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN e 189 " --> pdb=" O ILE e 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU e 192 " --> pdb=" O ASN e 189 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR e 193 " --> pdb=" O ALA e 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 219 No H-bonds generated for 'chain 'e' and resid 217 through 219' Processing helix chain 'e' and resid 269 through 293 removed outlier: 3.642A pdb=" N ALA e 274 " --> pdb=" O GLU e 270 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS e 277 " --> pdb=" O LYS e 273 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE e 287 " --> pdb=" O PHE e 283 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN e 288 " --> pdb=" O GLU e 284 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE e 290 " --> pdb=" O MET e 286 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS e 291 " --> pdb=" O ILE e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 306 through 315 removed outlier: 3.935A pdb=" N LEU e 311 " --> pdb=" O GLU e 307 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU e 312 " --> pdb=" O ALA e 308 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN e 314 " --> pdb=" O HIS e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 334 removed outlier: 3.659A pdb=" N LEU e 330 " --> pdb=" O PRO e 326 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE e 331 " --> pdb=" O GLU e 327 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA e 332 " --> pdb=" O ILE e 328 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA e 334 " --> pdb=" O LEU e 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 326 through 334' Processing helix chain 'e' and resid 390 through 412 removed outlier: 3.654A pdb=" N ARG e 398 " --> pdb=" O GLU e 394 " (cutoff:3.500A) Processing helix chain 'e' and resid 422 through 437 removed outlier: 3.622A pdb=" N LEU e 429 " --> pdb=" O ILE e 425 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP e 436 " --> pdb=" O SER e 432 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS e 437 " --> pdb=" O GLN e 433 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 463 removed outlier: 3.996A pdb=" N TYR e 444 " --> pdb=" O LEU e 441 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE e 449 " --> pdb=" O MET e 446 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA e 450 " --> pdb=" O ARG e 447 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA e 452 " --> pdb=" O PHE e 449 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU e 454 " --> pdb=" O ASP e 451 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE e 456 " --> pdb=" O LEU e 453 " (cutoff:3.500A) Proline residue: e 457 - end of helix removed outlier: 3.669A pdb=" N SER e 461 " --> pdb=" O MET e 458 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN e 463 " --> pdb=" O LEU e 460 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 478 removed outlier: 3.669A pdb=" N GLU e 474 " --> pdb=" O GLN e 470 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL e 475 " --> pdb=" O THR e 471 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG e 476 " --> pdb=" O MET e 472 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA e 477 " --> pdb=" O THR e 473 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG e 478 " --> pdb=" O GLU e 474 " (cutoff:3.500A) Processing helix chain 'e' and resid 508 through 526 Processing helix chain 'g' and resid 21 through 36 removed outlier: 3.586A pdb=" N ASN g 26 " --> pdb=" O VAL g 22 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE g 27 " --> pdb=" O GLN g 23 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE g 33 " --> pdb=" O ALA g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 removed outlier: 3.502A pdb=" N LEU g 67 " --> pdb=" O GLY g 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG g 68 " --> pdb=" O ASN g 64 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 63 through 69' Processing helix chain 'g' and resid 75 through 90 removed outlier: 3.860A pdb=" N MET g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE g 81 " --> pdb=" O ALA g 77 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR g 86 " --> pdb=" O GLU g 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU g 90 " --> pdb=" O THR g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 105 removed outlier: 3.663A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 139 removed outlier: 3.601A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP g 132 " --> pdb=" O LYS g 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER g 135 " --> pdb=" O ASP g 131 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 160 removed outlier: 3.597A pdb=" N ASN g 154 " --> pdb=" O ASP g 150 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE g 155 " --> pdb=" O MET g 151 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER g 158 " --> pdb=" O ASN g 154 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER g 159 " --> pdb=" O ILE g 155 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE g 160 " --> pdb=" O ILE g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 183 removed outlier: 3.736A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER g 169 " --> pdb=" O SER g 166 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA g 176 " --> pdb=" O CYS g 173 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU g 177 " --> pdb=" O ASN g 174 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP g 178 " --> pdb=" O ILE g 175 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA g 179 " --> pdb=" O ALA g 176 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL g 180 " --> pdb=" O LEU g 177 " (cutoff:3.500A) Processing helix chain 'g' and resid 195 through 198 No H-bonds generated for 'chain 'g' and resid 195 through 198' Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 269 through 280 removed outlier: 3.884A pdb=" N TYR g 274 " --> pdb=" O MET g 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE g 275 " --> pdb=" O GLU g 271 " (cutoff:3.500A) Processing helix chain 'g' and resid 300 through 306 Processing helix chain 'g' and resid 317 through 326 removed outlier: 3.548A pdb=" N ARG g 322 " --> pdb=" O THR g 318 " (cutoff:3.500A) Processing helix chain 'g' and resid 381 through 403 removed outlier: 3.561A pdb=" N ARG g 389 " --> pdb=" O SER g 385 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN g 392 " --> pdb=" O GLU g 388 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL g 397 " --> pdb=" O ASP g 393 " (cutoff:3.500A) Processing helix chain 'g' and resid 413 through 426 removed outlier: 3.852A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU g 424 " --> pdb=" O HIS g 420 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 455 removed outlier: 3.549A pdb=" N TRP g 435 " --> pdb=" O VAL g 432 " (cutoff:3.500A) Proline residue: g 436 - end of helix removed outlier: 3.635A pdb=" N VAL g 440 " --> pdb=" O TYR g 437 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU g 444 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU g 445 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE g 447 " --> pdb=" O LEU g 444 " (cutoff:3.500A) Proline residue: g 448 - end of helix removed outlier: 3.626A pdb=" N ILE g 452 " --> pdb=" O ARG g 449 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN g 454 " --> pdb=" O LEU g 451 " (cutoff:3.500A) Processing helix chain 'g' and resid 459 through 472 removed outlier: 3.810A pdb=" N ALA g 468 " --> pdb=" O THR g 464 " (cutoff:3.500A) Processing helix chain 'g' and resid 499 through 517 removed outlier: 3.520A pdb=" N ALA g 513 " --> pdb=" O ALA g 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 105 Processing helix chain 'G' and resid 119 through 139 removed outlier: 