Starting phenix.real_space_refine on Tue Mar 12 03:21:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0a_32922/03_2024/7x0a_32922.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0a_32922/03_2024/7x0a_32922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0a_32922/03_2024/7x0a_32922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0a_32922/03_2024/7x0a_32922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0a_32922/03_2024/7x0a_32922.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0a_32922/03_2024/7x0a_32922.pdb" } resolution = 3.1 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= 0.014 sd= 0.124 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: 4 Type Number sf(0) Gaussians S 379 5.16 5 C 38403 2.51 5 N 10664 2.21 5 O 11769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 15": "OE1" <-> "OE2" Residue "a GLU 68": "OE1" <-> "OE2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 261": "OD1" <-> "OD2" Residue "a ASP 294": "OD1" <-> "OD2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 302": "OE1" <-> "OE2" Residue "a ASP 358": "OD1" <-> "OD2" Residue "a PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 528": "OD1" <-> "OD2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 142": "OE1" <-> "OE2" 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 GLU 207": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 387": "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 "A ASP 528": "OD1" <-> "OD2" Residue "b PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 18": "OE1" <-> "OE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 66": "OD1" <-> "OD2" Residue "b ASP 86": "OD1" <-> "OD2" Residue "b PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 460": "OD1" <-> "OD2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "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 "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 400": "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 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 46": "OD1" <-> "OD2" Residue "d ASP 63": "OD1" <-> "OD2" Residue "d ASP 73": "OD1" <-> "OD2" Residue "d TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 219": "OD1" <-> "OD2" Residue "d ASP 268": "OD1" <-> "OD2" Residue "d TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 279": "OE1" <-> "OE2" Residue "d GLU 329": "OE1" <-> "OE2" Residue "d ASP 332": "OD1" <-> "OD2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d ASP 354": "OD1" <-> "OD2" Residue "d PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 533": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ASP 231": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 349": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 474": "OE1" <-> "OE2" Residue "E ASP 530": "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 ASP 243": "OD1" <-> "OD2" Residue "e TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 281": "OE1" <-> "OE2" Residue "e PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 305": "OD1" <-> "OD2" Residue "e PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 349": "OE1" <-> "OE2" Residue "e PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 394": "OE1" <-> "OE2" Residue "e GLU 395": "OE1" <-> "OE2" Residue "e TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 506": "OE1" <-> "OE2" Residue "g ASP 150": "OD1" <-> "OD2" Residue "g GLU 187": "OE1" <-> "OE2" Residue "g ASP 255": "OD1" <-> "OD2" Residue "g ASP 263": "OD1" <-> "OD2" Residue "g PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 280": "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 ASP 393": "OD1" <-> "OD2" Residue "g GLU 473": "OE1" <-> "OE2" Residue "g GLU 476": "OE1" <-> "OE2" Residue "G PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 272": "OE1" <-> "OE2" Residue "G ASP 298": "OD1" <-> "OD2" Residue "G ASP 341": "OD1" <-> "OD2" Residue "G PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 393": "OD1" <-> "OD2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 521": "OD1" <-> "OD2" Residue "h ASP 14": "OD1" <-> "OD2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "h PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 147": "OD1" <-> "OD2" Residue "h PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 188": "OD1" <-> "OD2" Residue "h PHE 216": "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 ASP 251": "OD1" <-> "OD2" Residue "h TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 147": "OD1" <-> "OD2" Residue "H ASP 187": "OD1" <-> "OD2" Residue "H PHE 216": "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 ASP 268": "OD1" <-> "OD2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 391": "OD1" <-> "OD2" 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 "Q PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 264": "OE1" <-> "OE2" Residue "Q PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q GLU 273": "OE1" <-> "OE2" Residue "Q TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 366": "OE1" <-> "OE2" Residue "Q ASP 369": "OD1" <-> "OD2" Residue "Q TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 485": "OE1" <-> "OE2" Residue "q PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 158": "OD1" <-> "OD2" Residue "q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 264": "OE1" <-> "OE2" Residue "q PHE 268": "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 GLU 366": "OE1" <-> "OE2" Residue "q TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 485": "OE1" <-> "OE2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z ASP 85": "OD1" <-> "OD2" Residue "Z ASP 107": "OD1" <-> "OD2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 213": "OD1" <-> "OD2" Residue "Z PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 269": "OD1" <-> "OD2" Residue "Z ASP 284": "OD1" <-> "OD2" Residue "Z PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 442": "OD1" <-> "OD2" Residue "Z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 472": "OE1" <-> "OE2" Residue "z ASP 32": "OD1" <-> "OD2" Residue "z ASP 107": "OD1" <-> "OD2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 166": "OD1" <-> "OD2" Residue "z PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 254": "OE1" <-> "OE2" Residue "z ASP 286": "OD1" <-> "OD2" Residue "z PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 337": "OD1" <-> "OD2" Residue "z ASP 342": "OD1" <-> "OD2" Residue "z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 357": "OE1" <-> "OE2" Residue "z PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 389": "OD1" <-> "OD2" Residue "z ASP 393": "OD1" <-> "OD2" Residue "z ASP 404": "OD1" <-> "OD2" Residue "z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61215 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4017 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 12, 'TRANS': 516} Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3548 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 11, 'TRANS': 458} Chain breaks: 3 Chain: "b" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3341 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 8, 'TRANS': 437} Chain breaks: 2 Chain: "B" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3213 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 7, 'TRANS': 421} Chain breaks: 5 Chain: "D" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3512 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 450} Chain breaks: 5 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: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4000 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 17, 'TRANS': 502} Chain: "e" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4000 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 17, 'TRANS': 502} Chain: "g" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3979 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain: "G" Number of atoms: 3763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3763 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "h" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3987 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "H" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3987 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "Q" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3987 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 508} Chain: "q" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3987 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 508} Chain: "Z" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3996 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "z" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3996 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Time building chain proxies: 24.22, per 1000 atoms: 0.40 Number of scatterers: 61215 At special positions: 0 Unit cell: (189.792, 197.7, 181.884, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 379 16.00 O 11769 8.00 N 10664 7.00 C 38403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.30 Conformation dependent library (CDL) restraints added in 8.8 seconds 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14950 Finding SS restraints... Secondary structure from input PDB file: 318 helices and 94 sheets defined 56.6% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'a' and resid 14 through 31 removed outlier: 4.307A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 removed outlier: 3.506A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.561A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 134 Processing helix chain 'a' and resid 148 through 157 Processing helix chain 'a' and resid 159 through 163 removed outlier: 3.603A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 3.836A pdb=" N PHE a 168 " --> pdb=" O ASN a 164 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET a 171 " --> pdb=" O PHE a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 208 removed outlier: 3.763A pdb=" N GLU a 207 " --> pdb=" O SER a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 256 through 281 removed outlier: 3.658A pdb=" N LEU a 260 " --> pdb=" O ASP a 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP a 261 " --> pdb=" O PRO a 257 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN a 262 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS a 272 " --> pdb=" O SER a 268 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU a 273 " --> pdb=" O ASP a 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR a 281 " --> pdb=" O LYS a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 304 Processing helix chain 'a' and resid 312 through 324 removed outlier: 3.524A pdb=" N ILE a 319 " --> pdb=" O ASP a 315 " (cutoff:3.500A) Processing helix chain 'a' and resid 381 through 405 removed outlier: 3.670A pdb=" N ARG a 390 " --> pdb=" O ASP a 386 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS a 397 " --> pdb=" O HIS a 393 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL a 402 " --> pdb=" O VAL a 398 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 431 removed outlier: 3.811A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 446 removed outlier: 3.554A pdb=" N LEU a 445 " --> pdb=" O PHE a 441 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.517A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN a 477 " --> pdb=" O GLU a 473 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'A' and resid 14 through 32 removed outlier: 3.937A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 113 through 135 Processing helix chain 'A' and resid 147 through 157 removed outlier: 4.155A pdb=" N ALA A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 6.975A pdb=" N ILE A 161 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 3.839A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.611A pdb=" N LEU A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 381 through 405 removed outlier: 3.820A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.679A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.564A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.804A pdb=" N ASN A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 removed outlier: 3.677A pdb=" N LEU A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 40 removed outlier: 3.755A pdb=" N LEU b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE b 29 " --> pdb=" O ARG b 25 " (cutoff:3.500A) removed outlier: 3.619A 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) Processing helix chain 'b' and resid 66 through 74 removed outlier: 3.572A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 95 removed outlier: 3.766A pdb=" N GLN b 91 " --> pdb=" O MET b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 119 removed outlier: 3.504A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 145 removed outlier: 3.580A pdb=" N GLY b 129 " --> pdb=" O THR b 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU b 141 " --> pdb=" O ALA b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 168 Processing helix chain 'b' and resid 170 through 174 removed outlier: 4.514A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 191 removed outlier: 3.564A pdb=" N PHE b 179 " --> pdb=" O HIS b 175 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS b 181 " --> pdb=" O ASP b 177 " (cutoff:3.500A) Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 297 through 307 removed outlier: 3.555A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 324 removed outlier: 3.643A pdb=" N ALA b 324 " --> pdb=" O VAL b 320 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 403 removed outlier: 3.625A pdb=" N LEU b 383 " --> pdb=" O THR b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 411 through 425 Processing helix chain 'b' and resid 429 through 455 removed outlier: 3.858A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER b 438 " --> pdb=" O VAL b 434 " (cutoff:3.500A) removed outlier: 3.907A 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 457 through 471 removed outlier: 3.667A pdb=" N GLU b 471 " --> pdb=" O ALA b 467 " (cutoff:3.500A) Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 removed outlier: 3.511A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 removed outlier: 3.647A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.790A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 94 removed outlier: 3.571A pdb=" N LYS B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.711A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 167 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.528A pdb=" N THR B 173 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.579A pdb=" N PHE B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.585A pdb=" N LEU B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 removed outlier: 3.857A pdb=" N LEU B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.761A pdb=" N ARG B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 399 " --> pdb=" O CYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 Processing helix chain 'B' and resid 429 through 455 removed outlier: 3.960A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.810A 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 457 through 470 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.708A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.529A pdb=" N GLN D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 3.768A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 172 Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.914A pdb=" N MET D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 277 through 293 Processing helix chain 'D' and resid 312 through 320 Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.509A pdb=" N ILE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 443 removed outlier: 3.725A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D 441 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.692A pdb=" N MET D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'd' and resid 30 through 50 removed outlier: 3.936A pdb=" N ARG d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR d 50 " --> pdb=" O ASP d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 80 Processing helix chain 'd' and resid 85 through 102 removed outlier: 3.691A pdb=" N LEU d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.958A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN d 125 " --> pdb=" O THR d 121 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS d 126 " --> pdb=" O LYS d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 151 removed outlier: 3.605A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 174 removed outlier: 3.835A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 195 removed outlier: 3.514A pdb=" N LEU d 183 " --> pdb=" O TYR d 179 " (cutoff:3.500A) Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 268 through 293 removed outlier: 3.675A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU d 286 " --> pdb=" O TYR d 282 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 320 removed outlier: 4.228A pdb=" N HIS d 315 " --> pdb=" O ASP d 311 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 329 through 341 removed outlier: 3.527A pdb=" N LYS