Starting phenix.real_space_refine on Mon Mar 18 23:02:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qw6_4658/03_2024/6qw6_4658_neut_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 280 5.49 5 Mg 1 5.21 5 S 439 5.16 5 C 55672 2.51 5 N 15582 2.21 5 O 17261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X GLU 102": "OE1" <-> "OE2" Residue "X ASP 121": "OD1" <-> "OD2" Residue "X TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 135": "NH1" <-> "NH2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 143": "NH1" <-> "NH2" Residue "X ARG 149": "NH1" <-> "NH2" Residue "41 GLU 56": "OE1" <-> "OE2" Residue "41 ARG 61": "NH1" <-> "NH2" Residue "42 GLU 23": "OE1" <-> "OE2" Residue "42 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "42 ARG 61": "NH1" <-> "NH2" Residue "42 GLU 68": "OE1" <-> "OE2" Residue "42 ARG 102": "NH1" <-> "NH2" Residue "42 ASP 104": "OD1" <-> "OD2" Residue "43 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "43 GLU 59": "OE1" <-> "OE2" Residue "43 ASP 75": "OD1" <-> "OD2" Residue "4A GLU 386": "OE1" <-> "OE2" Residue "4A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A GLU 444": "OE1" <-> "OE2" Residue "4A GLU 462": "OE1" <-> "OE2" Residue "4A ARG 507": "NH1" <-> "NH2" Residue "4A ARG 518": "NH1" <-> "NH2" Residue "4A ARG 525": "NH1" <-> "NH2" Residue "4A ARG 547": "NH1" <-> "NH2" Residue "4A ARG 549": "NH1" <-> "NH2" Residue "4A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A ASP 578": "OD1" <-> "OD2" Residue "4A ARG 596": "NH1" <-> "NH2" Residue "4A GLU 645": "OE1" <-> "OE2" Residue "4A GLU 659": "OE1" <-> "OE2" Residue "4A GLU 676": "OE1" <-> "OE2" Residue "4B GLU 201": "OE1" <-> "OE2" Residue "4B ARG 207": "NH1" <-> "NH2" Residue "4B ASP 231": "OD1" <-> "OD2" Residue "4B ARG 232": "NH1" <-> "NH2" Residue "4B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B ARG 270": "NH1" <-> "NH2" Residue "4B ASP 293": "OD1" <-> "OD2" Residue "4B ARG 325": "NH1" <-> "NH2" Residue "4B ARG 328": "NH1" <-> "NH2" Residue "4B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B ARG 345": "NH1" <-> "NH2" Residue "4B ARG 348": "NH1" <-> "NH2" Residue "4B ASP 351": "OD1" <-> "OD2" Residue "4B GLU 353": "OE1" <-> "OE2" Residue "4B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B ASP 376": "OD1" <-> "OD2" Residue "4B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B ARG 390": "NH1" <-> "NH2" Residue "4B ARG 395": "NH1" <-> "NH2" Residue "4B ARG 398": "NH1" <-> "NH2" Residue "4B ARG 437": "NH1" <-> "NH2" Residue "4B ARG 439": "NH1" <-> "NH2" Residue "4B ARG 440": "NH1" <-> "NH2" Residue "4B GLU 458": "OE1" <-> "OE2" Residue "4B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B GLU 492": "OE1" <-> "OE2" Residue "4B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C GLU 126": "OE1" <-> "OE2" Residue "4C ASP 147": "OD1" <-> "OD2" Residue "4C ARG 186": "NH1" <-> "NH2" Residue "4C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C ASP 306": "OD1" <-> "OD2" Residue "4C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C ASP 322": "OD1" <-> "OD2" Residue "4C ARG 351": "NH1" <-> "NH2" Residue "4C ARG 357": "NH1" <-> "NH2" Residue "4C ARG 360": "NH1" <-> "NH2" Residue "4C ARG 365": "NH1" <-> "NH2" Residue "4C ASP 386": "OD1" <-> "OD2" Residue "4C GLU 390": "OE1" <-> "OE2" Residue "4D ASP 24": "OD1" <-> "OD2" Residue "4D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D ASP 75": "OD1" <-> "OD2" Residue "4D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4b ASP 35": "OD1" <-> "OD2" Residue "4b GLU 47": "OE1" <-> "OE2" Residue "4b GLU 60": "OE1" <-> "OE2" Residue "4e ASP 59": "OD1" <-> "OD2" Residue "4e ARG 76": "NH1" <-> "NH2" Residue "4f TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4f ARG 73": "NH1" <-> "NH2" Residue "4g GLU 8": "OE1" <-> "OE2" Residue "4g PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4g ARG 32": "NH1" <-> "NH2" Residue "4g GLU 44": "OE1" <-> "OE2" Residue "51 GLU 56": "OE1" <-> "OE2" Residue "51 ARG 61": "NH1" <-> "NH2" Residue "52 PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "52 GLU 76": "OE1" <-> "OE2" Residue "52 ARG 102": "NH1" <-> "NH2" Residue "53 GLU 21": "OE1" <-> "OE2" Residue "53 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "53 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A GLU 32": "OE1" <-> "OE2" Residue "5A GLU 47": "OE1" <-> "OE2" Residue "5A GLU 59": "OE1" <-> "OE2" Residue "5A ARG 86": "NH1" <-> "NH2" Residue "5A ARG 114": "NH1" <-> "NH2" Residue "5A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 158": "NH1" <-> "NH2" Residue "5A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 163": "NH1" <-> "NH2" Residue "5A ARG 165": "NH1" <-> "NH2" Residue "5A ASP 170": "OD1" <-> "OD2" Residue "5A ASP 171": "OD1" <-> "OD2" Residue "5A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A GLU 189": "OE1" <-> "OE2" Residue "5A GLU 194": "OE1" <-> "OE2" Residue "5A ASP 205": "OD1" <-> "OD2" Residue "5A ASP 209": "OD1" <-> "OD2" Residue "5A ASP 215": "OD1" <-> "OD2" Residue "5A ARG 217": "NH1" <-> "NH2" Residue "5A ARG 227": "NH1" <-> "NH2" Residue "5A ASP 290": "OD1" <-> "OD2" Residue "5A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 305": "NH1" <-> "NH2" Residue "5A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 362": "NH1" <-> "NH2" Residue "5A GLU 376": "OE1" <-> "OE2" Residue "5A GLU 382": "OE1" <-> "OE2" Residue "5A GLU 385": "OE1" <-> "OE2" Residue "5A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 419": "NH1" <-> "NH2" Residue "5A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 474": "NH1" <-> "NH2" Residue "5A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 539": "NH1" <-> "NH2" Residue "5A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 548": "NH1" <-> "NH2" Residue "5A ARG 552": "NH1" <-> "NH2" Residue "5A ASP 559": "OD1" <-> "OD2" Residue "5A ASP 570": "OD1" <-> "OD2" Residue "5A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 686": "NH1" <-> "NH2" Residue "5A ARG 707": "NH1" <-> "NH2" Residue "5A GLU 715": "OE1" <-> "OE2" Residue "5A ARG 762": "NH1" <-> "NH2" Residue "5A TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ASP 835": "OD1" <-> "OD2" Residue "5A ARG 845": "NH1" <-> "NH2" Residue "5A ASP 872": "OD1" <-> "OD2" Residue "5A GLU 876": "OE1" <-> "OE2" Residue "5A ARG 883": "NH1" <-> "NH2" Residue "5A PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ASP 931": "OD1" <-> "OD2" Residue "5A ASP 944": "OD1" <-> "OD2" Residue "5A GLU 970": "OE1" <-> "OE2" Residue "5A ASP 989": "OD1" <-> "OD2" Residue "5A ARG 995": "NH1" <-> "NH2" Residue "5A PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ASP 1076": "OD1" <-> "OD2" Residue "5A GLU 1080": "OE1" <-> "OE2" Residue "5A TYR 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 1136": "NH1" <-> "NH2" Residue "5A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 1163": "NH1" <-> "NH2" Residue "5A TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A GLU 1205": "OE1" <-> "OE2" Residue "5A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A GLU 1321": "OE1" <-> "OE2" Residue "5A TYR 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 1370": "NH1" <-> "NH2" Residue "5A TYR 1371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 1401": "NH1" <-> "NH2" Residue "5A GLU 1409": "OE1" <-> "OE2" Residue "5A ARG 1414": "NH1" <-> "NH2" Residue "5A PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 1471": "NH1" <-> "NH2" Residue "5A GLU 1486": "OE1" <-> "OE2" Residue "5A PHE 1502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A GLU 1504": "OE1" <-> "OE2" Residue "5A ARG 1533": "NH1" <-> "NH2" Residue "5A PHE 1551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 1577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 1632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ASP 1650": "OD1" <-> "OD2" Residue "5A ASP 1672": "OD1" <-> "OD2" Residue "5A ASP 1686": "OD1" <-> "OD2" Residue "5A TYR 1709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 1754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 1762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ASP 1782": "OD1" <-> "OD2" Residue "5A GLU 1856": "OE1" <-> "OE2" Residue "5A ARG 1865": "NH1" <-> "NH2" Residue "5A ASP 1878": "OD1" <-> "OD2" Residue "5A PHE 1902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ASP 1921": "OD1" <-> "OD2" Residue "5A ASP 1948": "OD1" <-> "OD2" Residue "5A GLU 1963": "OE1" <-> "OE2" Residue "5A GLU 1975": "OE1" <-> "OE2" Residue "5A ARG 2008": "NH1" <-> "NH2" Residue "5A TYR 2102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A GLU 2141": "OE1" <-> "OE2" Residue "5A GLU 2167": "OE1" <-> "OE2" Residue "5A GLU 2209": "OE1" <-> "OE2" Residue "5A TYR 2228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ASP 2265": "OD1" <-> "OD2" Residue "5A PHE 2270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A GLU 2307": "OE1" <-> "OE2" Residue "5A TYR 2326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 51": "NH1" <-> "NH2" Residue "5B ARG 74": "NH1" <-> "NH2" Residue "5B ARG 78": "NH1" <-> "NH2" Residue "5B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 95": "OD1" <-> "OD2" Residue "5B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 149": "NH1" <-> "NH2" Residue "5B ARG 154": "NH1" <-> "NH2" Residue "5B ASP 165": "OD1" <-> "OD2" Residue "5B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 287": "OD1" <-> "OD2" Residue "5B GLU 288": "OE1" <-> "OE2" Residue "5B ASP 298": "OD1" <-> "OD2" Residue "5B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 322": "NH1" <-> "NH2" Residue "5B ARG 325": "NH1" <-> "NH2" Residue "5B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 342": "OE1" <-> "OE2" Residue "5B ARG 345": "NH1" <-> "NH2" Residue "5B ASP 353": "OD1" <-> "OD2" Residue "5B ASP 413": "OD1" <-> "OD2" Residue "5B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 436": "NH1" <-> "NH2" Residue "5B ARG 437": "NH1" <-> "NH2" Residue "5B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 476": "OE1" <-> "OE2" Residue "5B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 483": "NH1" <-> "NH2" Residue "5B ARG 490": "NH1" <-> "NH2" Residue "5B ARG 519": "NH1" <-> "NH2" Residue "5B ASP 535": "OD1" <-> "OD2" Residue "5B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 558": "NH1" <-> "NH2" Residue "5B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 572": "OD1" <-> "OD2" Residue "5B ASP 594": "OD1" <-> "OD2" Residue "5B ASP 615": "OD1" <-> "OD2" Residue "5B ASP 660": "OD1" <-> "OD2" Residue "5B ARG 666": "NH1" <-> "NH2" Residue "5B ASP 668": "OD1" <-> "OD2" Residue "5B PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 686": "OE1" <-> "OE2" Residue "5B GLU 694": "OE1" <-> "OE2" Residue "5B ARG 700": "NH1" <-> "NH2" Residue "5B PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 714": "OE1" <-> "OE2" Residue "5B ARG 728": "NH1" <-> "NH2" Residue "5B ARG 739": "NH1" <-> "NH2" Residue "5B ASP 740": "OD1" <-> "OD2" Residue "5B ASP 746": "OD1" <-> "OD2" Residue "5B ARG 753": "NH1" <-> "NH2" Residue "5B ARG 763": "NH1" <-> "NH2" Residue "5B GLU 767": "OE1" <-> "OE2" Residue "5B GLU 773": "OE1" <-> "OE2" Residue "5B ASP 793": "OD1" <-> "OD2" Residue "5B GLU 798": "OE1" <-> "OE2" Residue "5B GLU 843": "OE1" <-> "OE2" Residue "5B ASP 848": "OD1" <-> "OD2" Residue "5B TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 862": "OD1" <-> "OD2" Residue "5B TYR 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 904": "OE1" <-> "OE2" Residue "5B TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 931": "NH1" <-> "NH2" Residue "5B TYR 936": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 952": "NH1" <-> "NH2" Residue "5B GLU 983": "OE1" <-> "OE2" Residue "5B ARG 986": "NH1" <-> "NH2" Residue "5B TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 1073": "OE1" <-> "OE2" Residue "5B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 1090": "NH1" <-> "NH2" Residue "5B ARG 1093": "NH1" <-> "NH2" Residue "5B ASP 1109": "OD1" <-> "OD2" Residue "5B ASP 1119": "OD1" <-> "OD2" Residue "5B ARG 1121": "NH1" <-> "NH2" Residue "5B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 1152": "NH1" <-> "NH2" Residue "5B ARG 1166": "NH1" <-> "NH2" Residue "5B PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 1207": "OD1" <-> "OD2" Residue "5B GLU 1219": "OE1" <-> "OE2" Residue "5B PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 1273": "OD1" <-> "OD2" Residue "5B ARG 1274": "NH1" <-> "NH2" Residue "5B PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 1295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 1300": "OE1" <-> "OE2" Residue "5B TYR 1321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 1340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 1366": "NH1" <-> "NH2" Residue "5B GLU 1395": "OE1" <-> "OE2" Residue "5B ASP 1399": "OD1" <-> "OD2" Residue "5B ASP 1415": "OD1" <-> "OD2" Residue "5B GLU 1430": "OE1" <-> "OE2" Residue "5B ASP 1433": "OD1" <-> "OD2" Residue "5B ARG 1442": "NH1" <-> "NH2" Residue "5B GLU 1468": "OE1" <-> "OE2" Residue "5B PHE 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 1570": "NH1" <-> "NH2" Residue "5B ASP 1575": "OD1" <-> "OD2" Residue "5B ARG 1588": "NH1" <-> "NH2" Residue "5B PHE 1589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 1606": "OD1" <-> "OD2" Residue "5B TYR 1619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 1633": "OE1" <-> "OE2" Residue "5B ARG 1648": "NH1" <-> "NH2" Residue "5B ASP 1665": "OD1" <-> "OD2" Residue "5B TYR 1668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 1669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 1693": "NH1" <-> "NH2" Residue "5B ASP 1697": "OD1" <-> "OD2" Residue "5B ASP 1712": "OD1" <-> "OD2" Residue "5B PHE 1714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 1725": "OE1" <-> "OE2" Residue "5B ASP 1734": "OD1" <-> "OD2" Residue "5B PHE 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B TYR 1761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 1762": "NH1" <-> "NH2" Residue "5B TYR 1770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 1783": "OD1" <-> "OD2" Residue "5B ASP 1795": "OD1" <-> "OD2" Residue "5B GLU 1805": "OE1" <-> "OE2" Residue "5B TYR 1822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 1884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 1886": "OD1" <-> "OD2" Residue "5B GLU 1907": "OE1" <-> "OE2" Residue "5B PHE 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 1969": "OE1" <-> "OE2" Residue "5B PHE 1983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B GLU 1987": "OE1" <-> "OE2" Residue "5B GLU 1991": "OE1" <-> "OE2" Residue "5B ARG 1993": "NH1" <-> "NH2" Residue "5B ASP 2001": "OD1" <-> "OD2" Residue "5B PHE 2010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 2030": "NH1" <-> "NH2" Residue "5B GLU 2042": "OE1" <-> "OE2" Residue "5B ARG 2081": "NH1" <-> "NH2" Residue "5B PHE 2094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 2111": "OD1" <-> "OD2" Residue "5B ASP 2125": "OD1" <-> "OD2" Residue "5C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C ASP 147": "OD1" <-> "OD2" Residue "5C ASP 162": "OD1" <-> "OD2" Residue "5C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C ASP 192": "OD1" <-> "OD2" Residue "5C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C GLU 240": "OE1" <-> "OE2" Residue "5C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C GLU 450": "OE1" <-> "OE2" Residue "5C ASP 458": "OD1" <-> "OD2" Residue "5C ASP 467": "OD1" <-> "OD2" Residue "5C ASP 471": "OD1" <-> "OD2" Residue "5C ASP 486": "OD1" <-> "OD2" Residue "5C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C ASP 518": "OD1" <-> "OD2" Residue "5C TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C GLU 540": "OE1" <-> "OE2" Residue "5C GLU 553": "OE1" <-> "OE2" Residue "5C ARG 569": "NH1" <-> "NH2" Residue "5C GLU 622": "OE1" <-> "OE2" Residue "5C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C GLU 716": "OE1" <-> "OE2" Residue "5C PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C ARG 730": "NH1" <-> "NH2" Residue "5C GLU 753": "OE1" <-> "OE2" Residue "5C PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C ASP 793": "OD1" <-> "OD2" Residue "5C GLU 799": "OE1" <-> "OE2" Residue "5C ARG 814": "NH1" <-> "NH2" Residue "5C TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C ASP 841": "OD1" <-> "OD2" Residue "5C TYR 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C ASP 860": "OD1" <-> "OD2" Residue "5C ARG 940": "NH1" <-> "NH2" Residue "5C ASP 946": "OD1" <-> "OD2" Residue "5D TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D ASP 23": "OD1" <-> "OD2" Residue "5D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D GLU 65": "OE1" <-> "OE2" Residue "5D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D ASP 93": "OD1" <-> "OD2" Residue "5D GLU 107": "OE1" <-> "OE2" Residue "5D ASP 114": "OD1" <-> "OD2" Residue "5D ARG 121": "NH1" <-> "NH2" Residue "5D ARG 141": "NH1" <-> "NH2" Residue "5D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5J ARG 23": "NH1" <-> "NH2" Residue "5J PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5J ASP 72": "OD1" <-> "OD2" Residue "5J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5J ASP 97": "OD1" <-> "OD2" Residue "5J ASP 102": "OD1" <-> "OD2" Residue "5J GLU 114": "OE1" <-> "OE2" Residue "5J ARG 116": "NH1" <-> "NH2" Residue "5J GLU 118": "OE1" <-> "OE2" Residue "5J ARG 123": "NH1" <-> "NH2" Residue "5J ARG 132": "NH1" <-> "NH2" Residue "5J PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5J ASP 144": "OD1" <-> "OD2" Residue "5J GLU 156": "OE1" <-> "OE2" Residue "5J ASP 239": "OD1" <-> "OD2" Residue "5J GLU 348": "OE1" <-> "OE2" Residue "5J ARG 367": "NH1" <-> "NH2" Residue "5J ARG 374": "NH1" <-> "NH2" Residue "5J ARG 378": "NH1" <-> "NH2" Residue "5J ARG 391": "NH1" <-> "NH2" Residue "5J GLU 398": "OE1" <-> "OE2" Residue "5J ARG 405": "NH1" <-> "NH2" Residue "5J ARG 420": "NH1" <-> "NH2" Residue "5J ASP 463": "OD1" <-> "OD2" Residue "5J GLU 474": "OE1" <-> "OE2" Residue "5J GLU 484": "OE1" <-> "OE2" Residue "5J PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5J ARG 628": "NH1" <-> "NH2" Residue "5J ASP 656": "OD1" <-> "OD2" Residue "5J ARG 660": "NH1" <-> "NH2" Residue "5J ARG 662": "NH1" <-> "NH2" Residue "5J ARG 669": "NH1" <-> "NH2" Residue "5J ARG 676": "NH1" <-> "NH2" Residue "5J ARG 703": "NH1" <-> "NH2" Residue "5J ARG 729": "NH1" <-> "NH2" Residue "5J GLU 754": "OE1" <-> "OE2" Residue "5J ARG 770": "NH1" <-> "NH2" Residue "5J GLU 782": "OE1" <-> "OE2" Residue "5J GLU 806": "OE1" <-> "OE2" Residue "5J GLU 838": "OE1" <-> "OE2" Residue "5J ASP 840": "OD1" <-> "OD2" Residue "5J ARG 855": "NH1" <-> "NH2" Residue "5J ASP 873": "OD1" <-> "OD2" Residue "5J TYR 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5J GLU 885": "OE1" <-> "OE2" Residue "5J GLU 896": "OE1" <-> "OE2" Residue "5J ARG 907": "NH1" <-> "NH2" Residue "5J GLU 910": "OE1" <-> "OE2" Residue "5O ARG 52": "NH1" <-> "NH2" Residue "5O GLU 114": "OE1" <-> "OE2" Residue "5O GLU 142": "OE1" <-> "OE2" Residue "5O ARG 162": "NH1" <-> "NH2" Residue "5O GLU 246": "OE1" <-> "OE2" Residue "5O GLU 285": "OE1" <-> "OE2" Residue "5O GLU 355": "OE1" <-> "OE2" Residue "5X GLU 168": "OE1" <-> "OE2" Residue "5X GLU 172": "OE1" <-> "OE2" Residue "5X ARG 177": "NH1" <-> "NH2" Residue "5X GLU 191": "OE1" <-> "OE2" Residue "5X ARG 195": "NH1" <-> "NH2" Residue "5X PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X GLU 246": "OE1" <-> "OE2" Residue "5X PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X GLU 275": "OE1" <-> "OE2" Residue "5X ASP 277": "OD1" <-> "OD2" Residue "5X ASP 281": "OD1" <-> "OD2" Residue "5X TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X GLU 334": "OE1" <-> "OE2" Residue "5X GLU 337": "OE1" <-> "OE2" Residue "5X ARG 339": "NH1" <-> "NH2" Residue "5X GLU 347": "OE1" <-> "OE2" Residue "5X ASP 354": "OD1" <-> "OD2" Residue "5X PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X ARG 461": "NH1" <-> "NH2" Residue "5X TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X GLU 479": "OE1" <-> "OE2" Residue "5X GLU 485": "OE1" <-> "OE2" Residue "5X GLU 486": "OE1" <-> "OE2" Residue "5X ARG 498": "NH1" <-> "NH2" Residue "5X GLU 509": "OE1" <-> "OE2" Residue "5X ASP 510": "OD1" <-> "OD2" Residue "5X ASP 556": "OD1" <-> "OD2" Residue "5X GLU 560": "OE1" <-> "OE2" Residue "5X GLU 568": "OE1" <-> "OE2" Residue "5X GLU 583": "OE1" <-> "OE2" Residue "5X GLU 586": "OE1" <-> "OE2" Residue "5X PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X GLU 593": "OE1" <-> "OE2" Residue "5X TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X GLU 637": "OE1" <-> "OE2" Residue "5X GLU 640": "OE1" <-> "OE2" Residue "5X GLU 650": "OE1" <-> "OE2" Residue "5X GLU 660": "OE1" <-> "OE2" Residue "5X PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X ASP 678": "OD1" <-> "OD2" Residue "5X TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X ARG 703": "NH1" <-> "NH2" Residue "5X ASP 722": "OD1" <-> "OD2" Residue "5X ASP 729": "OD1" <-> "OD2" Residue "5X GLU 746": "OE1" <-> "OE2" Residue "5X ARG 751": "NH1" <-> "NH2" Residue "5X ARG 754": "NH1" <-> "NH2" Residue "5X ASP 772": "OD1" <-> "OD2" Residue "5X TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5X GLU 778": "OE1" <-> "OE2" Residue "5b ASP 23": "OD1" <-> "OD2" Residue "5b PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5b GLU 62": "OE1" <-> "OE2" Residue "5e TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5e GLU 44": "OE1" <-> "OE2" Residue "5e GLU 52": "OE1" <-> "OE2" Residue "5e ASP 59": "OD1" <-> "OD2" Residue "5e GLU 63": "OE1" <-> "OE2" Residue "5e ARG 76": "NH1" <-> "NH2" Residue "5f TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5f ARG 73": "NH1" <-> "NH2" Residue "5g GLU 8": "OE1" <-> "OE2" Residue "5g PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5g ARG 32": "NH1" <-> "NH2" Residue "5g GLU 44": "OE1" <-> "OE2" Residue "62 TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "62 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "63 ARG 22": "NH1" <-> "NH2" Residue "63 ARG 40": "NH1" <-> "NH2" Residue "63 ARG 42": "NH1" <-> "NH2" Residue "63 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "63 ASP 67": "OD1" <-> "OD2" Residue "63 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "63 TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "64 ARG 41": "NH1" <-> "NH2" Residue "64 ARG 48": "NH1" <-> "NH2" Residue "64 PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "64 ARG 55": "NH1" <-> "NH2" Residue "64 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "64 ARG 70": "NH1" <-> "NH2" Residue "65 ARG 25": "NH1" <-> "NH2" Residue "65 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "65 GLU 52": "OE1" <-> "OE2" Residue "65 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "65 ARG 64": "NH1" <-> "NH2" Residue "65 ARG 65": "NH1" <-> "NH2" Residue "66 ARG 18": "NH1" <-> "NH2" Residue "66 ARG 31": "NH1" <-> "NH2" Residue "66 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "66 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "66 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "66 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "67 PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "67 ARG 31": "NH1" <-> "NH2" Residue "67 PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "67 ARG 56": "NH1" <-> "NH2" Residue "67 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "68 ARG 11": "NH1" <-> "NH2" Residue "68 ARG 21": "NH1" <-> "NH2" Residue "68 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "68 ARG 44": "NH1" <-> "NH2" Residue "68 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "68 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "68 ARG 87": "NH1" <-> "NH2" Residue "R ASP 379": "OD1" <-> "OD2" Residue "R ARG 382": "NH1" <-> "NH2" Residue "R ASP 387": "OD1" <-> "OD2" Residue "R ARG 399": "NH1" <-> "NH2" Residue "R PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 437": "NH1" <-> "NH2" Residue "R TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 455": "NH1" <-> "NH2" Residue "R ARG 468": "NH1" <-> "NH2" Residue "S PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 565": "OE1" <-> "OE2" Residue "S TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 636": "NH1" <-> "NH2" Residue "S ASP 707": "OD1" <-> "OD2" Residue "S ASP 751": "OD1" <-> "OD2" Residue "S GLU 753": "OE1" <-> "OE2" Residue "U ARG 100": "NH1" <-> "NH2" Residue "U PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 177": "OD1" <-> "OD2" Residue "U TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 206": "OD1" <-> "OD2" Residue "U ARG 213": "NH1" <-> "NH2" Residue "U GLU 255": "OE1" <-> "OE2" Residue "U ARG 264": "NH1" <-> "NH2" Residue "U PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 279": "OE1" <-> "OE2" Residue "U ARG 282": "NH1" <-> "NH2" Residue "U ARG 288": "NH1" <-> "NH2" Residue "U ASP 318": "OD1" <-> "OD2" Residue "U ASP 347": "OD1" <-> "OD2" Residue "U PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 354": "NH1" <-> "NH2" Residue "U ASP 364": "OD1" <-> "OD2" Residue "U GLU 371": "OE1" <-> "OE2" Residue "U ASP 377": "OD1" <-> "OD2" Residue "U PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 394": "OD1" <-> "OD2" Residue "U ASP 403": "OD1" <-> "OD2" Residue "U GLU 429": "OE1" <-> "OE2" Residue "U PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 440": "NH1" <-> "NH2" Residue "U PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 487": "OE1" <-> "OE2" Residue "U ARG 515": "NH1" <-> "NH2" Residue "U TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 554": "NH1" <-> "NH2" Residue "U ARG 555": "NH1" <-> "NH2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 89236 Number of models: 1 Model: "" Number of chains: 42 Chain: "X" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain breaks: 1 Chain: "4" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2690 Unusual residues: {'M7M': 1} Inner-chain residues flagged as termini: ['pdbres=" G 4 85 "'] Classifications: {'RNA': 125, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 11, 'rna3p_pur': 54, 'rna3p_pyr': 50} Link IDs: {'rna2p': 21, 'rna3p': 103, None: 1} Not linked: pdbres="M7M 4 0 " pdbres=" A 4 1 " Chain breaks: 5 Chain: "41" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "42" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 737 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "43" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "4A" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1946 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "4B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2842 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 343} Chain: "4C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2375 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 290} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "4D" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 116} Chain: "4b" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 669 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "4e" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 631 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "4f" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 562 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "4g" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 577 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "5" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2192 Classifications: {'RNA': 104} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 38, 'rna3p_pyr': 43} Link IDs: {'rna2p': 22, 'rna3p': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "51" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "52" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Chain: "53" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "5A" Number of atoms: 18366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2212, 18366 Classifications: {'peptide': 2212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 123, 'TRANS': 2085} Chain breaks: 6 Chain: "5B" Number of atoms: 16077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2001, 16077 Classifications: {'peptide': 2001} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 83, 'TRANS': 1917} Chain breaks: 5 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "5C" Number of atoms: 6727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6727 Classifications: {'peptide': 852} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 801} Chain: "5D" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1169 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5J" Number of atoms: 6316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6316 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 772} Chain breaks: 4 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 Chain: "5O" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2394 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain: "5X" Number of atoms: 4780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 583, 4725 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 552} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 583, 4725 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 552} Chain breaks: 7 bond proxies already assigned to first conformer: 4742 Chain: "5b" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 594 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Chain: "5e" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "5f" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 567 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "5g" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 577 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "6" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 897 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 16} Link IDs: {'rna2p': 7, 'rna3p': 34} Chain breaks: 2 Chain: "62" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "63" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 699 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "64" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 596 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "65" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 587 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "66" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 567 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "67" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "68" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 722 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "R" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 874 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "S" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 947 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "U" Number of atoms: 3750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3750 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 432} Chain: "5A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "5C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85719 SG CYS U 136 91.034 108.226 137.254 1.00 25.65 S ATOM 85740 SG CYS U 139 94.126 106.286 138.130 1.00 16.97 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU5X 464 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU5X 464 " occ=0.51 residue: pdb=" N AGLU5X 479 " occ=0.33 ... (16 atoms not shown) pdb=" OE2BGLU5X 479 " occ=0.67 residue: pdb=" N AGLU5X 581 " occ=0.44 ... (16 atoms not shown) pdb=" OE2BGLU5X 581 " occ=0.56 residue: pdb=" N ASER5X 594 " occ=0.77 ... (10 atoms not shown) pdb=" OG BSER5X 594 " occ=0.23 residue: pdb=" N AGLN5X 601 " occ=0.52 ... (16 atoms not shown) pdb=" NE2BGLN5X 601 " occ=0.48 residue: pdb=" N ATHR5X 606 " occ=0.24 ... (12 atoms not shown) pdb=" CG2BTHR5X 606 " occ=0.76 residue: pdb=" N AILE5X 629 " occ=0.23 ... (14 atoms not shown) pdb=" CD1BILE5X 629 " occ=0.77 residue: pdb=" N AVAL5X 733 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL5X 733 " occ=0.50 Time building chain proxies: 35.56, per 1000 atoms: 0.40 Number of scatterers: 89236 At special positions: 0 Unit cell: (296.38, 213.598, 274.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 439 16.00 P 280 15.00 Mg 1 11.99 O 17261 8.00 N 15582 7.00 C 55672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS64 59 " - pdb=" SG CYS67 85 " distance=2.04 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 Atom "ATOM 15753 O5' U 5 7 .*. O " rejected from bonding due to valence issues. Atom "ATOM 17131 O4' G 5 77 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 28.39 Conformation dependent library (CDL) restraints added in 12.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN U 600 " pdb="ZN ZN U 600 " - pdb=" NE2 HIS U 155 " pdb="ZN ZN U 600 " - pdb=" ND1 HIS U 161 " pdb="ZN ZN U 600 " - pdb=" SG CYS U 136 " pdb="ZN ZN U 600 " - pdb=" SG CYS U 139 " Number of angles added : 1 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 372 helices and 106 sheets defined 37.0% alpha, 15.3% beta 90 base pairs and 147 stacking pairs defined. Time for finding SS restraints: 32.69 Creating SS restraints... Processing helix chain 'X' and resid 102 through 106 Processing helix chain 'X' and resid 123 through 125 No H-bonds generated for 'chain 'X' and resid 123 through 125' Processing helix chain '41' and resid 3 through 8 removed outlier: 3.606A pdb=" N MET41 8 " --> pdb=" O ARG41 5 " (cutoff:3.500A) Processing helix chain '41' and resid 62 through 64 No H-bonds generated for 'chain '41' and resid 62 through 64' Processing helix chain '42' and resid 28 through 33 removed outlier: 3.715A pdb=" N VAL42 31 " --> pdb=" O PRO42 28 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR42 33 " --> pdb=" O SER42 30 " (cutoff:3.500A) Processing helix chain '43' and resid 5 through 11 Processing helix chain '4A' and resid 389 through 394 Processing helix chain '4A' and resid 442 through 466 Processing helix chain '4A' and resid 494 through 516 Processing helix chain '4A' and resid 524 through 533 Processing helix chain '4A' and resid 554 through 566 Processing helix chain '4A' and resid 588 through 599 removed outlier: 3.567A pdb=" N LYS4A 593 " --> pdb=" O LYS4A 589 " (cutoff:3.500A) Processing helix chain '4A' and resid 654 through 663 Processing helix chain '4A' and resid 667 through 682 Processing helix chain '4B' and resid 172 through 201 Proline residue: 4B 187 - end of helix Processing helix chain '4B' and resid 204 through 220 removed outlier: 3.677A pdb=" N SER4B 220 " --> pdb=" O LYS4B 216 " (cutoff:3.500A) Processing helix chain '4C' and resid 60 through 72 removed outlier: 3.937A pdb=" N LYS4C 66 " --> pdb=" O GLU4C 62 " (cutoff:3.500A) Processing helix chain '4C' and resid 91 through 118 removed outlier: 4.546A pdb=" N ASN4C 105 " --> pdb=" O VAL4C 101 " (cutoff:3.500A) Processing helix chain '4C' and resid 125 through 128 No H-bonds generated for 'chain '4C' and resid 125 through 128' Processing helix chain '4C' and resid 132 through 141 Processing helix chain '4C' and resid 146 through 149 removed outlier: 3.782A pdb=" N CYS4C 149 " --> pdb=" O LEU4C 146 " (cutoff:3.500A) No H-bonds generated for 'chain '4C' and resid 146 through 149' Processing helix chain '4C' and resid 153 through 156 No H-bonds generated for 'chain '4C' and resid 153 through 156' Processing helix chain '4C' and resid 161 through 172 Processing helix chain '4C' and resid 181 through 215 Processing helix chain '4C' and resid 217 through 223 Processing helix chain '4C' and resid 225 through 235 removed outlier: 3.604A pdb=" N ALA4C 235 " --> pdb=" O ILE4C 231 " (cutoff:3.500A) Processing helix chain '4C' and resid 238 through 241 No H-bonds generated for 'chain '4C' and resid 238 through 241' Processing helix chain '4C' and resid 246 through 249 No H-bonds generated for 'chain '4C' and resid 246 through 249' Processing helix chain '4C' and resid 285 through 305 removed outlier: 3.860A pdb=" N ARG4C 288 " --> pdb=" O PRO4C 285 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG4C 289 " --> pdb=" O ASP4C 286 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS4C 290 " --> pdb=" O LEU4C 287 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA4C 296 " --> pdb=" O ARG4C 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA4C 297 " --> pdb=" O LEU4C 294 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS4C 298 " --> pdb=" O VAL4C 295 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS4C 299 " --> pdb=" O ALA4C 296 " (cutoff:3.500A) Processing helix chain '4C' and resid 315 through 331 Processing helix chain '4C' and resid 357 through 366 removed outlier: 4.112A pdb=" N ARG4C 365 " --> pdb=" O MET4C 362 " (cutoff:3.500A) Processing helix chain '4D' and resid 16 through 31 Processing helix chain '4D' and resid 39 through 47 Processing helix chain '4D' and resid 63 through 75 removed outlier: 5.610A pdb=" N HIS4D 68 " --> pdb=" O ILE4D 65 " (cutoff:3.500A) Proline residue: 4D 70 - end of helix Processing helix chain '4D' and resid 86 through 93 Processing helix chain '4D' and resid 113 through 123 Processing helix chain '4b' and resid 10 through 12 No H-bonds generated for 'chain '4b' and resid 10 through 12' Processing helix chain '4b' and resid 74 through 76 No H-bonds generated for 'chain '4b' and resid 74 through 76' Processing helix chain '4e' and resid 17 through 27 Processing helix chain '4e' and resid 81 through 83 No H-bonds generated for 'chain '4e' and resid 81 through 83' Processing helix chain '4f' and resid 7 through 14 Processing helix chain '4f' and resid 66 through 68 No H-bonds generated for 'chain '4f' and resid 66 through 68' Processing helix chain '4g' and resid 64 through 66 No H-bonds generated for 'chain '4g' and resid 64 through 66' Processing helix chain '51' and resid 3 through 8 removed outlier: 3.607A pdb=" N MET51 8 " --> pdb=" O ARG51 5 " (cutoff:3.500A) Processing helix chain '51' and resid 62 through 64 No H-bonds generated for 'chain '51' and resid 62 through 64' Processing helix chain '52' and resid 19 through 22 No H-bonds generated for 'chain '52' and resid 19 through 22' Processing helix chain '52' and resid 28 through 37 removed outlier: 3.762A pdb=" N VAL52 31 " --> pdb=" O PRO52 28 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN52 34 " --> pdb=" O VAL52 31 " (cutoff:3.500A) Processing helix chain '52' and resid 103 through 105 No H-bonds generated for 'chain '52' and resid 103 through 105' Processing helix chain '53' and resid 5 through 12 Processing helix chain '53' and resid 75 through 79 Processing helix chain '53' and resid 81 through 83 No H-bonds generated for 'chain '53' and resid 81 through 83' Processing helix chain '5A' and resid 28 through 44 removed outlier: 4.234A pdb=" N LYS5A 33 " --> pdb=" O LYS5A 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA5A 34 " --> pdb=" O LEU5A 30 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS5A 43 " --> pdb=" O GLN5A 39 " (cutoff:3.500A) Processing helix chain '5A' and resid 63 through 72 Processing helix chain '5A' and resid 85 through 104 removed outlier: 3.646A pdb=" N LYS5A 93 " --> pdb=" O LEU5A 89 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR5A 94 " --> pdb=" O GLY5A 90 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N MET5A 95 " --> pdb=" O ALA5A 91 " (cutoff:3.500A) Proline residue: 5A 96 - end of helix Processing helix chain '5A' and resid 137 through 157 Processing helix chain '5A' and resid 178 through 181 No H-bonds generated for 'chain '5A' and resid 178 through 181' Processing helix chain '5A' and resid 232 through 241 Processing helix chain '5A' and resid 243 through 245 No H-bonds generated for 'chain '5A' and resid 243 through 245' Processing helix chain '5A' and resid 260 through 268 Processing helix chain '5A' and resid 310 through 315 Processing helix chain '5A' and resid 398 through 405 Processing helix chain '5A' and resid 428 through 431 No H-bonds generated for 'chain '5A' and resid 428 through 431' Processing helix chain '5A' and resid 441 through 459 Processing helix chain '5A' and resid 472 through 477 Processing helix chain '5A' and resid 489 through 510 Processing helix chain '5A' and resid 532 through 537 Processing helix chain '5A' and resid 542 through 566 Processing helix chain '5A' and resid 571 through 583 Processing helix chain '5A' and resid 585 through 588 No H-bonds generated for 'chain '5A' and resid 585 through 588' Processing helix chain '5A' and resid 591 through 593 No H-bonds generated for 'chain '5A' and resid 591 through 593' Processing helix chain '5A' and resid 597 through 616 removed outlier: 4.237A pdb=" N TYR5A 613 " --> pdb=" O HIS5A 610 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR5A 614 " --> pdb=" O LEU5A 611 " (cutoff:3.500A) Processing helix chain '5A' and resid 631 through 655 removed outlier: 3.697A pdb=" N GLY5A 643 " --> pdb=" O PHE5A 639 " (cutoff:3.500A) Proline residue: 5A 646 - end of helix Processing helix chain '5A' and resid 681 through 695 Processing helix chain '5A' and resid 706 through 721 removed outlier: 3.574A pdb=" N LEU5A 710 " --> pdb=" O ALA5A 706 " (cutoff:3.500A) Processing helix chain '5A' and resid 733 through 763 Processing helix chain '5A' and resid 769 through 796 Processing helix chain '5A' and resid 803 through 819 Processing helix chain '5A' and resid 835 through 848 Processing helix chain '5A' and resid 858 through 872 Processing helix chain '5A' and resid 874 through 887 Processing helix chain '5A' and resid 913 through 932 Processing helix chain '5A' and resid 948 through 960 Processing helix chain '5A' and resid 990 through 1000 removed outlier: 3.605A pdb=" N LEU5A 999 " --> pdb=" O ARG5A 995 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE5A1000 " --> pdb=" O LEU5A 996 " (cutoff:3.500A) Processing helix chain '5A' and resid 1003 through 1013 removed outlier: 3.613A pdb=" N ASN5A1013 " --> pdb=" O MET5A1009 " (cutoff:3.500A) Processing helix chain '5A' and resid 1035 through 1062 removed outlier: 4.005A pdb=" N SER5A1038 " --> pdb=" O GLN5A1035 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL5A1041 " --> pdb=" O SER5A1038 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR5A1044 " --> pdb=" O VAL5A1041 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY5A1045 " --> pdb=" O GLN5A1042 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU5A1053 " --> pdb=" O LEU5A1050 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY5A1054 " --> pdb=" O LEU5A1051 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU5A1055 " --> pdb=" O VAL5A1052 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N HIS5A1056 " --> pdb=" O LEU5A1053 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG5A1057 " --> pdb=" O GLY5A1054 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA5A1058 " --> pdb=" O LEU5A1055 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA5A1062 " --> pdb=" O SER5A1059 " (cutoff:3.500A) Processing helix chain '5A' and resid 1077 through 1080 No H-bonds generated for 'chain '5A' and resid 1077 through 1080' Processing helix chain '5A' and resid 1103 through 1116 Processing helix chain '5A' and resid 1144 through 1160 removed outlier: 3.682A pdb=" N ARG5A1160 " --> pdb=" O ASP5A1156 " (cutoff:3.500A) Processing helix chain '5A' and resid 1234 through 1249 Processing helix chain '5A' and resid 1256 through 1273 Processing helix chain '5A' and resid 1275 through 1280 removed outlier: 4.048A pdb=" N VAL5A1279 " --> pdb=" O ARG5A1275 " (cutoff:3.500A) Processing helix chain '5A' and resid 1282 through 1303 Processing helix chain '5A' and resid 1313 through 1317 removed outlier: 3.851A pdb=" N TYR5A1317 " --> pdb=" O VAL5A1314 " (cutoff:3.500A) Processing helix chain '5A' and resid 1320 through 1322 No H-bonds generated for 'chain '5A' and resid 1320 through 1322' Processing helix chain '5A' and resid 1337 through 1340 removed outlier: 3.510A pdb=" N LEU5A1340 " --> pdb=" O GLN5A1337 " (cutoff:3.500A) No H-bonds generated for 'chain '5A' and resid 1337 through 1340' Processing helix chain '5A' and resid 1368 through 1371 Processing helix chain '5A' and resid 1375 through 1398 Processing helix chain '5A' and resid 1419 through 1423 Processing helix chain '5A' and resid 1425 through 1431 removed outlier: 4.421A pdb=" N HIS5A1428 " --> pdb=" O LYS5A1425 " (cutoff:3.500A) Processing helix chain '5A' and resid 1436 through 1445 removed outlier: 4.543A pdb=" N GLN5A1444 " --> pdb=" O THR5A1440 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR5A1445 " --> pdb=" O ASP5A1441 " (cutoff:3.500A) Processing helix chain '5A' and resid 1458 through 1461 No H-bonds generated for 'chain '5A' and resid 1458 through 1461' Processing helix chain '5A' and resid 1468 through 1478 Processing helix chain '5A' and resid 1480 through 1487 removed outlier: 4.546A pdb=" N HIS5A1487 " --> pdb=" O GLY5A1483 " (cutoff:3.500A) Processing helix chain '5A' and resid 1520 through 1542 Proline residue: 5A1530 - end of helix Proline residue: 5A1540 - end of helix Processing helix chain '5A' and resid 1567 through 1576 Processing helix chain '5A' and resid 1581 through 1599 Processing helix chain '5A' and resid 1602 through 1604 No H-bonds generated for 'chain '5A' and resid 1602 through 1604' Processing helix chain '5A' and resid 1676 through 1687 Processing helix chain '5A' and resid 1722 through 1736 Processing helix chain '5A' and resid 1738 through 1750 Processing helix chain '5A' and resid 1768 through 1772 removed outlier: 3.791A pdb=" N PHE5A1772 " --> pdb=" O GLY5A1769 " (cutoff:3.500A) Processing helix chain '5A' and resid 1783 through 1785 No H-bonds generated for 'chain '5A' and resid 1783 through 1785' Processing helix chain '5A' and resid 1824 through 1826 No H-bonds generated for 'chain '5A' and resid 1824 through 1826' Processing helix chain '5A' and resid 1834 through 1851 removed outlier: 4.963A pdb=" N TRP5A1839 " --> pdb=" O GLN5A1835 " (cutoff:3.500A) Processing helix chain '5A' and resid 1866 through 1875 removed outlier: 3.938A pdb=" N LEU5A1869 " --> pdb=" O LYS5A1866 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP5A1870 " --> pdb=" O GLY5A1867 " (cutoff:3.500A) Proline residue: 5A1871 - end of helix removed outlier: 3.735A pdb=" N HIS5A1875 " --> pdb=" O LEU5A1872 " (cutoff:3.500A) Processing helix chain '5A' and resid 1894 through 1898 Processing helix chain '5A' and resid 1900 through 1908 Processing helix chain '5A' and resid 1923 through 1925 No H-bonds generated for 'chain '5A' and resid 1923 through 1925' Processing helix chain '5A' and resid 1930 through 1945 Processing helix chain '5A' and resid 1947 through 1954 Processing helix chain '5A' and resid 1973 through 1994 Processing helix chain '5A' and resid 2004 through 2011 Processing helix chain '5A' and resid 2072 through 2086 removed outlier: 3.777A pdb=" N ASN5A2082 " --> pdb=" O ILE5A2078 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU5A2083 " --> pdb=" O SER5A2079 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N HIS5A2084 " --> pdb=" O ALA5A2080 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU5A2085 " --> pdb=" O ALA5A2081 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG5A2086 " --> pdb=" O ASN5A2082 " (cutoff:3.500A) Processing helix chain '5A' and resid 2108 through 2116 Processing helix chain '5A' and resid 2190 through 2202 Processing helix chain '5A' and resid 2232 through 2240 Processing helix chain '5A' and resid 2285 through 2287 No H-bonds generated for 'chain '5A' and resid 2285 through 2287' Processing helix chain '5A' and resid 2311 through 2314 No H-bonds