3.584A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 160 removed outlier: 3.579A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'G' and resid 169 through 183 removed outlier: 3.831A pdb=" N ASN G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL G 183 " --> pdb=" O ALA G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 188 No H-bonds generated for 'chain 'G' and resid 186 through 188' Processing helix chain 'G' and resid 195 through 198 No H-bonds generated for 'chain 'G' and resid 195 through 198' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 269 through 285 removed outlier: 3.588A pdb=" N GLU G 273 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU G 278 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP G 281 " --> pdb=" O GLN G 277 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 306 removed outlier: 3.648A pdb=" N HIS G 302 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU G 304 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG G 306 " --> pdb=" O HIS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 326 removed outlier: 3.961A pdb=" N ARG G 322 " --> pdb=" O THR G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 403 removed outlier: 3.557A pdb=" N ASN G 390 " --> pdb=" O GLU G 386 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP G 393 " --> pdb=" O ARG G 389 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA G 394 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN G 396 " --> pdb=" O GLN G 392 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G 403 " --> pdb=" O ARG G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.592A pdb=" N GLU G 424 " --> pdb=" O HIS G 420 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER G 426 " --> pdb=" O LEU G 422 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.720A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.655A pdb=" N VAL G 440 " --> pdb=" O TYR G 437 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA G 443 " --> pdb=" O VAL G 440 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 447 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Proline residue: G 448 - end of helix removed outlier: 3.939A pdb=" N ILE G 452 " --> pdb=" O ARG G 449 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN G 454 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 471 removed outlier: 3.578A pdb=" N HIS G 470 " --> pdb=" O LEU G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 517 removed outlier: 3.587A pdb=" N LYS G 507 " --> pdb=" O LEU G 503 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 39 removed outlier: 3.747A pdb=" N VAL h 31 " --> pdb=" O SER h 27 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR h 38 " --> pdb=" O GLU h 34 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 69 Processing helix chain 'h' and resid 74 through 89 removed outlier: 4.118A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP h 87 " --> pdb=" O ALA h 83 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA h 88 " --> pdb=" O LYS h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 107 removed outlier: 3.631A pdb=" N PHE h 104 " --> pdb=" O LEU h 100 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU h 105 " --> pdb=" O ALA h 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 112 No H-bonds generated for 'chain 'h' and resid 109 through 112' Processing helix chain 'h' and resid 118 through 139 removed outlier: 3.889A pdb=" N ILE h 122 " --> pdb=" O PRO h 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG h 123 " --> pdb=" O GLN h 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR h 127 " --> pdb=" O ARG h 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS h 137 " --> pdb=" O VAL h 133 " (cutoff:3.500A) Processing helix chain 'h' and resid 146 through 148 No H-bonds generated for 'chain 'h' and resid 146 through 148' Processing helix chain 'h' and resid 151 through 162 removed outlier: 3.572A pdb=" N GLU h 156 " --> pdb=" O ARG h 152 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR h 161 " --> pdb=" O LYS h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 172 through 184 removed outlier: 4.030A pdb=" N LYS h 177 " --> pdb=" O ALA h 173 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET h 178 " --> pdb=" O PHE h 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL h 180 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL h 183 " --> pdb=" O VAL h 179 " (cutoff:3.500A) Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 260 through 284 removed outlier: 4.155A pdb=" N GLN h 264 " --> pdb=" O VAL h 260 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL h 267 " --> pdb=" O TYR h 263 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU h 274 " --> pdb=" O GLU h 270 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE h 281 " --> pdb=" O LYS h 277 " (cutoff:3.500A) Processing helix chain 'h' and resid 297 through 305 removed outlier: 3.644A pdb=" N GLN h 301 " --> pdb=" O ASP h 297 " (cutoff:3.500A) Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 353 through 355 No H-bonds generated for 'chain 'h' and resid 353 through 355' Processing helix chain 'h' and resid 379 through 401 removed outlier: 3.512A pdb=" N GLU h 384 " --> pdb=" O GLN h 380 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 426 removed outlier: 3.568A pdb=" N GLU h 415 " --> pdb=" O ALA h 411 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 432 through 452 removed outlier: 3.790A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix removed outlier: 3.947A pdb=" N CYS h 450 " --> pdb=" O PRO h 446 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP h 451 " --> pdb=" O ARG h 447 " (cutoff:3.500A) Processing helix chain 'h' and resid 457 through 470 removed outlier: 3.807A pdb=" N ALA h 466 " --> pdb=" O ASN h 462 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG h 467 " --> pdb=" O LYS h 463 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS h 468 " --> pdb=" O LEU h 464 " (cutoff:3.500A) Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'H' and resid 19 through 35 removed outlier: 4.222A pdb=" N ILE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.508A pdb=" N LEU H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 89 removed outlier: 3.777A pdb=" N THR H 78 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 107 removed outlier: 3.732A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 112 No H-bonds generated for 'chain 'H' and resid 109 through 112' Processing helix chain 'H' and resid 118 through 139 removed outlier: 3.582A pdb=" N ILE H 122 " --> pdb=" O PRO H 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.580A pdb=" N THR H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 185 removed outlier: 3.554A pdb=" N MET H 178 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL H 179 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 284 removed outlier: 3.881A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS H 277 " --> pdb=" O ILE H 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS H 280 " --> pdb=" O ASP H 276 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 removed outlier: 3.758A pdb=" N GLN H 301 " --> pdb=" O ASP H 297 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 353 through 355 No H-bonds generated for 'chain 'H' and resid 353 through 355' Processing helix chain 'H' and resid 379 through 401 removed outlier: 3.528A pdb=" N GLU H 383 " --> pdb=" O GLU H 379 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS H 390 " --> pdb=" O GLU H 386 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET H 394 " --> pdb=" O HIS H 390 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 400 " --> pdb=" O VAL H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 