d 338 " --> pdb=" O GLU d 334 " (cutoff:3.500A) Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 394 through 418 removed outlier: 3.660A pdb=" N ALA d 401 " --> pdb=" O VAL d 397 " (cutoff:3.500A) Processing helix chain 'd' and resid 426 through 443 removed outlier: 3.564A pdb=" N ARG d 441 " --> pdb=" O THR d 437 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 459 removed outlier: 3.682A pdb=" N MET d 458 " --> pdb=" O PHE d 454 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU d 459 " --> pdb=" O ALA d 455 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 469 Processing helix chain 'd' and resid 472 through 487 removed outlier: 3.739A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 507 Processing helix chain 'd' and resid 512 through 531 Processing helix chain 'E' and resid 28 through 48 removed outlier: 3.520A pdb=" N MET E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR E 48 " --> pdb=" O ASN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 Processing helix chain 'E' and resid 83 through 100 removed outlier: 3.524A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 125 removed outlier: 3.635A pdb=" N VAL E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 149 removed outlier: 3.826A pdb=" N ASP E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 172 removed outlier: 3.847A pdb=" N ALA E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 178 removed outlier: 6.252A pdb=" N VAL E 176 " --> pdb=" O SER E 173 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER E 178 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 195 removed outlier: 3.655A pdb=" N MET E 183 " --> pdb=" O CYS E 179 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 184 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 186 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 268 through 294 removed outlier: 3.782A pdb=" N ALA E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 315 removed outlier: 3.582A pdb=" N LEU E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 4.169A pdb=" N GLU E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 346 Processing helix chain 'E' and resid 389 through 413 removed outlier: 3.581A pdb=" N ALA E 403 " --> pdb=" O SER E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 436 removed outlier: 3.938A pdb=" N ASP E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 454 removed outlier: 4.196A pdb=" N ALA E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 464 Processing helix chain 'E' and resid 467 through 479 Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.670A pdb=" N GLN E 502 " --> pdb=" O ASP E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 527 Processing helix chain 'e' and resid 28 through 47 removed outlier: 3.554A pdb=" N LEU e 32 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 50 No H-bonds generated for 'chain 'e' and resid 48 through 50' Processing helix chain 'e' and resid 71 through 79 Processing helix chain 'e' and resid 83 through 97 removed outlier: 4.132A pdb=" N SER e 93 " --> pdb=" O MET e 89 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS e 94 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 124 removed outlier: 3.861A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU e 121 " --> pdb=" O GLU e 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG e 124 " --> pdb=" O GLN e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 150 removed outlier: 3.568A pdb=" N ASP e 147 " --> pdb=" O ILE e 143 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 172 removed outlier: 3.522A pdb=" N ILE e 164 " --> pdb=" O THR e 160 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA e 167 " --> pdb=" O LEU e 163 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY e 172 " --> pdb=" O LYS e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 173 through 178 removed outlier: 6.675A pdb=" N VAL e 176 " --> pdb=" O SER e 173 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 179 through 195 removed outlier: 4.266A pdb=" N MET e 183 " --> pdb=" O CYS e 179 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA e 184 " --> pdb=" O HIS e 180 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU e 185 " --> pdb=" O ARG e 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE e 186 " --> pdb=" O GLN e 182 " (cutoff:3.500A) Processing helix chain 'e' and resid 216 through 220 Processing helix chain 'e' and resid 268 through 294 removed outlier: 3.830A pdb=" N ALA e 274 " --> pdb=" O GLU e 270 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS e 291 " --> pdb=" O ILE e 287 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU e 292 " --> pdb=" O GLN e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 305 through 316 removed outlier: 3.651A pdb=" N GLN e 314 " --> pdb=" O HIS e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 324 through 336 removed outlier: 3.561A pdb=" N GLU e 329 " --> pdb=" O GLY e 325 " (cutoff:3.500A) Processing helix chain 'e' and resid 342 through 346 Processing helix chain 'e' and resid 389 through 413 removed outlier: 3.547A pdb=" N LEU e 400 " --> pdb=" O ALA e 396 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA e 403 " --> pdb=" O SER e 399 " (cutoff:3.500A) Processing helix chain 'e' and resid 421 through 436 removed outlier: 3.559A pdb=" N LEU e 429 " --> pdb=" O ILE e 425 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP e 436 " --> pdb=" O SER e 432 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 454 removed outlier: 4.321A pdb=" N ALA e 445 " --> pdb=" O LEU e 441 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 465 Processing helix chain 'e' and resid 467 through 481 Processing helix chain 'e' and resid 498 through 503 removed outlier: 3.836A pdb=" N GLN e 502 " --> pdb=" O ASP e 498 " (cutoff:3.500A) Processing helix chain 'e' and resid 508 through 527 Processing helix chain 'g' and resid 19 through 37 removed outlier: 4.253A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 70 Processing helix chain 'g' and resid 74 through 91 removed outlier: 3.510A pdb=" N LYS g 78 " --> pdb=" O HIS g 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 94 through 107 removed outlier: 3.659A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.578A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 removed outlier: 4.024A pdb=" N MET g 152 " --> pdb=" O ASP g 148 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER g 158 " --> pdb=" O ASN g 154 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N SER g 159 " --> pdb=" O ILE g 155 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE g 160 " --> pdb=" O ILE g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.774A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 Processing helix chain 'g' and resid 185 through 189 removed outlier: 3.608A pdb=" N ASN g 188 " --> pdb=" O PHE g 185 " (cutoff:3.500A) Processing helix chain 'g' and resid 194 through 198 Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 260 through 283 removed outlier: 3.728A pdb=" N THR g 265 " --> pdb=" O GLU g 261 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG g 266 " --> pdb=" O GLU g 262 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR g 274 " --> pdb=" O MET g 270 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE g 275 " --> pdb=" O GLU g 271 " (cutoff:3.500A) Processing helix chain 'g' and resid 284 through 286 No H-bonds generated for 'chain 'g' and resid 284 through 286' Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.775A pdb=" N TYR g 303 " --> pdb=" O LEU g 299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU g 304 " --> pdb=" O ALA g 300 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 327 removed outlier: 3.660A pdb=" N ILE g 323 " --> pdb=" O ASP g 319 " (cutoff:3.500A) Processing helix chain 'g' and resid 380 through 404 removed outlier: 3.928A pdb=" N ASP g 393 " --> pdb=" O ARG g 389 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA g 394 " --> pdb=" O ASN g 390 " (cutoff:3.500A) Processing helix chain 'g' and resid 412 through 426 removed outlier: 3.546A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' Processing helix chain 'g' and resid 433 through 445 removed outlier: 3.821A pdb=" N ALA g 441 " --> pdb=" O TYR g 437 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) Processing helix chain 'g' and resid 445 through 456 removed outlier: 3.506A pdb=" N CYS g 455 " --> pdb=" O LEU g 451 " (cutoff:3.500A) Processing helix chain 'g' and resid 458 through 473 removed outlier: 3.514A pdb=" N LEU g 462 " --> pdb=" O SER g 458 " (cutoff:3.500A) Processing helix chain 'g' and resid 499 through 519 Processing helix chain 'G' and resid 19 through 37 removed outlier: 4.064A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 74 through 91 removed outlier: 3.638A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.626A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.760A pdb=" N LYS G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 removed outlier: 3.558A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 removed outlier: 3.674A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 269 through 285 removed outlier: 3.606A pdb=" N LEU G 278 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP G 281 " --> pdb=" O GLN G 277 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.548A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 removed outlier: 3.521A pdb=" N CYS G 327 " --> pdb=" O ILE G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 removed outlier: 3.848A pdb=" N GLU G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 426 Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 433 through 444 removed outlier: 3.778A pdb=" N ALA G 441 " --> pdb=" O TYR G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 473 Processing helix chain 'G' and resid 499 through 519 Processing helix chain 'h' and resid 18 through 35 Processing helix chain 'h' and resid 61 through 70 removed outlier: 3.875A pdb=" N ASP h 70 " --> pdb=" O LEU h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 90 removed outlier: 3.573A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 108 Processing helix chain 'h' and resid 108 through 114 Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.594A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA h 124 " --> pdb=" O ILE h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 145 through 149 Processing helix chain 'h' and resid 150 through 164 removed outlier: 3.538A pdb=" N LEU h 154 " --> pdb=" O GLU h 150 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 185 Processing helix chain 'h' and resid 259 through 285 removed outlier: 3.535A pdb=" N GLN h 264 " --> pdb=" O VAL h 260 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU h 274 " --> pdb=" O GLU h 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 306 removed outlier: 3.532A pdb=" N PHE h 303 " --> pdb=" O ALA h 299 " (cutoff:3.500A) Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 352 through 356 removed outlier: 3.861A pdb=" N GLU h 356 " --> pdb=" O ILE h 353 " (cutoff:3.500A) Processing helix chain 'h' and resid 378 through 402 removed outlier: 3.678A pdb=" N MET h 382 " --> pdb=" O ALA h 378 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG h 387 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA h 392 " --> pdb=" O SER h 388 " (cutoff:3.500A) Processing helix chain 'h' and resid 410 through 426 removed outlier: 3.993A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 442 removed outlier: 3.763A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU h 442 " --> pdb=" O TYR h 438 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 453 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.545A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 70 removed outlier: 3.576A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 90 removed outlier: 3.631A pdb=" N THR H 78 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 108 through 114 Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.623A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 150 through 163 removed outlier: 3.780A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 185 removed outlier: 3.502A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.938A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP H 268 " --> pdb=" O GLN H 264 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 333 through 337 removed outlier: 3.910A pdb=" N ALA H 336 " --> pdb=" O SER H 333 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU H 337 " --> pdb=" O VAL H 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 333 through 337' Processing helix chain 'H' and resid 352 through 356 Processing helix chain 'H' and resid 378 through 402 removed outlier: 3.562A pdb=" N MET H 382 " --> pdb=" O ALA H 378 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS H 401 " --> pdb=" O ARG H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 426 removed outlier: 3.550A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 442 removed outlier: 3.784A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 453 removed outlier: 3.538A pdb=" N LEU H 449 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 471 removed outlier: 3.501A pdb=" N ALA H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 27 through 45 removed outlier: 3.517A pdb=" N ASN Q 32 " --> pdb=" O ALA Q 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 95 removed outlier: 4.116A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN Q 95 " --> pdb=" O HIS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 122 removed outlier: 4.038A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE Q 121 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 143 removed outlier: 3.528A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 156 through 169 removed outlier: 3.504A pdb=" N SER Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 189 removed outlier: 3.551A pdb=" N LEU Q 179 " --> pdb=" O ASN Q 175 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER Q 189 " --> pdb=" O GLN Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 286 removed outlier: 3.505A pdb=" N ALA Q 284 " --> pdb=" O VAL Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 326 removed outlier: 3.559A pdb=" N LYS Q 326 " --> pdb=" O ARG Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 403 removed outlier: 3.530A pdb=" N ALA Q 391 " --> pdb=" O ASP Q 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR Q 398 " --> pdb=" O ASP Q 394 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE Q 399 " --> pdb=" O GLY Q 395 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 430 Processing helix chain 'Q' and resid 433 through 446 removed outlier: 4.305A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 456 Processing helix chain 'Q' and resid 459 through 473 removed outlier: 3.506A pdb=" N VAL Q 463 " --> pdb=" O LYS Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'q' and resid 27 through 45 removed outlier: 3.672A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 95 removed outlier: 4.128A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN q 95 " --> pdb=" O HIS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 122 removed outlier: 3.738A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 156 through 169 removed outlier: 3.554A pdb=" N ARG q 165 " --> pdb=" O SER q 161 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 175 through 188 removed outlier: 3.619A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 287 removed outlier: 3.585A pdb=" N GLU q 273 " --> pdb=" O SER q 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE q 283 " --> pdb=" O GLN q 279 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA q 284 " --> pdb=" O VAL q 280 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 removed outlier: 3.710A pdb=" N HIS q 303 " --> pdb=" O ASP q 299 " (cutoff:3.500A) Processing helix chain 'q' and resid 317 through 328 removed outlier: 3.581A pdb=" N LEU q 321 " --> pdb=" O SER q 317 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU q 324 " --> pdb=" O ASP q 320 " (cutoff:3.500A) Processing helix chain 'q' and resid 381 through 403 removed outlier: 3.579A pdb=" N ARG q 390 " --> pdb=" O ASP q 386 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) Processing helix chain 'q' and resid 413 through 430 Processing helix chain 'q' and resid 433 through 446 removed outlier: 4.254A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 456 removed outlier: 3.616A pdb=" N SER q 456 " --> pdb=" O LEU q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 459 through 473 removed outlier: 3.632A pdb=" N LYS q 466 " --> pdb=" O GLU q 462 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'Z' and resid 17 through 35 Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 71 through 88 removed outlier: 3.713A pdb=" N LEU Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 111 Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.750A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 157 Processing helix chain 'Z' and resid 158 through 160 No H-bonds generated for 'chain 'Z' and resid 158 through 160' Processing helix chain 'Z' and resid 163 through 180 removed outlier: 4.217A