generated for 'chain '5A' and resid 2311 through 2314' Processing helix chain '5B' and resid 64 through 77 Processing helix chain '5B' and resid 79 through 83 Processing helix chain '5B' and resid 109 through 124 Processing helix chain '5B' and resid 129 through 143 Processing helix chain '5B' and resid 153 through 161 removed outlier: 4.845A pdb=" N LEU5B 159 " --> pdb=" O LYS5B 155 " (cutoff:3.500A) Processing helix chain '5B' and resid 166 through 179 removed outlier: 4.603A pdb=" N ASN5B 174 " --> pdb=" O HIS5B 170 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU5B 175 " --> pdb=" O VAL5B 171 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY5B 176 " --> pdb=" O LEU5B 172 " (cutoff:3.500A) Processing helix chain '5B' and resid 267 through 274 removed outlier: 3.903A pdb=" N ARG5B 274 " --> pdb=" O ARG5B 270 " (cutoff:3.500A) Processing helix chain '5B' and resid 280 through 294 Processing helix chain '5B' and resid 299 through 310 Processing helix chain '5B' and resid 315 through 323 Processing helix chain '5B' and resid 325 through 335 Processing helix chain '5B' and resid 340 through 351 Processing helix chain '5B' and resid 354 through 364 removed outlier: 3.527A pdb=" N HIS5B 364 " --> pdb=" O LEU5B 360 " (cutoff:3.500A) Processing helix chain '5B' and resid 469 through 471 No H-bonds generated for 'chain '5B' and resid 469 through 471' Processing helix chain '5B' and resid 483 through 487 Processing helix chain '5B' and resid 489 through 492 No H-bonds generated for 'chain '5B' and resid 489 through 492' Processing helix chain '5B' and resid 510 through 521 Processing helix chain '5B' and resid 533 through 535 No H-bonds generated for 'chain '5B' and resid 533 through 535' Processing helix chain '5B' and resid 545 through 558 removed outlier: 3.872A pdb=" N GLY5B 553 " --> pdb=" O GLN5B 549 " (cutoff:3.500A) Processing helix chain '5B' and resid 573 through 582 Processing helix chain '5B' and resid 590 through 599 Processing helix chain '5B' and resid 603 through 605 No H-bonds generated for 'chain '5B' and resid 603 through 605' Processing helix chain '5B' and resid 617 through 620 Processing helix chain '5B' and resid 625 through 641 Processing helix chain '5B' and resid 658 through 664 Processing helix chain '5B' and resid 678 through 680 No H-bonds generated for 'chain '5B' and resid 678 through 680' Processing helix chain '5B' and resid 697 through 715 removed outlier: 3.687A pdb=" N HIS5B 715 " --> pdb=" O LYS5B 711 " (cutoff:3.500A) Processing helix chain '5B' and resid 728 through 744 removed outlier: 3.842A pdb=" N GLY5B 732 " --> pdb=" O ARG5B 728 " (cutoff:3.500A) Processing helix chain '5B' and resid 748 through 750 No H-bonds generated for 'chain '5B' and resid 748 through 750' Processing helix chain '5B' and resid 757 through 767 Processing helix chain '5B' and resid 791 through 802 Processing helix chain '5B' and resid 813 through 818 Processing helix chain '5B' and resid 846 through 854 Processing helix chain '5B' and resid 876 through 882 Processing helix chain '5B' and resid 897 through 906 Processing helix chain '5B' and resid 913 through 922 removed outlier: 3.651A pdb=" N TYR5B 922 " --> pdb=" O ASN5B 918 " (cutoff:3.500A) Processing helix chain '5B' and resid 924 through 931 Processing helix chain '5B' and resid 934 through 936 No H-bonds generated for 'chain '5B' and resid 934 through 936' Processing helix chain '5B' and resid 940 through 944 Processing helix chain '5B' and resid 950 through 966 Processing helix chain '5B' and resid 983 through 990 Processing helix chain '5B' and resid 995 through 1004 Processing helix chain '5B' and resid 1011 through 1019 removed outlier: 3.544A pdb=" N PHE5B1015 " --> pdb=" O GLU5B1011 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG5B1016 " --> pdb=" O ILE5B1012 " (cutoff:3.500A) Processing helix chain '5B' and resid 1022 through 1024 No H-bonds generated for 'chain '5B' and resid 1022 through 1024' Processing helix chain '5B' and resid 1031 through 1041 removed outlier: 5.508A pdb=" N LEU5B1035 " --> pdb=" O GLU5B1032 " (cutoff:3.500A) Processing helix chain '5B' and resid 1055 through 1067 Processing helix chain '5B' and resid 1075 through 1102 removed outlier: 4.665A pdb=" N ARG5B1090 " --> pdb=" O GLN5B1086 " (cutoff:3.500A) Processing helix chain '5B' and resid 1105 through 1120 Processing helix chain '5B' and resid 1128 through 1130 No H-bonds generated for 'chain '5B' and resid 1128 through 1130' Processing helix chain '5B' and resid 1137 through 1145 Processing helix chain '5B' and resid 1150 through 1154 removed outlier: 3.528A pdb=" N TYR5B1154 " --> pdb=" O GLU5B1151 " (cutoff:3.500A) Processing helix chain '5B' and resid 1158 through 1164 removed outlier: 3.566A pdb=" N GLY5B1162 " --> pdb=" O HIS5B1158 " (cutoff:3.500A) Processing helix chain '5B' and resid 1171 through 1179 Processing helix chain '5B' and resid 1243 through 1245 No H-bonds generated for 'chain '5B' and resid 1243 through 1245' Processing helix chain '5B' and resid 1309 through 1311 No H-bonds generated for 'chain '5B' and resid 1309 through 1311' Processing helix chain '5B' and resid 1315 through 1320 removed outlier: 3.983A pdb=" N LEU5B1320 " --> pdb=" O ALA5B1316 " (cutoff:3.500A) Processing helix chain '5B' and resid 1330 through 1339 removed outlier: 4.601A pdb=" N ASN5B1337 " --> pdb=" O THR5B1333 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR5B1338 " --> pdb=" O GLN5B1334 " (cutoff:3.500A) Processing helix chain '5B' and resid 1356 through 1370 Processing helix chain '5B' and resid 1383 through 1396 removed outlier: 3.737A pdb=" N GLU5B1395 " --> pdb=" O MET5B1391 " (cutoff:3.500A) Processing helix chain '5B' and resid 1412 through 1421 removed outlier: 3.626A pdb=" N LEU5B1416 " --> pdb=" O THR5B1412 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS5B1417 " --> pdb=" O SER5B1413 " (cutoff:3.500A) Processing helix chain '5B' and resid 1429 through 1438 removed outlier: 3.674A pdb=" N ILE5B1434 " --> pdb=" O GLU5B1430 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU5B1435 " --> pdb=" O LYS5B1431 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG5B1438 " --> pdb=" O ILE5B1434 " (cutoff:3.500A) Processing helix chain '5B' and resid 1443 through 1446 No H-bonds generated for 'chain '5B' and resid 1443 through 1446' Processing helix chain '5B' and resid 1456 through 1460 removed outlier: 3.709A pdb=" N GLY5B1460 " --> pdb=" O HIS5B1457 " (cutoff:3.500A) Processing helix chain '5B' and resid 1465 through 1478 removed outlier: 3.522A pdb=" N SER5B1478 " --> pdb=" O MET5B1474 " (cutoff:3.500A) Processing helix chain '5B' and resid 1497 through 1503 Processing helix chain '5B' and resid 1516 through 1518 No H-bonds generated for 'chain '5B' and resid 1516 through 1518' Processing helix chain '5B' and resid 1535 through 1553 removed outlier: 4.143A pdb=" N ALA5B1543 " --> pdb=" O LEU5B1539 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS5B1544 " --> pdb=" O LEU5B1540 " (cutoff:3.500A) Proline residue: 5B1545 - end of helix Processing helix chain '5B' and resid 1568 through 1582 removed outlier: 3.746A pdb=" N LEU5B1577 " --> pdb=" O ALA5B1573 " (cutoff:3.500A) Processing helix chain '5B' and resid 1598 through 1601 No H-bonds generated for 'chain '5B' and resid 1598 through 1601' Processing helix chain '5B' and resid 1607 through 1614 Processing helix chain '5B' and resid 1626 through 1637 Processing helix chain '5B' and resid 1648 through 1650 No H-bonds generated for 'chain '5B' and resid 1648 through 1650' Processing helix chain '5B' and resid 1681 through 1690 Processing helix chain '5B' and resid 1708 through 1717 removed outlier: 4.889A pdb=" N ASP5B1712 " --> pdb=" O SER5B1709 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE5B1713 " --> pdb=" O LYS5B1710 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS5B1716 " --> pdb=" O PHE5B1713 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE5B1717 " --> pdb=" O PHE5B1714 " (cutoff:3.500A) Processing helix chain '5B' and resid 1733 through 1741 Processing helix chain '5B' and resid 1748 through 1757 removed outlier: 4.114A pdb=" N TRP5B1757 " --> pdb=" O ASP5B1753 " (cutoff:3.500A) Processing helix chain '5B' and resid 1759 through 1764 Processing helix chain '5B' and resid 1768 through 1771 Processing helix chain '5B' and resid 1778 through 1798 Processing helix chain '5B' and resid 1814 through 1821 Processing helix chain '5B' and resid 1826 through 1835 removed outlier: 3.528A pdb=" N MET5B1834 " --> pdb=" O GLU5B1830 " (cutoff:3.500A) Processing helix chain '5B' and resid 1842 through 1850 removed outlier: 4.413A pdb=" N GLU5B1847 " --> pdb=" O ARG5B1843 " (cutoff:3.500A) Processing helix chain '5B' and resid 1853 through 1855 No H-bonds generated for 'chain '5B' and resid 1853 through 1855' Processing helix chain '5B' and resid 1865 through 1871 Processing helix chain '5B' and resid 1887 through 1899 Processing helix chain '5B' and resid 1906 through 1933 removed outlier: 3.614A pdb=" N ASP5B1911 " --> pdb=" O GLU5B1907 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU5B1914 " --> pdb=" O SER5B1910 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER5B1917 " --> pdb=" O GLU5B1913 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS5B1918 " --> pdb=" O GLU5B1914 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE5B1920 " --> pdb=" O LEU5B1916 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG5B1921 " --> pdb=" O SER5B1917 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU5B1922 " --> pdb=" O LYS5B1918 " (cutoff:3.500A) Processing helix chain '5B' and resid 1936 through 1951 Processing helix chain '5B' and resid 1968 through 1975 Processing helix chain '5B' and resid 1983 through 1986 No H-bonds generated for 'chain '5B' and resid 1983 through 1986' Processing helix chain '5B' and resid 1990 through 1994 Processing helix chain '5B' and resid 2003 through 2013 removed outlier: 3.838A pdb=" N ALA5B2008 " --> pdb=" O ILE5B2004 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG5B2009 " --> pdb=" O ALA5B2005 " (cutoff:3.500A) Processing helix chain '5C' and resid 116 through 122 Processing helix chain '5C' and resid 142 through 153 Processing helix chain '5C' and resid 172 through 177 Processing helix chain '5C' and resid 209 through 219 removed outlier: 4.653A pdb=" N ASP5C 213 " --> pdb=" O ASN5C 210 " (cutoff:3.500A) Processing helix chain '5C' and resid 237 through 248 Processing helix chain '5C' and resid 260 through 265 removed outlier: 4.230A pdb=" N LEU5C 265 " --> pdb=" O ARG5C 262 " (cutoff:3.500A) Processing helix chain '5C' and resid 271 through 292 Processing helix chain '5C' and resid 320 through 330 removed outlier: 3.541A pdb=" N TYR5C 327 " --> pdb=" O PHE5C 323 " (cutoff:3.500A) Processing helix chain '5C' and resid 336 through 343 Processing helix chain '5C' and resid 368 through 372 Processing helix chain '5C' and resid 374 through 385 Processing helix chain '5C' and resid 388 through 398 Proline residue: 5C 393 - end of helix Processing helix chain '5C' and resid 405 through 408 No H-bonds generated for 'chain '5C' and resid 405 through 408' Processing helix chain '5C' and resid 412 through 423 Processing helix chain '5C' and resid 428 through 436 Processing helix chain '5C' and resid 443 through 452 removed outlier: 3.846A pdb=" N LYS5C 446 " --> pdb=" O VAL5C 443 " (cutoff:3.500A) Proline residue: 5C 447 - end of helix removed outlier: 3.529A pdb=" N HIS5C 451 " --> pdb=" O LYS5C 448 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR5C 452 " --> pdb=" O ILE5C 449 " (cutoff:3.500A) Processing helix chain '5C' and resid 460 through 466 removed outlier: 3.733A pdb=" N ALA5C 464 " --> pdb=" O ASP5C 460 " (cutoff:3.500A) Processing helix chain '5C' and resid 597 through 613 Proline residue: 5C 601 - end of helix Processing helix chain '5C' and resid 634 through 646 Processing helix chain '5C' and resid 696 through 701 Processing helix chain '5C' and resid 711 through 722 removed outlier: 3.594A pdb=" N TYR5C 722 " --> pdb=" O PHE5C 718 " (cutoff:3.500A) Processing helix chain '5C' and resid 726 through 729 No H-bonds generated for 'chain '5C' and resid 726 through 729' Processing helix chain '5C' and resid 756 through 760 Processing helix chain '5C' and resid 763 through 776 Processing helix chain '5C' and resid 808 through 822 Processing helix chain '5C' and resid 843 through 852 removed outlier: 3.648A pdb=" N ARG5C 852 " --> pdb=" O THR5C 848 " (cutoff:3.500A) Processing helix chain '5C' and resid 883 through 890 Processing helix chain '5C' and resid 926 through 941 removed outlier: 5.963A pdb=" N ALA5C 930 " --> pdb=" O PRO5C 927 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET5C 934 " --> pdb=" O ARG5C 931 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE5C 935 " --> pdb=" O GLU5C 932 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS5C 936 " --> pdb=" O PHE5C 933 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR5C 937 " --> pdb=" O MET5C 934 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS5C 941 " --> pdb=" O ARG5C 938 " (cutoff:3.500A) Processing helix chain '5D' and resid 11 through 18 Processing helix chain '5D' and resid 36 through 47 Processing helix chain '5D' and resid 69 through 72 No H-bonds generated for 'chain '5D' and resid 69 through 72' Processing helix chain '5D' and resid 109 through 124 Processing helix chain '5J' and resid 96 through 114 Processing helix chain '5J' and resid 117 through 134 Processing helix chain '5J' and resid 138 through 149 removed outlier: 5.790A pdb=" N ASP5J 144 " --> pdb=" O GLN5J 140 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU5J 145 " --> pdb=" O GLN5J 141 " (cutoff:3.500A) Processing helix chain '5J' and resid 154 through 156 No H-bonds generated for 'chain '5J' and resid 154 through 156' Processing helix chain '5J' and resid 240 through 259 removed outlier: 4.007A pdb=" N GLY5J 244 " --> pdb=" O MET5J 240 " (cutoff:3.500A) Processing helix chain '5J' and resid 270 through 280 Processing helix chain '5J' and resid 288 through 304 Processing helix chain '5J' and resid 309 through 321 Processing helix chain '5J' and resid 325 through 338 removed outlier: 3.785A pdb=" N GLU5J 337 " --> pdb=" O MET5J 333 " (cutoff:3.500A) Processing helix chain '5J' and resid 343 through 352 Processing helix chain '5J' and resid 355 through 368 removed outlier: 4.007A pdb=" N ALA5J 360 " --> pdb=" O ASP5J 356 " (cutoff:3.500A) Processing helix chain '5J' and resid 373 through 382 Processing helix chain '5J' and resid 386 through 399 Processing helix chain '5J' and resid 404 through 413 removed outlier: 4.233A pdb=" N LEU5J 413 " --> pdb=" O ALA5J 409 " (cutoff:3.500A) Processing helix chain '5J' and resid 416 through 429 removed outlier: 3.627A pdb=" N ARG5J 425 " --> pdb=" O ILE5J 421 " (cutoff:3.500A) Processing helix chain '5J' and resid 434 through 442 Processing helix chain '5J' and resid 446 through 459 removed outlier: 4.143A pdb=" N LYS5J 451 " --> pdb=" O GLU5J 447 " (cutoff:3.500A) Processing helix chain '5J' and resid 465 through 476 Processing helix chain '5J' and resid 483 through 497 removed outlier: 3.709A pdb=" N THR5J 492 " --> pdb=" O ASP5J 488 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER5J 493 " --> pdb=" O ARG5J 489 " (cutoff:3.500A) Processing helix chain '5J' and resid 505 through 516 Processing helix chain '5J' and resid 519 through 531 Processing helix chain '5J' and resid 537 through 553 Processing helix chain '5J' and resid 557 through 569 Processing helix chain '5J' and resid 574 through 586 Processing helix chain '5J' and resid 591 through 603 Processing helix chain '5J' and resid 608 through 620 Processing helix chain '5J' and resid 624 through 637 removed outlier: 5.203A pdb=" N ARG5J 628 " --> pdb=" O PRO5J 625 " (cutoff:3.500A) Processing helix chain '5J' and resid 644 through 654 Processing helix chain '5J' and resid 658 through 671 removed outlier: 3.820A pdb=" N LEU5J 665 " --> pdb=" O ALA5J 661 " (cutoff:3.500A) Processing helix chain '5J' and resid 676 through 687 Processing helix chain '5J' and resid 692 through 704 removed outlier: 3.727A pdb=" N CYS5J 698 " --> pdb=" O ALA5J 694 " (cutoff:3.500A) Processing helix chain '5J' and resid 709 through 720 Processing helix chain '5J' and resid 726 through 738 Processing helix chain '5J' and resid 743 through 755 Processing helix chain '5J' and resid 759 through 772 Processing helix chain '5J' and resid 777 through 789 removed outlier: 3.537A pdb=" N GLU5J 782 " --> pdb=" O GLY5J 778 " (cutoff:3.500A) Processing helix chain '5J' and resid 793 through 806 removed outlier: 3.683A pdb=" N GLU5J 806 " --> pdb=" O LYS5J 802 " (cutoff:3.500A) Processing helix chain '5J' and resid 811 through 820 removed outlier: 3.809A pdb=" N PHE5J 819 " --> pdb=" O SER5J 815 " (cutoff:3.500A) Processing helix chain '5J' and resid 826 through 836 removed outlier: 3.731A pdb=" N VAL5J 831 " --> pdb=" O ARG5J 827 " (cutoff:3.500A) Processing helix chain '5J' and resid 841 through 853 Processing helix chain '5J' and resid 857 through 870 removed outlier: 4.015A pdb=" N GLU5J 862 " --> pdb=" O THR5J 858 " (cutoff:3.500A) Processing helix chain '5J' and resid 876 through 887 removed outlier: 4.000A pdb=" N PHE5J 881 " --> pdb=" O ALA5J 877 " (cutoff:3.500A) Processing helix chain '5J' and resid 891 through 903 removed outlier: 3.815A pdb=" N CYS5J 901 " --> pdb=" O VAL5J 897 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU5J 902 " --> pdb=" O ARG5J 898 " (cutoff:3.500A) Processing helix chain '5J' and resid 912 through 915 No H-bonds generated for 'chain '5J' and resid 912 through 915' Processing helix chain '5J' and resid 919 through 921 No H-bonds generated for 'chain '5J' and resid 919 through 921' Processing helix chain '5J' and resid 926 through 935 Processing helix chain '5X' and resid 166 through 200 Processing helix chain '5X' and resid 242 through 254 Processing helix chain '5X' and resid 288 through 291 No H-bonds generated for 'chain '5X' and resid 288 through 291' Processing helix chain '5X' and resid 309 through 315 Processing helix chain '5X' and resid 319 through 327 Processing helix chain '5X' and resid 330 through 353 Processing helix chain '5X' and resid 357 through 359 No H-bonds generated for 'chain '5X' and resid 357 through 359' Processing helix chain '5X' and resid 367 through 376 Processing helix chain '5X' and resid 400 through 409 Processing helix chain '5X' and resid 416 through 427 Proline residue: 5X 423 - end of helix Processing helix chain '5X' and resid 441 through 455 Proline residue: 5X 448 - end of helix Processing helix chain '5X' and resid 458 through 461 No H-bonds generated for 'chain '5X' and resid 458 through 461' Processing helix chain '5X' and resid 478 through 495 Proline residue: 5X 494 - end of helix Processing helix chain '5X' and resid 508 through 517 removed outlier: 3.621A pdb=" N ARG5X 516 " --> pdb=" O GLY5X 512 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET5X 517 " --> pdb=" O PHE5X 513 " (cutoff:3.500A) Processing helix chain '5X' and resid 526 through 534 Processing helix chain '5X' and resid 551 through 556 Processing helix chain '5X' and resid 560 through 569 removed outlier: 3.796A pdb=" N HIS5X 569 " --> pdb=" O LYS5X 565 " (cutoff:3.500A) Processing helix chain '5X' and resid 572 through 574 No H-bonds generated for 'chain '5X' and resid 572 through 574' Processing helix chain '5X' and resid 580 through 583 Processing helix chain '5X' and resid 585 through 593 Processing helix chain '5X' and resid 595 through 597 No H-bonds generated for 'chain '5X' and resid 595 through 597' Processing helix chain '5X' and resid 611 through 620 Processing helix chain '5X' and resid 635 through 637 No H-bonds generated for 'chain '5X' and resid 635 through 637' Processing helix chain '5X' and resid 648 through 661 removed outlier: 4.490A pdb=" N ARG5X 652 " --> pdb=" O SER5X 649 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS5X 653 " --> pdb=" O GLU5X 650 " (cutoff:3.500A) Processing helix chain '5X' and resid 674 through 686 Processing helix chain '5X' and resid 704 through 712 removed outlier: 3.520A pdb=" N ASN5X 709 " --> pdb=" O PHE5X 705 " (cutoff:3.500A) Processing helix chain '5X' and resid 745 through 755 removed outlier: 3.833A pdb=" N ARG5X 754 " --> pdb=" O HIS5X 750 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR5X 755 " --> pdb=" O ARG5X 751 " (cutoff:3.500A) Processing helix chain '5X' and resid 770 through 784 removed outlier: 3.541A pdb=" N SER5X 773 " --> pdb=" O LYS5X 770 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA5X 774 " --> pdb=" O GLU5X 771 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR5X 777 " --> pdb=" O ALA5X 774 " (cutoff:3.500A) Processing helix chain '5X' and resid 793 through 796 No H-bonds generated for 'chain '5X' and resid 793 through 796' Processing helix chain '5X' and resid 799 through 801 No H-bonds generated for 'chain '5X' and resid 799 through 801' Processing helix chain '5b' and resid 7 through 12 removed outlier: 4.812A pdb=" N HIS5b 12 " --> pdb=" O LYS5b 8 " (cutoff:3.500A) Processing helix chain '5b' and resid 74 through 76 No H-bonds generated for 'chain '5b' and resid 74 through 76' Processing helix chain '5e' and resid 17 through 27 Processing helix chain '5e' and resid 81 through 83 No H-bonds generated for 'chain '5e' and resid 81 through 83' Processing helix chain '5f' and resid 7 through 13 Processing helix chain '5f' and resid 66 through 68 No H-bonds generated for 'chain '5f' and resid 66 through 68' Processing helix chain '5g' and resid 64 through 66 No H-bonds generated for 'chain '5g' and resid 64 through 66' Processing helix chain '62' and resid 2 through 10 removed outlier: 3.631A pdb=" N LEU62 10 " --> pdb=" O PHE62 6 " (cutoff:3.500A) Processing helix chain '62' and resid 64 through 66 No H-bonds generated for 'chain '62' and resid 64 through 66' Processing helix chain '62' and resid 74 through 76 No H-bonds generated for 'chain '62' and resid 74 through 76' Processing helix chain '62' and resid 79 through 94 removed outlier: 3.641A pdb=" N LEU62 91 " --> pdb=" O ARG62 87 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS62 94 " --> pdb=" O ALA62 90 " (cutoff:3.500A) Processing helix chain '63' and resid 17 through 24 removed outlier: 3.532A pdb=" N LEU63 23 " --> pdb=" O ASP63 19 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER63 24 " --> pdb=" O LEU63 20 " (cutoff:3.500A) Processing helix chain '63' and resid 89 through 91 No H-bonds generated for 'chain '63' and resid 89 through 91' Processing helix chain '64' and resid 3 through 9 Processing helix chain '64' and resid 63 through 65 No H-bonds generated for 'chain '64' and resid 63 through 65' Processing helix chain '65' and resid 14 through 21 Processing helix chain '66' and resid 7 through 13 Processing helix chain '66' and resid 67 through 69 No H-bonds generated for 'chain '66' and resid 67 through 69' Processing helix chain '67' and resid 15 through 18 Processing helix chain '68' and resid 6 through 8 No H-bonds generated for 'chain '68' and resid 6 through 8' Processing helix chain '68' and resid 51 through 54 No H-bonds generated for 'chain '68' and resid 51 through 54' Processing helix chain 'R' and resid 373 through 375 No H-bonds generated for 'chain 'R' and resid 373 through 375' Processing helix chain 'R' and resid 396 through 401 Processing helix chain 'R' and resid 434 through 441 Processing helix chain 'R' and resid 462 through 472 removed outlier: 4.408A pdb=" N VAL R 467 " --> pdb=" O ASN R 463 " (cutoff:3.500A) Processing helix chain 'S' and resid 555 through 562 Processing helix chain 'S' and resid 568 through 570 No