426 removed outlier: 3.535A pdb=" N LEU H 416 " --> pdb=" O ILE H 412 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS H 418 " --> pdb=" O MET H 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG H 421 " --> pdb=" O SER H 417 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 452 removed outlier: 3.553A pdb=" N LYS H 440 " --> pdb=" O GLY H 436 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 469 removed outlier: 3.926A pdb=" N ALA H 466 " --> pdb=" O ASN H 462 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS H 468 " --> pdb=" O LEU H 464 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 514 removed outlier: 3.703A pdb=" N ILE H 513 " --> pdb=" O ALA H 509 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 40 removed outlier: 3.808A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 removed outlier: 3.540A pdb=" N ARG Q 74 " --> pdb=" O ALA Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 94 removed outlier: 3.976A pdb=" N MET Q 85 " --> pdb=" O PRO Q 81 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU Q 94 " --> pdb=" O SER Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 121 removed outlier: 3.621A pdb=" N ALA Q 108 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE Q 121 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 163 Processing helix chain 'Q' and resid 165 through 168 No H-bonds generated for 'chain 'Q' and resid 165 through 168' Processing helix chain 'Q' and resid 176 through 191 removed outlier: 3.561A pdb=" N LYS Q 181 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA Q 184 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER Q 189 " --> pdb=" O GLN Q 185 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 274 through 285 Processing helix chain 'Q' and resid 299 through 307 removed outlier: 3.627A pdb=" N HIS Q 303 " --> pdb=" O ASP Q 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Q 305 " --> pdb=" O ALA Q 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN Q 306 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) Processing helix chain 'Q' and resid 318 through 325 removed outlier: 3.791A pdb=" N LEU Q 324 " --> pdb=" O ASP Q 320 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS Q 325 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 402 removed outlier: 3.537A pdb=" N ASP Q 387 " --> pdb=" O ASN Q 383 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE Q 399 " --> pdb=" O GLY Q 395 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL Q 401 " --> pdb=" O ASN Q 397 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.564A pdb=" N GLN Q 422 " --> pdb=" O GLU Q 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER Q 425 " --> pdb=" O LYS Q 421 " (cutoff:3.500A) Processing helix chain 'Q' and resid 435 through 455 removed outlier: 3.688A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 472 removed outlier: 3.521A pdb=" N HIS Q 471 " --> pdb=" O LEU Q 467 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'q' and resid 30 through 44 removed outlier: 3.534A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 removed outlier: 3.829A pdb=" N LEU q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG q 74 " --> pdb=" O ALA q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 92 removed outlier: 3.927A pdb=" N MET q 85 " --> pdb=" O PRO q 81 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 121 removed outlier: 3.616A pdb=" N ALA q 108 " --> pdb=" O VAL q 104 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE q 121 " --> pdb=" O GLU q 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 125 through 142 removed outlier: 3.764A pdb=" N ARG q 137 " --> pdb=" O GLU q 133 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU q 141 " --> pdb=" O ARG q 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 157 through 168 removed outlier: 3.851A pdb=" N ARG q 165 " --> pdb=" O SER q 161 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 178 through 191 removed outlier: 3.590A pdb=" N ALA q 184 " --> pdb=" O ALA q 180 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER q 189 " --> pdb=" O GLN q 185 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE q 190 " --> pdb=" O ALA q 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 199 through 201 No H-bonds generated for 'chain 'q' and resid 199 through 201' Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 263 through 286 removed outlier: 3.506A pdb=" N PHE q 268 " --> pdb=" O GLU q 264 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU q 273 " --> pdb=" O SER q 269 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 removed outlier: 3.941A pdb=" N HIS q 303 " --> pdb=" O ASP q 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN q 306 " --> pdb=" O LEU q 302 " (cutoff:3.500A) Processing helix chain 'q' and resid 318 through 325 removed outlier: 3.780A pdb=" N LEU q 324 " --> pdb=" O ASP q 320 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS q 325 " --> pdb=" O LEU q 321 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 402 removed outlier: 3.615A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU q 402 " --> pdb=" O THR q 398 " (cutoff:3.500A) Processing helix chain 'q' and resid 415 through 429 removed outlier: 3.526A pdb=" N SER q 425 " --> pdb=" O LYS q 421 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 455 removed outlier: 3.952A pdb=" N TYR q 436 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE q 438 " --> pdb=" O GLN q 435 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS q 439 " --> pdb=" O TYR q 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS q 440 " --> pdb=" O ALA q 437 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA q 444 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE q 448 " --> pdb=" O PHE q 445 " (cutoff:3.500A) Proline residue: q 449 - end of helix removed outlier: 3.523A pdb=" N GLU q 454 " --> pdb=" O ALA q 451 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN q 455 " --> pdb=" O LEU q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 460 through 472 removed outlier: 3.557A pdb=" N HIS q 471 " --> pdb=" O LEU q 467 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 removed outlier: 3.896A pdb=" N TRP q 506 " --> pdb=" O LEU q 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 37 removed outlier: 3.925A pdb=" N ASN Z 23 " --> pdb=" O ALA Z 19 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN Z 37 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 65 No H-bonds generated for 'chain 'Z' and resid 62 through 65' Processing helix chain 'Z' and resid 72 through 87 removed outlier: 3.768A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS Z 79 " --> pdb=" O SER Z 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL Z 80 " --> pdb=" O LEU Z 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP Z 86 " --> pdb=" O THR Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 110 removed outlier: 3.632A pdb=" N VAL Z 96 " --> pdb=" O THR Z 92 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU Z 108 " --> pdb=" O LYS Z 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 removed outlier: 3.732A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 159 removed outlier: 3.665A pdb=" N ASP Z 150 " --> pdb=" O GLU Z 146 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR Z 154 " --> pdb=" O ASP Z 150 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS Z 159 " --> pdb=" O SER Z 155 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 179 removed outlier: 3.841A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE Z 179 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 253 through 280 removed outlier: 3.614A pdb=" N LYS Z 258 " --> pdb=" O GLU Z 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU Z 