pdb=" N VAL Z 167 " --> pdb=" O GLU Z 163 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE Z 176 " --> pdb=" O VAL Z 172 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE Z 179 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 252 through 281 removed outlier: 3.513A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP Z 269 " --> pdb=" O LYS Z 265 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS Z 273 " --> pdb=" O ASP Z 269 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE Z 275 " --> pdb=" O VAL Z 271 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 308 removed outlier: 3.683A pdb=" N LYS Z 307 " --> pdb=" O ASP Z 303 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 329 Processing helix chain 'Z' and resid 335 through 339 Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 Processing helix chain 'Z' and resid 412 through 424 Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.165A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU Z 445 " --> pdb=" O ALA Z 441 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 455 removed outlier: 3.539A pdb=" N ALA Z 452 " --> pdb=" O PRO Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 469 removed outlier: 3.565A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 517 Processing helix chain 'z' and resid 17 through 35 removed outlier: 3.518A pdb=" N ASN z 23 " --> pdb=" O ALA z 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 61 through 66 Processing helix chain 'z' and resid 71 through 88 removed outlier: 3.554A pdb=" N SER z 75 " --> pdb=" O HIS z 71 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU z 76 " --> pdb=" O PRO z 72 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE z 77 " --> pdb=" O THR z 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.589A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.780A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 157 removed outlier: 3.720A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 160 No H-bonds generated for 'chain 'z' and resid 158 through 160' Processing helix chain 'z' and resid 164 through 178 removed outlier: 3.848A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE z 176 " --> pdb=" O VAL z 172 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.957A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 252 through 281 removed outlier: 4.175A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 308 removed outlier: 3.515A pdb=" N ALA z 304 " --> pdb=" O PHE z 300 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 317 through 329 Processing helix chain 'z' and resid 335 through 339 Processing helix chain 'z' and resid 340 through 344 removed outlier: 3.686A pdb=" N CYS z 343 " --> pdb=" O SER z 340 " (cutoff:3.500A) Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.748A pdb=" N LEU z 384 " --> pdb=" O ASN z 380 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 424 Processing helix chain 'z' and resid 433 through 445 removed outlier: 3.558A pdb=" N LEU z 445 " --> pdb=" O ALA z 441 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 455 Processing helix chain 'z' and resid 458 through 469 removed outlier: 3.717A pdb=" N LEU z 463 " --> pdb=" O LEU z 459 " (cutoff:3.500A) Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 498 through 517 removed outlier: 3.590A pdb=" N VAL z 510 " --> pdb=" O HIS z 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 10 through 13 removed outlier: 6.363A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 44 through 46 Processing sheet with id=AA3, first strand: chain 'a' and resid 137 through 138 removed outlier: 3.622A pdb=" N ILE a 137 " --> pdb=" O VAL a 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 196 through 200 removed outlier: 6.328A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER a 374 " --> pdb=" O ILE a 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE a 376 " --> pdb=" O MET a 209 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET a 209 " --> pdb=" O ILE a 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 215 through 216 removed outlier: 3.600A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 285 through 287 removed outlier: 6.829A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.575A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 11 through 13 removed outlier: 4.717A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 61 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AB1, first strand: chain 'A' and resid 195 through 200 removed outlier: 3.680A pdb=" N ILE A 375 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AB3, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.680A pdb=" N ALA A 235 " --> pdb=" O LEU A 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AB5, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AB6, first strand: chain 'b' and resid 17 through 18 removed outlier: 6.140A pdb=" N ASP e 56 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN b 519 " --> pdb=" O ASP e 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 62 through 64 removed outlier: 6.444A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.624A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU b 375 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE b 202 " --> pdb=" O LEU b 375 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY b 377 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS b 204 " --> pdb=" O GLY b 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 238 through 240 removed outlier: 6.481A pdb=" N LEU b 238 " --> pdb=" O ILE b 291 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE b 290 " --> pdb=" O ILE b 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'b' and resid 351 through 353 Processing sheet with id=AC2, first strand: chain 'b' and resid 406 through 407 Processing sheet with id=AC3, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AC4, first strand: chain 'B' and resid 17 through 18 removed outlier: 4.473A pdb=" N VAL B 517 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET E 58 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN B 519 " --> pdb=" O MET E 58 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL E 60 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE B 521 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.638A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 199 through 205 removed outlier: 7.034A pdb=" N HIS B 200 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU B 375 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY B 377 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 239 through 240 Processing sheet with id=AC8, first strand: chain 'B' and resid 349 through 352 Processing sheet with id=AC9, first strand: chain 'B' and resid 406 through 407 Processing sheet with id=AD1, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AD2, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AD3, first strand: chain 'D' and resid 208 through 212 removed outlier: 6.821A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 227 through 229 removed outlier: 3.721A pdb=" N LEU D 229 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 373 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU D 360 " --> pdb=" O LYS D 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 246 through 248 removed outlier: 6.546A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU D 298 " --> pdb=" O ILE D 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.819A pdb=" N GLY D 492 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 208 through 214 removed outlier: 3.505A pdb=" N LYS d 209 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.625A pdb=" N LEU d 374 " --> pdb=" O LEU d 229 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY d 371 " --> pdb=" O LEU d 367 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU d 367 " --> pdb=" O GLY d 371 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR d 377 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU d 360 " --> pdb=" O LYS d 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 323 through 328 removed outlier: 3.783A pdb=" N LEU d 298 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE d 325 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP d 327 " --> pdb=" O ILE d 300 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N VAL d 345 " --> pdb=" O ILE d 246 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU d 248 " --> pdb=" O VAL d 345 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 421 through 423 Processing sheet with id=AE2, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AE3, first strand: chain 'E' and resid 207 through 213 removed outlier: 7.111A pdb=" N LYS E 208 " --> pdb=" O ILE E 383 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE E 385 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N GLY E 387 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS E 212 " --> pdb=" O GLY E 387 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 225 through 228 removed outlier: 3.514A pdb=" N VAL E 226 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 360 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 297 through 299 removed outlier: 6.165A pdb=" N ALA E 247 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL E 340 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE E 248 " --> pdb=" O VAL E 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AE7, first strand: chain 'E' and resid 531 through 532 removed outlier: 7.061A pdb=" N ARG E 532 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 23 through 27 removed outlier: 3.529A pdb=" N LYS e 533 " --> pdb=" O SER e 24 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU e 26 " --> pdb=" O ILE e 531 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE e 531 " --> pdb=" O LEU e 26 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE e 528 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU h 48 " --> pdb=" O ILE e 528 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP e 530 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL h 50 " --> pdb=" O ASP e 530 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG e 532 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'e' and resid 207 through 213 removed outlier: 3.727A pdb=" N GLY e 387 " --> pdb=" O LYS e 212 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 225 through 228 removed outlier: 3.876A pdb=" N VAL e 226 " --> pdb=" O ILE e 372 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP e 367 " --> pdb=" O PHE e 362 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE e 362 " --> pdb=" O ASP e 367 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE e 360 " --> pdb=" O MET e 369 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'e' and resid 246 through 249 removed outlier: 6.208A pdb=" N ALA e 247 " --> pdb=" O ILE e 299 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 416 through 418 Processing sheet with id=AF4, first strand: chain 'g' and resid 57 through 58 removed outlier: 6.626A pdb=" N MET g 47 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU z 520 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE z 521 " --> pdb=" O ALA z 14 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA z 14 " --> pdb=" O ILE z 521 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AF6, first strand: chain 'g' and resid 199 through 203 removed outlier: 3.791A pdb=" N ARG g 200 " --> pdb=" O CYS g 372 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE g 374 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU g 376 " --> pdb=" O GLU g 202 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 219 through 220 Processing sheet with id=AF8, first strand: chain 'g' and resid 232 through 233 Processing sheet with id=AF9, first strand: chain 'g' and resid 238 through 241 removed outlier: 5.830A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 57 through 58 removed outlier: 3.831A pdb=" N VAL G 58 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 50 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AG3, first strand: chain 'G' and resid 199 through 205 removed outlier: 3.725A pdb=" N ARG G 200 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY G 378 " --> pdb=" O ILE G 204 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AG5, first strand: chain 'G' and resid 232 through 233 removed outlier: 3.621A pdb=" N ILE G 233 " --> pdb=" O LEU G 350 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.771A pdb=" N LEU G 241 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL G 290 " --> pdb=" O ILE G 312 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 15 through 17 removed outlier: 4.101A pdb=" N SER h 16 " --> pdb=" O THR h 519 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR h 519 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL h 516 " --> pdb=" O ASN q 53 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET q 55 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU h 518 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE q 57 " --> pdb=" O GLU h 518 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AG9, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.860A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.381A pdb=" N VAL h 289 " --> pdb=" O ALA h 311 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'h' and resid 349 through 351 removed outlier: 3.601A pdb=" N GLU h 349 " --> pdb=" O PHE h 360 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE h 360 " --> pdb=" O GLU h 349 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 475 through 477 Processing sheet with id=AH4, first strand: chain 'H' and resid 16 through 17 removed outlier: 4.146A pdb=" N SER H 16 " --> pdb=" O THR H 519 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR H 519 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AH6, first strand: chain 'H' and resid 195 through 201 removed outlier: 7.125A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLY H 376 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL H 200 " --> pdb=" O GLY H 376 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 309 through 311 removed outlier: 6.482A pdb=" N VAL H 289 " --> pdb=" O ALA H 311 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU H 239 " --> pdb=" O GLN H 331 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.556A pdb=" N GLU H 349 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE H 360 " --> pdb=" O GLU H 349 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR H 351 " --> pdb=" O TYR H 358 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR H 358 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AI1, first strand: chain 'Q' and resid 202 through 208 Processing sheet with id=AI2, first strand: chain 'Q' and resid 233 through 234 Processing sheet with id=AI3, first strand: chain 'Q' and resid 240 through 242 removed outlier: 7.115A pdb=" N ALA Q 240 " --> pdb=" O VAL Q 292 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id=AI5, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AI6, first strand: chain 'Q' and resid 521 through 526 removed outlier: 4.677A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Z 45 " --> pdb=" O THR Z 57 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'q' and resid 202 through 208 removed outlier: 7.359A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'q' and resid 221 through 223 Processing sheet with id=AI9, first strand: chain 'q' and resid 311 through 314 removed outlier: 9.770A pdb=" N LEU q 333 " --> pdb=" O ILE q 239 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL q 241 " --> pdb=" O LEU q 333 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'q' and resid 408 through 410 Processing sheet with id=AJ2, first strand: chain 'q' and resid 478 through 480 removed outlier: 3.530A pdb=" N LYS q 490 " --> pdb=" O GLY q 479 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'q' and resid 521 through 526 removed outlier: 4.713A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.726A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Z' and resid 211 through 212 Processing sheet with id=AJ6, first strand: chain 'Z' and resid 229 through 231 removed outlier: 3.707A pdb=" N VAL Z 290 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL Z 311 " --> pdb=" O PHE Z 289 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 478 through 479 Processing sheet with id=AJ9, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.322A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'z' and resid 211 through 212 removed outlier: 3.523A pdb=" N PHE z 360 " --> pdb=" O TYR z 353 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'z' and resid 229 through 231 removed outlier: 7.374A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'z' and resid 407 through 409 Processing sheet with id=AK4, first strand: chain 'z' and resid 477 through 479 3292 hydrogen bonds defined for protein. 9534 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: 23.02 Time building geometry restraints manager: 20.