H-bonds generated for 'chain 'S' and resid 568 through 570' Processing helix chain 'S' and resid 639 through 648 Processing helix chain 'S' and resid 722 through 734 Processing helix chain 'S' and resid 740 through 757 Processing helix chain 'S' and resid 767 through 775 Processing helix chain 'U' and resid 106 through 108 No H-bonds generated for 'chain 'U' and resid 106 through 108' Processing helix chain 'U' and resid 151 through 159 Processing helix chain 'U' and resid 184 through 193 removed outlier: 4.451A pdb=" N ASP U 188 " --> pdb=" O SER U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 199 through 203 Processing helix chain 'U' and resid 234 through 243 Processing helix chain 'U' and resid 247 through 254 Processing helix chain 'U' and resid 256 through 258 No H-bonds generated for 'chain 'U' and resid 256 through 258' Processing helix chain 'U' and resid 270 through 284 removed outlier: 3.586A pdb=" N GLN U 275 " --> pdb=" O LEU U 272 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG U 276 " --> pdb=" O LEU U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 306 Processing helix chain 'U' and resid 319 through 333 Processing helix chain 'U' and resid 344 through 349 Processing helix chain 'U' and resid 367 through 376 removed outlier: 4.143A pdb=" N LEU U 374 " --> pdb=" O LYS U 370 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS U 375 " --> pdb=" O GLU U 371 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN U 376 " --> pdb=" O GLN U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 415 through 418 No H-bonds generated for 'chain 'U' and resid 415 through 418' Processing helix chain 'U' and resid 480 through 483 removed outlier: 3.515A pdb=" N TYR U 483 " --> pdb=" O LEU U 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 480 through 483' Processing sheet with id= A, first strand: chain '41' and resid 53 through 55 Processing sheet with id= B, first strand: chain '41' and resid 57 through 60 removed outlier: 5.837A pdb=" N LYS41 41 " --> pdb=" O ILE41 29 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE41 29 " --> pdb=" O LYS41 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '42' and resid 90 through 96 Processing sheet with id= D, first strand: chain '42' and resid 98 through 101 removed outlier: 6.099A pdb=" N GLU42 68 " --> pdb=" O VAL42 56 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL42 56 " --> pdb=" O GLU42 68 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '43' and resid 55 through 58 Processing sheet with id= F, first strand: chain '43' and resid 60 through 63 removed outlier: 5.496A pdb=" N SER43 44 " --> pdb=" O LEU43 32 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU43 32 " --> pdb=" O SER43 44 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '4A' and resid 570 through 574 removed outlier: 6.595A pdb=" N ARG4A 547 " --> pdb=" O LEU4A 632 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU4A 632 " --> pdb=" O ARG4A 547 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4B' and resid 221 through 224 Processing sheet with id= I, first strand: chain '4B' and resid 257 through 259 removed outlier: 3.710A pdb=" N TYR4B 236 " --> pdb=" O ALA4B 249 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '4B' and resid 279 through 281 Processing sheet with id= K, first strand: chain '4B' and resid 328 through 331 removed outlier: 3.964A pdb=" N ARG4B 328 " --> pdb=" O THR4B 341 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU4B 359 " --> pdb=" O LEU4B 349 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP4B 351 " --> pdb=" O GLU4B 357 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU4B 357 " --> pdb=" O ASP4B 351 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4B' and resid 379 through 381 Processing sheet with id= M, first strand: chain '4B' and resid 422 through 425 Processing sheet with id= N, first strand: chain '4B' and resid 455 through 457 removed outlier: 6.890A pdb=" N THR4B 478 " --> pdb=" O PRO4B 484 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4B' and resid 498 through 500 Processing sheet with id= P, first strand: chain '4D' and resid 35 through 37 removed outlier: 7.929A pdb=" N MET4D 56 " --> pdb=" O PRO4D 79 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL4D 81 " --> pdb=" O MET4D 56 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4b' and resid 15 through 20 removed outlier: 3.922A pdb=" N TYR4b 15 " --> pdb=" O PHE4b 31 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU4b 47 " --> pdb=" O VAL4b 66 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL4b 66 " --> pdb=" O GLU4b 47 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4b' and resid 70 through 72 removed outlier: 3.653A pdb=" N ALA4b 33 " --> pdb=" O ILE4b 41 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS4b 43 " --> pdb=" O PHE4b 31 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE4b 31 " --> pdb=" O CYS4b 43 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '4e' and resid 70 through 75 removed outlier: 5.837A pdb=" N ALA4e 61 " --> pdb=" O LEU4e 74 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N MET4e 41 " --> pdb=" O LEU4e 35 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU4e 35 " --> pdb=" O MET4e 41 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '4e' and resid 77 through 79 removed outlier: 4.035A pdb=" N GLY4e 49 " --> pdb=" O VAL4e 57 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASP4e 59 " --> pdb=" O ILE4e 47 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE4e 47 " --> pdb=" O ASP4e 59 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '4f' and resid 54 through 58 removed outlier: 6.702A pdb=" N GLU4f 49 " --> pdb=" O SER4f 56 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET4f 27 " --> pdb=" O LEU4f 23 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '4f' and resid 32 through 36 removed outlier: 6.601A pdb=" N GLN4f 43 " --> pdb=" O VAL4f 34 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY4f 60 " --> pdb=" O ASN4f 46 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '4g' and resid 69 through 72 removed outlier: 3.754A pdb=" N MET4g 69 " --> pdb=" O LYS4g 20 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL4g 41 " --> pdb=" O ARG4g 32 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '51' and resid 53 through 55 Processing sheet with id= Y, first strand: chain '51' and resid 57 through 60 removed outlier: 5.837A pdb=" N LYS51 41 " --> pdb=" O ILE51 29 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE51 29 " --> pdb=" O LYS51 41 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '52' and resid 90 through 96 Processing sheet with id= AA, first strand: chain '52' and resid 98 through 101 removed outlier: 3.829A pdb=" N ASN52 64 " --> pdb=" O ASP52 60 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP52 60 " --> pdb=" O ASN52 64 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA52 58 " --> pdb=" O VAL52 66 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU52 68 " --> pdb=" O VAL52 56 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL52 56 " --> pdb=" O GLU52 68 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '53' and resid 55 through 58 Processing sheet with id= AC, first strand: chain '53' and resid 60 through 63 removed outlier: 6.381A pdb=" N SER53 44 " --> pdb=" O LEU53 32 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU53 32 " --> pdb=" O SER53 44 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '5A' and resid 482 through 488 Processing sheet with id= AE, first strand: chain '5A' and resid 227 through 229 Processing sheet with id= AF, first strand: chain '5A' and resid 516 through 518 Processing sheet with id= AG, first strand: chain '5A' and resid 895 through 900 Processing sheet with id= AH, first strand: chain '5A' and resid 1174 through 1178 removed outlier: 6.414A pdb=" N ARG5A1100 " --> pdb=" O ILE5A1085 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE5A1085 " --> pdb=" O ARG5A1100 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '5A' and resid 1016 through 1018 Processing sheet with id= AJ, first strand: chain '5A' and resid 1184 through 1189 removed outlier: 7.132A pdb=" N LEU5A1216 " --> pdb=" O THR5A1225 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN5A1227 " --> pdb=" O TRP5A1214 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TRP5A1214 " --> pdb=" O GLN5A1227 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '5A' and resid 1342 through 1346 Processing sheet with id= AL, first strand: chain '5A' and resid 1501 through 1503 Processing sheet with id= AM, first strand: chain '5A' and resid 1608 through 1611 Processing sheet with id= AN, first strand: chain '5A' and resid 1916 through 1918 removed outlier: 4.215A pdb=" N GLN5A1816 " --> pdb=" O ASN5A1811 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN5A1860 " --> pdb=" O TRP5A1778 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL5A1780 " --> pdb=" O GLN5A1860 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE5A1862 " --> pdb=" O VAL5A1780 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL5A1883 " --> pdb=" O ILE5A1861 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL5A1863 " --> pdb=" O VAL5A1883 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS5A1885 " --> pdb=" O VAL5A1863 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '5A' and resid 1787 through 1792 removed outlier: 4.295A pdb=" N ARG5A1787 " --> pdb=" O ILE5A1803 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '5A' and resid 2090 through 2092 removed outlier: 6.260A pdb=" N CYS5A2223 " --> pdb=" O TYR5A2091 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU5A2128 " --> pdb=" O LEU5A2175 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP5A2177 " --> pdb=" O GLY5A2126 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY5A2126 " --> pdb=" O TRP5A2177 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL5A2131 " --> pdb=" O ILE5A2142 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE5A2142 " --> pdb=" O VAL5A2131 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR5A2103 " --> pdb=" O LYS5A2140 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE5A2142 " --> pdb=" O THR5A2103 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE5A2105 " --> pdb=" O ILE5A2142 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N CYS5A2144 " --> pdb=" O ILE5A2105 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N VAL5A2146 " --> pdb=" O PRO5A2107 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN5A2260 " --> pdb=" O TYR5A2104 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU5A2106 " --> pdb=" O GLN5A2260 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU5A2262 " --> pdb=" O LEU5A2106 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '5A' and resid 2144 through 2146 removed outlier: 6.488A pdb=" N PHE5A2270 " --> pdb=" O ILE5A2145 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain '5A' and resid 2228 through 2230 Processing sheet with id= AS, first strand: chain '5A' and resid 1637 through 1640 removed outlier: 3.890A pdb=" N VAL5A1639 " --> pdb=" O THR5A1655 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N THR5A1655 " --> pdb=" O VAL5A1639 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '5B' and resid 436 through 438 removed outlier: 6.402A pdb=" N GLY5B 865 " --> pdb=" O GLU5B 686 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR5B 688 " --> pdb=" O GLY5B 865 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY5B 867 " --> pdb=" O THR5B 688 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL5B 690 " --> pdb=" O GLY5B 867 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU5B 869 " --> pdb=" O VAL5B 690 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE5B 692 " --> pdb=" O LEU5B 869 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR5B 871 " --> pdb=" O ILE5B 692 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '5B' and resid 673 through 675 removed outlier: 6.121A pdb=" N LEU5B 500 " --> pdb=" O PHE5B 674 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LYS5B 537 " --> pdb=" O ARG5B 610 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE5B 612 " --> pdb=" O LYS5B 537 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE5B 539 " --> pdb=" O ILE5B 612 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU5B 614 " --> pdb=" O ILE5B 539 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE5B 541 " --> pdb=" O LEU5B 614 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '5B' and resid 832 through 835 Processing sheet with id= AW, first strand: chain '5B' and resid 970 through 972 Processing sheet with id= AX, first strand: chain '5B' and resid 1184 through 1192 Processing sheet with id= AY, first strand: chain '5B' and resid 1279 through 1285 Processing sheet with id= AZ, first strand: chain '5B' and resid 1511 through 1513 removed outlier: 6.533A pdb=" N PHE5B1347 " --> pdb=" O PHE5B1512 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '5B' and resid 1522 through 1530 Processing sheet with id= BB, first strand: chain '5B' and resid 1667 through 1670 Processing sheet with id= BC, first strand: chain '5B' and resid 1802 through 1805 Processing sheet with id= BD, first strand: chain '5B' and resid 2017 through 2023 Processing sheet with id= BE, first strand: chain '5B' and resid 2118 through 2124 removed outlier: 3.710A pdb=" N GLN5B2118 " --> pdb=" O PHE5B2108 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP5B2070 " --> pdb=" O LEU5B2076 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU5B2076 " --> pdb=" O ASP5B2070 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '5C' and resid 316 through 318 removed outlier: 9.095A pdb=" N CYS5C 308 " --> pdb=" O VAL5C 253 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL5C 255 " --> pdb=" O CYS5C 308 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER5C 310 " --> pdb=" O VAL5C 255 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE5C 257 " --> pdb=" O SER5C 310 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ARG5C 130 " --> pdb=" O SER5C 197 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU5C 199 " --> pdb=" O ARG5C 130 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL5C 132 " --> pdb=" O LEU5C 199 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN5C 201 " --> pdb=" O VAL5C 132 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU5C 134 " --> pdb=" O ASN5C 201 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N MET5C 203 " --> pdb=" O LEU5C 134 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY5C 136 " --> pdb=" O MET5C 203 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '5C' and resid 348 through 350 Processing sheet with id= BH, first strand: chain '5C' and resid 522 through 526 removed outlier: 6.643A pdb=" N PHE5C 493 " --> pdb=" O THR5C 479 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET5C 481 " --> pdb=" O HIS5C 491 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS5C 491 " --> pdb=" O MET5C 481 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain '5C' and resid 530 through 533 removed outlier: 4.006A pdb=" N LEU5C 530 " --> pdb=" O VAL5C 541 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain '5C' and resid 653 through 655 removed outlier: 4.085A pdb=" N HIS5C 627 " --> pdb=" O VAL5C 592 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR5C 618 " --> pdb=" O LEU5C 630 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain '5C' and resid 663 through 666 removed outlier: 3.507A pdb=" N HIS5C 903 " --> pdb=" O TYR5C 831 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE5C 833 " --> pdb=" O PHE5C 901 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE5C 901 " --> pdb=" O PHE5C 833 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU5C 835 " --> pdb=" O SER5C 899 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N SER5C 899 " --> pdb=" O GLU5C 835 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN5C 837 " --> pdb=" O SER5C 897 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER5C 897 " --> pdb=" O GLN5C 837 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain '5C' and resid 674 through 676 removed outlier: 6.619A pdb=" N ILE5C 688 " --> pdb=" O ILE5C 791 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE5C 791 " --> pdb=" O ILE5C 688 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU5C 690 " --> pdb=" O PHE5C 789 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE5C 789 " --> pdb=" O GLU5C 690 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE5C 744 " --> pdb=" O PHE5C 789 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE5C 791 " --> pdb=" O ILE5C 744 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL5C 746 " --> pdb=" O ILE5C 791 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP5C 793 " --> pdb=" O VAL5C 746 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain '5C' and resid 831 through 839 removed outlier: 6.269A pdb=" N PHE5C 874 " --> pdb=" O VAL5C 857 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL5C 857 " --> pdb=" O PHE5C 874 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain '5D' and resid 6 through 8 removed outlier: 5.898A pdb=" N VAL5D 25 " --> pdb=" O VAL5D 57 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR5D 59 " --> pdb=" O VAL5D 25 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL5D 27 " --> pdb=" O TYR5D 59 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL5D 61 " --> pdb=" O VAL5D 27 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG5D 29 " --> pdb=" O VAL5D 61 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE5D 83 " --> pdb=" O ILE5D 90 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain '5D' and resid 91 through 93 Processing sheet with id= BP, first strand: chain '5O' and resid 61 through 63 Processing sheet with id= BQ, first strand: chain '5O' and resid 69 through 74 removed outlier: 7.154A pdb=" N ALA5O 84 " --> pdb=" O TYR5O 70 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS5O 72 " --> pdb=" O ALA5O 82 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA5O 82 " --> pdb=" O CYS5O 72 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE5O 74 " --> pdb=" O THR5O 80 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR5O 80 " --> pdb=" O PHE5O 74 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY5O 85 " --> pdb=" O LEU5O 89 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU5O 89 " --> pdb=" O GLY5O 85 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA5O 103 " --> pdb=" O LEU5O 92 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN5O 94 " --> pdb=" O ASN5O 101 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN5O 101 " --> pdb=" O ASN5O 94 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain '5O' and resid 112 through 117 removed outlier: 6.602A pdb=" N ALA5O 127 " --> pdb=" O MET5O 113 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU5O 115 " --> pdb=" O PHE5O 125 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE5O 125 " --> pdb=" O LEU5O 115 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR5O 117 " --> pdb=" O MET5O 123 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N MET5O 123 " --> pdb=" O TYR5O 117 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP5O 137 " --> pdb=" O ARG5O 143 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG5O 143 " --> pdb=" O ASP5O 137 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain '5O' and resid 175 through 177 Processing sheet with id= BT, first strand: chain '5O' and resid 230 through 232 removed outlier: 5.226A pdb=" N ASP5O 216 " --> pdb=" O GLY5O 212 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY5O 212 " --> pdb=" O ASP5O 216 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain '5O' and resid 238 through 243 removed outlier: 6.607A pdb=" N ASN5O 253 " --> pdb=" O THR5O 239 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU5O 241 " --> pdb=" O LEU5O 251 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU5O 251 " --> pdb=" O LEU5O 241 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU5O 243 " --> pdb=" O TYR5O 249 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR5O 249 " --> pdb=" O LEU5O 243 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA5O 254 " --> pdb=" O THR5O 258 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR5O 258 " --> pdb=" O ALA5O 254 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS5O 275 " --> pdb=" O VAL5O 261 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP5O 263 " --> pdb=" O CYS5O 273 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N CYS5O 273 " --> pdb=" O ASP5O 263 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain '5O' and resid 291 through 293 Processing sheet with id= BW, first strand: chain '5O' and resid 154 through 159 removed outlier: 6.610A pdb=" N GLY5O 170 " --> pdb=" O ASN5O 155 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS5O 157 " --> pdb=" O CYS5O 168 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS5O 168 " --> pdb=" O CYS5O 157 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain '5O' and resid 309 through 312 Processing sheet with id= BY, first strand: chain '5O' and resid 330 through 335 removed outlier: 6.808A pdb=" N ALA5O 345 " --> pdb=" O ASN5O 331 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL5O 333 " --> pdb=" O ILE5O 343 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE5O 343 " --> pdb=" O VAL5O 333 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain '5X' and resid 379 through 382 Processing sheet with id= CA, first strand: chain '5X' and resid 640 through 645 removed outlier: 6.648A pdb=" N ILE5X 668 " --> pdb=" O VAL5X 737 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain '5b' and resid 63 through 68 removed outlier: 3.950A pdb=" N GLU5b 63 " --> pdb=" O ARG5b 49 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG5b 49 " --> pdb=" O GLU5b 63 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N CYS5b 45 " --> pdb=" O LEU5b 67 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG5b 18 " --> pdb=" O VAL5b 82 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL5b 82 " --> pdb=" O ARG5b 18 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE5b 20 " --> pdb=" O MET5b 80 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N MET5b 80 " --> pdb=" O ILE5b 20 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain '5b' and resid 70 through 72 removed outlier: 6.675A pdb=" N CYS5b 43 " --> pdb=" O PHE5b 31 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE5b 31 " --> pdb=" O CYS5b 43 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain '5e' and resid 42 through 44 removed outlier: 3.582A pdb=" N ALA5e 61 " --> pdb=" O GLY5e 75 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY5e 75 " --> pdb=" O ALA5e 61 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU5e 63 " --> pdb=" O GLN5e 73 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN5e 73 " --> pdb=" O GLU5e 63 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain '5e' and resid 56 through 58 Processing sheet with id= CF, first strand: chain '5f' and resid 48 through 51 removed outlier: 4.858A pdb=" N MET5f 27 " --> pdb=" O LEU5f 23 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain '5f' and resid 62 through 64 removed outlier: 6.330A pdb=" N ALA5f 45 " --> pdb=" O LEU5f 33 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU5f 33 " --> pdb=" O ALA5f 45 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain '5g' and resid 69 through 72 removed outlier: 3.753A pdb=" N MET5g 69 " --> pdb=" O LYS5g 20 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL5g 41 " --> pdb=" O ARG5g 32 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain '62' and resid 67 through 71 removed outlier: 6.844A pdb=" N GLU62 18 " --> pdb=" O ARG62 68 