259 " --> pdb=" O GLU Z 255 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP Z 269 " --> pdb=" O LYS Z 265 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL Z 271 " --> pdb=" O ILE Z 267 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS Z 272 " --> pdb=" O GLU Z 268 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE Z 274 " --> pdb=" O ARG Z 270 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 306 Processing helix chain 'Z' and resid 318 through 328 removed outlier: 3.554A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU Z 326 " --> pdb=" O GLU Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 336 through 338 No H-bonds generated for 'chain 'Z' and resid 336 through 338' Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 removed outlier: 3.511A pdb=" N GLN Z 386 " --> pdb=" O HIS Z 382 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG Z 392 " --> pdb=" O LYS Z 388 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA Z 397 " --> pdb=" O ASP Z 393 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL Z 398 " --> pdb=" O GLY Z 394 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 423 removed outlier: 3.542A pdb=" N ALA Z 417 " --> pdb=" O ALA Z 413 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU Z 420 " --> pdb=" O VAL Z 416 " (cutoff:3.500A) Processing helix chain 'Z' and resid 432 through 454 removed outlier: 3.562A pdb=" N LEU Z 435 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA Z 443 " --> pdb=" O PHE Z 440 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU Z 444 " --> pdb=" O ALA Z 441 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Z 445 " --> pdb=" O ASP Z 442 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE Z 446 " --> pdb=" O ALA Z 443 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix removed outlier: 4.072A pdb=" N LEU Z 451 " --> pdb=" O PRO Z 448 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA Z 452 " --> pdb=" O LYS Z 449 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN Z 454 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 459 through 468 removed outlier: 3.683A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS Z 465 " --> pdb=" O GLU Z 461 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE Z 466 " --> pdb=" O THR Z 462 " (cutoff:3.500A) Processing helix chain 'Z' and resid 489 through 492 No H-bonds generated for 'chain 'Z' and resid 489 through 492' Processing helix chain 'Z' and resid 498 through 516 removed outlier: 3.817A pdb=" N THR Z 509 " --> pdb=" O LEU Z 505 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL Z 510 " --> pdb=" O HIS Z 506 " (cutoff:3.500A) Processing helix chain 'z' and resid 18 through 33 removed outlier: 3.649A pdb=" N VAL z 22 " --> pdb=" O ALA z 18 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN z 23 " --> pdb=" O ALA z 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU z 30 " --> pdb=" O ALA z 26 " (cutoff:3.500A) Processing helix chain 'z' and resid 62 through 65 No H-bonds generated for 'chain 'z' and resid 62 through 65' Processing helix chain 'z' and resid 72 through 85 removed outlier: 3.672A pdb=" N LEU z 76 " --> pdb=" O PRO z 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE z 77 " --> pdb=" O THR z 73 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS z 79 " --> pdb=" O SER z 75 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL z 80 " --> pdb=" O LEU z 76 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA z 81 " --> pdb=" O ILE z 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR z 82 " --> pdb=" O ALA z 78 " (cutoff:3.500A) Processing helix chain 'z' and resid 92 through 110 removed outlier: 3.564A pdb=" N VAL z 96 " --> pdb=" O THR z 92 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 removed outlier: 3.841A pdb=" N GLU z 128 " --> pdb=" O GLU z 124 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL z 137 " --> pdb=" O PHE z 133 " (cutoff:3.500A) Processing helix chain 'z' and resid 145 through 159 removed outlier: 3.830A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR z 154 " --> pdb=" O ASP z 150 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG z 157 " --> pdb=" O ARG z 153 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS z 159 " --> pdb=" O SER z 155 " (cutoff:3.500A) Processing helix chain 'z' and resid 165 through 179 removed outlier: 3.849A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE z 179 " --> pdb=" O SER z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 253 through 280 removed outlier: 3.686A pdb=" N GLU z 257 " --> pdb=" O ALA z 253 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS z 258 " --> pdb=" O GLU z 254 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA z 262 " --> pdb=" O LYS z 258 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS z 273 " --> pdb=" O ASP z 269 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE z 274 " --> pdb=" O ARG z 270 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE z 275 " --> pdb=" O VAL z 271 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 307 removed outlier: 3.730A pdb=" N LYS z 307 " --> pdb=" O ASP z 303 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 328 removed outlier: 3.665A pdb=" N LEU z 326 " --> pdb=" O GLU z 322 " (cutoff:3.500A) Processing helix chain 'z' and resid 336 through 338 No H-bonds generated for 'chain 'z' and resid 336 through 338' Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 removed outlier: 3.676A pdb=" N ALA z 397 " --> pdb=" O ASP z 393 " (cutoff:3.500A) Processing helix chain 'z' and resid 413 through 423 Processing helix chain 'z' and resid 432 through 455 removed outlier: 3.518A pdb=" N PHE z 440 " --> pdb=" O VAL z 437 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA z 441 " --> pdb=" O GLN z 438 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU z 444 " --> pdb=" O ALA z 441 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU z 445 " --> pdb=" O ASP z 442 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix removed outlier: 3.927A pdb=" N LEU z 451 " --> pdb=" O PRO z 448 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN z 454 " --> pdb=" O LEU z 451 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER z 455 " --> pdb=" O ALA z 452 " (cutoff:3.500A) Processing helix chain 'z' and resid 461 through 467 removed outlier: 3.590A pdb=" N ILE z 466 " --> pdb=" O THR z 462 " (cutoff:3.500A) Processing helix chain 'z' and resid 498 through 516 removed outlier: 3.541A pdb=" N HIS z 506 " --> pdb=" O LYS z 502 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR z 509 " --> pdb=" O LEU z 505 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= B, first strand: chain 'a' and resid 196 through 201 Processing sheet with id= C, first strand: chain 'a' and resid 234 through 237 removed outlier: 6.142A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'a' and resid 350 through 353 removed outlier: 3.749A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= F, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.572A pdb=" N ASP a 489 " --> pdb=" O LYS a 494 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 43 through 46 removed outlier: 3.585A pdb=" N LYS A 43 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 196 through 199 removed outlier: 3.957A pdb=" N ILE A 375 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 198 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 209 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.263A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.728A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 361 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= L, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.548A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= N, first