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 20734 1.35 - 1.47: 11760 1.47 - 1.59: 28777 1.59 - 1.71: 0 1.71 - 1.83: 626 Bond restraints: 61897 Sorted by residual: bond pdb=" C ASN A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.331 1.346 -0.015 7.90e-03 1.60e+04 3.49e+00 bond pdb=" CA PHE b 12 " pdb=" CB PHE b 12 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.35e-02 5.49e+03 1.49e+00 bond pdb=" N GLY A 9 " pdb=" CA GLY A 9 " ideal model delta sigma weight residual 1.453 1.443 0.010 8.60e-03 1.35e+04 1.36e+00 bond pdb=" CB ILE H 197 " pdb=" CG2 ILE H 197 " ideal model delta sigma weight residual 1.521 1.559 -0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" C SER G 333 " pdb=" N ARG G 334 " ideal model delta sigma weight residual 1.325 1.339 -0.014 1.25e-02 6.40e+03 1.31e+00 ... (remaining 61892 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.73: 1273 106.73 - 113.56: 35949 113.56 - 120.38: 21797 120.38 - 127.21: 24062 127.21 - 134.03: 419 Bond angle restraints: 83500 Sorted by residual: angle pdb=" C SER D 234 " pdb=" N ASN D 235 " pdb=" CA ASN D 235 " ideal model delta sigma weight residual 121.70 128.34 -6.64 1.80e+00 3.09e-01 1.36e+01 angle pdb=" N ILE G 495 " pdb=" CA ILE G 495 " pdb=" C ILE G 495 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" N ILE g 495 " pdb=" CA ILE g 495 " pdb=" C ILE g 495 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" N VAL Z 429 " pdb=" CA VAL Z 429 " pdb=" C VAL Z 429 " ideal model delta sigma weight residual 112.12 109.33 2.79 8.40e-01 1.42e+00 1.10e+01 angle pdb=" N GLN A 187 " pdb=" CA GLN A 187 " pdb=" C GLN A 187 " ideal model delta sigma weight residual 109.81 116.67 -6.86 2.21e+00 2.05e-01 9.62e+00 ... (remaining 83495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 35906 17.94 - 35.87: 2182 35.87 - 53.81: 223 53.81 - 71.75: 56 71.75 - 89.69: 36 Dihedral angle restraints: 38403 sinusoidal: 15339 harmonic: 23064 Sorted by residual: 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 -125.96 -54.04 0 5.00e+00 4.00e-02 1.17e+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 -127.08 -52.92 0 5.00e+00 4.00e-02 1.12e+02 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 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.33e+01 ... (remaining 38400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 7091 0.032 - 0.065: 1845 0.065 - 0.097: 562 0.097 - 0.129: 487 0.129 - 0.162: 38 Chirality restraints: 10023 Sorted by residual: chirality pdb=" CA PRO A 188 " pdb=" N PRO A 188 " pdb=" C PRO A 188 " pdb=" CB PRO A 188 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA PRO a 188 " pdb=" N PRO a 188 " pdb=" C PRO a 188 " pdb=" CB PRO a 188 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 10020 not shown) Planarity restraints: 10715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 187 " 0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO a 188 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO a 188 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO a 188 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 187 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO A 188 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Q 191 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO Q 192 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO Q 192 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO Q 192 " -0.030 5.00e-02 4.00e+02 ... (remaining 10712 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 49 2.32 - 2.97: 25987 2.97 - 3.61: 89553 3.61 - 4.26: 138723 4.26 - 4.90: 229115 Nonbonded interactions: 483427 Sorted by model distance: nonbonded pdb=" NZ LYS e 527 " pdb=" OE2 GLU h 384 " model vdw 1.679 2.520 nonbonded pdb=" OD1 ASP a 462 " pdb=" NZ LYS H 430 " model vdw 1.944 2.520 nonbonded pdb=" NZ LYS q 16 " pdb=" O LEU z 63 " model vdw 1.970 2.520 nonbonded pdb=" OG SER d 358 " pdb=" O CYS d 379 " model vdw 2.079 2.440 nonbonded pdb=" NZ LYS b 50 " pdb=" OD1 ASP d 534 " model vdw 2.091 2.520 ... (remaining 483422 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 5 through 237 or resid 285 through 331 or resid 338 throug \ h 354 or resid 361 through 533)) } ncs_group { reference = (chain 'B' and (resid 10 through 240 or resid 289 through 326 or resid 349 or re \ sid 351 or resid 358 through 526)) selection = (chain 'b' and (resid 10 through 227 or resid 235 through 306 or resid 317 throu \ gh 326 or resid 354 or resid 356 or resid 358 through 526)) } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 24 through 173 or resid 181 through 249 or resid 276 throu \ gh 300 or resid 311 through 352 or resid 356 through 366 or resid 372 through 53 \ 9)) } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = (chain 'g' and (resid 15 through 241 or resid 268 through 526)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 6.200 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 127.220 Find NCS groups from input model: 5.380 Set up NCS constraints: 0.390 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:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 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 0.038 61897 Z= 0.185 Angle : 0.502 6.855 83500 Z= 0.270 Chirality : 0.040 0.162 10023 Planarity : 0.003 0.087 10715 Dihedral : 11.700 89.685 23453 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % 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: -3.71 (0.07), residues: 7955 helix: -2.48 (0.05), residues: 4076 sheet: -2.62 (0.17), residues: 671 loop : -2.15 (0.10), residues: 3208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP g 478 HIS 0.002 0.001 HIS q 59 PHE 0.014 0.001 PHE G 112 TYR 0.008 0.001 TYR H 263 ARG 0.005 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2145 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2142 time to evaluate : 5.384 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: a 167 PHE cc_start: 0.4716 (t80) cc_final: 0.4363 (t80) REVERT: a 299 TYR cc_start: 0.1561 (m-80) cc_final: 0.1326 (m-80) REVERT: a 460 SER cc_start: 0.8402 (p) cc_final: 0.8199 (p) REVERT: A 20 GLN cc_start: 0.8680 (mt0) cc_final: 0.8322 (mt0) REVERT: A 52 VAL cc_start: 0.7787 (p) cc_final: 0.7556 (t) REVERT: A 156 MET cc_start: 0.3887 (mtp) cc_final: 0.3446 (ptt) REVERT: A 168 PHE cc_start: 0.5955 (m-80) cc_final: 0.5617 (m-80) REVERT: A 171 MET cc_start: 0.5947 (mtt) cc_final: 0.5480 (ttm) REVERT: A 489 ASP cc_start: 0.1866 (t0) cc_final: 0.1212 (t70) REVERT: b 48 MET cc_start: 0.8346 (mmm) cc_final: 0.8120 (mmp) REVERT: b 97 ASP cc_start: 0.5651 (t0) cc_final: 0.5072 (m-30) REVERT: b 120 LYS cc_start: 0.8421 (mtmt) cc_final: 0.7773 (mmtm) REVERT: b 177 ASP cc_start: 0.6132 (m-30) cc_final: 0.5469 (t0) REVERT: b 452 ASP cc_start: 0.7114 (m-30) cc_final: 0.6700 (m-30) REVERT: b 495 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6220 (mt-10) REVERT: B 52 LEU cc_start: 0.8127 (mt) cc_final: 0.7661 (mt) REVERT: B 65 ASN cc_start: 0.8176 (p0) cc_final: 0.7966 (p0) REVERT: B 177 ASP cc_start: 0.6350 (m-30) cc_final: 0.6109 (p0) REVERT: B 216 GLU cc_start: 0.4631 (pt0) cc_final: 0.4293 (tt0) REVERT: B 448 THR cc_start: 0.7934 (m) cc_final: 0.7265 (p) REVERT: B 449 ILE cc_start: 0.8453 (mt) cc_final: 0.8025 (mm) REVERT: B 452 ASP cc_start: 0.6549 (m-30) cc_final: 0.6154 (m-30) REVERT: B 522 LYS cc_start: 0.8406 (mttt) cc_final: 0.8011 (ptpt) REVERT: D 57 MET cc_start: 0.8447 (mmm) cc_final: 0.7696 (mmm) REVERT: D 76 THR cc_start: 0.8865 (m) cc_final: 0.8658 (t) REVERT: D 205 LEU cc_start: 0.5729 (mt) cc_final: 0.5257 (pt) REVERT: D 460 VAL cc_start: 0.7975 (p) cc_final: 0.7647 (t) REVERT: d 58 ASP cc_start: 0.7423 (m-30) cc_final: 0.7209 (m-30) REVERT: E 33 LYS cc_start: 0.8346 (mttm) cc_final: 0.7828 (mttp) REVERT: E 58 MET cc_start: 0.8525 (ttm) cc_final: 0.8270 (ttm) REVERT: E 65 ASP cc_start: 0.6706 (m-30) cc_final: 0.6344 (t0) REVERT: E 71 ASP cc_start: 0.7624 (t70) cc_final: 0.7391 (t0) REVERT: E 76 LEU cc_start: 0.8726 (mt) cc_final: 0.8204 (pp) REVERT: E 79 MET cc_start: 0.8140 (mtp) cc_final: 0.7716 (tpp) REVERT: E 82 ASP cc_start: 0.7063 (m-30) cc_final: 0.6842 (m-30) REVERT: E 88 LEU cc_start: 0.8379 (mt) cc_final: 0.7674 (mm) REVERT: E 197 MET cc_start: 0.2341 (mtp) cc_final: 0.1792 (mtp) REVERT: E 365 THR cc_start: 0.4948 (m) cc_final: 0.4662 (p) REVERT: E 413 ASP cc_start: 0.8380 (t0) cc_final: 0.8017 (t0) REVERT: E 474 GLU cc_start: 0.5703 (mt-10) cc_final: 0.5005 (mt-10) REVERT: e 32 LEU cc_start: 0.8329 (mt) cc_final: 0.7914 (tp) REVERT: e 87 LYS cc_start: 0.8558 (mttt) cc_final: 0.7609 (mttp) REVERT: e 115 LEU cc_start: 0.9296 (mt) cc_final: 0.9000 (mt) REVERT: G 145 ASP cc_start: 0.7006 (t0) cc_final: 0.6554 (m-30) REVERT: G 237 ARG cc_start: 0.6645 (mtt180) cc_final: 0.6204 (mtp85) REVERT: G 392 GLN cc_start: 0.8149 (mt0) cc_final: 0.7816 (mt0) REVERT: G 395 MET cc_start: 0.7883 (mtt) cc_final: 0.7668 (mtm) REVERT: G 495 ILE cc_start: 0.7464 (mm) cc_final: 0.6861 (mm) REVERT: h 46 ASP cc_start: 0.7526 (m-30) cc_final: 0.7182 (m-30) REVERT: h 49 ILE cc_start: 0.8960 (mt) cc_final: 0.8673 (mm) REVERT: h 57 THR cc_start: 0.8741 (m) cc_final: 0.8492 (p) REVERT: h 77 LYS cc_start: 0.8245 (mttt) cc_final: 0.8008 (mttm) REVERT: h 197 ILE cc_start: 0.6216 (mt) cc_final: 0.5974 (mm) REVERT: h 274 LEU cc_start: 0.1360 (tp) cc_final: 0.1068 (mm) REVERT: h 282 HIS cc_start: 0.4328 (t70) cc_final: 0.4040 (t-170) REVERT: H 160 MET cc_start: 0.6399 (ptp) cc_final: 0.6117 (ptp) REVERT: H 178 MET cc_start: 0.7494 (mmp) cc_final: 0.7103 (tpp) REVERT: H 180 VAL cc_start: 0.6937 (t) cc_final: 0.6632 (m) REVERT: H 484 ILE cc_start: 0.8113 (pt) cc_final: 0.7791 (pt) REVERT: H 519 THR cc_start: 0.7887 (m) cc_final: 0.7575 (t) REVERT: H 521 LYS cc_start: 0.8142 (tttt) cc_final: 0.7688 (ttpp) REVERT: Q 63 LEU cc_start: 0.8364 (tp) cc_final: 0.8120 (tp) REVERT: Q 377 LEU cc_start: 0.9130 (mt) cc_final: 0.8737 (mp) REVERT: Q 386 ASP cc_start: 0.8193 (m-30) cc_final: 0.7987 (t0) REVERT: q 31 ARG cc_start: 0.8094 (mmt180) cc_final: 0.7751 (mmt-90) REVERT: q 34 GLN cc_start: 0.8270 (tp40) cc_final: 0.7900 (mm110) REVERT: q 357 ASP cc_start: 0.6888 (m-30) cc_final: 0.6513 (m-30) REVERT: Z 61 ASN cc_start: 0.6739 (t0) cc_final: 0.6486 (t0) REVERT: Z 150 ASP cc_start: 0.6605 (m-30) cc_final: 0.6046 (m-30) REVERT: Z 351 TYR cc_start: 0.3206 (p90) cc_final: 0.2526 (p90) REVERT: Z 453 GLN cc_start: 0.7574 (mt0) cc_final: 0.7262 (mt0) REVERT: Z 521 ILE cc_start: 0.8243 (mt) cc_final: 0.7734 (mt) REVERT: z 37 ASN cc_start: 0.8092 (p0) cc_final: 0.7877 (p0) REVERT: z 66 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7706 (mt-10) REVERT: z 355 LEU cc_start: 0.4688 (mp) cc_final: 0.4237 (mt) REVERT: z 414 VAL cc_start: 0.8600 (t) cc_final: 0.8331 (t) REVERT: z 453 GLN cc_start: 0.7920 (mt0) cc_final: 0.7220 (mt0) outliers start: 3 outliers final: 0 residues processed: 2143 average time/residue: 0.6199 time to fit residues: 2150.3758 Evaluate side-chains 1145 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1145 time to evaluate : 5.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 6.9990 chunk 602 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 205 optimal weight: 0.4980 chunk 406 optimal weight: 8.9990 chunk 321 optimal weight: 0.5980 chunk 623 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 378 optimal weight: 0.9990 chunk 463 optimal weight: 7.9990 chunk 721 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 135 ASN a 150 ASN a 164 ASN ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 187 GLN A 393 HIS A 475 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN b 175 HIS B 175 HIS ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 62 GLN D 85 HIS D 98 GLN D 394 ASN D 406 HIS ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 165 ASN E 301 GLN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS g 154 ASN g 277 GLN g 320 ASN g 472 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN G 321 ASN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 233 HIS H 21 GLN H 209 GLN H 331 GLN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 175 ASN q 477 ASN Z 132 GLN Z 293 ASN Z 434 GLN z 497 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 61897 Z= 0.261 Angle : 0.637 12.016 83500 Z= 0.333 Chirality : 0.044 0.260 10023 Planarity : 0.005 0.081 10715 Dihedral : 3.764 54.660 8501 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.90 % Rotamer: Outliers : 2.49 % Allowed : 12.02 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.09), residues: 7955 helix: 0.18 (0.07), residues: 4207 sheet: -2.05 (0.17), residues: 718 loop : -1.77 (0.10), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP h 271 HIS 0.011 0.001 HIS B 178 PHE 0.026 0.002 PHE a 516 TYR 0.021 0.002 TYR h 419 ARG 0.013 0.001 ARG Z 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1270 time to evaluate : 5.399 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: a 78 LEU cc_start: 0.7852 (mt) cc_final: 0.7631 (mt) REVERT: a 99 GLU cc_start: 0.7395 (tp30) cc_final: 0.7186 (tp30) REVERT: a 102 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8517 (ttpt) REVERT: a 388 MET cc_start: 0.6662 (ptp) cc_final: 0.6445 (ptt) REVERT: A 168 PHE cc_start: 0.5300 (m-80) cc_final: 0.5099 (m-80) REVERT: A 345 LEU cc_start: 0.4117 (mm) cc_final: 0.3423 (pp) REVERT: A 400 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7166 (pttt) REVERT: A 462 ASP cc_start: 0.6843 (m-30) cc_final: 0.6620 (m-30) REVERT: A 528 ASP cc_start: 0.8308 (p0) cc_final: 0.7975 (p0) REVERT: b 48 MET cc_start: 0.8311 (mmm) cc_final: 0.7910 (mmm) REVERT: b 97 ASP cc_start: 0.6465 (t0) cc_final: 0.5113 (m-30) REVERT: b 120 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8660 (mmtm) REVERT: b 177 ASP cc_start: 0.6020 (m-30) cc_final: 0.5581 (t0) REVERT: b 353 MET cc_start: 0.3645 (mmp) cc_final: 0.3217 (mmp) REVERT: b 452 ASP cc_start: 0.7690 (m-30) cc_final: 0.7194 (m-30) REVERT: B 91 GLN cc_start: 0.7322 (tp40) cc_final: 0.7079 (tp40) REVERT: B 177 ASP cc_start: 0.7249 (m-30) cc_final: 0.6992 (p0) REVERT: B 448 THR cc_start: 0.8502 (m) cc_final: 0.7997 (p) REVERT: B 452 ASP cc_start: 0.7251 (m-30) cc_final: 0.6565 (m-30) REVERT: B 457 ASP cc_start: 0.7202 (p0) cc_final: 0.6903 (p0) REVERT: D 32 GLN cc_start: 0.7827 (pt0) cc_final: 0.7533 (pm20) REVERT: D 46 ASP cc_start: 0.7556 (m-30) cc_final: 0.7308 (m-30) REVERT: D 57 MET cc_start: 0.8504 (mmm) cc_final: 0.7767 (mmm) REVERT: D 399 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6458 (mp0) REVERT: d 319 LYS cc_start: 0.5215 (mttt) cc_final: 0.4811 (pttt) REVERT: d 361 LEU cc_start: 0.6448 (tp) cc_final: 0.5929 (pp) REVERT: d 446 MET cc_start: 0.7043 (mmm) cc_final: 0.6703 (mmm) REVERT: E 46 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7870 (mmm) REVERT: E 58 MET cc_start: 0.8534 (ttm) cc_final: 0.8128 (ttm) REVERT: E 65 ASP cc_start: 0.6729 (m-30) cc_final: 0.5981 (t70) REVERT: E 413 ASP cc_start: 0.8638 (t0) cc_final: 0.8283 (t0) REVERT: g 48 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7196 (mmtm) REVERT: g 229 MET cc_start: 0.0948 (mtt) cc_final: -0.0538 (mmt) REVERT: g 305 MET cc_start: 0.6356 (ptm) cc_final: 0.5459 (mmt) REVERT: g 306 ARG cc_start: 0.4576 (ttp80) cc_final: 0.3155 (ttp80) REVERT: g 385 SER cc_start: 0.7128 (t) cc_final: 0.6204 (m) REVERT: g 518 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7469 (mtp85) REVERT: G 152 MET cc_start: 0.8160 (mtp) cc_final: 0.7909 (mtp) REVERT: G 362 PHE cc_start: 0.5411 (m-10) cc_final: 0.5199 (m-10) REVERT: G 392 GLN cc_start: 0.8345 (mt0) cc_final: 0.7922 (mt0) REVERT: h 49 ILE cc_start: 0.9039 (mt) cc_final: 0.8729 (mm) REVERT: h 51 ASP cc_start: 0.7672 (p0) cc_final: 0.7256 (p0) REVERT: h 57 THR cc_start: 0.9101 (m) cc_final: 0.8891 (p) REVERT: h 194 MET cc_start: 0.6158 (mmm) cc_final: 0.5436 (ptm) REVERT: h 274 LEU cc_start: 0.0271 (tp) cc_final: -0.0001 (mm) REVERT: h 324 MET cc_start: 0.6580 (mmm) cc_final: 0.6368 (mmm) REVERT: H 87 ASP cc_start: 0.5700 (t0) cc_final: 0.5459 (t0) REVERT: H 106 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7807 (ttpt) REVERT: H 160 MET cc_start: 0.6748 (ptp) cc_final: 0.6482 (ptm) REVERT: H 178 MET cc_start: 0.7825 (mmp) cc_final: 0.7528 (mmp) REVERT: H 382 MET cc_start: 0.4339 (mtm) cc_final: 0.3589 (mtt) REVERT: H 521 LYS cc_start: 0.8239 (tttt) cc_final: 0.7725 (ttpp) REVERT: Q 14 MET cc_start: 0.4589 (ppp) cc_final: 0.3256 (ptt) REVERT: Q 79 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8472 (mp10) REVERT: Q 196 HIS cc_start: 0.6009 (t70) cc_final: 0.5688 (t70) REVERT: Q 382 ASP cc_start: 0.8596 (m-30) cc_final: 0.8268 (m-30) REVERT: q 27 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7115 (mm-30) REVERT: q 61 GLU cc_start: 0.7159 (mp0) cc_final: 0.6959 (mp0) REVERT: q 75 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6578 (mm-30) REVERT: q 114 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8773 (mm) REVERT: q 357 ASP cc_start: 0.7240 (m-30) cc_final: 0.6880 (m-30) REVERT: q 523 GLN cc_start: 0.8066 (tt0) cc_final: 0.7594 (tp40) REVERT: q 526 MET cc_start: 0.6014 (mtm) cc_final: 0.5738 (mpp) REVERT: Z 61 ASN cc_start: 0.6988 (t0) cc_final: 0.6649 (t0) REVERT: Z 163 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6765 (mm-30) REVERT: Z 221 MET cc_start: 0.3986 (mmt) cc_final: 0.2389 (tmm) REVERT: Z 520 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6341 (tm-30) REVERT: z 59 ASP cc_start: 0.7394 (t70) cc_final: 0.7082 (t70) REVERT: z 143 MET cc_start: 0.6533 (pmm) cc_final: 0.6247 (pmm) REVERT: z 179 ILE cc_start: 0.7088 (pt) cc_final: 0.6852 (pt) REVERT: z 446 ILE cc_start: 0.8921 (tp) cc_final: 0.8600 (tp) outliers start: 166 outliers final: 91 residues processed: 1382 average time/residue: 0.5643 time to fit residues: 1311.5695 Evaluate side-chains 1096 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1002 time to evaluate : 5.