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL62 70 " --> pdb=" O VAL62 16 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL62 16 " --> pdb=" O VAL62 70 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS62 39 " --> pdb=" O HIS62 30 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain '63' and resid 73 through 82 removed outlier: 3.573A pdb=" N ARG63 37 " --> pdb=" O MET63 33 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain '63' and resid 84 through 87 removed outlier: 6.699A pdb=" N GLY63 55 " --> pdb=" O LEU63 43 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU63 43 " --> pdb=" O GLY63 55 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain '64' and resid 52 through 56 removed outlier: 7.100A pdb=" N CYS64 45 " --> pdb=" O PHE64 53 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG64 55 " --> pdb=" O VAL64 43 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL64 43 " --> pdb=" O ARG64 55 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain '64' and resid 58 through 61 removed outlier: 5.811A pdb=" N ARG64 41 " --> pdb=" O LEU64 29 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU64 29 " --> pdb=" O ARG64 41 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain '65' and resid 63 through 67 removed outlier: 6.827A pdb=" N GLU65 56 " --> pdb=" O ARG65 65 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LYS65 34 " --> pdb=" O MET65 30 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain '65' and resid 71 through 74 removed outlier: 3.646A pdb=" N GLY65 42 " --> pdb=" O VAL65 50 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU65 52 " --> pdb=" O LEU65 40 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU65 40 " --> pdb=" O GLU65 52 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain '66' and resid 55 through 58 removed outlier: 6.586A pdb=" N GLU66 50 " --> pdb=" O LEU66 56 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain '66' and resid 63 through 65 removed outlier: 6.848A pdb=" N GLU66 46 " --> pdb=" O LEU66 34 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU66 34 " --> pdb=" O GLU66 46 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain '67' and resid 68 through 72 removed outlier: 5.689A pdb=" N THR67 51 " --> pdb=" O LEU67 71 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain '67' and resid 74 through 76 removed outlier: 6.119A pdb=" N ASP67 49 " --> pdb=" O LEU67 37 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU67 37 " --> pdb=" O ASP67 49 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain '68' and resid 67 through 72 removed outlier: 6.499A pdb=" N ILE68 16 " --> pdb=" O ALA68 68 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE68 70 " --> pdb=" O ALA68 14 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA68 14 " --> pdb=" O ILE68 70 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLU68 72 " --> pdb=" O THR68 12 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR68 12 " --> pdb=" O GLU68 72 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG68 21 " --> pdb=" O THR68 17 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE68 37 " --> pdb=" O LYS68 28 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'R' and resid 453 through 456 Processing sheet with id= CV, first strand: chain 'U' and resid 142 through 144 Processing sheet with id= CW, first strand: chain 'U' and resid 172 through 174 removed outlier: 4.251A pdb=" N PHE U 172 " --> pdb=" O ILE U 181 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'U' and resid 351 through 353 Processing sheet with id= CY, first strand: chain 'U' and resid 390 through 394 removed outlier: 8.101A pdb=" N LEU U 391 " --> pdb=" O TYR U 449 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE U 451 " --> pdb=" O LEU U 391 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU U 393 " --> pdb=" O ILE U 451 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N CYS U 453 " --> pdb=" O LEU U 393 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS U 553 " --> pdb=" O LEU U 499 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU U 499 " --> pdb=" O LYS U 553 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE U 500 " --> pdb=" O LEU U 519 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP U 526 " --> pdb=" O ILE U 537 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'U' and resid 412 through 414 removed outlier: 6.007A pdb=" N ILE U 470 " --> pdb=" O VAL U 413 " (cutoff:3.500A) No H-bonds generated for sheet with id= CZ Processing sheet with id= DA, first strand: chain 'U' and resid 427 through 432 Processing sheet with id= DB, first strand: chain 'U' and resid 457 through 459 3224 hydrogen bonds defined for protein. 8826 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 224 hydrogen bonds 404 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 147 stacking parallelities Total time for adding SS restraints: 53.39 Time building geometry restraints manager: 31.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 14141 1.26 - 1.41: 23605 1.41 - 1.57: 52561 1.57 - 1.72: 599 1.72 - 1.87: 723 Bond restraints: 91629 Sorted by residual: bond pdb=" CBQ M7M 4 0 " pdb=" CBX M7M 4 0 " ideal model delta sigma weight residual 1.295 1.510 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C VAL66 70 " pdb=" O VAL66 70 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.03e-02 9.43e+03 9.98e+01 bond pdb=" CBQ M7M 4 0 " pdb=" OBR M7M 4 0 " ideal model delta sigma weight residual 1.618 1.422 0.196 2.00e-02 2.50e+03 9.57e+01 bond pdb=" C GLN67 61 " pdb=" O GLN67 61 " ideal model delta sigma weight residual 1.233 1.111 0.123 1.26e-02 6.30e+03 9.46e+01 bond pdb=" O3' C 4 87 " pdb=" P G 4 88 " ideal model delta sigma weight residual 1.607 1.745 -0.138 1.50e-02 4.44e+03 8.47e+01 ... (remaining 91624 not shown) Histogram of bond angle deviations from ideal: 87.31 - 98.50: 38 98.50 - 109.69: 17487 109.69 - 120.88: 80130 120.88 - 132.07: 27251 132.07 - 143.26: 251 Bond angle restraints: 125157 Sorted by residual: angle pdb=" CA ASP65 70 " pdb=" CB ASP65 70 " pdb=" CG ASP65 70 " ideal model delta sigma weight residual 112.60 124.97 -12.37 1.00e+00 1.00e+00 1.53e+02 angle pdb=" N GLY5A1550 " pdb=" CA GLY5A1550 " pdb=" C GLY5A1550 " ideal model delta sigma weight residual 111.03 127.03 -16.00 1.40e+00 5.10e-01 1.31e+02 angle pdb=" N PHE5A1551 " pdb=" CA PHE5A1551 " pdb=" C PHE5A1551 " ideal model delta sigma weight residual 109.56 89.05 20.51 1.84e+00 2.95e-01 1.24e+02 angle pdb=" N VAL5A 384 " pdb=" CA VAL5A 384 " pdb=" C VAL5A 384 " ideal model delta sigma weight residual 109.58 123.64 -14.06 1.29e+00 6.01e-01 1.19e+02 angle pdb=" O3' C 4 87 " pdb=" P G 4 88 " pdb=" O5' G 4 88 " ideal model delta sigma weight residual 104.00 119.38 -15.38 1.50e+00 4.44e-01 1.05e+02 ... (remaining 125152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 54155 35.83 - 71.65: 1779 71.65 - 107.48: 153 107.48 - 143.31: 5 143.31 - 179.14: 12 Dihedral angle restraints: 56104 sinusoidal: 25864 harmonic: 30240 Sorted by residual: dihedral pdb=" CA GLN4C 350 " pdb=" C GLN4C 350 " pdb=" N ARG4C 351 " pdb=" CA ARG4C 351 " ideal model delta harmonic sigma weight residual 180.00 122.75 57.25 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA ILE S 566 " pdb=" C ILE S 566 " pdb=" N PRO S 567 " pdb=" CA PRO S 567 " ideal model delta harmonic sigma weight residual 180.00 122.75 57.25 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA SER4A 538 " pdb=" C SER4A 538 " pdb=" N GLN4A 539 " pdb=" CA GLN4A 539 " ideal model delta harmonic sigma weight residual -180.00 -126.77 -53.23 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 56101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 13980 0.224 - 0.448: 131 0.448 - 0.672: 5 0.672 - 0.896: 0 0.896 - 1.120: 1 Chirality restraints: 14117 Sorted by residual: chirality pdb=" CA PRO R 405 " pdb=" N PRO R 405 " pdb=" C PRO R 405 " pdb=" CB PRO R 405 " both_signs ideal model delta sigma weight residual False 2.72 1.60 1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CA LEU68 59 " pdb=" N LEU68 59 " pdb=" C LEU68 59 " pdb=" CB LEU68 59 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" CA ASP65 53 " pdb=" N ASP65 53 " pdb=" C ASP65 53 " pdb=" CB ASP65 53 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 ... (remaining 14114 not shown) Planarity restraints: 15038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR63 30 " -0.179 2.00e-02 2.50e+03 1.15e-01 2.66e+02 pdb=" CG TYR63 30 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR63 30 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 TYR63 30 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR63 30 " 0.086 2.00e-02 2.50e+03 pdb=" CE2 TYR63 30 " 0.104 2.00e-02 2.50e+03 pdb=" CZ TYR63 30 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR63 30 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR66 51 " -0.174 2.00e-02 2.50e+03 1.10e-01 2.42e+02 pdb=" CG TYR66 51 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR66 51 " 0.103 2.00e-02 2.50e+03 pdb=" CD2 TYR66 51 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR66 51 " 0.072 2.00e-02 2.50e+03 pdb=" CE2 TYR66 51 " 0.114 2.00e-02 2.50e+03 pdb=" CZ TYR66 51 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR66 51 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR63 46 " 0.206 2.00e-02 2.50e+03 1.08e-01 2.32e+02 pdb=" CG TYR63 46 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR63 46 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR63 46 " -0.135 2.00e-02 2.50e+03 pdb=" CE1 TYR63 46 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR63 46 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR63 46 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR63 46 " 0.121 2.00e-02 2.50e+03 ... (remaining 15035 not shown) Histogram of nonbonded interaction distances: 0.64 - 1.50: 11 1.50 - 2.35: 156 2.35 - 3.20: 76977 3.20 - 4.05: 248948 4.05 - 4.90: 448614 Warning: very small nonbonded interaction distances. Nonbonded interactions: 774706 Sorted by model distance: nonbonded pdb=" CE1 PHE R 404 " pdb=" OD1 ASP R 434 " model vdw 0.644 3.340 nonbonded pdb=" CZ PHE R 404 " pdb=" OD1 ASP R 434 " model vdw 0.767 3.340 nonbonded pdb=" CZ ARG X 135 " pdb=" NE2 GLN5A1595 " model vdw 0.880 3.350 nonbonded pdb=" NE ARG X 135 " pdb=" NE2 GLN5A1595 " model vdw 1.050 3.200 nonbonded pdb=" C1' G 5 77 " pdb=" NZ LYS5O 184 " model vdw 1.106 3.550 ... (remaining 774701 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 '41' selection = chain '51' } ncs_group { reference = (chain '42' and (resid 22 through 77 or resid 87 through 113)) selection = (chain '52' and resid 22 through 113) } ncs_group { reference = (chain '43' and resid 3 through 84) selection = (chain '53' and resid 3 through 84) } ncs_group { reference = (chain '4b' and (resid 8 through 50 or resid 61 through 88)) selection = (chain '5b' and resid 8 through 88) } ncs_group { reference = chain '4e' selection = (chain '5e' and resid 14 through 89) } ncs_group { reference = chain '4f' selection = (chain '5f' and resid 4 through 75) } ncs_group { reference = chain '4g' selection = chain '5g' } 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=0.01 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 19.070 Check model and map are aligned: 1.320 Set scattering table: 0.860 Process input model: 229.650 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.370 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:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 267.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 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 : 0.010 0.215 91629 Z= 0.644 Angle : 1.215 34.029 125157 Z= 0.695 Chirality : 0.069 1.120 14117 Planarity : 0.009 0.250 15038 Dihedral : 17.139 179.136 36509 Min Nonbonded Distance : 0.644 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.11 % Favored : 94.50 % Rotamer: Outliers : 1.79 % Allowed : 7.33 % Favored : 90.89 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.22 % 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: -3.43 (0.07), residues: 10226 helix: -2.59 (0.06), residues: 4004 sheet: -1.73 (0.12), residues: 1583 loop : -2.03 (0.08), residues: 4639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP5A 750 HIS 0.025 0.002 HIS65 27 PHE 0.074 0.004 PHE62 3 TYR 0.206 0.006 TYR63 46 ARG 0.067 0.001 ARG67 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2072 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1910 time to evaluate : 7.719 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: X 104 MET cc_start: 0.2951 (mmt) cc_final: 0.1521 (tmm) REVERT: 41 8 MET cc_start: 0.3253 (OUTLIER) cc_final: 0.2662 (tmt) REVERT: 41 57 THR cc_start: 0.4347 (OUTLIER) cc_final: 0.4088 (t) REVERT: 41 79 LEU cc_start: 0.6573 (mt) cc_final: 0.5896 (tt) REVERT: 4A 504 MET cc_start: 0.5691 (ttp) cc_final: 0.5274 (ptp) REVERT: 4C 100 THR cc_start: 0.7545 (t) cc_final: 0.7094 (m) REVERT: 4C 193 MET cc_start: 0.7446 (ppp) cc_final: 0.7110 (ppp) REVERT: 4C 331 TRP cc_start: 0.6222 (m-10) cc_final: 0.5890 (m-10) REVERT: 4C 341 LYS cc_start: 0.5970 (tttt) cc_final: 0.5745 (mptp) REVERT: 4C 359 TYR cc_start: 0.5805 (m-80) cc_final: 0.5235 (m-80) REVERT: 4C 361 LYS cc_start: 0.5848 (mttt) cc_final: 0.5227 (mmtm) REVERT: 4C 362 MET cc_start: 0.5528 (mmm) cc_final: 0.5246 (mmm) REVERT: 4D 113 LYS cc_start: 0.6912 (tptt) cc_final: 0.6628 (tppt) REVERT: 4b 17 MET cc_start: 0.2371 (tpp) cc_final: 0.2070 (tpp) REVERT: 4b 28 ILE cc_start: 0.6241 (mt) cc_final: 0.5929 (pp) REVERT: 4e 14 MET cc_start: 0.1769 (tpp) cc_final: 0.1339 (mmp) REVERT: 4g 13 MET cc_start: 0.2788 (mmm) cc_final: 0.2391 (pp-130) REVERT: 4g 43 ASP cc_start: 0.5498 (OUTLIER) cc_final: 0.4715 (t70) REVERT: 4g 44 GLU cc_start: 0.4073 (OUTLIER) cc_final: 0.3355 (mp0) REVERT: 51 44 LYS cc_start: 0.4689 (OUTLIER) cc_final: 0.4226 (mmmm) REVERT: 53 19 THR cc_start: 0.7805 (t) cc_final: 0.7200 (m) REVERT: 5A 736 GLU cc_start: 0.7787 (tt0) cc_final: 0.7443 (tp30) REVERT: 5A 1070 ASP cc_start: 0.7591 (p0) cc_final: 0.7131 (t0) REVERT: 5A 1143 MET cc_start: 0.8389 (mmm) cc_final: 0.8188 (mmt) REVERT: 5A 1400 ASN cc_start: 0.7476 (t0) cc_final: 0.7265 (t160) REVERT: 5A 1604 LEU cc_start: 0.8361 (mt) cc_final: 0.8098 (mm) REVERT: 5A 1607 GLU cc_start: 0.7498 (tt0) cc_final: 0.7259 (tt0) REVERT: 5A 1843 GLU cc_start: 0.7174 (pt0) cc_final: 0.6760 (pp20) REVERT: 5A 1888 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6479 (mm-30) REVERT: 5A 1911 GLU cc_start: 0.6706 (tt0) cc_final: 0.6273 (tp30) REVERT: 5A 2014 MET cc_start: 0.4836 (ttt) cc_final: 0.4449 (ttm) REVERT: 5B 67 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7421 (mtt-85) REVERT: 5B 929 MET cc_start: 0.7521 (mtm) cc_final: 0.7277 (mtm) REVERT: 5B 1050 GLU cc_start: 0.7684 (mp0) cc_final: 0.7246 (mt-10) REVERT: 5B 1081 MET cc_start: 0.8318 (ttp) cc_final: 0.8062 (ttp) REVERT: 5B 1187 SER cc_start: 0.8195 (m) cc_final: 0.7982 (p) REVERT: 5B 1196 SER cc_start: 0.7877 (t) cc_final: 0.7674 (m) REVERT: 5B 1207 ASP cc_start: 0.6366 (t0) cc_final: 0.6136 (t0) REVERT: 5B 1229 ASP cc_start: 0.7353 (m-30) cc_final: 0.6961 (m-30) REVERT: 5B 1631 LEU cc_start: 0.8402 (tp) cc_final: 0.8176 (mt) REVERT: 5B 1687 MET cc_start: 0.8929 (mtt) cc_final: 0.8681 (mtt) REVERT: 5B 1986 MET cc_start: 0.1383 (ptp) cc_final: 0.0281 (tpt) REVERT: 5C 298 LEU cc_start: 0.7185 (pt) cc_final: 0.5498 (pt) REVERT: 5C 350 ASN cc_start: 0.8077 (t0) cc_final: 0.7864 (t0) REVERT: 5C 355 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8143 (tttt) REVERT: 5C 726 LEU cc_start: 0.8109 (pp) cc_final: 0.7815 (pt) REVERT: 5C 837 GLN cc_start: 0.7827 (tt0) cc_final: 0.7558 (tt0) REVERT: 5D 53 LYS cc_start: 0.7730 (ttpp) cc_final: 0.7463 (ttpp) REVERT: 5D 93 ASP cc_start: 0.8178 (t70) cc_final: 0.7929 (t70) REVERT: 5D 141 ARG cc_start: 0.7530 (mtp85) cc_final: 0.7233 (mmm160) REVERT: 5J 133 MET cc_start: 0.7391 (mmm) cc_final: 0.7094 (tpt) REVERT: 5J 317 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7248 (ttp-110) REVERT: 5J 341 LYS cc_start: 0.7378 (mmtp) cc_final: 0.6654 (mmmt) REVERT: 5J 367 ARG cc_start: 0.5728 (ttm-80) cc_final: 0.5481 (tpm170) REVERT: 5J 505 GLN cc_start: 0.6185 (mt0) cc_final: 0.5542 (tp-100) REVERT: 5J 642 GLU cc_start: 0.2928 (mp0) cc_final: 0.2588 (pm20) REVERT: 5J 878 TRP cc_start: 0.5770 (m100) cc_final: 0.5445 (m100) REVERT: 5X 186 ARG cc_start: 0.7570 (tmm160) cc_final: 0.7070 (ptm-80) REVERT: 5X 352 TRP cc_start: 0.4788 (t-100) cc_final: 0.4583 (t-100) REVERT: 5X 359 GLN cc_start: 0.3996 (pt0) cc_final: 0.3720 (mp10) REVERT: 5X 369 ASP cc_start: 0.5383 (t0) cc_final: 0.5056 (m-30) REVERT: 5X 375 GLU cc_start: 0.6555 (tm-30) cc_final: 0.6084 (tm-30) REVERT: 5b 30 THR cc_start: 0.7644 (m) cc_final: 0.7404 (m) REVERT: 5b 36 LYS cc_start: 0.6650 (pttt) cc_final: 0.6049 (mptt) REVERT: 5b 76 ASN cc_start: 0.5880 (m110) cc_final: 0.5342 (t0) REVERT: 5f 11 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.4775 (mt) REVERT: 62 54 MET cc_start: 0.1950 (mtt) cc_final: 0.0987 (ptm) REVERT: 64 56 MET cc_start: -0.0451 (mtm) cc_final: -0.1562 (tmm) REVERT: 68 91 LEU cc_start: 0.1608 (OUTLIER) cc_final: 0.1024 (mt) REVERT: R 445 LYS cc_start: 0.7111 (tttm) cc_final: 0.6849 (mmpt) REVERT: S 719 LYS cc_start: 0.6231 (mmtm) cc_final: 0.5839 (tmtt) REVERT: S 747 MET cc_start: 0.7066 (ttt) cc_final: 0.6812 (ttm) REVERT: S 750 LEU cc_start: 0.7281 (mt) cc_final: 0.6476 (pp) REVERT: U 107 TYR cc_start: 0.8582 (m-80) cc_final: 0.8248 (m-80) REVERT: U 340 LYS cc_start: 0.7136 (tppt) cc_final: 0.6751 (tptp) REVERT: U 389 MET cc_start: 0.8663 (mmt) cc_final: 0.8427 (tpp) REVERT: U 402 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7836 (pptt) REVERT: U 541 MET cc_start: 0.7738 (mtp) cc_final: 0.7391 (mmt) outliers start: 162 outliers final: 28 residues processed: 2048 average time/residue: 1.7513 time to fit residues: 4806.9188 Evaluate side-chains 1079 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1044 time to evaluate : 7.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 41 residue 8 MET Chi-restraints excluded: chain 41 residue 15 VAL Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 55 LEU Chi-restraints excluded: chain 41 residue 57 THR Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4g residue 43 ASP Chi-restraints excluded: chain 4g residue 44 GLU Chi-restraints excluded: chain 51 residue 4 VAL Chi-restraints excluded: chain 51 residue 44 LYS Chi-restraints excluded: chain 51 residue 57 THR Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1606 ILE Chi-restraints excluded: chain 5B residue 203 VAL Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1228 VAL Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1698 ASP Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 507 VAL Chi-restraints excluded: chain 5D residue 68 ASP Chi-restraints excluded: chain 5J residue 296 LEU Chi-restraints excluded: chain 5J residue 501 ILE Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5f residue 11 LEU Chi-restraints excluded: chain 5g residue 44 GLU Chi-restraints excluded: chain 62 residue 44 SER Chi-restraints excluded: chain 63 residue 34 ARG Chi-restraints excluded: chain 68 residue 13 VAL Chi-restraints excluded: chain 68 residue 90 PRO Chi-restraints excluded: chain 68 residue 91 LEU Chi-restraints excluded: chain S residue 559 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 883 optimal weight: 4.9990 chunk 792 optimal weight: 0.4980 chunk 439 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 534 optimal weight: 0.9980 chunk 423 optimal weight: 0.8980 chunk 819 optimal weight: 20.0000 chunk 317 optimal weight: 0.0470 chunk 498 optimal weight: 0.9980 chunk 610 optimal weight: 20.0000 chunk 949 optimal weight: 0.0570 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 41 24 GLN 42 49 ASN 42 69 ASN 42 112 ASN 4A 425 ASN 4A 508 GLN 4A 600 HIS 4A 650 GLN 4B 183 ASN ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 360 HIS 4B 414 ASN 4C 111 HIS 4C 332 GLN 4C 389 GLN 4D 47 ASN 4D 68 HIS 4f 6 ASN 4g 26 HIS 51 64 ASN 52 41 GLN ** 53 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 210 HIS ** 5A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 243 ASN 5A 325 HIS 5A 434 HIS 5A 448 GLN 5A 495 GLN 5A 505 ASN 5A 542 ASN 5A 563 GLN 5A 691 HIS 5A 775 ASN 5A 875 HIS 5A1003 HIS 5A1014 ASN 5A1096 HIS 5A1159 ASN 5A1241 HIS 5A1296 GLN 5A1332 HIS 5A1345 GLN 5A1543 ASN 5A1595 GLN 5A1658 GLN 5A1737 ASN 5A1830 GLN 5A2084 HIS 5A2166 HIS 5A2203 ASN 5A2246 ASN 5A2260 GLN 5A2276 GLN 5A2306 HIS 5A2321 GLN 5B 64 GLN ** 5B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 304 ASN 5B 313 ASN 5B 323 GLN 5B 446 HIS 5B 485 GLN 5B 524 HIS 5B 574 GLN 5B 638 ASN 5B 687 GLN 5B 785 HIS 5B 832 GLN 5B 884 ASN ** 5B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1003 GLN 5B1086 GLN 5B1235 HIS 5B1250 HIS ** 5B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1441 GLN 5B1591 HIS 5B1655 ASN ** 5B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1674 HIS ** 5B1749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1769 ASN 5B1924 GLN ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 154 HIS 5C 542 ASN 5C 548 ASN ** 5C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 583 ASN 5C 719 GLN 5C 743 ASN 5C 771 GLN ** 5C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 903 HIS 5D 7 HIS 5J 305 ASN 5J 364 GLN 5J 371 GLN ** 5J 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 587 HIS ** 5J 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 797 ASN ** 5J 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5O 101 ASN 5O 165 GLN 5O 225 ASN ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5X 311 GLN 5X 350 GLN ** 5X 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5X 428 ASN 5X 535 ASN 5X 569 HIS 5X 597 HIS 5X 731 GLN 5b 22 GLN ** 5e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5f 6 ASN 5g 26 HIS 5g 54 GLN 62 53 HIS 66 69 ASN ** 68 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 68 54 GLN 68 66 ASN R 393 ASN R 471 GLN S 554 ASN ** S 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 ASN U 144 GLN U 158 GLN U 162 HIS U 204 ASN ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 245 ASN U 297 HIS U 412 GLN U 521 HIS U 530 GLN U 540 GLN Total number of N/Q/H flips: 122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 91629 Z= 0.227 Angle : 0.705 16.009 125157 Z= 0.363 Chirality : 0.045 0.320 14117 Planarity : 0.006 0.174 15038 Dihedral : 14.916 179.778 15570 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.48 % Rotamer: Outliers : 3.67 % Allowed : 16.80 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.07), residues: 10226 helix: -1.23 (0.07), residues: 4013 sheet: -1.40 (0.12), residues: 1621 loop : -1.70 (0.08), residues: 4592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP4B 482 HIS 0.009 0.001 HIS5J 842 PHE 0.026 0.002 PHE5X 445 TYR 0.029 0.002 TYR5A 520 ARG 0.012 0.000 ARG53 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1153 time to evaluate : 9.288 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: X 103 MET cc_start: 0.1118 (ppp) cc_final: -0.0084 (tpt) REVERT: X 104 MET cc_start: 0.2872 (mmt) cc_final: 0.1022 (tmm) REVERT: X 129 ILE cc_start: 0.6147 (mp) cc_final: 0.5945 (mt) REVERT: 41 8 MET cc_start: 0.3447 (mtm) cc_final: 0.2895 (tmt) REVERT: 41 46 THR cc_start: 0.5713 (OUTLIER) cc_final: 0.5509 (m) REVERT: 41 57 THR cc_start: 0.4343 (OUTLIER) cc_final: 0.4108 (t) REVERT: 4A 443 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7242 (ttpp) REVERT: 4A 504 MET cc_start: 0.5582 (ttp) cc_final: 0.5256 (mtm) REVERT: 4A 559 LYS cc_start: 0.3859 (OUTLIER) cc_final: 0.3640 (mtmm) REVERT: 4B 347 TRP cc_start: 0.3835 (OUTLIER) cc_final: 0.3361 (p90) REVERT: 4B 415 PHE cc_start: 0.4384 (m-80) cc_final: 0.3981 (m-10) REVERT: 4C 100 THR cc_start: 0.7685 (t) cc_final: 0.7169 (m) REVERT: 4C 102 GLU cc_start: 0.6450 (tm-30) cc_final: 0.5977 (pt0) REVERT: 4C 173 THR cc_start: 0.6743 (OUTLIER) cc_final: 0.6451 (p) REVERT: 4C 193 MET cc_start: 0.7239 (ppp) cc_final: 0.6808 (ppp) REVERT: 4C 331 TRP cc_start: 0.6060 (m-10) cc_final: 0.5849 (m-10) REVERT: 4C 341 LYS cc_start: 0.5989 (tttt) cc_final: 0.5682 (mptp) REVERT: 4C 361 LYS cc_start: 0.5795 (mttt) cc_final: 0.5360 (mmtm) REVERT: 4C 364 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: 4D 15 ASP cc_start: 0.5614 (OUTLIER) cc_final: 0.5252 (m-30) REVERT: 4b 17 MET cc_start: 0.2781 (tpp) cc_final: 0.2490 (mmt) REVERT: 4b 28 ILE cc_start: 0.6007 (mt) cc_final: 0.5610 (pp) REVERT: 4b 38 MET cc_start: 0.3682 (OUTLIER) cc_final: 0.2972 (mpp) REVERT: 4g 44 GLU cc_start: 0.4103 (OUTLIER) cc_final: 0.3577 (mp0) REVERT: 51 10 LEU cc_start: 0.6577 (tm) cc_final: 0.4808 (mt) REVERT: 5A 519 ASP cc_start: 0.7275 (p0) cc_final: 0.7073 (p0) REVERT: 5A 533 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7552 (tptp) REVERT: 5A 641 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7663 (mmm) REVERT: 5A 964 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7322 (p0) REVERT: 5A 1070 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7130 (t0) REVERT: 5A 1239 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7173 (tpm170) REVERT: 5A 1321 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: 5A 1394 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6714 (pt0) REVERT: 5A 1400 ASN cc_start: 0.7441 (t0) cc_final: 0.7220 (t160) REVERT: 5A 1474 MET cc_start: 0.8152 (tpp) cc_final: 0.7746 (tpp) REVERT: 5A 1587 GLU cc_start: 0.7384 (tp30) cc_final: 0.7168 (tp30) REVERT: 5A 1599 GLN cc_start: 0.6847 (tp-100) cc_final: 0.6117 (tp40) REVERT: 5A 1678 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7562 (mtt-85) REVERT: 5A 1694 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7850 (mm) REVERT: 5A 1784 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: 5A 1798 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6275 (tp) REVERT: 5A 1816 GLN cc_start: 0.7163 (tt0) cc_final: 0.6676 (tp-100) REVERT: 5A 1843 GLU cc_start: 0.7176 (pt0) cc_final: 0.6688 (pp20) REVERT: 5A 1894 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5883 (pt0) REVERT: 5A 1911 GLU cc_start: 0.6728 (tt0) cc_final: 0.6256 (tp30) REVERT: 5A 1917 PHE cc_start: 0.7465 (m-80) cc_final: 0.6829 (m-80) REVERT: 5A 2163 LEU cc_start: 0.8186 (mt) cc_final: 0.7973 (tp) REVERT: 5A 2171 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7135 (pt0) REVERT: 5B 415 VAL cc_start: 0.8494 (m) cc_final: 0.8264 (m) REVERT: 5B 643 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6091 (mp10) REVERT: 5B 748 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7076 (tm) REVERT: 5B 929 MET cc_start: 0.7485 (mtm) cc_final: 0.7204 (mtm) REVERT: 5B 1050 GLU cc_start: 0.7652 (mp0) cc_final: 0.7220 (mt-10) REVERT: 5B 1081 MET cc_start: 0.8237 (ttp) cc_final: 0.7947 (ttp) REVERT: 5B 1196 SER cc_start: 0.7934 (t) cc_final: 0.7676 (m) REVERT: 5B 1344 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6323 (m-30) REVERT: 5B 1631 LEU cc_start: 0.8256 (tp) cc_final: 0.8041 (mt) REVERT: 5B 1682 TYR cc_start: 0.7891 (m-80) cc_final: 0.7645 (m-80) REVERT: 5B 1687 MET cc_start: 0.8942 (mtt) cc_final: 0.8710 (mtt) REVERT: 5B 1705 MET cc_start: 0.8626 (mtt) cc_final: 0.8178 (mtm) REVERT: 5B 1986 MET cc_start: 0.1231 (ptp) cc_final: 0.0241 (tpt) REVERT: 5B 2114 MET cc_start: 0.2078 (mmm) cc_final: 0.0319 (tpt) REVERT: 5C 350 ASN cc_start: 0.7947 (t0) cc_final: 0.7593 (t0) REVERT: 5C 355 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8188 (tttt) REVERT: 5C 406 GLU cc_start: 0.7156 (tp30) cc_final: 0.6876 (tp30) REVERT: 5D 4 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.5633 (mmm) REVERT: 5D 53 LYS cc_start: 0.7604 (ttpp) cc_final: 0.7383 (ttpp) REVERT: 5D 92 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7103 (mt) REVERT: 5D 93 ASP cc_start: 0.8173 (t70) cc_final: 0.7898 (t70) REVERT: 5D 141 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7250 (mmm160) REVERT: 5J 133 MET cc_start: 0.7284 (mmm) cc_final: 0.7055 (tpt) REVERT: 5J 253 MET cc_start: 0.7913 (tmm) cc_final: 0.7686 (tmm) REVERT: 5J 341 LYS cc_start: 0.7375 (mmtp) cc_final: 0.6697 (mmmt) REVERT: 5X 186 ARG cc_start: 0.7555 (tmm160) cc_final: 0.7091 (ptm-80) REVERT: 5X 352 TRP cc_start: 0.5004 (t-100) cc_final: 0.4709 (t-100) REVERT: 5X 359 GLN cc_start: 0.4125 (pt0) cc_final: 0.3827 (mp10) REVERT: 5X 570 MET cc_start: 0.3435 (pp-130) cc_final: 0.0444 (ttm) REVERT: 5b 14 ASP cc_start: 0.7402 (t0) cc_final: 0.7106 (t0) REVERT: 5b 36 LYS cc_start: 0.6857 (pttt) cc_final: 0.6108 (mptt) REVERT: 5b 76 ASN cc_start: 0.5451 (m110) cc_final: 0.5103 (t0) REVERT: 5b 81 THR cc_start: 0.7086 (t) cc_final: 0.6774 (t) REVERT: 5g 41 VAL cc_start: 0.6663 (OUTLIER) cc_final: 0.6274 (p) REVERT: 62 54 MET cc_start: 0.1970 (mtt) cc_final: 0.0887 (ptm) REVERT: 63 94 LEU cc_start: 0.1894 (OUTLIER) cc_final: 0.1438 (mp) REVERT: 65 49 MET cc_start: 0.4091 (ttt) cc_final: 0.3886 (ttp) REVERT: S 746 ARG cc_start: 0.7193 (mtt-85) cc_final: 0.6890 (mtt-85) REVERT: U 107 TYR cc_start: 0.8508 (m-80) cc_final: 0.8265 (m-80) REVERT: U 234 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8097 (p0) REVERT: U 340 LYS cc_start: 0.7377 (tppt) cc_final: 0.7024 (tmtt) REVERT: U 402 LYS cc_start: 0.7969 (ptmt) cc_final: 0.7744 (pptt) REVERT: U 525 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7338 (mmtm) outliers start: 334 outliers final: 100 residues processed: 1379 average time/residue: 1.6576 time to fit residues: 3126.0636 Evaluate side-chains 1092 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 960 time to evaluate : 7.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 41 residue 15 VAL Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 30 THR Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 41 residue 53 VAL Chi-restraints excluded: chain 41 residue 57 THR Chi-restraints excluded: chain 42 residue 66 VAL Chi-restraints excluded: chain 4A residue 443 LYS Chi-restraints excluded: chain 4A residue 508 GLN Chi-restraints excluded: chain 4A residue 559 LYS Chi-restraints excluded: chain 4A residue 579 VAL Chi-restraints excluded: chain 4B residue 181 ILE Chi-restraints excluded: chain 4B residue 268 THR Chi-restraints excluded: chain 4B residue 347 TRP Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4C residue 172 SER Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 307 SER Chi-restraints excluded: chain 4C residue 332 GLN Chi-restraints excluded: chain 4C residue 364 GLU Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 87 GLN Chi-restraints excluded: chain 4b residue 38 MET Chi-restraints excluded: chain 4g residue 44 GLU Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 52 residue 66 VAL Chi-restraints excluded: chain 52 residue 99 MET Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 36 GLU Chi-restraints excluded: chain 5A residue 115 ASP Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 533 LYS Chi-restraints excluded: chain 5A residue 641 MET Chi-restraints excluded: chain 5A residue 701 ILE Chi-restraints excluded: chain 5A residue 897 GLU Chi-restraints excluded: chain 5A residue 964 ASP Chi-restraints excluded: chain 5A residue 973 CYS Chi-restraints excluded: chain 5A residue 1021 ASP Chi-restraints excluded: chain 5A residue 1070 ASP Chi-restraints excluded: chain 5A residue 1116 GLU Chi-restraints excluded: chain 5A residue 1239 ARG Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1321 GLU Chi-restraints excluded: chain 5A residue 1346 THR Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1381 ASP Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1394 GLN Chi-restraints excluded: chain 5A residue 1395 GLU Chi-restraints excluded: chain 5A residue 1410 ASP Chi-restraints excluded: chain 5A residue 1557 LEU Chi-restraints excluded: chain 5A residue 1606 ILE Chi-restraints excluded: chain 5A residue 1639 VAL Chi-restraints excluded: chain 5A residue 1678 ARG Chi-restraints excluded: chain 5A residue 1694 ILE Chi-restraints excluded: chain 5A residue 1784 ASN Chi-restraints excluded: chain 5A residue 1798 LEU Chi-restraints excluded: chain 5A residue 1800 THR Chi-restraints excluded: chain 5A residue 1809 ILE Chi-restraints excluded: chain 5A residue 1869 LEU Chi-restraints excluded: chain 5A residue 1894 GLN Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 2096 ASP Chi-restraints excluded: chain 5A residue 2171 GLU Chi-restraints excluded: chain 5B residue 203 VAL Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 290 LEU Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 550 GLU Chi-restraints excluded: chain 5B residue 643 GLN Chi-restraints excluded: chain 5B residue 710 GLU Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1163 GLU Chi-restraints excluded: chain 5B residue 1231 GLU Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1344 ASP Chi-restraints excluded: chain 5B residue 1400 ARG Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1910 SER Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 442 LYS Chi-restraints excluded: chain 5C residue 501 ILE Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 669 THR Chi-restraints excluded: chain 5C residue 707 ILE Chi-restraints excluded: chain 5C residue 725 ASP Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 856 HIS Chi-restraints excluded: chain 5D residue 4 MET Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5J residue 93 PRO Chi-restraints excluded: chain 5J residue 377 ILE Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 404 VAL Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5O residue 130 ASP Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 245 SER Chi-restraints excluded: chain 5X residue 366 THR Chi-restraints excluded: chain 5X residue 434 VAL Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 9 MET Chi-restraints excluded: chain 5b residue 47 GLU Chi-restraints excluded: chain 5f residue 47 THR Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5g residue 17 LEU Chi-restraints excluded: chain 5g residue 41 VAL Chi-restraints excluded: chain 5g residue 44 GLU Chi-restraints excluded: chain 5g residue 56 ASN Chi-restraints excluded: chain 5g residue 73 LEU Chi-restraints excluded: chain 62 residue 44 SER Chi-restraints excluded: chain 63 residue 94 LEU Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain 68 residue 13 VAL Chi-restraints excluded: chain R residue 447 VAL Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 525 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 527 optimal weight: 9.9990 chunk 294 optimal weight: 0.9980 chunk 790 optimal weight: 6.9990 chunk 646 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 chunk 951 optimal weight: 30.0000 chunk 1027 optimal weight: 9.9990 chunk 847 optimal weight: 4.9990 chunk 943 optimal weight: 0.0040 chunk 324 optimal weight: 2.9990 chunk 763 optimal weight: 5.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 42 49 ASN 4A 539 GLN 4A 600 HIS 4B 264 ASN ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 361 GLN 4B 449 GLN ** 4C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4D 47 ASN 4g 22 ASN 4g 54 GLN 52 17 GLN ** 53 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 294 ASN 5A 563 GLN 5A1066 GLN 5A1241 HIS 5A1282 GLN 5A1367 ASN ** 5A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A1466 ASN 5A1487 HIS 5A1522 GLN 5A1528 GLN 5A1658 GLN ** 5A1811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A1875 HIS ** 5A2150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A2246 ASN ** 5B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 446 HIS 5B 687 GLN 5B 702 GLN 5B 771 ASN ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1568 GLN 5B1591 HIS ** 5B1615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1994 ASN ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 548 ASN ** 5C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 583 ASN 5C 596 ASN 5C 890 HIS 5D 89 HIS 5D 103 ASN ** 5J 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 842 HIS 5J 887 GLN ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5O 116 HIS 5O 357 GLN ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5X 359 GLN 5X 388 ASN 5e 16 GLN ** 5e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 68 35 ASN S 646 GLN U 228 ASN U 245 ASN U 293 HIS U 530 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 91629 Z= 0.393 Angle : 0.726 15.065 125157 Z= 0.368 Chirality : 0.047 0.285 14117 Planarity : 0.006 0.154 15038 Dihedral : 14.697 179.953 15533 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 4.75 % Allowed : 18.35 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.08 % 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: -1.73 (0.08), residues: 10226 helix: -0.62 (0.08), residues: 4018 sheet: -1.20 (0.12), residues: 1655 loop : -1.51 (0.09), residues: 4553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP4B 482 HIS 0.032 0.002 HIS5C 856 PHE 0.027 0.002 PHE5X 445 TYR 0.036 0.002 TYR4B 443 ARG 0.010 0.001 ARG5X 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 1059 time to evaluate : 7.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 103 MET cc_start: 0.1032 (ppp) cc_final: -0.0185 (tpt) REVERT: X 104 MET cc_start: 0.2931 (mmt) cc_final: 0.1061 (tmm) REVERT: X 136 LYS cc_start: 0.7204 (tmtt) cc_final: 0.6873 (tmtt) REVERT: 41 8 MET cc_start: 0.3205 (mtm) cc_final: 0.2962 (tmt) REVERT: 41 57 THR cc_start: 0.4331 (OUTLIER) cc_final: 0.4068 (t) REVERT: 43 43 MET cc_start: 0.2596 (mpm) cc_final: 0.1445 (mtt) REVERT: 4A 504 MET cc_start: 0.5350 (ttp) cc_final: 0.5131 (mtm) REVERT: 4B 291 PRO cc_start: 0.6114 (Cg_endo) cc_final: 0.5899 (Cg_exo) REVERT: 4B 522 GLU cc_start: 0.4307 (mm-30) cc_final: 0.4076 (mm-30) REVERT: 4C 59 MET cc_start: 0.4698 (OUTLIER) cc_final: 0.3773 (mpt) REVERT: 4C 95 ASP cc_start: 0.4946 (OUTLIER) cc_final: 0.4629 (m-30) REVERT: 4C 102 GLU cc_start: 0.6313 (tm-30) cc_final: 0.5832 (pt0) REVERT: 4C 157 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.5223 (mp10) REVERT: 4C 173 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6514 (p) REVERT: 4C 189 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6149 (pt0) REVERT: 4C 193 MET cc_start: 0.7320 (ppp) cc_final: 0.6770 (ppp) REVERT: 4C 331 TRP cc_start: 0.5880 (m-10) cc_final: 0.5667 (m-10) REVERT: 4C 361 LYS cc_start: 0.5842 (mttt) cc_final: 0.5211 (mmtm) REVERT: 4C 364 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6246 (mt-10) REVERT: 4D 45 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6382 (p) REVERT: 4b 17 MET cc_start: 0.2622 (tpp) cc_final: 0.2075 (mmt) REVERT: 4b 28 ILE cc_start: 0.6019 (mt) cc_final: 0.5529 (pp) REVERT: 4g 44 GLU cc_start: 0.4033 (OUTLIER) cc_final: 0.3436 (mp0) REVERT: 4g 48 MET cc_start: 0.1700 (OUTLIER) cc_final: -0.0618 (tmm) REVERT: 4g 69 MET cc_start: -0.0251 (ttm) cc_final: -0.0839 (pp-130) REVERT: 51 10 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.5365 (mt) REVERT: 52 11 MET cc_start: 0.3152 (OUTLIER) cc_final: 0.2464 (ppp) REVERT: 5A 153 ARG cc_start: 0.7455 (mtp85) cc_final: 0.7214 (mtt-85) REVERT: 5A 175 PRO cc_start: 0.6956 (Cg_endo) cc_final: 0.6750 (Cg_exo) REVERT: 5A 533 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7604 (tptp) REVERT: 5A 641 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7808 (mtt) REVERT: 5A 964 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7524 (p0) REVERT: 5A 978 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7181 (pt0) REVERT: 5A 1116 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: 5A 1136 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7593 (ttm-80) REVERT: 5A 1239 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8130 (tpm170) REVERT: 5A 1354 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.3961 (mtm-85) REVERT: 5A 1450 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: 5A 1474 MET cc_start: 0.8303 (tpp) cc_final: 0.7863 (tpp) REVERT: 5A 1587 GLU cc_start: 0.7589 (tp30) cc_final: 0.7351 (tp30) REVERT: 5A 1607 GLU cc_start: 0.7716 (tt0) cc_final: 0.7045 (tt0) REVERT: 5A 1694 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7803 (mm) REVERT: 5A 1843 GLU cc_start: 0.7179 (pt0) cc_final: 0.6661 (pp20) REVERT: 5A 1873 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6730 (OUTLIER) REVERT: 5A 1894 GLN cc_start: 0.6178 (OUTLIER) cc_final: 0.5768 (pt0) REVERT: 5A 1911 GLU cc_start: 0.6608 (tt0) cc_final: 0.6373 (tp30) REVERT: 5A 2150 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7285 (pm20) REVERT: 5B 48 GLU cc_start: 0.6688 (pm20) cc_final: 0.6395 (mp0) REVERT: 5B 415 VAL cc_start: 0.8694 (m) cc_final: 0.8429 (m) REVERT: 5B 712 ILE cc_start: 0.7965 (mp) cc_final: 0.7736 (mp) REVERT: 5B 773 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6323 (mt-10) REVERT: 5B 929 MET cc_start: 0.7534 (mtm) cc_final: 0.7269 (mtm) REVERT: 5B 1207 ASP cc_start: 0.6711 (t0) cc_final: 0.6349 (t0) REVERT: 5B 1300 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7064 (mm-30) REVERT: 5B 1687 MET cc_start: 0.8852 (mtt) cc_final: 0.8540 (mtt) REVERT: 5B 1705 MET cc_start: 0.8658 (mtt) cc_final: 0.8161 (mtm) REVERT: 5B 1791 GLN cc_start: 0.7374 (tp40) cc_final: 0.6795 (tp40) REVERT: 5B 1795 ASP cc_start: 0.6976 (m-30) cc_final: 0.6642 (m-30) REVERT: 5B 1807 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: 5B 1908 LEU cc_start: 0.7621 (tp) cc_final: 0.7387 (tp) REVERT: 5B 2114 MET cc_start: 0.2419 (OUTLIER) cc_final: 0.0626 (tpt) REVERT: 5C 350 ASN cc_start: 0.8080 (t0) cc_final: 0.7633 (t0) REVERT: 5C 422 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8369 (mttm) REVERT: 5C 623 GLU cc_start: 0.7550 (mp0) cc_final: 0.7247 (mm-30) REVERT: 5D 4 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5522 (mmm) REVERT: 5D 53 LYS cc_start: 0.7758 (ttpp) cc_final: 0.7408 (ttpp) REVERT: 5D 91 MET cc_start: 0.7705 (mtp) cc_final: 0.7399 (mtm) REVERT: 5D 92 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7151 (mt) REVERT: 5D 93 ASP cc_start: 0.8239 (t70) cc_final: 0.7955 (t70) REVERT: 5D 141 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7289 (mtp-110) REVERT: 5J 154 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5686 (tm-30) REVERT: 5J 320 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: 5J 341 LYS cc_start: 0.7501 (mmtp) cc_final: 0.7239 (mmmm) REVERT: 5J 724 MET cc_start: 0.4079 (tpp) cc_final: 0.3724 (mtm) REVERT: 5O 116 HIS cc_start: 0.2487 (OUTLIER) cc_final: 0.1332 (t-90) REVERT: 5O 223 ARG cc_start: 0.1477 (OUTLIER) cc_final: 0.0832 (mtt-85) REVERT: 5X 186 ARG cc_start: 0.7585 (tmm160) cc_final: 0.7122 (ptm-80) REVERT: 5X 352 TRP cc_start: 0.4880 (t-100) cc_final: 0.4581 (t-100) REVERT: 5X 375 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6539 (tm-30) REVERT: 5X 491 PHE cc_start: -0.1032 (OUTLIER) cc_final: -0.2150 (m-10) REVERT: 5X 570 MET cc_start: 0.2783 (pp-130) cc_final: 0.0683 (ttm) REVERT: 5X 741 MET cc_start: -0.0688 (tpt) cc_final: -0.1497 (tpt) REVERT: 5b 14 ASP cc_start: 0.7338 (t0) cc_final: 0.7083 (t0) REVERT: 5b 36 LYS cc_start: 0.6870 (pttt) cc_final: 0.6092 (mptt) REVERT: 5e 48 ILE cc_start: 0.3671 (OUTLIER) cc_final: 0.3301 (mm) REVERT: 5e 72 LYS cc_start: 0.5495 (mtmt) cc_final: 0.4906 (tttp) REVERT: 5f 40 MET cc_start: 0.4244 (mpm) cc_final: 0.3771 (mtt) REVERT: 5g 20 LYS cc_start: 0.6769 (mtpp) cc_final: 0.6384 (mppt) REVERT: 5g 47 GLU cc_start: 0.5680 (OUTLIER) cc_final: 0.5007 (tp30) REVERT: 62 54 MET cc_start: 0.2433 (mtt) cc_final: 0.1220 (ptm) REVERT: 63 94 LEU cc_start: 0.1504 (OUTLIER) cc_final: 0.1237 (mp) REVERT: 64 15 MET cc_start: 0.1034 (mmm) cc_final: 0.0064 (mmt) REVERT: 64 36 MET cc_start: 0.1985 (tpp) cc_final: 0.0339 (mtm) REVERT: 65 81 MET cc_start: 0.2707 (mpp) cc_final: 0.2267 (ptt) REVERT: R 411 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6859 (ttmm) REVERT: R 434 ASP cc_start: 0.4874 (OUTLIER) cc_final: 0.4470 (m-30) REVERT: R 442 MET cc_start: 0.6900 (tpp) cc_final: 0.6445 (tpp) REVERT: S 746 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6841 (mtt-85) REVERT: U 101 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7184 (ptt-90) REVERT: U 340 LYS cc_start: 0.7483 (tppt) cc_final: 0.7058 (tmtt) REVERT: U 394 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: U 402 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7819 (pptt) REVERT: U 525 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7804 (mmtm) REVERT: U 537 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8686 (tt) REVERT: U 541 MET cc_start: 0.7714 (mmm) cc_final: 0.7488 (mmt) outliers start: 433 outliers final: 160 residues processed: 1365 average time/residue: 1.6250 time to fit residues: 3045.5749 Evaluate side-chains 1128 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 924 time to evaluate : 7.