strand: chain 'b' and resid 199 through 204 removed outlier: 6.930A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'b' and resid 237 through 240 removed outlier: 6.787A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'b' and resid 348 through 351 Processing sheet with id= Q, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= R, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.521A pdb=" N LEU B 52 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= T, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= U, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.570A pdb=" N ILE D 61 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 209 through 214 removed outlier: 3.851A pdb=" N LYS D 213 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 392 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 240 through 242 removed outlier: 3.673A pdb=" N VAL D 241 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 365 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU D 373 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 246 through 248 removed outlier: 7.146A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= Z, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= AA, first strand: chain 'd' and resid 59 through 62 removed outlier: 3.511A pdb=" N LYS d 59 " --> pdb=" O THR d 71 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.939A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.517A pdb=" N LEU d 229 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU d 367 " --> pdb=" O GLY d 371 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU d 373 " --> pdb=" O VAL d 365 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'd' and resid 246 through 249 removed outlier: 6.461A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= AF, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= AG, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= AH, first strand: chain 'E' and resid 207 through 211 removed outlier: 7.061A pdb=" N VAL E 381 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLU E 210 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE E 383 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 225 through 228 removed outlier: 3.756A pdb=" N ILE E 360 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 246 through 248 removed outlier: 6.565A pdb=" N LEU E 297 " --> pdb=" O ALA E 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'E' and resid 416 through 418 removed outlier: 3.832A pdb=" N VAL E 417 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU E 506 " --> pdb=" O VAL E 417 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'e' and resid 57 through 60 removed outlier: 3.685A pdb=" N THR e 69 " --> pdb=" O LYS e 57 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR e 67 " --> pdb=" O MET e 59 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'e' and resid 207 through 213 removed outlier: 6.891A pdb=" N VAL e 381 " --> pdb=" O LYS e 208 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU e 210 " --> pdb=" O VAL e 381 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE e 383 " --> pdb=" O GLU e 210 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LYS e 212 " --> pdb=" O ILE e 383 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE e 385 " --> pdb=" O LYS e 212 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'e' and resid 225 through 228 removed outlier: 3.729A pdb=" N VAL e 226 " --> pdb=" O ILE e 372 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE e 372 " --> pdb=" O VAL e 226 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL e 228 " --> pdb=" O LEU e 370 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET e 369 " --> pdb=" O ILE e 360 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE e 360 " --> pdb=" O MET e 369 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'e' and resid 246 through 248 removed outlier: 6.517A pdb=" N LEU e 297 " --> pdb=" O ALA e 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'g' and resid 199 through 205 removed outlier: 6.950A pdb=" N CYS g 372 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU g 202 " --> pdb=" O CYS g 372 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE g 374 " --> pdb=" O GLU g 202 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE g 204 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU g 376 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'g' and resid 238 through 241 removed outlier: 7.117A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= AS, first strand: chain 'G' and resid 202 through 205 removed outlier: 4.149A pdb=" N GLY G 378 " --> pdb=" O ILE G 204 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'G' and resid 238 through 240 removed outlier: 6.943A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AV, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= AW, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.037A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.803A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= AZ, first strand: chain 'h' and resid 475 through 477 Processing sheet with id= BA, first strand: chain 'H' and resid 195 through 199 removed outlier: 6.238A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE H 373 " --> pdb=" O GLN H 209 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.788A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.564A pdb=" N PHE H 360 " --> pdb=" O GLU H 349 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR H 358 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= BE, first strand: chain 'H' and resid 475 through 477 Processing sheet with id= BF, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= BG, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.549A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Q' and resid 221 through 223 removed outlier: 3.521A pdb=" N MET Q 221 " --> pdb=" O PHE Q 363 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Q 361 " --> pdb=" O PHE Q 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR Q 351 " --> pdb=" O VAL Q 362 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Q' and resid 311 through 314 removed outlier: 8.324A pdb=" N LYS Q 238 " --> pdb=" O ASN Q 289 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL Q 291 " --> pdb=" O LYS Q 238 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA Q 240 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR Q 293 " --> pdb=" O ALA Q 240 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TYR Q 242 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id= BK, first strand: chain 'Q' and resid 478 through 480 removed outlier: 3.787A pdb=" N LYS Q 490 " --> pdb=" O GLY Q 479 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'q' and resid 54 through 58 removed outlier: 3.974A pdb=" N LYS q 62 " --> pdb=" O ASN q 58 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.469A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'q' and resid 221 through 223 removed outlier: 3.548A pdb=" N LYS q 364 " --> pdb=" O SER q 349 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER q 349 " --> pdb=" O LYS q 364 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'q' and resid 239 through 242 removed outlier: 6.901A pdb=" N VAL q 290 " --> pdb=" O ALA q 240 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR q 242 " --> pdb=" O VAL q 290 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL q 292 " --> pdb=" O TYR q 242 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= BQ, first strand: chain 'Z' and resid 45 through 48 removed outlier: 3.576A pdb=" N LYS Z 45 " --> pdb=" O THR Z 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR Z 57 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.817A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'Z' and resid 229 through 231 Processing sheet with id= BT, first strand: chain 'Z' and resid 351 through 354 Processing sheet with id= BU, first strand: chain 'Z' and resid 407 through 409 removed outlier: 3.593A pdb=" N VAL Z 408 " --> pdb=" O ASP Z 496 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= BW, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.744A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR z 373 " --> pdb=" O ILE z 207 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'z' and resid 229 through 231 removed outlier: 3.577A pdb=" N LEU z 231 " --> pdb=" O VAL z 290 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'z' and resid 350 through 354 removed outlier: 3.552A pdb=" N PHE z 360 " --> pdb=" O TYR z 353 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= CA, first strand: chain 'z' and resid 477 through 479 2267 hydrogen bonds defined for protein. 