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 376 ILE Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain a residue 492 ASN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 135 GLU Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain e residue 400 LEU Chi-restraints excluded: chain e residue 531 ILE Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 302 HIS Chi-restraints excluded: chain g residue 372 CYS Chi-restraints excluded: chain g residue 488 VAL Chi-restraints excluded: chain g residue 501 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 374 LEU Chi-restraints excluded: chain h residue 459 ASN Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 172 LYS Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 319 TRP Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 119 LEU Chi-restraints excluded: chain q residue 153 ASN Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 300 MET Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain Z residue 30 LEU Chi-restraints excluded: chain Z residue 166 ASP Chi-restraints excluded: chain Z residue 323 ARG Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 212 LEU Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 335 SER Chi-restraints excluded: chain z residue 408 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 600 optimal weight: 4.9990 chunk 491 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 723 optimal weight: 6.9990 chunk 781 optimal weight: 2.9990 chunk 644 optimal weight: 6.9990 chunk 717 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 580 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN b 361 HIS B 65 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN D 37 ASN ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 84 GLN ** g 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS g 226 HIS ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN G 400 ASN G 434 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 352 GLN h 359 ASN ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 462 ASN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN q 13 GLN q 50 ASN ** q 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 GLN Z 386 GLN ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 467 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 61897 Z= 0.256 Angle : 0.608 9.401 83500 Z= 0.315 Chirality : 0.044 0.193 10023 Planarity : 0.004 0.087 10715 Dihedral : 4.008 54.725 8501 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.19 % Allowed : 13.97 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.09), residues: 7955 helix: 0.93 (0.08), residues: 4218 sheet: -1.73 (0.17), residues: 767 loop : -1.57 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 302 HIS 0.017 0.001 HIS z 161 PHE 0.024 0.002 PHE a 167 TYR 0.020 0.002 TYR h 438 ARG 0.006 0.001 ARG d 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1097 time to evaluate : 5.467 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: a 111 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8862 (mmmm) REVERT: a 357 CYS cc_start: 0.3080 (p) cc_final: 0.2656 (t) REVERT: A 147 CYS cc_start: 0.6545 (t) cc_final: 0.6270 (m) REVERT: A 156 MET cc_start: 0.3396 (mtt) cc_final: 0.3035 (ptm) REVERT: A 168 PHE cc_start: 0.5399 (m-80) cc_final: 0.5063 (m-80) REVERT: A 344 MET cc_start: 0.4462 (pmm) cc_final: 0.4199 (mpp) REVERT: A 345 LEU cc_start: 0.5105 (mm) cc_final: 0.4619 (pp) REVERT: A 384 MET cc_start: 0.3946 (ppp) cc_final: 0.3465 (ppp) REVERT: A 397 CYS cc_start: 0.7434 (m) cc_final: 0.6777 (p) REVERT: A 400 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6990 (pttt) REVERT: b 97 ASP cc_start: 0.6656 (t0) cc_final: 0.5378 (m-30) REVERT: b 120 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8804 (mmtm) REVERT: b 162 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7783 (tt) REVERT: b 177 ASP cc_start: 0.5911 (m-30) cc_final: 0.5560 (t0) REVERT: b 353 MET cc_start: 0.4519 (mmp) cc_final: 0.3962 (mmp) REVERT: b 441 LYS cc_start: 0.8897 (mptt) cc_final: 0.8384 (mptt) REVERT: b 480 MET cc_start: 0.6511 (pmm) cc_final: 0.6147 (mpp) REVERT: B 85 VAL cc_start: 0.8920 (t) cc_final: 0.8503 (p) REVERT: B 91 GLN cc_start: 0.7409 (tp-100) cc_final: 0.6996 (tp40) REVERT: B 157 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6603 (pt0) REVERT: B 177 ASP cc_start: 0.7269 (m-30) cc_final: 0.6975 (p0) REVERT: B 448 THR cc_start: 0.8732 (m) cc_final: 0.8169 (p) REVERT: B 452 ASP cc_start: 0.7551 (m-30) cc_final: 0.6942 (m-30) REVERT: D 32 GLN cc_start: 0.8220 (pt0) cc_final: 0.7876 (pm20) REVERT: D 46 ASP cc_start: 0.7851 (m-30) cc_final: 0.7507 (m-30) REVERT: D 57 MET cc_start: 0.8579 (mmm) cc_final: 0.7913 (mmm) REVERT: D 399 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6708 (mp0) REVERT: d 446 MET cc_start: 0.7353 (mmm) cc_final: 0.6878 (mmm) REVERT: E 58 MET cc_start: 0.8117 (ttm) cc_final: 0.7703 (ttm) REVERT: E 65 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6010 (t70) REVERT: E 78 MET cc_start: 0.8491 (mmm) cc_final: 0.8153 (mmm) REVERT: E 80 ASP cc_start: 0.7862 (p0) cc_final: 0.7636 (p0) REVERT: E 370 LEU cc_start: 0.5495 (pp) cc_final: 0.4748 (tp) REVERT: E 409 ASN cc_start: 0.8764 (m-40) cc_final: 0.8147 (m110) REVERT: E 413 ASP cc_start: 0.8777 (t0) cc_final: 0.8443 (t0) REVERT: e 393 ILE cc_start: 0.6711 (mt) cc_final: 0.6386 (tt) REVERT: e 521 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7562 (ttm) REVERT: g 38 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.8149 (mtp85) REVERT: g 229 MET cc_start: 0.1201 (mtt) cc_final: 0.0901 (mtp) REVERT: g 305 MET cc_start: 0.5960 (ptm) cc_final: 0.4954 (mmp) REVERT: g 319 ASP cc_start: 0.4196 (OUTLIER) cc_final: 0.3830 (t0) REVERT: G 152 MET cc_start: 0.8231 (mtp) cc_final: 0.7968 (mtp) REVERT: G 198 TYR cc_start: 0.7182 (m-80) cc_final: 0.6619 (m-80) REVERT: G 305 MET cc_start: 0.0498 (tmm) cc_final: 0.0216 (tmm) REVERT: G 392 GLN cc_start: 0.8560 (mt0) cc_final: 0.8257 (mt0) REVERT: G 395 MET cc_start: 0.7392 (mtt) cc_final: 0.6960 (mmt) REVERT: h 49 ILE cc_start: 0.8990 (mt) cc_final: 0.8768 (mm) REVERT: h 57 THR cc_start: 0.9193 (m) cc_final: 0.8986 (p) REVERT: h 194 MET cc_start: 0.6421 (mmm) cc_final: 0.5753 (mmm) REVERT: h 274 LEU cc_start: 0.0588 (tp) cc_final: 0.0240 (mm) REVERT: h 382 MET cc_start: 0.5963 (mmp) cc_final: 0.5582 (mpp) REVERT: H 106 LYS cc_start: 0.8271 (ttpt) cc_final: 0.7852 (ttpt) REVERT: H 160 MET cc_start: 0.6824 (ptp) cc_final: 0.6542 (ptm) REVERT: H 322 THR cc_start: 0.7104 (m) cc_final: 0.6579 (p) REVERT: H 382 MET cc_start: 0.4897 (mtm) cc_final: 0.4229 (mtt) REVERT: H 394 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.4167 (mtt) REVERT: H 481 ASN cc_start: 0.7137 (t0) cc_final: 0.6904 (t0) REVERT: H 521 LYS cc_start: 0.8172 (tttt) cc_final: 0.7693 (ttpp) REVERT: Q 14 MET cc_start: 0.4368 (ppp) cc_final: 0.3140 (ptt) REVERT: Q 79 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8424 (mp10) REVERT: Q 120 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6948 (mmt180) REVERT: Q 172 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7221 (tm-30) REVERT: Q 178 PHE cc_start: 0.6999 (t80) cc_final: 0.6729 (t80) REVERT: Q 196 HIS cc_start: 0.6018 (t70) cc_final: 0.5730 (t70) REVERT: Q 389 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7841 (tm-30) REVERT: q 31 ARG cc_start: 0.7618 (mmt180) cc_final: 0.7167 (mmt180) REVERT: q 114 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8750 (mm) REVERT: q 357 ASP cc_start: 0.7147 (m-30) cc_final: 0.6869 (m-30) REVERT: q 523 GLN cc_start: 0.7906 (tt0) cc_final: 0.7589 (tp40) REVERT: q 526 MET cc_start: 0.6369 (mtm) cc_final: 0.6086 (mpp) REVERT: Z 61 ASN cc_start: 0.7285 (t0) cc_final: 0.6970 (t0) REVERT: Z 85 ASP cc_start: 0.6219 (t0) cc_final: 0.5822 (t0) REVERT: Z 221 MET cc_start: 0.4222 (mmt) cc_final: 0.2988 (tmm) REVERT: Z 265 LYS cc_start: 0.7540 (mttt) cc_final: 0.6975 (tppt) REVERT: z 23 ASN cc_start: 0.8324 (m-40) cc_final: 0.8044 (m-40) REVERT: z 59 ASP cc_start: 0.7494 (t70) cc_final: 0.7233 (t70) REVERT: z 143 MET cc_start: 0.6642 (pmm) cc_final: 0.6362 (pmm) REVERT: z 144 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.6169 (p0) outliers start: 213 outliers final: 119 residues processed: 1235 average time/residue: 0.5525 time to fit residues: 1160.6379 Evaluate side-chains 1067 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 939 time to evaluate : 5.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 ILE Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 376 ILE Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain a residue 492 ASN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 493 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 201 ASP Chi-restraints excluded: chain e residue 400 LEU Chi-restraints excluded: chain e residue 411 ILE Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain e residue 531 ILE Chi-restraints excluded: chain g residue 97 SER Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 319 ASP Chi-restraints excluded: chain g residue 490 MET Chi-restraints excluded: chain g residue 501 VAL Chi-restraints excluded: chain g residue 523 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 512 LEU Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 172 LYS Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 394 MET Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 319 TRP Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 119 LEU Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 153 ASN Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 166 ASP Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 144 ASP Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 212 LEU Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 374 LEU Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 408 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 3.9990 chunk 543 optimal weight: 0.1980 chunk 375 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 345 optimal weight: 1.9990 chunk 485 optimal weight: 10.0000 chunk 725 optimal weight: 20.0000 chunk 768 optimal weight: 0.9990 chunk 379 optimal weight: 4.9990 chunk 687 optimal weight: 10.0000 chunk 207 optimal weight: 0.0020 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 170 ASN ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 228 GLN B 65 ASN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 ASN g 111 HIS g 320 ASN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN G 400 ASN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 140 HIS Q 435 GLN Q 472 GLN q 140 HIS ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 234 ASN Z 380 ASN ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 61897 Z= 0.180 Angle : 0.554 10.501 83500 Z= 0.285 Chirality : 0.042 0.263 10023 Planarity : 0.004 0.088 10715 Dihedral : 3.932 55.044 8501 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.98 % Allowed : 15.75 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.09), residues: 7955 helix: 1.25 (0.08), residues: 4230 sheet: -1.41 (0.18), residues: 736 loop : -1.41 (0.11), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 302 HIS 0.013 0.001 HIS z 161 PHE 0.018 0.001 PHE Q 399 TYR 0.016 0.001 TYR B 456 ARG 0.011 0.000 ARG g 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1055 time to evaluate : 5.640 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: a 99 GLU cc_start: 0.7435 (tp30) cc_final: 0.7187 (tp30) REVERT: a 111 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8841 (mmmm) REVERT: a 357 CYS cc_start: 0.2554 (p) cc_final: 0.2171 (t) REVERT: A 156 MET cc_start: 0.3331 (mtt) cc_final: 0.3025 (ptm) REVERT: A 168 PHE cc_start: 0.5584 (m-80) cc_final: 0.5202 (m-80) REVERT: A 171 MET cc_start: 0.5250 (mpp) cc_final: 0.4911 (mpp) REVERT: A 344 MET cc_start: 0.4388 (pmm) cc_final: 0.3820 (mpp) REVERT: A 345 LEU cc_start: 0.5264 (mm) cc_final: 0.4845 (pp) REVERT: A 384 MET cc_start: 0.4289 (ppp) cc_final: 0.3771 (ppp) REVERT: A 397 CYS cc_start: 0.7401 (m) cc_final: 0.6723 (p) REVERT: A 400 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6943 (pttt) REVERT: b 97 ASP cc_start: 0.6368 (t0) cc_final: 0.4977 (m-30) REVERT: b 142 LEU cc_start: 0.8610 (tp) cc_final: 0.8306 (tp) REVERT: b 162 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7785 (tt) REVERT: b 177 ASP cc_start: 0.5833 (m-30) cc_final: 0.5457 (t0) REVERT: b 353 MET cc_start: 0.4528 (mmp) cc_final: 0.3980 (mmp) REVERT: b 441 LYS cc_start: 0.8876 (mptt) cc_final: 0.8379 (mptt) REVERT: b 512 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6920 (tm-30) REVERT: B 85 VAL cc_start: 0.8989 (t) cc_final: 0.8658 (p) REVERT: B 91 GLN cc_start: 0.7597 (tp-100) cc_final: 0.7066 (tp40) REVERT: B 157 GLN cc_start: 0.6916 (mm-40) cc_final: 0.6668 (pt0) REVERT: B 177 ASP cc_start: 0.7267 (m-30) cc_final: 0.6990 (p0) REVERT: B 448 THR cc_start: 0.8679 (m) cc_final: 0.8098 (p) REVERT: B 452 ASP cc_start: 0.7588 (m-30) cc_final: 0.6977 (m-30) REVERT: B 522 LYS cc_start: 0.8145 (mttt) cc_final: 0.7917 (pttm) REVERT: D 32 GLN cc_start: 0.8168 (pt0) cc_final: 0.7829 (pm20) REVERT: D 46 ASP cc_start: 0.7873 (m-30) cc_final: 0.7505 (m-30) REVERT: D 57 MET cc_start: 0.8566 (mmm) cc_final: 0.7921 (mmm) REVERT: D 399 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6762 (mp0) REVERT: d 446 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6774 (mmm) REVERT: E 58 MET cc_start: 0.8274 (ttm) cc_final: 0.7867 (ttp) REVERT: E 65 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6439 (t0) REVERT: E 78 MET cc_start: 0.8491 (mmm) cc_final: 0.8144 (mmm) REVERT: E 174 LYS cc_start: 0.7031 (tppt) cc_final: 0.6291 (tppt) REVERT: E 395 GLU cc_start: 0.7989 (tp30) cc_final: 0.7525 (tp30) REVERT: E 401 HIS cc_start: 0.8669 (t70) cc_final: 0.7999 (t70) REVERT: E 413 ASP cc_start: 0.8749 (t0) cc_final: 0.8413 (t0) REVERT: e 46 MET cc_start: 0.8668 (mmm) cc_final: 0.8288 (mmm) REVERT: e 447 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.7227 (mtm180) REVERT: e 521 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7539 (ttm) REVERT: e 533 LYS cc_start: 0.7504 (tptm) cc_final: 0.7259 (tptm) REVERT: g 38 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8133 (mtp85) REVERT: g 229 MET cc_start: 0.1472 (mtt) cc_final: 0.1128 (mtp) REVERT: g 305 MET cc_start: 0.5585 (ptm) cc_final: 0.4973 (mmp) REVERT: G 305 MET cc_start: 0.0347 (tmm) cc_final: 0.0043 (tmm) REVERT: G 392 GLN cc_start: 0.8582 (mt0) cc_final: 0.8179 (mt0) REVERT: h 194 MET cc_start: 0.6395 (mmm) cc_final: 0.5985 (mmm) REVERT: h 274 LEU cc_start: 0.0580 (tp) cc_final: 0.0205 (mm) REVERT: h 382 MET cc_start: 0.6183 (OUTLIER) cc_final: 0.5801 (mpp) REVERT: h 394 MET cc_start: 0.7202 (mmm) cc_final: 0.6954 (mmp) REVERT: H 106 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7870 (ttpt) REVERT: H 160 MET cc_start: 0.6900 (ptp) cc_final: 0.6527 (ptm) REVERT: H 178 MET cc_start: 0.8175 (mmt) cc_final: 0.7921 (mmm) REVERT: H 374 LEU cc_start: 0.7862 (mt) cc_final: 0.7406 (mt) REVERT: H 382 MET cc_start: 0.4901 (mtm) cc_final: 0.4183 (mtt) REVERT: H 394 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.4520 (mtt) REVERT: H 521 LYS cc_start: 0.8197 (tttt) cc_final: 0.7728 (ttpp) REVERT: Q 14 MET cc_start: 0.4254 (ppp) cc_final: 0.3240 (ptt) REVERT: Q 41 GLN cc_start: 0.8206 (mm110) cc_final: 0.7854 (tp40) REVERT: Q 79 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8384 (mp10) REVERT: Q 116 GLU cc_start: 0.7095 (tp30) cc_final: 0.6774 (tp30) REVERT: Q 120 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6428 (mmt-90) REVERT: Q 172 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7095 (tm-30) REVERT: Q 178 PHE cc_start: 0.6901 (t80) cc_final: 0.6684 (t80) REVERT: Q 276 MET cc_start: 0.4797 (tpp) cc_final: 0.4387 (tpp) REVERT: Q 387 ASP cc_start: 0.8576 (p0) cc_final: 0.8305 (p0) REVERT: Q 389 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7729 (tm-30) REVERT: q 73 LEU cc_start: 0.8751 (mt) cc_final: 0.8456 (mt) REVERT: q 114 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8728 (mm) REVERT: q 249 MET cc_start: 0.1300 (OUTLIER) cc_final: 0.0825 (mpp) REVERT: q 357 ASP cc_start: 0.7180 (m-30) cc_final: 0.6950 (m-30) REVERT: q 523 GLN cc_start: 0.8094 (tt0) cc_final: 0.7835 (tp40) REVERT: q 526 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.5917 (mpp) REVERT: Z 61 ASN cc_start: 0.7386 (t0) cc_final: 0.7078 (t0) REVERT: Z 85 ASP cc_start: 0.6471 (t0) cc_final: 0.6130 (t0) REVERT: Z 221 MET cc_start: 0.4264 (mmt) cc_final: 0.3232 (tmm) REVERT: Z 265 LYS cc_start: 0.7541 (mttt) cc_final: 0.6972 (tppt) REVERT: Z 286 ASP cc_start: 0.5270 (OUTLIER) cc_final: 0.4101 (t0) REVERT: Z 387 ILE cc_start: 0.9423 (mm) cc_final: 0.9203 (mt) REVERT: Z 520 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7306 (tm-30) REVERT: z 23 ASN cc_start: 0.8252 (m-40) cc_final: 0.8038 (m-40) REVERT: z 59 ASP cc_start: 0.7548 (t70) cc_final: 0.7273 (t70) REVERT: z 99 ILE cc_start: 0.8924 (mt) cc_final: 0.8624 (mm) outliers start: 199 outliers final: 122 residues processed: 1177 average time/residue: 0.6046 time to fit residues: 1219.5357 Evaluate side-chains 1080 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 946 time to evaluate : 5.