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain 41 residue 15 VAL Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 28 THR Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 41 residue 57 THR Chi-restraints excluded: chain 42 residue 56 VAL Chi-restraints excluded: chain 42 residue 66 VAL Chi-restraints excluded: chain 42 residue 70 VAL Chi-restraints excluded: chain 4A residue 443 LYS Chi-restraints excluded: chain 4A residue 579 VAL Chi-restraints excluded: chain 4A residue 637 THR Chi-restraints excluded: chain 4B residue 181 ILE Chi-restraints excluded: chain 4B residue 268 THR Chi-restraints excluded: chain 4B residue 357 GLU Chi-restraints excluded: chain 4B residue 382 THR Chi-restraints excluded: chain 4B residue 401 MET Chi-restraints excluded: chain 4B residue 448 HIS Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4B residue 496 MET Chi-restraints excluded: chain 4C residue 59 MET Chi-restraints excluded: chain 4C residue 95 ASP Chi-restraints excluded: chain 4C residue 147 ASP Chi-restraints excluded: chain 4C residue 157 GLN Chi-restraints excluded: chain 4C residue 172 SER Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 189 GLU Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 274 ILE Chi-restraints excluded: chain 4C residue 307 SER Chi-restraints excluded: chain 4C residue 364 GLU Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 45 THR Chi-restraints excluded: chain 4D residue 85 SER Chi-restraints excluded: chain 4D residue 87 GLN Chi-restraints excluded: chain 4g residue 44 GLU Chi-restraints excluded: chain 4g residue 48 MET Chi-restraints excluded: chain 4g residue 51 SER Chi-restraints excluded: chain 51 residue 10 LEU Chi-restraints excluded: chain 51 residue 28 THR Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 51 residue 59 SER Chi-restraints excluded: chain 51 residue 81 VAL Chi-restraints excluded: chain 52 residue 11 MET Chi-restraints excluded: chain 52 residue 56 VAL Chi-restraints excluded: chain 52 residue 66 VAL Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 36 GLU Chi-restraints excluded: chain 53 residue 44 SER Chi-restraints excluded: chain 53 residue 66 SER Chi-restraints excluded: chain 53 residue 71 LEU Chi-restraints excluded: chain 53 residue 72 ILE Chi-restraints excluded: chain 5A residue 85 LYS Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 322 ASN Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 533 LYS Chi-restraints excluded: chain 5A residue 560 SER Chi-restraints excluded: chain 5A residue 641 MET Chi-restraints excluded: chain 5A residue 680 HIS Chi-restraints excluded: chain 5A residue 697 MET Chi-restraints excluded: chain 5A residue 701 ILE Chi-restraints excluded: chain 5A residue 772 CYS Chi-restraints excluded: chain 5A residue 804 GLU Chi-restraints excluded: chain 5A residue 964 ASP Chi-restraints excluded: chain 5A residue 978 GLU Chi-restraints excluded: chain 5A residue 1116 GLU Chi-restraints excluded: chain 5A residue 1136 ARG Chi-restraints excluded: chain 5A residue 1194 CYS Chi-restraints excluded: chain 5A residue 1220 VAL Chi-restraints excluded: chain 5A residue 1239 ARG Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1346 THR Chi-restraints excluded: chain 5A residue 1354 ARG Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1410 ASP Chi-restraints excluded: chain 5A residue 1416 ILE Chi-restraints excluded: chain 5A residue 1450 GLN Chi-restraints excluded: chain 5A residue 1639 VAL Chi-restraints excluded: chain 5A residue 1694 ILE Chi-restraints excluded: chain 5A residue 1800 THR Chi-restraints excluded: chain 5A residue 1809 ILE Chi-restraints excluded: chain 5A residue 1869 LEU Chi-restraints excluded: chain 5A residue 1873 GLU Chi-restraints excluded: chain 5A residue 1894 GLN Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 1966 HIS Chi-restraints excluded: chain 5A residue 2096 ASP Chi-restraints excluded: chain 5A residue 2150 GLN Chi-restraints excluded: chain 5A residue 2265 ASP Chi-restraints excluded: chain 5A residue 2284 MET Chi-restraints excluded: chain 5B residue 142 VAL Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 312 PHE Chi-restraints excluded: chain 5B residue 314 THR Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 550 GLU Chi-restraints excluded: chain 5B residue 557 LYS Chi-restraints excluded: chain 5B residue 654 THR Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 773 GLU Chi-restraints excluded: chain 5B residue 778 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 871 THR Chi-restraints excluded: chain 5B residue 976 THR Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1138 GLU Chi-restraints excluded: chain 5B residue 1163 GLU Chi-restraints excluded: chain 5B residue 1187 SER Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1400 ARG Chi-restraints excluded: chain 5B residue 1456 VAL Chi-restraints excluded: chain 5B residue 1509 THR Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1729 ASP Chi-restraints excluded: chain 5B residue 1807 GLU Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1910 SER Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5B residue 2114 MET Chi-restraints excluded: chain 5B residue 2124 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 147 ASP Chi-restraints excluded: chain 5C residue 165 LEU Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 422 LYS Chi-restraints excluded: chain 5C residue 442 LYS Chi-restraints excluded: chain 5C residue 501 ILE Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 562 THR Chi-restraints excluded: chain 5C residue 566 THR Chi-restraints excluded: chain 5C residue 587 VAL Chi-restraints excluded: chain 5C residue 668 GLU Chi-restraints excluded: chain 5C residue 669 THR Chi-restraints excluded: chain 5C residue 705 VAL Chi-restraints excluded: chain 5C residue 707 ILE Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 870 THR Chi-restraints excluded: chain 5C residue 884 GLU Chi-restraints excluded: chain 5D residue 4 MET Chi-restraints excluded: chain 5D residue 5 LEU Chi-restraints excluded: chain 5D residue 37 THR Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5D residue 138 THR Chi-restraints excluded: chain 5J residue 154 GLU Chi-restraints excluded: chain 5J residue 267 VAL Chi-restraints excluded: chain 5J residue 320 GLU Chi-restraints excluded: chain 5J residue 398 GLU Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 404 VAL Chi-restraints excluded: chain 5J residue 434 VAL Chi-restraints excluded: chain 5J residue 480 THR Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5J residue 859 LYS Chi-restraints excluded: chain 5J residue 930 LEU Chi-restraints excluded: chain 5O residue 116 HIS Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 223 ARG Chi-restraints excluded: chain 5O residue 276 ILE Chi-restraints excluded: chain 5X residue 378 SER Chi-restraints excluded: chain 5X residue 491 PHE Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 47 GLU Chi-restraints excluded: chain 5b residue 81 THR Chi-restraints excluded: chain 5e residue 48 ILE Chi-restraints excluded: chain 5f residue 47 THR Chi-restraints excluded: chain 5f residue 63 LEU Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5g residue 11 LYS Chi-restraints excluded: chain 5g residue 31 LEU Chi-restraints excluded: chain 5g residue 44 GLU Chi-restraints excluded: chain 5g residue 47 GLU Chi-restraints excluded: chain 5g residue 56 ASN Chi-restraints excluded: chain 5g residue 73 LEU Chi-restraints excluded: chain 63 residue 94 LEU Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain 68 residue 13 VAL Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 387 ASP Chi-restraints excluded: chain R residue 411 LYS Chi-restraints excluded: chain R residue 434 ASP Chi-restraints excluded: chain R residue 435 TYR Chi-restraints excluded: chain R residue 447 VAL Chi-restraints excluded: chain S residue 716 THR Chi-restraints excluded: chain U residue 101 ARG Chi-restraints excluded: chain U residue 128 LEU Chi-restraints excluded: chain U residue 129 SER Chi-restraints excluded: chain U residue 270 MET Chi-restraints excluded: chain U residue 324 SER Chi-restraints excluded: chain U residue 346 THR Chi-restraints excluded: chain U residue 353 MET Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 525 LYS Chi-restraints excluded: chain U residue 537 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 940 optimal weight: 8.9990 chunk 715 optimal weight: 5.9990 chunk 493 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 454 optimal weight: 10.0000 chunk 638 optimal weight: 0.8980 chunk 955 optimal weight: 8.9990 chunk 1011 optimal weight: 1.9990 chunk 498 optimal weight: 0.8980 chunk 905 optimal weight: 10.0000 chunk 272 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 42 49 ASN 4A 600 HIS ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4C 108 ASN 4D 28 GLN 4D 34 GLN 4D 47 ASN 4D 115 GLN ** 4D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 51 26 HIS ** 53 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 563 GLN 5A1400 ASN 5A1528 GLN 5A1875 HIS ** 5A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A2150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 64 GLN ** 5B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 687 GLN ** 5B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1568 GLN 5B1591 HIS ** 5B1615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 402 HIS 5D 32 HIS 5D 103 ASN 5J 502 ASN ** 5J 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 704 HIS ** 5J 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 646 GLN U 178 ASN ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 530 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 91629 Z= 0.297 Angle : 0.664 13.320 125157 Z= 0.336 Chirality : 0.045 0.289 14117 Planarity : 0.005 0.143 15038 Dihedral : 14.548 177.401 15529 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 4.27 % Allowed : 20.12 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.05 % 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: -1.39 (0.08), residues: 10226 helix: -0.23 (0.08), residues: 4025 sheet: -1.14 (0.12), residues: 1671 loop : -1.38 (0.09), residues: 4530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP4B 482 HIS 0.014 0.001 HIS5O 116 PHE 0.025 0.002 PHE5X 445 TYR 0.033 0.002 TYR5A 520 ARG 0.009 0.001 ARG5A 861 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 389 poor density : 1029 time to evaluate : 7.430 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: X 103 MET cc_start: 0.0805 (ppp) cc_final: -0.0164 (tpt) REVERT: X 104 MET cc_start: 0.3132 (mmt) cc_final: 0.1160 (tmm) REVERT: X 136 LYS cc_start: 0.7080 (tmtt) cc_final: 0.6776 (tmtt) REVERT: 41 39 HIS cc_start: 0.6513 (m170) cc_final: 0.5965 (m-70) REVERT: 41 46 THR cc_start: 0.6013 (OUTLIER) cc_final: 0.5689 (m) REVERT: 4A 443 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7484 (tttp) REVERT: 4A 447 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7437 (mtpm) REVERT: 4A 504 MET cc_start: 0.5206 (ttp) cc_final: 0.4960 (mtm) REVERT: 4B 418 ASN cc_start: 0.4187 (OUTLIER) cc_final: 0.3802 (m-40) REVERT: 4B 522 GLU cc_start: 0.4483 (mm-30) cc_final: 0.4009 (mm-30) REVERT: 4C 59 MET cc_start: 0.4637 (OUTLIER) cc_final: 0.3722 (mpt) REVERT: 4C 64 MET cc_start: 0.6415 (tmm) cc_final: 0.6085 (mmt) REVERT: 4C 95 ASP cc_start: 0.4917 (OUTLIER) cc_final: 0.4634 (m-30) REVERT: 4C 102 GLU cc_start: 0.6308 (tm-30) cc_final: 0.5808 (pt0) REVERT: 4C 156 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6382 (mp10) REVERT: 4C 157 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.5177 (mp10) REVERT: 4C 173 THR cc_start: 0.6841 (OUTLIER) cc_final: 0.6578 (p) REVERT: 4C 177 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: 4C 189 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6120 (pt0) REVERT: 4C 193 MET cc_start: 0.7349 (ppp) cc_final: 0.6888 (ppp) REVERT: 4C 331 TRP cc_start: 0.5934 (m-10) cc_final: 0.5726 (m-10) REVERT: 4C 361 LYS cc_start: 0.5600 (mttt) cc_final: 0.4947 (mmtm) REVERT: 4D 15 ASP cc_start: 0.5827 (OUTLIER) cc_final: 0.5204 (m-30) REVERT: 4b 17 MET cc_start: 0.2925 (tpp) cc_final: 0.2527 (mmt) REVERT: 4b 28 ILE cc_start: 0.5890 (mt) cc_final: 0.5485 (pp) REVERT: 4g 13 MET cc_start: 0.2953 (mmm) cc_final: 0.0757 (ppp) REVERT: 4g 48 MET cc_start: 0.1309 (OUTLIER) cc_final: -0.1067 (tmm) REVERT: 4g 69 MET cc_start: -0.0114 (OUTLIER) cc_final: -0.0777 (pp-130) REVERT: 51 10 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.5423 (mt) REVERT: 5A 175 PRO cc_start: 0.6718 (Cg_endo) cc_final: 0.6510 (Cg_exo) REVERT: 5A 533 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7585 (tptp) REVERT: 5A 641 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7748 (mtt) REVERT: 5A 1136 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7575 (ttm-80) REVERT: 5A 1474 MET cc_start: 0.8319 (tpp) cc_final: 0.7987 (tpp) REVERT: 5A 1499 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: 5A 1587 GLU cc_start: 0.7446 (tp30) cc_final: 0.7221 (tp30) REVERT: 5A 1607 GLU cc_start: 0.7759 (tt0) cc_final: 0.7092 (tt0) REVERT: 5A 1776 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6159 (mp) REVERT: 5A 1786 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: 5A 1843 GLU cc_start: 0.7233 (pt0) cc_final: 0.6674 (pp20) REVERT: 5A 1873 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: 5A 1911 GLU cc_start: 0.6668 (tt0) cc_final: 0.6459 (tp30) REVERT: 5A 2099 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7897 (mm-30) REVERT: 5A 2150 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: 5B 48 GLU cc_start: 0.6688 (pm20) cc_final: 0.6377 (mp0) REVERT: 5B 415 VAL cc_start: 0.8691 (m) cc_final: 0.8461 (m) REVERT: 5B 615 ASP cc_start: 0.7349 (t0) cc_final: 0.7059 (t0) REVERT: 5B 616 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6884 (mm-30) REVERT: 5B 748 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7265 (tm) REVERT: 5B 773 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6432 (mt-10) REVERT: 5B 1207 ASP cc_start: 0.6643 (t0) cc_final: 0.6352 (t0) REVERT: 5B 1300 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7027 (mm-30) REVERT: 5B 1344 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6404 (m-30) REVERT: 5B 1687 MET cc_start: 0.8872 (mtt) cc_final: 0.8572 (mtt) REVERT: 5B 1705 MET cc_start: 0.8633 (mtt) cc_final: 0.8365 (mtp) REVERT: 5B 1791 GLN cc_start: 0.7136 (tp40) cc_final: 0.6697 (tp40) REVERT: 5B 1795 ASP cc_start: 0.6746 (m-30) cc_final: 0.6527 (m-30) REVERT: 5B 1807 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6482 (tt0) REVERT: 5B 1908 LEU cc_start: 0.7666 (tp) cc_final: 0.7431 (tp) REVERT: 5B 2114 MET cc_start: 0.2538 (OUTLIER) cc_final: 0.0759 (tpt) REVERT: 5C 623 GLU cc_start: 0.7589 (mp0) cc_final: 0.7289 (mm-30) REVERT: 5C 668 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: 5D 22 GLU cc_start: 0.7512 (mp0) cc_final: 0.7241 (mp0) REVERT: 5D 50 GLU cc_start: 0.7269 (pm20) cc_final: 0.7020 (tt0) REVERT: 5D 53 LYS cc_start: 0.7755 (ttpp) cc_final: 0.7382 (ttpp) REVERT: 5D 91 MET cc_start: 0.7709 (mtp) cc_final: 0.7391 (mtm) REVERT: 5D 92 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7089 (mp) REVERT: 5D 93 ASP cc_start: 0.8196 (t70) cc_final: 0.7903 (t70) REVERT: 5D 106 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7945 (mtm) REVERT: 5D 141 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7292 (mtp-110) REVERT: 5J 137 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6998 (tttp) REVERT: 5J 154 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5813 (tm-30) REVERT: 5J 341 LYS cc_start: 0.7488 (mmtp) cc_final: 0.7236 (mmmm) REVERT: 5J 714 MET cc_start: 0.4549 (tmm) cc_final: 0.4295 (tmm) REVERT: 5O 223 ARG cc_start: 0.1478 (OUTLIER) cc_final: 0.0806 (mtt-85) REVERT: 5X 186 ARG cc_start: 0.7598 (tmm160) cc_final: 0.7140 (ptm-80) REVERT: 5X 337 GLU cc_start: 0.7000 (tp30) cc_final: 0.6503 (mt-10) REVERT: 5X 352 TRP cc_start: 0.4939 (t-100) cc_final: 0.4597 (t-100) REVERT: 5X 375 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: 5X 491 PHE cc_start: -0.1019 (OUTLIER) cc_final: -0.2233 (m-10) REVERT: 5X 493 LYS cc_start: 0.3759 (mmpt) cc_final: 0.3253 (mmtt) REVERT: 5b 14 ASP cc_start: 0.7244 (t0) cc_final: 0.7011 (t0) REVERT: 5b 36 LYS cc_start: 0.6845 (pttt) cc_final: 0.6055 (mptt) REVERT: 5e 72 LYS cc_start: 0.5583 (mtmt) cc_final: 0.5031 (tttp) REVERT: 5f 40 MET cc_start: 0.4030 (mpm) cc_final: 0.3624 (mtt) REVERT: 5g 9 LEU cc_start: 0.7746 (mt) cc_final: 0.7497 (mm) REVERT: 5g 20 LYS cc_start: 0.6648 (mtpp) cc_final: 0.6286 (mmpt) REVERT: 5g 32 ARG cc_start: 0.5857 (tpp80) cc_final: 0.5657 (tpp80) REVERT: 5g 47 GLU cc_start: 0.5693 (OUTLIER) cc_final: 0.5024 (tp30) REVERT: 5g 57 ILE cc_start: 0.4631 (mp) cc_final: 0.4363 (pp) REVERT: 62 54 MET cc_start: 0.2176 (mtt) cc_final: 0.0933 (ptm) REVERT: 64 36 MET cc_start: 0.1883 (tpp) cc_final: 0.0223 (mtm) REVERT: R 416 LYS cc_start: 0.2476 (OUTLIER) cc_final: 0.2241 (pttt) REVERT: R 442 MET cc_start: 0.6940 (tpp) cc_final: 0.6442 (tpp) REVERT: R 465 ASP cc_start: 0.6742 (t70) cc_final: 0.6466 (t70) REVERT: S 746 ARG cc_start: 0.7206 (mtt-85) cc_final: 0.6827 (mtt-85) REVERT: U 178 ASN cc_start: 0.8183 (p0) cc_final: 0.7864 (p0) REVERT: U 394 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: U 402 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7815 (pttp) REVERT: U 537 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8662 (tt) outliers start: 389 outliers final: 160 residues processed: 1288 average time/residue: 1.5842 time to fit residues: 2809.2307 Evaluate side-chains 1138 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 937 time to evaluate : 7.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 41 residue 15 VAL Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 30 THR Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 42 residue 56 VAL Chi-restraints excluded: chain 42 residue 66 VAL Chi-restraints excluded: chain 42 residue 99 MET Chi-restraints excluded: chain 4A residue 443 LYS Chi-restraints excluded: chain 4A residue 447 LYS Chi-restraints excluded: chain 4A residue 526 LYS Chi-restraints excluded: chain 4A residue 579 VAL Chi-restraints excluded: chain 4A residue 631 VAL Chi-restraints excluded: chain 4A residue 637 THR Chi-restraints excluded: chain 4B residue 180 TRP Chi-restraints excluded: chain 4B residue 268 THR Chi-restraints excluded: chain 4B residue 357 GLU Chi-restraints excluded: chain 4B residue 418 ASN Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4B residue 477 TRP Chi-restraints excluded: chain 4B residue 496 MET Chi-restraints excluded: chain 4B residue 518 LEU Chi-restraints excluded: chain 4C residue 59 MET Chi-restraints excluded: chain 4C residue 95 ASP Chi-restraints excluded: chain 4C residue 147 ASP Chi-restraints excluded: chain 4C residue 156 GLN Chi-restraints excluded: chain 4C residue 157 GLN Chi-restraints excluded: chain 4C residue 172 SER Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 177 GLN Chi-restraints excluded: chain 4C residue 189 GLU Chi-restraints excluded: chain 4C residue 209 GLU Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 274 ILE Chi-restraints excluded: chain 4C residue 299 CYS Chi-restraints excluded: chain 4C residue 305 VAL Chi-restraints excluded: chain 4C residue 307 SER Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 28 GLN Chi-restraints excluded: chain 4D residue 45 THR Chi-restraints excluded: chain 4D residue 51 SER Chi-restraints excluded: chain 4D residue 85 SER Chi-restraints excluded: chain 4D residue 87 GLN Chi-restraints excluded: chain 4g residue 48 MET Chi-restraints excluded: chain 4g residue 51 SER Chi-restraints excluded: chain 4g residue 69 MET Chi-restraints excluded: chain 51 residue 10 LEU Chi-restraints excluded: chain 51 residue 28 THR Chi-restraints excluded: chain 51 residue 29 ILE Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 52 residue 31 VAL Chi-restraints excluded: chain 52 residue 56 VAL Chi-restraints excluded: chain 53 residue 20 CYS Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 36 GLU Chi-restraints excluded: chain 53 residue 47 THR Chi-restraints excluded: chain 53 residue 66 SER Chi-restraints excluded: chain 53 residue 72 ILE Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 533 LYS Chi-restraints excluded: chain 5A residue 560 SER Chi-restraints excluded: chain 5A residue 641 MET Chi-restraints excluded: chain 5A residue 680 HIS Chi-restraints excluded: chain 5A residue 697 MET Chi-restraints excluded: chain 5A residue 701 ILE Chi-restraints excluded: chain 5A residue 733 THR Chi-restraints excluded: chain 5A residue 772 CYS Chi-restraints excluded: chain 5A residue 804 GLU Chi-restraints excluded: chain 5A residue 973 CYS Chi-restraints excluded: chain 5A residue 1116 GLU Chi-restraints excluded: chain 5A residue 1136 ARG Chi-restraints excluded: chain 5A residue 1164 SER Chi-restraints excluded: chain 5A residue 1167 THR Chi-restraints excluded: chain 5A residue 1194 CYS Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1330 MET Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1410 ASP Chi-restraints excluded: chain 5A residue 1499 GLU Chi-restraints excluded: chain 5A residue 1509 PHE Chi-restraints excluded: chain 5A residue 1639 VAL Chi-restraints excluded: chain 5A residue 1776 ILE Chi-restraints excluded: chain 5A residue 1784 ASN Chi-restraints excluded: chain 5A residue 1786 TYR Chi-restraints excluded: chain 5A residue 1800 THR Chi-restraints excluded: chain 5A residue 1809 ILE Chi-restraints excluded: chain 5A residue 1869 LEU Chi-restraints excluded: chain 5A residue 1873 GLU Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 1966 HIS Chi-restraints excluded: chain 5A residue 2096 ASP Chi-restraints excluded: chain 5A residue 2099 GLU Chi-restraints excluded: chain 5A residue 2150 GLN Chi-restraints excluded: chain 5A residue 2265 ASP Chi-restraints excluded: chain 5A residue 2284 MET Chi-restraints excluded: chain 5B residue 142 VAL Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 312 PHE Chi-restraints excluded: chain 5B residue 314 THR Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 550 GLU Chi-restraints excluded: chain 5B residue 557 LYS Chi-restraints excluded: chain 5B residue 654 THR Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 773 GLU Chi-restraints excluded: chain 5B residue 778 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 912 ASN Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1138 GLU Chi-restraints excluded: chain 5B residue 1320 LEU Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1344 ASP Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1400 ARG Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1807 GLU Chi-restraints excluded: chain 5B residue 1830 GLU Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1910 SER Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5B residue 2114 MET Chi-restraints excluded: chain 5B residue 2124 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 147 ASP Chi-restraints excluded: chain 5C residue 165 LEU Chi-restraints excluded: chain 5C residue 291 MET Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 507 VAL Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 562 THR Chi-restraints excluded: chain 5C residue 566 THR Chi-restraints excluded: chain 5C residue 587 VAL Chi-restraints excluded: chain 5C residue 655 VAL Chi-restraints excluded: chain 5C residue 668 GLU Chi-restraints excluded: chain 5C residue 673 LYS Chi-restraints excluded: chain 5C residue 705 VAL Chi-restraints excluded: chain 5C residue 707 ILE Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 856 HIS Chi-restraints excluded: chain 5C residue 870 THR Chi-restraints excluded: chain 5C residue 884 GLU Chi-restraints excluded: chain 5C residue 917 VAL Chi-restraints excluded: chain 5D residue 5 LEU Chi-restraints excluded: chain 5D residue 37 THR Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 106 MET Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5D residue 138 THR Chi-restraints excluded: chain 5J residue 88 LEU Chi-restraints excluded: chain 5J residue 137 LYS Chi-restraints excluded: chain 5J residue 154 GLU Chi-restraints excluded: chain 5J residue 242 LYS Chi-restraints excluded: chain 5J residue 267 VAL Chi-restraints excluded: chain 5J residue 373 VAL Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 404 VAL Chi-restraints excluded: chain 5J residue 576 VAL Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5J residue 783 SER Chi-restraints excluded: chain 5J residue 930 LEU Chi-restraints excluded: chain 5O residue 69 VAL Chi-restraints excluded: chain 5O residue 154 VAL Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 223 ARG Chi-restraints excluded: chain 5O residue 245 SER Chi-restraints excluded: chain 5X residue 375 GLU Chi-restraints excluded: chain 5X residue 434 VAL Chi-restraints excluded: chain 5X residue 491 PHE Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 521 ILE Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 9 MET Chi-restraints excluded: chain 5b residue 81 THR Chi-restraints excluded: chain 5e residue 82 ASP Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5f residue 75 VAL Chi-restraints excluded: chain 5g residue 31 LEU Chi-restraints excluded: chain 5g residue 47 GLU Chi-restraints excluded: chain 5g residue 73 LEU Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 416 LYS Chi-restraints excluded: chain R residue 435 TYR Chi-restraints excluded: chain S residue 714 ASP Chi-restraints excluded: chain S residue 716 THR Chi-restraints excluded: chain U residue 129 SER Chi-restraints excluded: chain U residue 324 SER Chi-restraints excluded: chain U residue 346 THR Chi-restraints excluded: chain U residue 353 MET Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain U residue 525 LYS Chi-restraints excluded: chain U residue 537 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 842 optimal weight: 0.0870 chunk 573 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 752 optimal weight: 10.0000 chunk 417 optimal weight: 0.9980 chunk 862 optimal weight: 6.9990 chunk 698 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 516 optimal weight: 4.9990 chunk 907 optimal weight: 0.0970 chunk 255 optimal weight: 1.