6318 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: 18.97 Time building geometry restraints manager: 18.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 19776 1.34 - 1.46: 9959 1.46 - 1.58: 28864 1.58 - 1.69: 18 1.69 - 1.81: 599 Bond restraints: 59216 Sorted by residual: bond pdb=" C4' ADP Q 601 " pdb=" O4' ADP Q 601 " ideal model delta sigma weight residual 1.426 1.481 -0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" C1' ADP Q 601 " pdb=" O4' ADP Q 601 " ideal model delta sigma weight residual 1.426 1.470 -0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" C6 ADP Z 601 " pdb=" N1 ADP Z 601 " ideal model delta sigma weight residual 1.350 1.393 -0.043 2.00e-02 2.50e+03 4.68e+00 bond pdb=" C2 ADP Z 601 " pdb=" N1 ADP Z 601 " ideal model delta sigma weight residual 1.337 1.376 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" CD1 TYR Q 47 " pdb=" CE1 TYR Q 47 " ideal model delta sigma weight residual 1.382 1.438 -0.056 3.00e-02 1.11e+03 3.44e+00 ... (remaining 59211 not shown) Histogram of bond angle deviations from ideal: 99.96 - 107.37: 1575 107.37 - 114.78: 36940 114.78 - 122.19: 30007 122.19 - 129.60: 11133 129.60 - 137.01: 293 Bond angle restraints: 79948 Sorted by residual: angle pdb=" CA VAL a 409 " pdb=" C VAL a 409 " pdb=" N PRO a 410 " ideal model delta sigma weight residual 116.57 120.19 -3.62 9.80e-01 1.04e+00 1.36e+01 angle pdb=" N ASP A 358 " pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " ideal model delta sigma weight residual 114.17 110.02 4.15 1.14e+00 7.69e-01 1.32e+01 angle pdb=" C SER D 234 " pdb=" N ASN D 235 " pdb=" CA ASN D 235 " ideal model delta sigma weight residual 121.70 127.81 -6.11 1.80e+00 3.09e-01 1.15e+01 angle pdb=" N ILE Q 417 " pdb=" CA ILE Q 417 " pdb=" C ILE Q 417 " ideal model delta sigma weight residual 111.58 108.17 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" CA VAL g 408 " pdb=" C VAL g 408 " pdb=" N PRO g 409 " ideal model delta sigma weight residual 116.57 119.59 -3.02 9.80e-01 1.04e+00 9.51e+00 ... (remaining 79943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 35537 23.61 - 47.22: 1010 47.22 - 70.83: 119 70.83 - 94.44: 29 94.44 - 118.06: 4 Dihedral angle restraints: 36699 sinusoidal: 14672 harmonic: 22027 Sorted by residual: dihedral pdb=" CA ASP a 146 " pdb=" C ASP a 146 " pdb=" N CYS a 147 " pdb=" CA CYS a 147 " ideal model delta harmonic sigma weight residual 180.00 121.01 58.99 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA GLN A 187 " pdb=" C GLN A 187 " pdb=" N PRO A 188 " pdb=" CA PRO A 188 " ideal model delta harmonic sigma weight residual 180.00 -126.56 -53.44 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA GLN a 187 " pdb=" C GLN a 187 " pdb=" N PRO a 188 " pdb=" CA PRO a 188 " ideal model delta harmonic sigma weight residual -180.00 -126.80 -53.20 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 36696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 9581 0.132 - 0.264: 28 0.264 - 0.397: 0 0.397 - 0.529: 0 0.529 - 0.661: 1 Chirality restraints: 9610 Sorted by residual: chirality pdb=" C4' ADP Q 601 " pdb=" C3' ADP Q 601 " pdb=" C5' ADP Q 601 " pdb=" O4' ADP Q 601 " both_signs ideal model delta sigma weight residual False -2.50 -3.16 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CG LEU Z 481 " pdb=" CB LEU Z 481 " pdb=" CD1 LEU Z 481 " pdb=" CD2 LEU Z 481 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA ILE g 204 " pdb=" N ILE g 204 " pdb=" C ILE g 204 " pdb=" CB ILE g 204 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 9607 not shown) Planarity restraints: 10225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 187 " 0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO a 188 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO a 188 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO a 188 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' ADP Z 601 " 0.010 2.00e-02 2.50e+03 1.69e-02 7.90e+00 pdb=" C2 ADP Z 601 " -0.027 2.00e-02 2.50e+03 pdb=" C4 ADP Z 601 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP Z 601 " -0.009 2.00e-02 2.50e+03 pdb=" C6 ADP Z 601 " -0.013 2.00e-02 2.50e+03 pdb=" C8 ADP Z 601 " 0.005 2.00e-02 2.50e+03 pdb=" N1 ADP Z 601 " 0.044 2.00e-02 2.50e+03 pdb=" N3 ADP Z 601 " 0.000 2.00e-02 2.50e+03 pdb=" N6 ADP Z 601 " -0.005 2.00e-02 2.50e+03 pdb=" N7 ADP Z 601 " 0.004 2.00e-02 2.50e+03 pdb=" N9 ADP Z 601 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 187 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 188 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.036 5.00e-02 4.00e+02 ... (remaining 10222 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 486 2.60 - 3.17: 49319 3.17 - 3.75: 86608 3.75 - 4.32: 124047 4.32 - 4.90: 199472 Nonbonded interactions: 459932 Sorted by model distance: nonbonded pdb=" OG SER q 170 " pdb=" O2A ADP q 601 " model vdw 2.022 2.440 nonbonded pdb=" O ALA Z 165 " pdb=" OG1 THR Z 169 " model vdw 2.078 2.440 nonbonded pdb=" O GLY A 213 " pdb=" OG SER A 374 " model vdw 2.089 2.440 nonbonded pdb=" O LYS e 512 " pdb=" OG SER e 516 " model vdw 2.111 2.440 nonbonded pdb=" N TYR a 190 " pdb=" OE2 GLU a 404 " model vdw 2.121 2.520 ... (remaining 459927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'a' and (resid 14 through 237 or resid 282 through 533)) } ncs_group { reference = (chain 'E' and resid 25 through 534) selection = chain 'e' } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 18 through 524) } ncs_group { reference = chain 'Q' selection = (chain 'q' and (resid 28 through 242 or resid 273 through 529 or resid 601)) } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 17 through 525 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.670 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 117.040 Find NCS groups from input model: 4.600 Set up NCS constraints: 0.290 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5115 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 : 0.003 0.056 59216 Z= 0.201 Angle : 0.580 9.167 79948 Z= 0.321 Chirality : 0.041 0.661 9610 Planarity : 0.003 0.074 10225 Dihedral : 11.642 118.055 22419 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.78 % Favored : 97.21 % Rotamer: Outliers : 0.06 % Allowed : 1.19 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.07), residues: 7598 helix: -3.34 (0.05), residues: 3667 sheet: -2.48 (0.18), residues: 617 loop : -2.08 (0.09), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP q 319 HIS 0.003 0.000 HIS Z 161 PHE 0.017 0.001 PHE e 362 TYR 0.011 0.001 TYR Q 47 ARG 0.004 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1728 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1724 time to evaluate : 4.