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain a residue 492 ASN Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 396 LEU Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 201 ASP Chi-restraints excluded: chain e residue 237 MET Chi-restraints excluded: chain e residue 400 LEU Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 97 SER Chi-restraints excluded: chain g residue 362 PHE Chi-restraints excluded: chain g residue 372 CYS Chi-restraints excluded: chain g residue 503 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 193 LYS Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 358 TYR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 394 MET Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 319 TRP Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 119 LEU Chi-restraints excluded: chain q residue 133 GLU Chi-restraints excluded: chain q residue 153 ASN Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 173 TYR Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 187 ASP Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 212 LEU Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 406 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 6.9990 chunk 436 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 572 optimal weight: 6.9990 chunk 317 optimal weight: 9.9990 chunk 655 optimal weight: 10.0000 chunk 531 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 392 optimal weight: 6.9990 chunk 689 optimal weight: 0.6980 chunk 193 optimal weight: 0.0970 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 HIS ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 296 ASN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN g 23 GLN g 111 HIS ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 ASN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 306 ASN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 61897 Z= 0.203 Angle : 0.571 11.002 83500 Z= 0.292 Chirality : 0.043 0.295 10023 Planarity : 0.004 0.089 10715 Dihedral : 3.987 54.896 8501 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.37 % Allowed : 16.33 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 7955 helix: 1.36 (0.08), residues: 4243 sheet: -1.35 (0.18), residues: 741 loop : -1.35 (0.11), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 302 HIS 0.009 0.001 HIS z 161 PHE 0.024 0.001 PHE Q 399 TYR 0.017 0.001 TYR H 358 ARG 0.013 0.000 ARG h 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 998 time to evaluate : 5.563 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: a 111 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8864 (mmmm) REVERT: a 357 CYS cc_start: 0.2413 (p) cc_final: 0.1978 (t) REVERT: A 99 GLU cc_start: 0.6916 (tp30) cc_final: 0.6671 (tp30) REVERT: A 110 GLN cc_start: 0.7578 (mp10) cc_final: 0.7265 (mp10) REVERT: A 156 MET cc_start: 0.3391 (mtt) cc_final: 0.2844 (ptm) REVERT: A 168 PHE cc_start: 0.5627 (m-80) cc_final: 0.5171 (m-80) REVERT: A 171 MET cc_start: 0.5475 (mpp) cc_final: 0.5205 (mpp) REVERT: A 209 MET cc_start: 0.7394 (tpt) cc_final: 0.6880 (ptp) REVERT: A 344 MET cc_start: 0.4597 (pmm) cc_final: 0.4031 (mpp) REVERT: A 345 LEU cc_start: 0.5475 (mm) cc_final: 0.4905 (pp) REVERT: A 384 MET cc_start: 0.4444 (ppp) cc_final: 0.3861 (ppp) REVERT: A 397 CYS cc_start: 0.6841 (m) cc_final: 0.6296 (p) REVERT: A 400 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6917 (pttt) REVERT: b 97 ASP cc_start: 0.6460 (t0) cc_final: 0.5067 (m-30) REVERT: b 142 LEU cc_start: 0.8427 (tp) cc_final: 0.8120 (tp) REVERT: b 162 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7823 (tt) REVERT: b 177 ASP cc_start: 0.5891 (m-30) cc_final: 0.5464 (t0) REVERT: b 353 MET cc_start: 0.4676 (mmp) cc_final: 0.4142 (mmp) REVERT: b 389 SER cc_start: 0.4985 (OUTLIER) cc_final: 0.4753 (p) REVERT: b 441 LYS cc_start: 0.8863 (mptt) cc_final: 0.8421 (mptt) REVERT: b 512 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7106 (tm-30) REVERT: B 85 VAL cc_start: 0.8986 (t) cc_final: 0.8744 (p) REVERT: B 91 GLN cc_start: 0.7627 (tp-100) cc_final: 0.7157 (tp-100) REVERT: B 522 LYS cc_start: 0.8146 (mttt) cc_final: 0.7937 (pttm) REVERT: D 32 GLN cc_start: 0.8167 (pt0) cc_final: 0.7850 (pm20) REVERT: D 57 MET cc_start: 0.8599 (mmm) cc_final: 0.7934 (mmm) REVERT: D 399 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6783 (mp0) REVERT: E 58 MET cc_start: 0.8252 (ttm) cc_final: 0.7847 (ttp) REVERT: E 59 MET cc_start: 0.8093 (mtm) cc_final: 0.7831 (mtp) REVERT: E 65 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6159 (t0) REVERT: E 78 MET cc_start: 0.8491 (mmm) cc_final: 0.8142 (mmm) REVERT: E 80 ASP cc_start: 0.7751 (p0) cc_final: 0.7519 (p0) REVERT: E 174 LYS cc_start: 0.6935 (tppt) cc_final: 0.6257 (tppt) REVERT: E 395 GLU cc_start: 0.8175 (tp30) cc_final: 0.7721 (tp30) REVERT: E 401 HIS cc_start: 0.8703 (t70) cc_final: 0.8050 (t70) REVERT: E 413 ASP cc_start: 0.8792 (t0) cc_final: 0.8480 (t0) REVERT: e 30 GLU cc_start: 0.8691 (mp0) cc_final: 0.7949 (pp20) REVERT: e 58 MET cc_start: 0.8667 (ttm) cc_final: 0.8455 (ttm) REVERT: e 183 MET cc_start: 0.6320 (mtt) cc_final: 0.5939 (mtm) REVERT: e 447 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7261 (mtm180) REVERT: e 521 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7570 (ttm) REVERT: e 531 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8796 (mm) REVERT: g 38 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8141 (mtp85) REVERT: g 229 MET cc_start: 0.1595 (mtt) cc_final: 0.1183 (mtp) REVERT: g 305 MET cc_start: 0.5629 (ptm) cc_final: 0.4991 (mmp) REVERT: G 182 MET cc_start: 0.6519 (ttt) cc_final: 0.6223 (ptm) REVERT: G 289 VAL cc_start: 0.2240 (OUTLIER) cc_final: 0.1855 (t) REVERT: G 305 MET cc_start: 0.0467 (tmm) cc_final: 0.0170 (tmm) REVERT: G 392 GLN cc_start: 0.8361 (mt0) cc_final: 0.8033 (mt0) REVERT: G 395 MET cc_start: 0.7430 (mtm) cc_final: 0.6974 (mmt) REVERT: h 274 LEU cc_start: 0.0258 (tp) cc_final: -0.0114 (mm) REVERT: h 382 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5683 (mpp) REVERT: h 394 MET cc_start: 0.7438 (mmm) cc_final: 0.7185 (mmp) REVERT: h 444 ILE cc_start: 0.8612 (tp) cc_final: 0.8396 (tp) REVERT: H 79 LEU cc_start: 0.8516 (mp) cc_final: 0.8036 (mt) REVERT: H 103 GLU cc_start: 0.7036 (tp30) cc_final: 0.6759 (tp30) REVERT: H 106 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7957 (ttpt) REVERT: H 113 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7830 (mm-30) REVERT: H 178 MET cc_start: 0.8290 (mmt) cc_final: 0.7869 (mmm) REVERT: H 233 HIS cc_start: 0.6195 (m-70) cc_final: 0.5774 (m-70) REVERT: H 374 LEU cc_start: 0.7624 (mt) cc_final: 0.7263 (mt) REVERT: H 382 MET cc_start: 0.5034 (mtm) cc_final: 0.4317 (mtt) REVERT: H 394 MET cc_start: 0.5010 (OUTLIER) cc_final: 0.3536 (mtt) REVERT: H 521 LYS cc_start: 0.8247 (tttt) cc_final: 0.7776 (ttpp) REVERT: Q 14 MET cc_start: 0.4760 (ppp) cc_final: 0.3859 (ptt) REVERT: Q 41 GLN cc_start: 0.8215 (mm110) cc_final: 0.7942 (tp40) REVERT: Q 90 SER cc_start: 0.9396 (OUTLIER) cc_final: 0.9076 (p) REVERT: Q 116 GLU cc_start: 0.6970 (tp30) cc_final: 0.6708 (tp30) REVERT: Q 120 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6395 (mmt-90) REVERT: Q 172 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7434 (tm-30) REVERT: Q 196 HIS cc_start: 0.5995 (t70) cc_final: 0.5719 (t70) REVERT: Q 276 MET cc_start: 0.5016 (tpp) cc_final: 0.4636 (tpp) REVERT: q 34 GLN cc_start: 0.8047 (tp40) cc_final: 0.7743 (mm110) REVERT: q 114 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8703 (mm) REVERT: q 249 MET cc_start: 0.1716 (OUTLIER) cc_final: 0.1151 (mpp) REVERT: q 357 ASP cc_start: 0.7205 (m-30) cc_final: 0.6988 (m-30) REVERT: Z 61 ASN cc_start: 0.7475 (t0) cc_final: 0.7143 (t0) REVERT: Z 85 ASP cc_start: 0.6758 (t0) cc_final: 0.6398 (t0) REVERT: Z 221 MET cc_start: 0.4283 (mmt) cc_final: 0.3294 (tmm) REVERT: Z 265 LYS cc_start: 0.7603 (mttt) cc_final: 0.6940 (tppt) REVERT: Z 286 ASP cc_start: 0.5576 (OUTLIER) cc_final: 0.4100 (t0) REVERT: z 23 ASN cc_start: 0.8226 (m-40) cc_final: 0.7779 (m110) REVERT: z 59 ASP cc_start: 0.7649 (t70) cc_final: 0.7336 (t70) REVERT: z 99 ILE cc_start: 0.8788 (mt) cc_final: 0.8578 (mm) outliers start: 225 outliers final: 145 residues processed: 1136 average time/residue: 0.5609 time to fit residues: 1086.4355 Evaluate side-chains 1082 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 923 time to evaluate : 5.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain a residue 376 ILE Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain a residue 492 ASN Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain d residue 46 ASP Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 207 ASP Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 396 LEU Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 201 ASP Chi-restraints excluded: chain e residue 283 PHE Chi-restraints excluded: chain e residue 400 LEU Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain e residue 531 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 362 PHE Chi-restraints excluded: chain g residue 503 LEU Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 193 LYS Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 358 TYR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 394 MET Chi-restraints excluded: chain Q residue 31 ARG Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 319 TRP Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain Q residue 504 LYS Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 119 LEU Chi-restraints excluded: chain q residue 153 ASN Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 343 GLU Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 406 LYS Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain Z residue 30 LEU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 166 ASP Chi-restraints excluded: chain Z residue 187 ASP Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 160 VAL Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 361 THR Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 10.0000 chunk 692 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 451 optimal weight: 0.0570 chunk 189 optimal weight: 0.0870 chunk 769 optimal weight: 1.9990 chunk 638 optimal weight: 3.9990 chunk 356 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 254 optimal weight: 9.9990 chunk 403 optimal weight: 0.0170 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 450 ASN ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 520 GLN ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS g 434 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 ASN h 21 GLN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 306 ASN Q 461 ASN q 175 ASN q 267 ASN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 HIS ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 61897 Z= 0.153 Angle : 0.549 14.192 83500 Z= 0.279 Chirality : 0.042 0.363 10023 Planarity : 0.003 0.087 10715 Dihedral : 3.863 54.262 8501 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.53 % Allowed : 17.25 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 7955 helix: 1.55 (0.08), residues: 4232 sheet: -1.11 (0.19), residues: 731 loop : -1.22 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 302 HIS 0.007 0.001 HIS z 161 PHE 0.025 0.001 PHE Q 399 TYR 0.019 0.001 TYR a 426 ARG 0.008 0.000 ARG h 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1016 time to evaluate : 5.539 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: a 111 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8859 (mmmm) REVERT: A 20 GLN cc_start: 0.8782 (mt0) cc_final: 0.8444 (mt0) REVERT: A 99 GLU cc_start: 0.6875 (tp30) cc_final: 0.6570 (tp30) REVERT: A 110 GLN cc_start: 0.7716 (mp10) cc_final: 0.7507 (mp10) REVERT: A 156 MET cc_start: 0.3598 (mtt) cc_final: 0.3275 (ptm) REVERT: A 168 PHE cc_start: 0.5643 (m-80) cc_final: 0.5116 (m-80) REVERT: A 171 MET cc_start: 0.5793 (mpp) cc_final: 0.5563 (mpp) REVERT: A 209 MET cc_start: 0.7357 (tpt) cc_final: 0.6902 (ptp) REVERT: A 344 MET cc_start: 0.4549 (pmm) cc_final: 0.4029 (mpp) REVERT: A 345 LEU cc_start: 0.5686 (mm) cc_final: 0.5011 (pp) REVERT: A 384 MET cc_start: 0.4301 (ppp) cc_final: 0.3707 (ppp) REVERT: A 397 CYS cc_start: 0.6597 (m) cc_final: 0.5975 (p) REVERT: A 400 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6904 (pttp) REVERT: A 404 GLU cc_start: 0.5598 (tp30) cc_final: 0.5330 (tt0) REVERT: b 48 MET cc_start: 0.8360 (mmp) cc_final: 0.8066 (mmm) REVERT: b 97 ASP cc_start: 0.6356 (t0) cc_final: 0.5148 (m-30) REVERT: b 142 LEU cc_start: 0.8377 (tp) cc_final: 0.8057 (tp) REVERT: b 162 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7824 (tt) REVERT: b 177 ASP cc_start: 0.5923 (m-30) cc_final: 0.5535 (t0) REVERT: b 353 MET cc_start: 0.4686 (mmp) cc_final: 0.4168 (mmp) REVERT: b 441 LYS cc_start: 0.8834 (mptt) cc_final: 0.8375 (mptt) REVERT: b 512 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7036 (tm-30) REVERT: B 85 VAL cc_start: 0.8982 (t) cc_final: 0.8711 (p) REVERT: B 91 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7258 (tp40) REVERT: D 57 MET cc_start: 0.8556 (mmm) cc_final: 0.7863 (mmm) REVERT: D 192 MET cc_start: 0.5025 (tpp) cc_final: 0.4501 (tpp) REVERT: D 399 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6715 (mp0) REVERT: E 58 MET cc_start: 0.8212 (ttm) cc_final: 0.7894 (ttp) REVERT: E 59 MET cc_start: 0.8042 (mtm) cc_final: 0.7761 (mtp) REVERT: E 65 ASP cc_start: 0.6848 (m-30) cc_final: 0.6128 (t0) REVERT: E 71 ASP cc_start: 0.7500 (t0) cc_final: 0.7163 (p0) REVERT: E 78 MET cc_start: 0.8426 (mmm) cc_final: 0.8075 (mmm) REVERT: E 80 ASP cc_start: 0.7495 (p0) cc_final: 0.7244 (p0) REVERT: E 105 THR cc_start: 0.8912 (p) cc_final: 0.8563 (p) REVERT: E 174 LYS cc_start: 0.7041 (tppt) cc_final: 0.6607 (tppt) REVERT: E 395 GLU cc_start: 0.8215 (tp30) cc_final: 0.7701 (tp30) REVERT: E 401 HIS cc_start: 0.8765 (t70) cc_final: 0.8130 (t70) REVERT: E 413 ASP cc_start: 0.8719 (t0) cc_final: 0.8382 (t0) REVERT: E 502 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: e 30 GLU cc_start: 0.8691 (mp0) cc_final: 0.7978 (pp20) REVERT: e 58 MET cc_start: 0.8682 (ttm) cc_final: 0.8385 (ttm) REVERT: e 391 MET cc_start: 0.6368 (mpp) cc_final: 0.6155 (mmp) REVERT: e 447 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.7216 (mtm180) REVERT: e 463 ASN cc_start: 0.8602 (m-40) cc_final: 0.8257 (m110) REVERT: e 521 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7535 (ttm) REVERT: e 531 ILE cc_start: 0.9045 (pt) cc_final: 0.8782 (mm) REVERT: g 38 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.8103 (mtp85) REVERT: g 229 MET cc_start: 0.1434 (mtt) cc_final: 0.1051 (mtp) REVERT: g 305 MET cc_start: 0.5713 (ptm) cc_final: 0.5053 (mmp) REVERT: g 518 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7399 (mtp85) REVERT: G 305 MET cc_start: 0.0569 (tmm) cc_final: 0.0244 (tmm) REVERT: G 392 GLN cc_start: 0.8357 (mt0) cc_final: 0.8033 (mt0) REVERT: G 395 MET cc_start: 0.7446 (mtm) cc_final: 0.6987 (mmt) REVERT: G 415 GLU cc_start: 0.7452 (mp0) cc_final: 0.7022 (mp0) REVERT: h 274 LEU cc_start: 0.0239 (tp) cc_final: -0.0116 (mm) REVERT: h 382 MET cc_start: 0.5457 (mmp) cc_final: 0.4978 (mpp) REVERT: h 394 MET cc_start: 0.7433 (mmm) cc_final: 0.7147 (mmp) REVERT: H 113 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7782 (mm-30) REVERT: H 178 MET cc_start: 0.8314 (mmt) cc_final: 0.7940 (mmm) REVERT: H 233 HIS cc_start: 0.6231 (m-70) cc_final: 0.5908 (m-70) REVERT: H 374 LEU cc_start: 0.7508 (mt) cc_final: 0.7145 (mt) REVERT: H 382 MET cc_start: 0.4659 (mtm) cc_final: 0.3921 (mtt) REVERT: H 521 LYS cc_start: 0.8308 (tttt) cc_final: 0.7787 (ttpp) REVERT: Q 14 MET cc_start: 0.4367 (ppp) cc_final: 0.3418 (ptt) REVERT: Q 41 GLN cc_start: 0.8139 (mm110) cc_final: 0.7892 (tp40) REVERT: Q 90 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.9133 (p) REVERT: Q 116 GLU cc_start: 0.6970 (tp30) cc_final: 0.6688 (tp30) REVERT: Q 172 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7383 (tm-30) REVERT: Q 178 PHE cc_start: 0.6255 (t80) cc_final: 0.5939 (t80) REVERT: Q 276 MET cc_start: 0.5004 (tpp) cc_final: 0.4596 (mpp) REVERT: Q 302 LEU cc_start: 0.6836 (pp) cc_final: 0.6376 (tt) REVERT: q 30 TYR cc_start: 0.8148 (m-10) cc_final: 0.7120 (m-10) REVERT: q 34 GLN cc_start: 0.8062 (tp40) cc_final: 0.7649 (mm110) REVERT: q 114 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8717 (mm) REVERT: q 249 MET cc_start: 0.1815 (OUTLIER) cc_final: 0.1330 (mpp) REVERT: q 357 ASP cc_start: 0.7249 (m-30) cc_final: 0.7010 (m-30) REVERT: Z 61 ASN cc_start: 0.7389 (t0) cc_final: 0.7103 (t0) REVERT: Z 85 ASP cc_start: 0.7244 (t0) cc_final: 0.6853 (t0) REVERT: Z 95 ASN cc_start: 0.8218 (t0) cc_final: 0.7987 (t0) REVERT: Z 195 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6485 (tt0) REVERT: Z 221 MET cc_start: 0.3890 (mmt) cc_final: 0.3165 (tmm) REVERT: Z 265 LYS cc_start: 0.7622 (mttt) cc_final: 0.7008 (tppt) REVERT: Z 286 ASP cc_start: 0.5345 (OUTLIER) cc_final: 0.4092 (t0) REVERT: z 59 ASP cc_start: 0.7637 (t70) cc_final: 0.7322 (t70) outliers start: 169 outliers final: 112 residues processed: 1117 average time/residue: 0.5616 time to fit residues: 1071.8142 Evaluate side-chains 1044 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 924 time to evaluate : 5.