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 146 ASP cc_start: 0.7581 (t0) cc_final: 0.7376 (t0) REVERT: a 233 LYS cc_start: 0.3401 (mtmm) cc_final: 0.3131 (mtmm) REVERT: a 421 ILE cc_start: 0.7059 (mm) cc_final: 0.6581 (mm) REVERT: A 133 ASN cc_start: 0.6885 (m-40) cc_final: 0.6558 (t0) REVERT: A 344 MET cc_start: 0.2917 (mtt) cc_final: 0.2647 (mpp) REVERT: A 528 ASP cc_start: 0.5710 (t0) cc_final: 0.5330 (t0) REVERT: b 66 ASP cc_start: 0.6758 (t70) cc_final: 0.6362 (t70) REVERT: b 112 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6716 (mm-30) REVERT: b 135 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7976 (ptmm) REVERT: b 203 LYS cc_start: 0.5236 (mtmt) cc_final: 0.4378 (mtpt) REVERT: b 228 GLN cc_start: 0.2568 (mm-40) cc_final: 0.2168 (mt0) REVERT: b 275 MET cc_start: 0.3400 (mmt) cc_final: 0.3200 (mmt) REVERT: b 460 ASP cc_start: 0.7329 (m-30) cc_final: 0.7064 (m-30) REVERT: B 112 GLU cc_start: 0.6897 (tp30) cc_final: 0.6680 (tp30) REVERT: B 484 THR cc_start: 0.3431 (t) cc_final: 0.1871 (t) REVERT: B 521 ILE cc_start: 0.7410 (mt) cc_final: 0.6835 (mt) REVERT: D 90 MET cc_start: 0.7124 (mtm) cc_final: 0.6769 (mtp) REVERT: D 98 GLN cc_start: 0.7710 (tp40) cc_final: 0.7327 (tp40) REVERT: D 148 LEU cc_start: 0.7228 (mt) cc_final: 0.6869 (tt) REVERT: D 320 MET cc_start: -0.1757 (mmt) cc_final: -0.2265 (ptp) REVERT: D 345 VAL cc_start: 0.2487 (t) cc_final: 0.2166 (t) REVERT: D 385 THR cc_start: 0.2291 (p) cc_final: 0.1336 (p) REVERT: D 446 MET cc_start: 0.5282 (mtt) cc_final: 0.4397 (mmm) REVERT: D 479 GLU cc_start: 0.5966 (tt0) cc_final: 0.5591 (tp30) REVERT: D 512 LEU cc_start: 0.5153 (tp) cc_final: 0.4007 (tp) REVERT: d 52 LEU cc_start: 0.6560 (tp) cc_final: 0.6254 (tp) REVERT: d 211 VAL cc_start: 0.4992 (t) cc_final: 0.4548 (m) REVERT: d 415 LEU cc_start: 0.7878 (mt) cc_final: 0.7279 (tp) REVERT: E 66 VAL cc_start: 0.5355 (t) cc_final: 0.4596 (m) REVERT: E 75 ILE cc_start: 0.6635 (mt) cc_final: 0.6390 (mt) REVERT: E 205 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6744 (mt-10) REVERT: E 216 ARG cc_start: 0.6298 (mmt-90) cc_final: 0.5696 (mpp-170) REVERT: E 345 GLU cc_start: 0.5091 (mm-30) cc_final: 0.4412 (mp0) REVERT: E 366 LYS cc_start: -0.0316 (tmtt) cc_final: -0.0763 (ptmm) REVERT: E 369 MET cc_start: 0.3048 (mtp) cc_final: 0.2646 (mtm) REVERT: E 484 ASN cc_start: 0.5454 (m-40) cc_final: 0.5234 (m-40) REVERT: E 491 CYS cc_start: 0.7889 (p) cc_final: 0.7474 (p) REVERT: E 521 MET cc_start: 0.6470 (tpt) cc_final: 0.4781 (ttm) REVERT: e 26 LEU cc_start: 0.7794 (mp) cc_final: 0.7000 (tp) REVERT: e 30 GLU cc_start: 0.7245 (mp0) cc_final: 0.5982 (pt0) REVERT: e 46 MET cc_start: 0.6502 (mtp) cc_final: 0.6022 (mmp) REVERT: e 59 MET cc_start: 0.7341 (mmp) cc_final: 0.6964 (mmp) REVERT: e 63 ASP cc_start: 0.6030 (m-30) cc_final: 0.5468 (m-30) REVERT: e 78 MET cc_start: 0.7797 (tpt) cc_final: 0.7319 (tpt) REVERT: e 117 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6553 (mm-30) REVERT: e 296 ASN cc_start: 0.5439 (m-40) cc_final: 0.4393 (t0) REVERT: e 345 GLU cc_start: 0.4632 (mm-30) cc_final: 0.3885 (pt0) REVERT: e 456 ILE cc_start: 0.8358 (mt) cc_final: 0.7790 (mt) REVERT: e 513 GLN cc_start: 0.6616 (mm-40) cc_final: 0.5914 (mm-40) REVERT: g 50 LEU cc_start: 0.8170 (mp) cc_final: 0.7536 (mp) REVERT: g 59 MET cc_start: 0.7062 (tpp) cc_final: 0.6666 (mmm) REVERT: g 78 LYS cc_start: 0.7395 (mttt) cc_final: 0.6766 (ttmt) REVERT: g 112 PHE cc_start: 0.4547 (m-80) cc_final: 0.3816 (m-80) REVERT: g 113 LEU cc_start: 0.7044 (mp) cc_final: 0.6838 (mp) REVERT: g 237 ARG cc_start: 0.7525 (mtt180) cc_final: 0.6728 (ttm-80) REVERT: G 153 LEU cc_start: 0.7418 (tp) cc_final: 0.7023 (tp) REVERT: G 157 ASN cc_start: 0.7551 (m-40) cc_final: 0.7122 (p0) REVERT: G 229 MET cc_start: 0.0490 (mtt) cc_final: 0.0278 (mtt) REVERT: G 305 MET cc_start: 0.3497 (mtm) cc_final: 0.3264 (tpp) REVERT: h 117 HIS cc_start: 0.6314 (t-90) cc_final: 0.5913 (t-90) REVERT: h 217 LYS cc_start: 0.4474 (tttt) cc_final: 0.3991 (mppt) REVERT: H 116 LEU cc_start: 0.7823 (tp) cc_final: 0.7206 (mm) REVERT: H 184 MET cc_start: 0.2802 (mtp) cc_final: 0.1250 (tpp) REVERT: H 418 LYS cc_start: 0.7429 (tttm) cc_final: 0.7092 (tmtt) REVERT: H 517 ASP cc_start: 0.6115 (m-30) cc_final: 0.5653 (m-30) REVERT: Q 92 MET cc_start: 0.7066 (mmm) cc_final: 0.6546 (mmp) REVERT: Q 153 ASN cc_start: 0.5912 (t0) cc_final: 0.5639 (t0) REVERT: Q 196 HIS cc_start: 0.5896 (m90) cc_final: 0.5461 (t70) REVERT: Q 318 LYS cc_start: 0.4690 (mttt) cc_final: 0.4175 (pptt) REVERT: Q 320 ASP cc_start: 0.4444 (m-30) cc_final: 0.3936 (m-30) REVERT: Q 388 ILE cc_start: 0.8851 (mt) cc_final: 0.8550 (tt) REVERT: Q 491 ASP cc_start: 0.6094 (t0) cc_final: 0.5454 (t70) REVERT: q 62 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7660 (tptm) REVERT: q 101 THR cc_start: 0.7576 (m) cc_final: 0.7333 (p) REVERT: q 315 LEU cc_start: 0.6384 (mt) cc_final: 0.5896 (tp) REVERT: q 385 MET cc_start: 0.4833 (ttp) cc_final: 0.4360 (ttp) REVERT: Z 71 HIS cc_start: 0.6114 (t-90) cc_final: 0.5859 (t-90) REVERT: Z 187 ASP cc_start: 0.1690 (t0) cc_final: 0.1034 (t0) REVERT: Z 355 LEU cc_start: 0.5935 (mt) cc_final: 0.5706 (mt) REVERT: Z 393 ASP cc_start: 0.5206 (m-30) cc_final: 0.4848 (m-30) REVERT: z 292 ILE cc_start: 0.3285 (pt) cc_final: 0.2674 (tp) REVERT: z 521 ILE cc_start: 0.7208 (mt) cc_final: 0.6873 (mp) outliers start: 4 outliers final: 1 residues processed: 1728 average time/residue: 0.5798 time to fit residues: 1641.6359 Evaluate side-chains 1008 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1007 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 640 optimal weight: 20.0000 chunk 575 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 196 optimal weight: 0.0050 chunk 388 optimal weight: 0.6980 chunk 307 optimal weight: 7.9990 chunk 594 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 361 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 689 optimal weight: 7.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 ASN a 187 GLN a 425 ASN a 472 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN b 174 HIS b 361 HIS b 399 GLN ** b 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 347 HIS ** d 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 84 GLN ** g 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 308 ASN g 390 ASN g 392 GLN g 400 ASN G 235 ASN G 390 ASN G 392 GLN h 86 GLN h 151 GLN ** h 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 432 GLN h 448 GLN H 25 ASN H 130 GLN H 234 ASN ** H 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 HIS Q 102 ASN ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS Q 397 ASN Q 477 ASN q 50 ASN q 306 ASN q 477 ASN Z 23 ASN Z 161 HIS Z 245 ASN Z 434 GLN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 294 GLN z 320 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5303 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 59216 Z= 0.202 Angle : 0.594 11.651 79948 Z= 0.301 Chirality : 0.043 0.201 9610 Planarity : 0.004 0.078 10225 Dihedral : 4.624 98.430 8179 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.98 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.08), residues: 7598 helix: -1.35 (0.07), residues: 3785 sheet: -1.97 (0.17), residues: 711 loop : -1.69 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 493 HIS 0.006 0.001 HIS b 122 PHE 0.025 0.002 PHE Q 399 TYR 0.020 0.002 TYR H 275 ARG 0.013 0.001 ARG b 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15196 Ramachandran restraints generated. 7598 Oldfield, 0 Emsley, 7598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1289 time to evaluate : 4.