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 376 ILE Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain a residue 492 ASN Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain d residue 46 ASP Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 396 LEU Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 502 GLN Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 201 ASP Chi-restraints excluded: chain e residue 283 PHE Chi-restraints excluded: chain e residue 400 LEU Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 362 PHE Chi-restraints excluded: chain g residue 503 LEU Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 193 LYS Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 358 TYR Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 116 GLU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 153 ASN Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 173 TYR Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 187 ASP Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 160 VAL Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 361 THR Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 438 optimal weight: 0.9980 chunk 561 optimal weight: 3.9990 chunk 435 optimal weight: 4.9990 chunk 647 optimal weight: 8.9990 chunk 429 optimal weight: 0.7980 chunk 766 optimal weight: 1.9990 chunk 479 optimal weight: 0.9990 chunk 467 optimal weight: 2.9990 chunk 353 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 484 HIS ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 520 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 301 GLN h 459 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 461 ASN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 214 HIS ** z 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 386 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 61897 Z= 0.172 Angle : 0.559 12.006 83500 Z= 0.284 Chirality : 0.042 0.310 10023 Planarity : 0.003 0.087 10715 Dihedral : 3.854 54.079 8501 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.53 % Allowed : 17.92 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.09), residues: 7955 helix: 1.60 (0.08), residues: 4236 sheet: -1.02 (0.19), residues: 733 loop : -1.18 (0.11), residues: 2986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 319 HIS 0.010 0.001 HIS b 391 PHE 0.030 0.001 PHE Q 399 TYR 0.022 0.001 TYR a 426 ARG 0.007 0.000 ARG z 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 952 time to evaluate : 5.450 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: A 20 GLN cc_start: 0.8871 (mt0) cc_final: 0.8535 (mt0) REVERT: A 110 GLN cc_start: 0.7735 (mp10) cc_final: 0.7412 (mp10) REVERT: A 156 MET cc_start: 0.3497 (mtt) cc_final: 0.3293 (ptm) REVERT: A 168 PHE cc_start: 0.5550 (m-80) cc_final: 0.5211 (m-80) REVERT: A 171 MET cc_start: 0.5791 (mpp) cc_final: 0.5553 (mpp) REVERT: A 209 MET cc_start: 0.7445 (tpt) cc_final: 0.6944 (ptp) REVERT: A 344 MET cc_start: 0.4478 (pmm) cc_final: 0.4091 (mpp) REVERT: A 345 LEU cc_start: 0.5762 (mm) cc_final: 0.5103 (pp) REVERT: A 384 MET cc_start: 0.4315 (ppp) cc_final: 0.3714 (ppp) REVERT: A 397 CYS cc_start: 0.6586 (m) cc_final: 0.6266 (m) REVERT: A 400 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6838 (pttp) REVERT: A 404 GLU cc_start: 0.5604 (tp30) cc_final: 0.5304 (tt0) REVERT: b 97 ASP cc_start: 0.6341 (t0) cc_final: 0.5142 (m-30) REVERT: b 162 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7849 (tt) REVERT: b 353 MET cc_start: 0.4719 (mmp) cc_final: 0.4205 (mmp) REVERT: b 441 LYS cc_start: 0.8829 (mptt) cc_final: 0.8433 (mptt) REVERT: b 512 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7088 (tm-30) REVERT: B 85 VAL cc_start: 0.8985 (t) cc_final: 0.8683 (p) REVERT: B 91 GLN cc_start: 0.7816 (tp-100) cc_final: 0.7476 (tp40) REVERT: B 438 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8673 (p) REVERT: D 32 GLN cc_start: 0.8250 (pt0) cc_final: 0.8004 (pt0) REVERT: D 57 MET cc_start: 0.8584 (mmm) cc_final: 0.7937 (mmm) REVERT: D 192 MET cc_start: 0.5306 (tpp) cc_final: 0.4770 (tpp) REVERT: D 322 ILE cc_start: 0.0123 (mt) cc_final: -0.0106 (mt) REVERT: D 399 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6428 (mp0) REVERT: d 333 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4823 (mt) REVERT: E 58 MET cc_start: 0.8181 (ttm) cc_final: 0.7881 (ttp) REVERT: E 65 ASP cc_start: 0.6727 (m-30) cc_final: 0.6009 (t0) REVERT: E 80 ASP cc_start: 0.7474 (p0) cc_final: 0.7193 (p0) REVERT: E 133 ASP cc_start: 0.7546 (t0) cc_final: 0.7094 (t0) REVERT: E 174 LYS cc_start: 0.7077 (tppt) cc_final: 0.6677 (tppt) REVERT: E 197 MET cc_start: 0.2409 (mtm) cc_final: 0.2151 (mtm) REVERT: E 314 GLN cc_start: 0.4412 (OUTLIER) cc_final: 0.3981 (mt0) REVERT: E 369 MET cc_start: 0.5022 (tpp) cc_final: 0.4643 (tpp) REVERT: E 390 LYS cc_start: 0.8299 (tmmt) cc_final: 0.7722 (tptt) REVERT: E 395 GLU cc_start: 0.8234 (tp30) cc_final: 0.7728 (tp30) REVERT: E 401 HIS cc_start: 0.8775 (t70) cc_final: 0.8166 (t70) REVERT: E 413 ASP cc_start: 0.8746 (t0) cc_final: 0.8415 (t0) REVERT: E 472 MET cc_start: 0.6938 (mmm) cc_final: 0.6618 (mmm) REVERT: e 30 GLU cc_start: 0.8692 (mp0) cc_final: 0.7976 (pp20) REVERT: e 391 MET cc_start: 0.6496 (mpp) cc_final: 0.6215 (mmp) REVERT: e 447 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7352 (mtm180) REVERT: e 463 ASN cc_start: 0.8577 (m-40) cc_final: 0.8257 (m110) REVERT: e 521 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7582 (ttm) REVERT: e 531 ILE cc_start: 0.9022 (pt) cc_final: 0.8778 (mm) REVERT: g 38 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8126 (mtp85) REVERT: g 171 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7456 (tp) REVERT: g 229 MET cc_start: 0.1551 (mtt) cc_final: 0.1138 (mtp) REVERT: g 305 MET cc_start: 0.5695 (ptm) cc_final: 0.5057 (mmp) REVERT: g 306 ARG cc_start: 0.4773 (ttp80) cc_final: 0.3497 (ttp80) REVERT: g 395 MET cc_start: 0.7941 (ptt) cc_final: 0.7439 (ptm) REVERT: G 305 MET cc_start: 0.0359 (tmm) cc_final: 0.0010 (tmm) REVERT: G 392 GLN cc_start: 0.8215 (mt0) cc_final: 0.7902 (mt0) REVERT: G 395 MET cc_start: 0.7506 (mtm) cc_final: 0.6823 (tpp) REVERT: h 382 MET cc_start: 0.5656 (mmp) cc_final: 0.5116 (mpp) REVERT: h 394 MET cc_start: 0.7492 (mmm) cc_final: 0.7164 (mmp) REVERT: H 113 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7708 (mm-30) REVERT: H 178 MET cc_start: 0.8325 (mmt) cc_final: 0.7985 (mmm) REVERT: H 382 MET cc_start: 0.4719 (mtm) cc_final: 0.3944 (mtt) REVERT: H 521 LYS cc_start: 0.8326 (tttt) cc_final: 0.7562 (tmtt) REVERT: Q 14 MET cc_start: 0.4481 (ppp) cc_final: 0.3553 (ptt) REVERT: Q 41 GLN cc_start: 0.8105 (mm110) cc_final: 0.7837 (tp40) REVERT: Q 90 SER cc_start: 0.9396 (OUTLIER) cc_final: 0.9141 (p) REVERT: Q 116 GLU cc_start: 0.7028 (tp30) cc_final: 0.6760 (tp30) REVERT: Q 172 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7402 (tm-30) REVERT: Q 178 PHE cc_start: 0.6655 (t80) cc_final: 0.6299 (t80) REVERT: Q 276 MET cc_start: 0.5010 (tpp) cc_final: 0.4601 (mpp) REVERT: Q 302 LEU cc_start: 0.6978 (pp) cc_final: 0.6277 (tp) REVERT: q 34 GLN cc_start: 0.7996 (tp40) cc_final: 0.7676 (mm110) REVERT: q 249 MET cc_start: 0.2262 (OUTLIER) cc_final: 0.1805 (mpp) REVERT: q 357 ASP cc_start: 0.7334 (m-30) cc_final: 0.7099 (m-30) REVERT: Z 61 ASN cc_start: 0.7392 (t0) cc_final: 0.7088 (t0) REVERT: Z 85 ASP cc_start: 0.7259 (t0) cc_final: 0.6791 (t0) REVERT: Z 221 MET cc_start: 0.3935 (mmt) cc_final: 0.3214 (tmm) REVERT: Z 265 LYS cc_start: 0.7662 (mttt) cc_final: 0.6960 (tppt) REVERT: Z 286 ASP cc_start: 0.5560 (OUTLIER) cc_final: 0.4105 (t0) REVERT: z 59 ASP cc_start: 0.7623 (t70) cc_final: 0.7342 (t70) outliers start: 169 outliers final: 122 residues processed: 1058 average time/residue: 0.5591 time to fit residues: 1005.7532 Evaluate side-chains 1038 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 906 time to evaluate : 5.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 376 ILE Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain d residue 46 ASP Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain d residue 207 ASP Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 333 ILE Chi-restraints excluded: chain d residue 396 LEU Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 201 ASP Chi-restraints excluded: chain e residue 283 PHE Chi-restraints excluded: chain e residue 349 GLU Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 171 LEU Chi-restraints excluded: chain g residue 362 PHE Chi-restraints excluded: chain g residue 503 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 193 LYS Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 358 TYR Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 119 LEU Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 173 TYR Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 343 GLU Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 166 ASP Chi-restraints excluded: chain Z residue 187 ASP Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 160 VAL Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 361 THR Chi-restraints excluded: chain z residue 374 LEU Chi-restraints excluded: chain z residue 402 ILE Chi-restraints excluded: chain z residue 406 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 457 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 487 optimal weight: 10.0000 chunk 522 optimal weight: 0.9980 chunk 378 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 602 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN A 135 ASN ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN b 148 HIS b 391 HIS B 65 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 409 ASN ** g 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 228 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 383 ASN q 306 ASN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 346 HIS z 497 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 61897 Z= 0.343 Angle : 0.708 13.800 83500 Z= 0.365 Chirality : 0.046 0.397 10023 Planarity : 0.005 0.092 10715 Dihedral : 4.587 57.344 8501 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.55 % Favored : 95.44 % Rotamer: Outliers : 2.99 % Allowed : 18.31 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 7955 helix: 1.17 (0.08), residues: 4250 sheet: -1.14 (0.18), residues: 749 loop : -1.42 (0.11), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP g 435 HIS 0.012 0.002 HIS z 214 PHE 0.025 0.002 PHE a 300 TYR 0.034 0.002 TYR H 423 ARG 0.010 0.001 ARG h 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 965 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 355 ARG cc_start: 0.3860 (OUTLIER) cc_final: 0.2850 (ptt-90) REVERT: A 106 GLU cc_start: 0.7764 (pt0) cc_final: 0.7413 (pt0) REVERT: A 110 GLN cc_start: 0.7829 (mp10) cc_final: 0.7565 (mp10) REVERT: A 156 MET cc_start: 0.3845 (mtt) cc_final: 0.3586 (ptm) REVERT: A 209 MET cc_start: 0.7535 (tpt) cc_final: 0.6865 (ptp) REVERT: A 345 LEU cc_start: 0.6044 (mm) cc_final: 0.5545 (pp) REVERT: A 384 MET cc_start: 0.4397 (ppp) cc_final: 0.3891 (ppp) REVERT: A 397 CYS cc_start: 0.6802 (m) cc_final: 0.6543 (m) REVERT: A 400 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7000 (pttt) REVERT: b 97 ASP cc_start: 0.6051 (t0) cc_final: 0.4901 (m-30) REVERT: b 353 MET cc_start: 0.4684 (mmp) cc_final: 0.4390 (mmt) REVERT: b 408 TYR cc_start: 0.8137 (m-80) cc_final: 0.7780 (m-10) REVERT: b 441 LYS cc_start: 0.8799 (mptt) cc_final: 0.8417 (mptt) REVERT: B 85 VAL cc_start: 0.9048 (t) cc_final: 0.8778 (p) REVERT: B 438 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8777 (p) REVERT: B 488 MET cc_start: 0.7476 (mmm) cc_final: 0.6635 (mmm) REVERT: D 32 GLN cc_start: 0.8422 (pt0) cc_final: 0.8188 (pm20) REVERT: D 57 MET cc_start: 0.8621 (mmm) cc_final: 0.7977 (mmm) REVERT: D 192 MET cc_start: 0.5149 (tpp) cc_final: 0.4780 (tpp) REVERT: D 399 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6467 (mp0) REVERT: d 319 LYS cc_start: 0.4675 (mttt) cc_final: 0.3488 (pttt) REVERT: d 403 ARG cc_start: 0.7317 (tmm160) cc_final: 0.7114 (tmm160) REVERT: E 46 MET cc_start: 0.8187 (mmm) cc_final: 0.7853 (mmm) REVERT: E 58 MET cc_start: 0.8139 (ttm) cc_final: 0.7754 (ttp) REVERT: E 65 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.5783 (t0) REVERT: E 78 MET cc_start: 0.8727 (mtm) cc_final: 0.8346 (ptm) REVERT: E 80 ASP cc_start: 0.7123 (p0) cc_final: 0.6707 (p0) REVERT: E 105 THR cc_start: 0.9191 (p) cc_final: 0.8911 (p) REVERT: E 117 GLU cc_start: 0.7632 (tp30) cc_final: 0.7359 (tp30) REVERT: E 133 ASP cc_start: 0.7605 (t0) cc_final: 0.7189 (t0) REVERT: E 369 MET cc_start: 0.4690 (tpp) cc_final: 0.4356 (tpp) REVERT: E 390 LYS cc_start: 0.8196 (tmmt) cc_final: 0.7651 (tptt) REVERT: E 401 HIS cc_start: 0.8851 (t70) cc_final: 0.8299 (t70) REVERT: E 472 MET cc_start: 0.6899 (mmm) cc_final: 0.6645 (mmm) REVERT: e 447 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7343 (mtm180) REVERT: e 521 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7693 (ttm) REVERT: g 229 MET cc_start: 0.1241 (mtt) cc_final: 0.0677 (mtt) REVERT: g 305 MET cc_start: 0.6060 (ptm) cc_final: 0.5196 (mmp) REVERT: g 362 PHE cc_start: 0.4723 (OUTLIER) cc_final: 0.3971 (m-80) REVERT: g 395 MET cc_start: 0.8043 (ptt) cc_final: 0.7537 (ptm) REVERT: G 294 LYS cc_start: 0.6481 (mttt) cc_final: 0.6113 (mtmm) REVERT: G 305 MET cc_start: 0.0870 (tmm) cc_final: 0.0519 (tmm) REVERT: G 395 MET cc_start: 0.7470 (mtm) cc_final: 0.6867 (tpp) REVERT: h 382 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.5136 (mpp) REVERT: h 394 MET cc_start: 0.7715 (mmm) cc_final: 0.7464 (mmp) REVERT: H 106 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8126 (ttpt) REVERT: H 113 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7781 (mm-30) REVERT: H 154 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7415 (tp) REVERT: H 178 MET cc_start: 0.8361 (mmt) cc_final: 0.7990 (mmm) REVERT: H 382 MET cc_start: 0.5170 (mtm) cc_final: 0.4313 (mtt) REVERT: H 521 LYS cc_start: 0.8683 (tttt) cc_final: 0.7994 (tmtt) REVERT: Q 14 MET cc_start: 0.4570 (OUTLIER) cc_final: 0.3487 (ptp) REVERT: Q 41 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7838 (tp40) REVERT: Q 90 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9126 (p) REVERT: Q 116 GLU cc_start: 0.7219 (tp30) cc_final: 0.6949 (tp30) REVERT: Q 178 PHE cc_start: 0.7237 (t80) cc_final: 0.6803 (t80) REVERT: q 31 ARG cc_start: 0.7661 (mmt180) cc_final: 0.7333 (mmt180) REVERT: q 34 GLN cc_start: 0.8103 (tp40) cc_final: 0.7813 (mm110) REVERT: q 224 LYS cc_start: 0.8593 (pttt) cc_final: 0.8209 (tptt) REVERT: q 249 MET cc_start: 0.2858 (OUTLIER) cc_final: 0.1644 (mpp) REVERT: q 276 MET cc_start: 0.2563 (ttp) cc_final: 0.2320 (ttt) REVERT: q 526 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.5916 (mmm) REVERT: Z 61 ASN cc_start: 0.7645 (t0) cc_final: 0.7362 (t0) REVERT: Z 85 ASP cc_start: 0.7742 (t0) cc_final: 0.7377 (t0) REVERT: Z 221 MET cc_start: 0.3863 (mmt) cc_final: 0.3021 (tmm) REVERT: Z 265 LYS cc_start: 0.7915 (mttt) cc_final: 0.7203 (tppt) REVERT: Z 520 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7124 (tm-30) REVERT: z 59 ASP cc_start: 0.7967 (t70) cc_final: 0.7564 (t70) REVERT: z 67 MET cc_start: 0.7338 (mtt) cc_final: 0.6836 (mtt) outliers start: 200 outliers final: 146 residues processed: 1095 average time/residue: 0.5622 time to fit residues: 1050.8951 Evaluate side-chains 1034 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 875 time to evaluate : 5.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain a residue 355 ARG Chi-restraints excluded: chain a residue 376 ILE Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 434 GLU Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain d residue 46 ASP Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 207 ASP Chi-restraints excluded: chain d residue 225 GLU Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 396 LEU Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 201 ASP Chi-restraints excluded: chain e residue 283 PHE Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain e residue 525 ILE Chi-restraints excluded: chain e residue 531 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 171 LEU Chi-restraints excluded: chain g residue 362 PHE Chi-restraints excluded: chain g residue 503 LEU Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 358 TYR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain Q residue 14 MET Chi-restraints excluded: chain Q residue 41 GLN Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 463 VAL Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain Q residue 504 LYS Chi-restraints excluded: chain Q residue 518 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 343 GLU Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 166 ASP Chi-restraints excluded: chain Z residue 187 ASP Chi-restraints excluded: chain Z residue 276 GLU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 160 VAL Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 361 THR Chi-restraints excluded: chain z residue 374 LEU Chi-restraints excluded: chain z residue 406 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 4.9990 chunk 734 optimal weight: 0.8980 chunk 669 optimal weight: 3.9990 chunk 714 optimal weight: 3.9990 chunk 733 optimal weight: 8.9990 chunk 429 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 560 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 645 optimal weight: 2.9990 chunk 675 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 20 GLN a 139 ASN ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS B 65 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN ** e 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 228 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 GLN H 462 ASN Q 153 ASN Q 383 ASN Z 182 GLN z 84 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 61897 Z= 0.274 Angle : 0.664 13.482 83500 Z= 0.342 Chirality : 0.045 0.400 10023 Planarity : 0.004 0.095 10715 Dihedral : 4.571 56.970 8501 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.70 % Allowed : 19.45 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.09), residues: 7955 helix: 1.18 (0.08), residues: 4234 sheet: -1.08 (0.19), residues: 744 loop : -1.43 (0.11), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 435 HIS 0.010 0.001 HIS b 391 PHE 0.022 0.002 PHE a 300 TYR 0.025 0.002 TYR H 423 ARG 0.014 0.001 ARG Z 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 974 time to evaluate : 5.508 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: A 20 GLN cc_start: 0.8791 (mt0) cc_final: 0.8190 (mp10) REVERT: A 105 ASP cc_start: 0.8049 (t0) cc_final: 0.7792 (t0) REVERT: A 106 GLU cc_start: 0.7967 (pt0) cc_final: 0.7728 (pt0) REVERT: A 109 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8599 (mmtp) REVERT: A 156 MET cc_start: 0.3488 (mtt) cc_final: 0.2771 (ptm) REVERT: A 209 MET cc_start: 0.7659 (tpt) cc_final: 0.7001 (ptp) REVERT: A 345 LEU cc_start: 0.5885 (mm) cc_final: 0.5296 (pp) REVERT: A 397 CYS cc_start: 0.6743 (m) cc_final: 0.6511 (m) REVERT: A 400 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7053 (pttt) REVERT: b 97 ASP cc_start: 0.5974 (t0) cc_final: 0.5066 (m-30) REVERT: b 353 MET cc_start: 0.4657 (mmp) cc_final: 0.4359 (mmt) REVERT: b 408 TYR cc_start: 0.8008 (m-80) cc_final: 0.7781 (m-10) REVERT: b 512 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 30 ILE cc_start: 0.7514 (mm) cc_final: 0.7004 (tt) REVERT: B 91 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7372 (tp40) REVERT: B 120 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8807 (mmmt) REVERT: B 488 MET cc_start: 0.7490 (mmm) cc_final: 0.6271 (mmm) REVERT: D 57 MET cc_start: 0.8622 (mmm) cc_final: 0.7991 (mmm) REVERT: D 192 MET cc_start: 0.5252 (tpp) cc_final: 0.4794 (tpp) REVERT: D 399 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6540 (tp30) REVERT: d 77 ILE cc_start: 0.8784 (mp) cc_final: 0.8071 (mt) REVERT: d 80 GLN cc_start: 0.7942 (mp10) cc_final: 0.7719 (mp10) REVERT: d 90 MET cc_start: 0.6984 (mtm) cc_final: 0.6083 (mtm) REVERT: d 319 LYS cc_start: 0.4747 (mttt) cc_final: 0.3600 (pttt) REVERT: E 46 MET cc_start: 0.8076 (mmm) cc_final: 0.7437 (mmt) REVERT: E 58 MET cc_start: 0.8233 (ttm) cc_final: 0.7866 (ttp) REVERT: E 65 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.5754 (t70) REVERT: E 78 MET cc_start: 0.8497 (mtm) cc_final: 0.8024 (ptt) REVERT: E 80 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6875 (p0) REVERT: E 105 THR cc_start: 0.9277 (p) cc_final: 0.9009 (p) REVERT: E 117 GLU cc_start: 0.7640 (tp30) cc_final: 0.7398 (tp30) REVERT: E 133 ASP cc_start: 0.7565 (t0) cc_final: 0.7139 (t0) REVERT: E 237 MET cc_start: 0.2513 (mtt) cc_final: 0.1904 (mtm) REVERT: E 278 TYR cc_start: 0.2186 (m-10) cc_final: 0.1735 (m-80) REVERT: E 369 MET cc_start: 0.4749 (tpp) cc_final: 0.4529 (tpp) REVERT: E 390 LYS cc_start: 0.8312 (tmmt) cc_final: 0.7815 (tptt) REVERT: E 397 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8373 (mtmm) REVERT: E 398 ARG cc_start: 0.8898 (mpp80) cc_final: 0.8669 (mtt-85) REVERT: E 472 MET cc_start: 0.6884 (mmm) cc_final: 0.6654 (mmm) REVERT: e 447 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7270 (mtm180) REVERT: e 521 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7585 (ttm) REVERT: g 229 MET cc_start: 0.0620 (mtt) cc_final: 0.0043 (mtt) REVERT: g 305 MET cc_start: 0.6083 (ptm) cc_final: 0.5264 (mmt) REVERT: g 362 PHE cc_start: 0.4511 (OUTLIER) cc_final: 0.3609 (m-80) REVERT: g 395 MET cc_start: 0.7892 (ptt) cc_final: 0.7346 (ptm) REVERT: G 305 MET cc_start: 0.0822 (tmm) cc_final: 0.0339 (tmm) REVERT: G 395 MET cc_start: 0.7490 (mtm) cc_final: 0.6680 (mmt) REVERT: G 415 GLU cc_start: 0.7437 (mp0) cc_final: 0.7121 (mp0) REVERT: h 61 ASP cc_start: 0.7463 (t70) cc_final: 0.7219 (t70) REVERT: h 382 MET cc_start: 0.5753 (mmp) cc_final: 0.4963 (mpp) REVERT: h 394 MET cc_start: 0.7689 (mmm) cc_final: 0.7469 (mmp) REVERT: h 443 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7257 (mt-10) REVERT: H 106 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8181 (ttpt) REVERT: H 178 MET cc_start: 0.8356 (mmt) cc_final: 0.7962 (mmm) REVERT: H 382 MET cc_start: 0.4906 (mtm) cc_final: 0.4146 (mtt) REVERT: H 521 LYS cc_start: 0.8678 (tttt) cc_final: 0.8039 (tmtt) REVERT: Q 14 MET cc_start: 0.4709 (OUTLIER) cc_final: 0.4058 (ptp) REVERT: Q 31 ARG cc_start: 0.7363 (mtt-85) cc_final: 0.7041 (mtt-85) REVERT: Q 41 GLN cc_start: 0.8138 (mm110) cc_final: 0.7880 (tp40) REVERT: Q 90 SER cc_start: 0.9432 (OUTLIER) cc_final: 0.9168 (p) REVERT: Q 116 GLU cc_start: 0.7156 (tp30) cc_final: 0.6888 (tp30) REVERT: q 31 ARG cc_start: 0.7618 (mmt180) cc_final: 0.7271 (mmt180) REVERT: q 34 GLN cc_start: 0.8242 (tp40) cc_final: 0.7879 (mm110) REVERT: q 224 LYS cc_start: 0.8752 (pttt) cc_final: 0.8297 (tptt) REVERT: q 276 MET cc_start: 0.2292 (ttp) cc_final: 0.2019 (ttt) REVERT: q 526 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.5888 (mmm) REVERT: Z 221 MET cc_start: 0.4103 (mmt) cc_final: 0.3305 (tmm) REVERT: Z 265 LYS cc_start: 0.7898 (mttt) cc_final: 0.7194 (tppt) REVERT: Z 377 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7925 (mtpt) REVERT: Z 520 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7105 (tm-30) REVERT: z 59 ASP cc_start: 0.7992 (t70) cc_final: 0.7619 (t70) REVERT: z 67 MET cc_start: 0.7428 (mtt) cc_final: 0.6882 (mtt) outliers start: 180 outliers final: 141 residues processed: 1087 average time/residue: 0.5789 time to fit residues: 1072.6954 Evaluate side-chains 1040 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 890 time to evaluate : 5.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 301 VAL Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain a residue 376 ILE Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain d residue 46 ASP Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain d residue 199 THR Chi-restraints excluded: chain d residue 207 ASP Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 396 LEU Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 197 MET Chi-restraints excluded: chain e residue 201 ASP Chi-restraints excluded: chain e residue 283 PHE Chi-restraints excluded: chain e residue 521 MET Chi-restraints excluded: chain e residue 525 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 171 LEU Chi-restraints excluded: chain g residue 362 PHE Chi-restraints excluded: chain g residue 444 LEU Chi-restraints excluded: chain g residue 503 LEU Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 358 TYR Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain Q residue 14 MET Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 319 TRP Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 463 VAL Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain Q residue 504 LYS Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 119 LEU Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 343 GLU Chi-restraints excluded: chain q residue 406 LYS Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 187 ASP Chi-restraints excluded: chain Z residue 276 GLU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 377 LYS Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 107 ASP Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 160 VAL Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 361 THR Chi-restraints excluded: chain z residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 3.9990 chunk 468 optimal weight: 5.9990 chunk 755 optimal weight: 0.9990 chunk 460 optimal weight: 6.9990 chunk 358 optimal weight: 3.9990 chunk 524 optimal weight: 0.2980 chunk 792 optimal weight: 0.5980 chunk 728 optimal weight: 6.9990 chunk 630 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 487 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 435 GLN ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 ASN G 390 ASN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.7443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 61897 Z= 0.174 Angle : 0.622 14.001 83500 Z= 0.316 Chirality : 0.043 0.324 10023 Planarity : 0.004 0.091 10715 Dihedral : 4.277 55.271 8501 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.02 % Allowed : 20.71 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.09), residues: 7955 helix: 1.42 (0.08), residues: 4218 sheet: -0.96 (0.19), residues: 717 loop : -1.28 (0.11), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 435 HIS 0.011 0.001 HIS b 391 PHE 0.031 0.001 PHE d 335 TYR 0.020 0.001 TYR a 426 ARG 0.012 0.000 ARG D 391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15910 Ramachandran restraints generated. 7955 Oldfield, 0 Emsley, 7955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 982 time to evaluate : 5.765 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: a 105 ASP cc_start: 0.7592 (m-30) cc_final: 0.7314 (m-30) REVERT: a 361 LEU cc_start: 0.6353 (mt) cc_final: 0.5764 (tt) REVERT: A 105 ASP cc_start: 0.8006 (t0) cc_final: 0.7681 (t0) REVERT: A 109 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8471 (mmtp) REVERT: A 156 MET cc_start: 0.3308 (mtt) cc_final: 0.2440 (ptm) REVERT: A 209 MET cc_start: 0.7482 (tpt) cc_final: 0.6996 (ptp) REVERT: A 345 LEU cc_start: 0.5655 (mm) cc_final: 0.5084 (pp) REVERT: b 97 ASP cc_start: 0.5292 (t0) cc_final: 0.4521 (m-30) REVERT: b 353 MET cc_start: 0.5177 (mmp) cc_final: 0.4905 (mmt) REVERT: b 408 TYR cc_start: 0.8075 (m-80) cc_final: 0.7747 (m-10) REVERT: B 30 ILE cc_start: 0.7406 (mm) cc_final: 0.6882 (tt) REVERT: B 91 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7489 (tp40) REVERT: B 120 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8747 (mmmt) REVERT: B 417 MET cc_start: 0.7895 (mtt) cc_final: 0.7672 (mtt) REVERT: B 488 MET cc_start: 0.7484 (mmm) cc_final: 0.5979 (mmm) REVERT: D 57 MET cc_start: 0.8622 (mmm) cc_final: 0.7949 (mmm) REVERT: D 192 MET cc_start: 0.5422 (tpp) cc_final: 0.4949 (tpp) REVERT: D 399 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6571 (tp30) REVERT: d 319 LYS cc_start: 0.5107 (mttt) cc_final: 0.4037 (pttp) REVERT: d 355 MET cc_start: -0.1637 (tmm) cc_final: -0.1893 (tmm) REVERT: E 58 MET cc_start: 0.8256 (ttm) cc_final: 0.7840 (ttp) REVERT: E 65 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6038 (t0) REVERT: E 78 MET cc_start: 0.8519 (mtm) cc_final: 0.8088 (ptt) REVERT: E 80 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6469 (p0) REVERT: E 105 THR cc_start: 0.9261 (p) cc_final: 0.9025 (p) REVERT: E 278 TYR cc_start: 0.2254 (m-10) cc_final: 0.1753 (m-80) REVERT: E 369 MET cc_start: 0.4561 (tpp) cc_final: 0.4098 (tpp) REVERT: E 390 LYS cc_start: 0.8333 (tmmt) cc_final: 0.7797 (tptt) REVERT: E 401 HIS cc_start: 0.8892 (t70) cc_final: 0.8416 (t70) REVERT: E 413 ASP cc_start: 0.8978 (t0) cc_final: 0.8486 (t0) REVERT: E 472 MET cc_start: 0.6722 (mmm) cc_final: 0.6490 (mmm) REVERT: e 46 MET cc_start: 0.8542 (mmp) cc_final: 0.8217 (mmm) REVERT: e 447 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.7221 (mtm180) REVERT: g 171 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7586 (tp) REVERT: g 190 ARG cc_start: 0.6960 (mmp80) cc_final: 0.6627 (mmp-170) REVERT: g 229 MET cc_start: 0.1910 (mtt) cc_final: 0.1317 (mtt) REVERT: g 305 MET cc_start: 0.6090 (ptm) cc_final: 0.5244 (mmp) REVERT: g 362 PHE cc_start: 0.4234 (OUTLIER) cc_final: 0.3313 (m-80) REVERT: g 507 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8276 (mtmm) REVERT: G 152 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7669 (mpp) REVERT: G 305 MET cc_start: 0.0802 (tmm) cc_final: 0.0457 (tmm) REVERT: G 395 MET cc_start: 0.7464 (mtm) cc_final: 0.6713 (mmt) REVERT: G 415 GLU cc_start: 0.7413 (mp0) cc_final: 0.7089 (mp0) REVERT: h 383 GLU cc_start: 0.5370 (tp30) cc_final: 0.4994 (tm-30) REVERT: h 384 GLU cc_start: 0.5361 (tt0) cc_final: 0.4846 (tt0) REVERT: h 394 MET cc_start: 0.7676 (mmm) cc_final: 0.7434 (mmp) REVERT: H 178 MET cc_start: 0.8444 (mmt) cc_final: 0.8188 (mtt) REVERT: H 194 MET cc_start: 0.4818 (mtt) cc_final: 0.4476 (mtt) REVERT: H 382 MET cc_start: 0.4708 (mtm) cc_final: 0.4355 (mtt) REVERT: H 521 LYS cc_start: 0.8616 (tttt) cc_final: 0.8051 (tmtt) REVERT: Q 14 MET cc_start: 0.4643 (ppp) cc_final: 0.3688 (ptp) REVERT: Q 90 SER cc_start: 0.9369 (OUTLIER) cc_final: 0.9152 (p) REVERT: Q 116 GLU cc_start: 0.7141 (tp30) cc_final: 0.6872 (tp30) REVERT: q 31 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7223 (mmt180) REVERT: q 34 GLN cc_start: 0.8157 (tp40) cc_final: 0.7744 (mm110) REVERT: q 224 LYS cc_start: 0.8726 (pttt) cc_final: 0.8351 (tptt) REVERT: q 276 MET cc_start: 0.2050 (ttp) cc_final: 0.1488 (ttp) REVERT: q 492 MET cc_start: 0.6634 (mmm) cc_final: 0.6405 (mmm) REVERT: Z 221 MET cc_start: 0.4260 (mmt) cc_final: 0.3637 (tmm) REVERT: Z 265 LYS cc_start: 0.7854 (mttt) cc_final: 0.7108 (tppt) REVERT: Z 377 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8172 (mtpt) REVERT: z 35 ARG cc_start: 0.8527 (ptm160) cc_final: 0.8204 (ttp80) REVERT: z 59 ASP cc_start: 0.7874 (t70) cc_final: 0.7447 (t70) REVERT: z 67 MET cc_start: 0.7368 (mtt) cc_final: 0.6806 (mtt) outliers start: 135 outliers final: 107 residues processed: 1068 average time/residue: 0.5692 time to fit residues: 1029.6722 Evaluate side-chains 1040 residues out of total 6679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 926 time to evaluate : 5.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 490 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 213 TYR Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain d residue 46 ASP Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 396 LEU Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 201 ASP Chi-restraints excluded: chain e residue 283 PHE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 171 LEU Chi-restraints excluded: chain g residue 362 PHE Chi-restraints excluded: chain g residue 444 LEU Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 193 LYS Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 358 TYR Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain Q residue 504 LYS Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 119 LEU Chi-restraints excluded: chain q residue 157 ILE Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 303 HIS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 317 SER Chi-restraints excluded: chain q residue 406 LYS Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 517 THR Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 187 ASP Chi-restraints excluded: chain Z residue 276 GLU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 377 LYS Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 160 VAL Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 0.9990 chunk 500 optimal weight: 5.9990 chunk 671 optimal weight: 0.2980 chunk 193 optimal weight: 6.9990 chunk 581 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 631 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 648 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS B 65 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN Q 41 GLN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.160994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.140956 restraints weight = 146851.984| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 3.57 r_work: 0.4087 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.7591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 61897 Z= 0.206 Angle : 0.631 13.962 83500 Z= 0.321 Chirality : 0.043 0.294 10023 Planarity : 0.004 0.091 10715 Dihedral : 4.282 55.119 8501 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.13 % Allowed : 21.14 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.09), residues: 7955 helix: 1.41 (0.08), residues: 4232 sheet: -0.84 (0.19), residues: 725 loop : -1.25 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 478 HIS 0.011 0.001 HIS b 391 PHE 0.027 0.002 PHE H 175 TYR 0.026 0.001 TYR a 426 ARG 0.011 0.000 ARG Q 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18218.74 seconds wall clock time: 318 minutes 31.75 seconds (19111.75 seconds total)