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 17 ILE cc_start: 0.6726 (mp) cc_final: 0.6289 (mp) REVERT: a 73 LYS cc_start: 0.7121 (mmtt) cc_final: 0.6254 (mmtt) REVERT: a 76 CYS cc_start: 0.7285 (m) cc_final: 0.6966 (p) REVERT: a 171 MET cc_start: 0.3644 (mmm) cc_final: 0.1619 (tmm) REVERT: a 233 LYS cc_start: 0.3554 (mtmm) cc_final: 0.3278 (mtmm) REVERT: a 425 ASN cc_start: 0.6427 (m-40) cc_final: 0.5883 (p0) REVERT: A 206 MET cc_start: 0.3831 (mmm) cc_final: 0.3495 (mmm) REVERT: A 209 MET cc_start: 0.3664 (mmt) cc_final: 0.3440 (mmt) REVERT: A 344 MET cc_start: 0.2667 (mtt) cc_final: 0.2175 (mpp) REVERT: A 447 VAL cc_start: 0.7169 (t) cc_final: 0.6601 (p) REVERT: b 112 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6982 (mm-30) REVERT: b 228 GLN cc_start: 0.1745 (mm-40) cc_final: 0.1460 (mt0) REVERT: b 275 MET cc_start: 0.3223 (mmt) cc_final: 0.2979 (mmt) REVERT: b 460 ASP cc_start: 0.7422 (m-30) cc_final: 0.6850 (m-30) REVERT: B 119 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8024 (tptp) REVERT: B 402 LYS cc_start: 0.8595 (tttt) cc_final: 0.8072 (mptt) REVERT: B 445 MET cc_start: 0.6751 (mmm) cc_final: 0.6343 (tpt) REVERT: B 488 MET cc_start: 0.7668 (mmm) cc_final: 0.7354 (mmm) REVERT: B 518 ASP cc_start: 0.7878 (p0) cc_final: 0.7322 (p0) REVERT: D 79 LYS cc_start: 0.6406 (ptpt) cc_final: 0.6011 (ptpp) REVERT: D 96 LYS cc_start: 0.7758 (mttt) cc_final: 0.7383 (tptt) REVERT: D 138 GLN cc_start: 0.4280 (pp30) cc_final: 0.3009 (pp30) REVERT: D 141 LEU cc_start: 0.6784 (pp) cc_final: 0.6549 (tt) REVERT: D 320 MET cc_start: -0.2604 (mmt) cc_final: -0.3041 (ptp) REVERT: D 345 VAL cc_start: 0.1779 (t) cc_final: 0.1448 (t) REVERT: D 364 GLU cc_start: 0.3491 (mt-10) cc_final: 0.3024 (pp20) REVERT: D 479 GLU cc_start: 0.5912 (tt0) cc_final: 0.5630 (tp30) REVERT: D 512 LEU cc_start: 0.5068 (tp) cc_final: 0.4106 (mp) REVERT: d 109 VAL cc_start: 0.7835 (t) cc_final: 0.7570 (t) REVERT: d 192 MET cc_start: 0.5402 (mmp) cc_final: 0.4467 (tmm) REVERT: d 211 VAL cc_start: 0.3647 (t) cc_final: 0.3361 (m) REVERT: d 214 LEU cc_start: 0.6056 (pt) cc_final: 0.5779 (pt) REVERT: d 415 LEU cc_start: 0.7519 (mt) cc_final: 0.6734 (tp) REVERT: E 181 ARG cc_start: 0.6825 (tpt170) cc_final: 0.6352 (mtm-85) REVERT: E 201 ASP cc_start: 0.3659 (m-30) cc_final: 0.3172 (m-30) REVERT: E 216 ARG cc_start: 0.6341 (mmt-90) cc_final: 0.6101 (tpm170) REVERT: E 286 MET cc_start: 0.4669 (mmt) cc_final: 0.4302 (mmt) REVERT: E 369 MET cc_start: 0.2969 (mtp) cc_final: 0.2308 (mtm) REVERT: E 491 CYS cc_start: 0.7912 (p) cc_final: 0.7514 (p) REVERT: E 521 MET cc_start: 0.5578 (OUTLIER) cc_final: 0.5171 (ttm) REVERT: e 30 GLU cc_start: 0.7475 (mp0) cc_final: 0.5939 (pt0) REVERT: e 78 MET cc_start: 0.7858 (tpt) cc_final: 0.7634 (tpt) REVERT: e 79 MET cc_start: 0.6359 (mtm) cc_final: 0.5891 (mtm) REVERT: e 116 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6695 (tm-30) REVERT: e 296 ASN cc_start: 0.5844 (m-40) cc_final: 0.4659 (t0) REVERT: e 345 GLU cc_start: 0.3740 (mm-30) cc_final: 0.3209 (pt0) REVERT: e 369 MET cc_start: -0.2624 (mtp) cc_final: -0.4585 (ptp) REVERT: g 112 PHE cc_start: 0.4747 (m-80) cc_final: 0.3902 (m-80) REVERT: g 237 ARG cc_start: 0.7461 (mtt180) cc_final: 0.7136 (ttt90) REVERT: g 517 LEU cc_start: 0.7262 (mt) cc_final: 0.6921 (mt) REVERT: G 153 LEU cc_start: 0.7205 (tp) cc_final: 0.6391 (tp) REVERT: G 157 ASN cc_start: 0.7663 (m-40) cc_final: 0.7168 (p0) REVERT: G 416 MET cc_start: 0.5105 (mmm) cc_final: 0.4897 (mmm) REVERT: G 483 GLU cc_start: 0.6526 (mm-30) cc_final: 0.5827 (mp0) REVERT: h 170 GLN cc_start: 0.6283 (mt0) cc_final: 0.5694 (mp10) REVERT: h 185 MET cc_start: 0.6939 (ppp) cc_final: 0.6188 (ppp) REVERT: h 217 LYS cc_start: 0.4742 (tttt) cc_final: 0.4140 (mttp) REVERT: h 251 ASP cc_start: 0.3902 (m-30) cc_final: 0.3567 (t0) REVERT: h 324 MET cc_start: 0.3583 (ppp) cc_final: 0.3349 (ppp) REVERT: h 383 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7449 (tt0) REVERT: h 500 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6057 (tt) REVERT: H 95 THR cc_start: 0.7920 (m) cc_final: 0.7582 (m) REVERT: H 134 ASN cc_start: 0.7054 (m-40) cc_final: 0.6837 (m110) REVERT: H 211 VAL cc_start: 0.3799 (t) cc_final: 0.3585 (t) REVERT: H 358 TYR cc_start: 0.3428 (m-80) cc_final: 0.3180 (m-80) REVERT: H 370 CYS cc_start: 0.5428 (p) cc_final: 0.5170 (p) REVERT: H 418 LYS cc_start: 0.7649 (tttm) cc_final: 0.7278 (tppt) REVERT: Q 153 ASN cc_start: 0.6103 (t0) cc_final: 0.5336 (t0) REVERT: Q 196 HIS cc_start: 0.5942 (m90) cc_final: 0.4866 (t70) REVERT: Q 320 ASP cc_start: 0.4340 (m-30) cc_final: 0.4063 (m-30) REVERT: q 315 LEU cc_start: 0.6772 (mt) cc_final: 0.6307 (tp) REVERT: q 454 GLU cc_start: 0.6727 (mm-30) cc_final: 0.5900 (mm-30) REVERT: Z 179 ILE cc_start: 0.5543 (pt) cc_final: 0.4139 (pt) REVERT: Z 385 THR cc_start: 0.7070 (m) cc_final: 0.6692 (m) REVERT: z 73 THR cc_start: 0.7550 (m) cc_final: 0.7331 (m) REVERT: z 143 MET cc_start: 0.5549 (ppp) cc_final: 0.3702 (ptt) REVERT: z 196 MET cc_start: 0.5295 (mmm) cc_final: 0.5088 (mmm) REVERT: z 208 ARG cc_start: 0.5097 (mmp80) cc_final: 0.4771 (mmp80) REVERT: z 370 ARG cc_start: 0.6924 (mtp-110) cc_final: 0.6638 (ttp-110) outliers start: 7 outliers final: 1 residues processed: 1291 average time/residue: 0.5461 time to fit residues: 1185.6090 Evaluate side-chains 952 residues out of total 6374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 949 time to evaluate : 4.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3511 > 50: distance: 40 - 45: 9.684 distance: 45 - 46: 19.562 distance: 46 - 47: 15.713 distance: 46 - 49: 22.772 distance: 47 - 48: 29.847 distance: 47 - 50: 12.564 distance: 50 - 51: 6.802 distance: 51 - 52: 6.464 distance: 51 - 54: 23.348 distance: 52 - 53: 28.908 distance: 52 - 59: 14.380 distance: 54 - 55: 20.515 distance: 55 - 56: 24.008 distance: 56 - 57: 10.936 distance: 56 - 58: 12.689 distance: 59 - 60: 17.184 distance: 60 - 61: 15.840 distance: 60 - 63: 22.585 distance: 61 - 62: 13.443 distance: 61 - 69: 10.340 distance: 63 - 64: 20.275 distance: 64 - 65: 13.523 distance: 64 - 66: 3.958 distance: 65 - 67: 14.640 distance: 66 - 68: 17.261 distance: 67 - 68: 8.453 distance: 69 - 70: 19.194 distance: 70 - 71: 11.469 distance: 70 - 73: 15.083 distance: 71 - 72: 12.948 distance: 71 - 80: 11.522 distance: 73 - 74: 12.076 distance: 74 - 75: 7.442 distance: 74 - 76: 15.253 distance: 75 - 77: 15.484 distance: 76 - 78: 15.878 distance: 77 - 79: 6.836 distance: 78 - 79: 12.143 distance: 80 - 81: 6.365 distance: 81 - 82: 22.895 distance: 81 - 84: 16.887 distance: 82 - 83: 35.717 distance: 82 - 88: 12.303 distance: 84 - 85: 22.942 distance: 85 - 86: 21.643 distance: 85 - 87: 23.333 distance: 88 - 89: 16.868 distance: 89 - 90: 16.666 distance: 89 - 92: 31.666 distance: 90 - 91: 40.659 distance: 90 - 97: 9.473 distance: 92 - 93: 20.033 distance: 93 - 94: 9.613 distance: 94 - 95: 8.465 distance: 94 - 96: 11.022 distance: 97 - 98: 21.977 distance: 98 - 99: 15.841 distance: 98 - 101: 23.317 distance: 99 - 100: 12.049 distance: 99 - 106: 24.914 distance: 101 - 102: 25.694 distance: 102 - 103: 21.122 distance: 103 - 104: 8.149 distance: 103 - 105: 11.589 distance: 106 - 107: 24.298 distance: 107 - 108: 17.302 distance: 107 - 110: 10.693 distance: 108 - 109: 21.293 distance: 108 - 115: 10.406 distance: 110 - 111: 17.822 distance: 112 - 113: 5.980 distance: 112 - 114: 6.542 distance: 115 - 116: 4.977 distance: 116 - 117: 21.300 distance: 116 - 119: 15.162 distance: 117 - 118: 17.710 distance: 117 - 123: 10.419 distance: 119 - 120: 22.899 distance: 120 - 121: 19.924 distance: 121 - 122: 38.430 distance: 123 - 124: 7.615 distance: 124 - 125: 11.958 distance: 124 - 127: 10.490 distance: 125 - 126: 31.233 distance: 125 - 133: 4.994 distance: 127 - 128: 14.298 distance: 128 - 129: 7.723 distance: 128 - 130: 8.463 distance: 129 - 131: 7.968 distance: 130 - 132: 11.099 distance: 131 - 132: 7.374