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 42 49 ASN 4A 600 HIS 4B 242 ASN ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 421 HIS 4C 108 ASN 4D 27 GLN 4D 28 GLN 4D 34 GLN 4D 47 ASN 4D 115 GLN 4D 117 GLN ** 4e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 51 63 ASN 52 48 ASN 5A 563 GLN 5A 711 GLN 5A 994 ASN 5A1241 HIS 5A1400 ASN 5A1528 GLN 5A1875 HIS ** 5A2150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 64 GLN ** 5B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 771 ASN ** 5B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1591 HIS 5B1615 ASN ** 5B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 402 HIS 5C 583 ASN ** 5D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 502 ASN ** 5J 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 842 HIS ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 91629 Z= 0.199 Angle : 0.618 11.993 125157 Z= 0.311 Chirality : 0.043 0.278 14117 Planarity : 0.005 0.143 15038 Dihedral : 14.357 175.143 15521 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 4.04 % Allowed : 20.97 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -1.09 (0.08), residues: 10226 helix: 0.07 (0.08), residues: 4046 sheet: -1.03 (0.12), residues: 1682 loop : -1.25 (0.09), residues: 4498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP4B 482 HIS 0.013 0.001 HIS5J 865 PHE 0.035 0.001 PHE4D 53 TYR 0.031 0.001 TYR5A 520 ARG 0.010 0.000 ARG5A 861 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1041 time to evaluate : 7.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 103 MET cc_start: 0.0496 (ppp) cc_final: -0.0366 (tpt) REVERT: X 104 MET cc_start: 0.2997 (mmt) cc_final: 0.0939 (tmm) REVERT: X 129 ILE cc_start: 0.6406 (OUTLIER) cc_final: 0.6205 (tp) REVERT: 41 8 MET cc_start: 0.2972 (tmt) cc_final: 0.2219 (tmt) REVERT: 41 39 HIS cc_start: 0.6322 (m170) cc_final: 0.5862 (m-70) REVERT: 41 46 THR cc_start: 0.6024 (OUTLIER) cc_final: 0.5639 (m) REVERT: 42 71 LYS cc_start: 0.5543 (tppt) cc_final: 0.4726 (tttt) REVERT: 4A 443 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7479 (tttp) REVERT: 4A 497 GLU cc_start: 0.2701 (tp30) cc_final: 0.1923 (mp0) REVERT: 4B 418 ASN cc_start: 0.3894 (OUTLIER) cc_final: 0.3512 (m-40) REVERT: 4B 522 GLU cc_start: 0.4539 (mm-30) cc_final: 0.4330 (mm-30) REVERT: 4C 64 MET cc_start: 0.6254 (tmm) cc_final: 0.6029 (tpt) REVERT: 4C 95 ASP cc_start: 0.4743 (m-30) cc_final: 0.4498 (m-30) REVERT: 4C 102 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5783 (pt0) REVERT: 4C 109 ILE cc_start: 0.6998 (mm) cc_final: 0.6736 (pt) REVERT: 4C 156 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6363 (mp10) REVERT: 4C 157 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5093 (mp10) REVERT: 4C 173 THR cc_start: 0.6851 (OUTLIER) cc_final: 0.6586 (p) REVERT: 4C 177 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: 4C 189 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6108 (pt0) REVERT: 4C 231 ILE cc_start: 0.7832 (mt) cc_final: 0.7594 (mm) REVERT: 4C 361 LYS cc_start: 0.5519 (mttt) cc_final: 0.4876 (mmtm) REVERT: 4D 15 ASP cc_start: 0.5919 (OUTLIER) cc_final: 0.5423 (m-30) REVERT: 4D 97 ARG cc_start: 0.5253 (mmm-85) cc_final: 0.5034 (mmt180) REVERT: 4b 17 MET cc_start: 0.2606 (tpp) cc_final: 0.2074 (mmt) REVERT: 4b 28 ILE cc_start: 0.5954 (mt) cc_final: 0.5600 (pp) REVERT: 4b 38 MET cc_start: 0.4474 (mtp) cc_final: 0.4156 (ttt) REVERT: 4g 13 MET cc_start: 0.3266 (mmm) cc_final: 0.0922 (ppp) REVERT: 4g 48 MET cc_start: 0.1522 (OUTLIER) cc_final: -0.0535 (tmm) REVERT: 51 10 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.5459 (mt) REVERT: 52 111 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.5117 (ttp80) REVERT: 53 54 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.5372 (mtm110) REVERT: 53 69 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7290 (ttm-80) REVERT: 5A 533 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7559 (tptm) REVERT: 5A 573 GLN cc_start: 0.7737 (mt0) cc_final: 0.7453 (mt0) REVERT: 5A 804 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: 5A 1023 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8293 (p0) REVERT: 5A 1116 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: 5A 1474 MET cc_start: 0.8269 (tpp) cc_final: 0.7807 (tpp) REVERT: 5A 1499 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: 5A 1528 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7506 (mm-40) REVERT: 5A 1587 GLU cc_start: 0.7361 (tp30) cc_final: 0.7139 (tp30) REVERT: 5A 1599 GLN cc_start: 0.6933 (tp-100) cc_final: 0.6425 (tp40) REVERT: 5A 1656 THR cc_start: 0.6960 (t) cc_final: 0.6704 (t) REVERT: 5A 1694 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7561 (mm) REVERT: 5A 1776 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.6109 (mp) REVERT: 5A 1786 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: 5A 1843 GLU cc_start: 0.7279 (pt0) cc_final: 0.6785 (pp20) REVERT: 5A 1873 GLU cc_start: 0.7208 (tp30) cc_final: 0.6676 (tt0) REVERT: 5A 1917 PHE cc_start: 0.7449 (m-80) cc_final: 0.7237 (m-10) REVERT: 5A 2150 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: 5A 2171 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7091 (pt0) REVERT: 5B 48 GLU cc_start: 0.6771 (pm20) cc_final: 0.6413 (mp0) REVERT: 5B 415 VAL cc_start: 0.8630 (m) cc_final: 0.8413 (m) REVERT: 5B 748 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7166 (tm) REVERT: 5B 773 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6400 (mt-10) REVERT: 5B 1207 ASP cc_start: 0.6627 (t0) cc_final: 0.6326 (t0) REVERT: 5B 1300 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6915 (mm-30) REVERT: 5B 1344 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6373 (m-30) REVERT: 5B 1687 MET cc_start: 0.8910 (mtt) cc_final: 0.8568 (mtt) REVERT: 5B 1705 MET cc_start: 0.8602 (mtt) cc_final: 0.8344 (mtp) REVERT: 5B 1791 GLN cc_start: 0.7011 (tp40) cc_final: 0.6799 (tp40) REVERT: 5B 1807 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6422 (tt0) REVERT: 5B 1834 MET cc_start: 0.7688 (mmm) cc_final: 0.7480 (mmt) REVERT: 5B 1908 LEU cc_start: 0.7670 (tp) cc_final: 0.7455 (tp) REVERT: 5B 2085 GLN cc_start: 0.4227 (OUTLIER) cc_final: 0.2963 (mm-40) REVERT: 5B 2086 GLN cc_start: 0.2812 (OUTLIER) cc_final: 0.2191 (pm20) REVERT: 5B 2114 MET cc_start: 0.2618 (OUTLIER) cc_final: 0.0701 (tpt) REVERT: 5C 366 GLN cc_start: 0.8001 (mt0) cc_final: 0.7734 (mt0) REVERT: 5C 623 GLU cc_start: 0.7549 (mp0) cc_final: 0.7270 (mm-30) REVERT: 5C 668 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: 5D 16 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7459 (mm110) REVERT: 5D 22 GLU cc_start: 0.7444 (mp0) cc_final: 0.7182 (mp0) REVERT: 5D 50 GLU cc_start: 0.7244 (pm20) cc_final: 0.7003 (tt0) REVERT: 5D 53 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7369 (ttpp) REVERT: 5D 91 MET cc_start: 0.7729 (mtp) cc_final: 0.7471 (mtm) REVERT: 5D 92 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7070 (mp) REVERT: 5D 93 ASP cc_start: 0.8014 (t70) cc_final: 0.7717 (t70) REVERT: 5D 141 ARG cc_start: 0.7647 (mtp85) cc_final: 0.7349 (mmm160) REVERT: 5J 137 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6977 (tttp) REVERT: 5J 341 LYS cc_start: 0.7385 (mmtp) cc_final: 0.7142 (mmmm) REVERT: 5J 714 MET cc_start: 0.4560 (OUTLIER) cc_final: 0.4339 (tmm) REVERT: 5J 724 MET cc_start: 0.4233 (ppp) cc_final: 0.3968 (pmm) REVERT: 5O 223 ARG cc_start: 0.1468 (OUTLIER) cc_final: 0.0806 (mtt-85) REVERT: 5X 186 ARG cc_start: 0.7607 (tmm160) cc_final: 0.6927 (ptm-80) REVERT: 5X 352 TRP cc_start: 0.4943 (t-100) cc_final: 0.4607 (t-100) REVERT: 5X 375 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6418 (tm-30) REVERT: 5X 570 MET cc_start: 0.2770 (pp-130) cc_final: 0.0811 (ttm) REVERT: 5X 588 MET cc_start: 0.2861 (mtm) cc_final: 0.2658 (mtm) REVERT: 5X 646 MET cc_start: -0.0676 (ptp) cc_final: -0.1258 (ptm) REVERT: 5X 741 MET cc_start: -0.0802 (tpt) cc_final: -0.1535 (tpt) REVERT: 5b 14 ASP cc_start: 0.7252 (t0) cc_final: 0.7025 (t0) REVERT: 5b 36 LYS cc_start: 0.6815 (pttt) cc_final: 0.5858 (mmtt) REVERT: 5e 72 LYS cc_start: 0.5554 (mtmt) cc_final: 0.5007 (tttp) REVERT: 5g 20 LYS cc_start: 0.6500 (mtpp) cc_final: 0.6089 (mmpt) REVERT: 5g 47 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.4903 (tt0) REVERT: 5g 57 ILE cc_start: 0.4914 (mp) cc_final: 0.4711 (pp) REVERT: 62 54 MET cc_start: 0.2182 (mtt) cc_final: 0.1003 (ptm) REVERT: 63 84 MET cc_start: 0.1530 (mpt) cc_final: 0.0945 (ptp) REVERT: 64 15 MET cc_start: 0.1193 (mmm) cc_final: 0.0057 (mmt) REVERT: 64 36 MET cc_start: 0.2008 (tpp) cc_final: 0.0472 (mtm) REVERT: 65 81 MET cc_start: 0.3010 (mpp) cc_final: 0.2587 (ptt) REVERT: R 416 LYS cc_start: 0.2623 (OUTLIER) cc_final: 0.2339 (pttt) REVERT: R 442 MET cc_start: 0.6962 (tpp) cc_final: 0.6432 (tpp) REVERT: R 465 ASP cc_start: 0.6761 (t70) cc_final: 0.6528 (t0) REVERT: S 711 GLU cc_start: 0.7658 (pt0) cc_final: 0.7439 (pt0) REVERT: S 746 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6948 (mtt-85) REVERT: U 101 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7105 (ptt-90) REVERT: U 178 ASN cc_start: 0.8143 (p0) cc_final: 0.7801 (p0) REVERT: U 394 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: U 402 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7840 (pttp) REVERT: U 533 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7652 (pt0) outliers start: 368 outliers final: 139 residues processed: 1299 average time/residue: 1.6601 time to fit residues: 3008.6070 Evaluate side-chains 1111 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 929 time to evaluate : 7.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 129 ILE Chi-restraints excluded: chain 41 residue 15 VAL Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 30 THR Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 42 residue 56 VAL Chi-restraints excluded: chain 42 residue 66 VAL Chi-restraints excluded: chain 42 residue 99 MET Chi-restraints excluded: chain 42 residue 110 LEU Chi-restraints excluded: chain 4A residue 443 LYS Chi-restraints excluded: chain 4A residue 526 LYS Chi-restraints excluded: chain 4A residue 579 VAL Chi-restraints excluded: chain 4A residue 631 VAL Chi-restraints excluded: chain 4A residue 637 THR Chi-restraints excluded: chain 4B residue 401 MET Chi-restraints excluded: chain 4B residue 418 ASN Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4C residue 156 GLN Chi-restraints excluded: chain 4C residue 157 GLN Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 177 GLN Chi-restraints excluded: chain 4C residue 189 GLU Chi-restraints excluded: chain 4C residue 209 GLU Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 274 ILE Chi-restraints excluded: chain 4C residue 305 VAL Chi-restraints excluded: chain 4C residue 307 SER Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 51 SER Chi-restraints excluded: chain 4D residue 85 SER Chi-restraints excluded: chain 4D residue 87 GLN Chi-restraints excluded: chain 4D residue 121 GLN Chi-restraints excluded: chain 4b residue 26 ILE Chi-restraints excluded: chain 4e residue 14 MET Chi-restraints excluded: chain 4g residue 48 MET Chi-restraints excluded: chain 4g residue 51 SER Chi-restraints excluded: chain 4g residue 61 VAL Chi-restraints excluded: chain 51 residue 10 LEU Chi-restraints excluded: chain 51 residue 28 THR Chi-restraints excluded: chain 51 residue 29 ILE Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 51 residue 59 SER Chi-restraints excluded: chain 52 residue 31 VAL Chi-restraints excluded: chain 52 residue 66 VAL Chi-restraints excluded: chain 52 residue 99 MET Chi-restraints excluded: chain 52 residue 111 ARG Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 36 GLU Chi-restraints excluded: chain 53 residue 38 ASN Chi-restraints excluded: chain 53 residue 54 ARG Chi-restraints excluded: chain 53 residue 66 SER Chi-restraints excluded: chain 53 residue 72 ILE Chi-restraints excluded: chain 5A residue 85 LYS Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 533 LYS Chi-restraints excluded: chain 5A residue 560 SER Chi-restraints excluded: chain 5A residue 697 MET Chi-restraints excluded: chain 5A residue 701 ILE Chi-restraints excluded: chain 5A residue 804 GLU Chi-restraints excluded: chain 5A residue 897 GLU Chi-restraints excluded: chain 5A residue 973 CYS Chi-restraints excluded: chain 5A residue 1023 ASN Chi-restraints excluded: chain 5A residue 1116 GLU Chi-restraints excluded: chain 5A residue 1164 SER Chi-restraints excluded: chain 5A residue 1194 CYS Chi-restraints excluded: chain 5A residue 1220 VAL Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1416 ILE Chi-restraints excluded: chain 5A residue 1499 GLU Chi-restraints excluded: chain 5A residue 1528 GLN Chi-restraints excluded: chain 5A residue 1606 ILE Chi-restraints excluded: chain 5A residue 1639 VAL Chi-restraints excluded: chain 5A residue 1694 ILE Chi-restraints excluded: chain 5A residue 1776 ILE Chi-restraints excluded: chain 5A residue 1784 ASN Chi-restraints excluded: chain 5A residue 1786 TYR Chi-restraints excluded: chain 5A residue 1800 THR Chi-restraints excluded: chain 5A residue 1809 ILE Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 1943 LEU Chi-restraints excluded: chain 5A residue 1966 HIS Chi-restraints excluded: chain 5A residue 2096 ASP Chi-restraints excluded: chain 5A residue 2150 GLN Chi-restraints excluded: chain 5A residue 2171 GLU Chi-restraints excluded: chain 5A residue 2284 MET Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 312 PHE Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 557 LYS Chi-restraints excluded: chain 5B residue 654 THR Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 773 GLU Chi-restraints excluded: chain 5B residue 778 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 871 THR Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1344 ASP Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1400 ARG Chi-restraints excluded: chain 5B residue 1456 VAL Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1627 MET Chi-restraints excluded: chain 5B residue 1729 ASP Chi-restraints excluded: chain 5B residue 1807 GLU Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1910 SER Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5B residue 2085 GLN Chi-restraints excluded: chain 5B residue 2086 GLN Chi-restraints excluded: chain 5B residue 2114 MET Chi-restraints excluded: chain 5B residue 2124 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 291 MET Chi-restraints excluded: chain 5C residue 308 CYS Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 397 ASP Chi-restraints excluded: chain 5C residue 507 VAL Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 566 THR Chi-restraints excluded: chain 5C residue 587 VAL Chi-restraints excluded: chain 5C residue 668 GLU Chi-restraints excluded: chain 5C residue 669 THR Chi-restraints excluded: chain 5C residue 707 ILE Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 856 HIS Chi-restraints excluded: chain 5D residue 5 LEU Chi-restraints excluded: chain 5D residue 16 GLN Chi-restraints excluded: chain 5D residue 37 THR Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5D residue 138 THR Chi-restraints excluded: chain 5J residue 88 LEU Chi-restraints excluded: chain 5J residue 128 ILE Chi-restraints excluded: chain 5J residue 137 LYS Chi-restraints excluded: chain 5J residue 242 LYS Chi-restraints excluded: chain 5J residue 267 VAL Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 404 VAL Chi-restraints excluded: chain 5J residue 576 VAL Chi-restraints excluded: chain 5J residue 714 MET Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5J residue 930 LEU Chi-restraints excluded: chain 5O residue 69 VAL Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 219 VAL Chi-restraints excluded: chain 5O residue 223 ARG Chi-restraints excluded: chain 5X residue 282 THR Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 9 MET Chi-restraints excluded: chain 5b residue 66 VAL Chi-restraints excluded: chain 5b residue 81 THR Chi-restraints excluded: chain 5f residue 33 LEU Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5f residue 75 VAL Chi-restraints excluded: chain 5g residue 31 LEU Chi-restraints excluded: chain 5g residue 47 GLU Chi-restraints excluded: chain 5g residue 73 LEU Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain 65 residue 72 ILE Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 416 LYS Chi-restraints excluded: chain S residue 714 ASP Chi-restraints excluded: chain S residue 716 THR Chi-restraints excluded: chain U residue 101 ARG Chi-restraints excluded: chain U residue 129 SER Chi-restraints excluded: chain U residue 324 SER Chi-restraints excluded: chain U residue 346 THR Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 525 LYS Chi-restraints excluded: chain U residue 529 LEU Chi-restraints excluded: chain U residue 533 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 340 optimal weight: 0.9980 chunk 910 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 593 optimal weight: 9.9990 chunk 249 optimal weight: 0.1980 chunk 1012 optimal weight: 4.9990 chunk 840 optimal weight: 10.0000 chunk 468 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 334 optimal weight: 0.8980 chunk 531 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 42 49 ASN 42 62 HIS 4A 445 GLN 4A 508 GLN 4A 600 HIS ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4C 108 ASN 4D 34 GLN 4D 47 ASN ** 4e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 563 GLN 5A1066 GLN 5A1875 HIS ** 5A2150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 64 GLN ** 5B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 885 GLN ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1038 GLN 5B1157 ASN 5B1502 HIS 5B1568 GLN 5B1591 HIS ** 5B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 548 ASN 5C 583 ASN ** 5D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5D 103 ASN ** 5J 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 758 GLN ** 5J 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5O 287 ASN 5X 287 ASN ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5b 37 HIS ** 5b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 166 ASN ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 245 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 91629 Z= 0.198 Angle : 0.607 11.584 125157 Z= 0.304 Chirality : 0.043 0.257 14117 Planarity : 0.004 0.126 15038 Dihedral : 14.229 174.933 15521 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 3.81 % Allowed : 21.93 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -0.88 (0.08), residues: 10226 helix: 0.28 (0.08), residues: 4056 sheet: -0.95 (0.12), residues: 1686 loop : -1.16 (0.09), residues: 4484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP4B 392 HIS 0.010 0.001 HIS4A 600 PHE 0.029 0.001 PHE4D 53 TYR 0.029 0.001 TYR5A 520 ARG 0.011 0.000 ARG5B 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1016 time to evaluate : 7.230 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: X 103 MET cc_start: 0.0496 (ppp) cc_final: -0.0339 (tpt) REVERT: X 104 MET cc_start: 0.3037 (mmt) cc_final: 0.1006 (tmm) REVERT: 41 8 MET cc_start: 0.3306 (tmt) cc_final: 0.2832 (tmt) REVERT: 41 46 THR cc_start: 0.6128 (OUTLIER) cc_final: 0.5688 (m) REVERT: 42 71 LYS cc_start: 0.5543 (tppt) cc_final: 0.4795 (tttt) REVERT: 42 110 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6330 (tm) REVERT: 4A 443 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7471 (tttp) REVERT: 4A 447 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7232 (mmtp) REVERT: 4A 497 GLU cc_start: 0.2673 (tp30) cc_final: 0.1996 (mp0) REVERT: 4B 418 ASN cc_start: 0.4073 (OUTLIER) cc_final: 0.3682 (m-40) REVERT: 4B 522 GLU cc_start: 0.4474 (mm-30) cc_final: 0.4270 (mm-30) REVERT: 4C 64 MET cc_start: 0.6357 (tmm) cc_final: 0.5979 (tpt) REVERT: 4C 102 GLU cc_start: 0.6222 (tm-30) cc_final: 0.5800 (pt0) REVERT: 4C 109 ILE cc_start: 0.7016 (mm) cc_final: 0.6760 (pt) REVERT: 4C 157 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.5246 (mp10) REVERT: 4C 173 THR cc_start: 0.6869 (OUTLIER) cc_final: 0.6605 (p) REVERT: 4C 177 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: 4C 189 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6118 (pt0) REVERT: 4C 231 ILE cc_start: 0.7775 (mt) cc_final: 0.7541 (mm) REVERT: 4C 361 LYS cc_start: 0.5575 (mttt) cc_final: 0.4980 (mmtm) REVERT: 4D 15 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5432 (m-30) REVERT: 4b 28 ILE cc_start: 0.5811 (mt) cc_final: 0.5481 (pp) REVERT: 4g 48 MET cc_start: 0.1540 (OUTLIER) cc_final: -0.0388 (tmm) REVERT: 51 10 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.5446 (mt) REVERT: 52 11 MET cc_start: 0.3183 (OUTLIER) cc_final: 0.2491 (ppp) REVERT: 52 111 ARG cc_start: 0.5583 (OUTLIER) cc_final: 0.4721 (ttp80) REVERT: 53 54 ARG cc_start: 0.5873 (ptm160) cc_final: 0.5408 (mtm110) REVERT: 5A 170 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6736 (p0) REVERT: 5A 528 LYS cc_start: 0.6261 (ptmm) cc_final: 0.5892 (pttt) REVERT: 5A 533 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7571 (tptm) REVERT: 5A 573 GLN cc_start: 0.7729 (mt0) cc_final: 0.7457 (mt0) REVERT: 5A 804 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: 5A 1023 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8283 (p0) REVERT: 5A 1450 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: 5A 1474 MET cc_start: 0.8237 (tpp) cc_final: 0.7893 (tpp) REVERT: 5A 1513 MET cc_start: 0.4431 (OUTLIER) cc_final: 0.4152 (ptp) REVERT: 5A 1587 GLU cc_start: 0.7401 (tp30) cc_final: 0.7190 (tp30) REVERT: 5A 1656 THR cc_start: 0.6968 (t) cc_final: 0.6634 (t) REVERT: 5A 1776 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.6075 (mp) REVERT: 5A 1786 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: 5A 1843 GLU cc_start: 0.7289 (pt0) cc_final: 0.6766 (pp20) REVERT: 5A 1873 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6751 (tt0) REVERT: 5A 2150 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: 5A 2171 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7045 (pt0) REVERT: 5B 48 GLU cc_start: 0.6779 (pm20) cc_final: 0.6423 (mp0) REVERT: 5B 748 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7175 (tm) REVERT: 5B 773 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6336 (mt-10) REVERT: 5B 1207 ASP cc_start: 0.6523 (t0) cc_final: 0.6226 (t0) REVERT: 5B 1300 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6833 (mm-30) REVERT: 5B 1344 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.6394 (m-30) REVERT: 5B 1687 MET cc_start: 0.8935 (mtt) cc_final: 0.8615 (mtt) REVERT: 5B 1705 MET cc_start: 0.8571 (mtt) cc_final: 0.8323 (mtp) REVERT: 5B 1795 ASP cc_start: 0.6456 (m-30) cc_final: 0.6028 (m-30) REVERT: 5B 1807 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6401 (tt0) REVERT: 5B 2085 GLN cc_start: 0.4244 (OUTLIER) cc_final: 0.2972 (mm-40) REVERT: 5B 2086 GLN cc_start: 0.2754 (OUTLIER) cc_final: 0.2165 (pm20) REVERT: 5B 2114 MET cc_start: 0.2578 (OUTLIER) cc_final: 0.0693 (tpt) REVERT: 5C 366 GLN cc_start: 0.7992 (mt0) cc_final: 0.7727 (mt0) REVERT: 5C 407 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7746 (mt-10) REVERT: 5C 623 GLU cc_start: 0.7526 (mp0) cc_final: 0.7205 (mm-30) REVERT: 5C 668 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: 5D 16 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7347 (mm110) REVERT: 5D 22 GLU cc_start: 0.7446 (mp0) cc_final: 0.7223 (mp0) REVERT: 5D 39 MET cc_start: 0.7432 (mtm) cc_final: 0.7138 (mtp) REVERT: 5D 53 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7395 (ttpp) REVERT: 5D 91 MET cc_start: 0.7721 (mtp) cc_final: 0.7496 (mtm) REVERT: 5D 92 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7088 (mp) REVERT: 5D 93 ASP cc_start: 0.7982 (t70) cc_final: 0.7660 (t70) REVERT: 5D 106 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7824 (mtm) REVERT: 5D 141 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7418 (mmm160) REVERT: 5J 137 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6988 (tttp) REVERT: 5J 341 LYS cc_start: 0.7359 (mmtp) cc_final: 0.6950 (mmmm) REVERT: 5J 473 LEU cc_start: 0.4684 (OUTLIER) cc_final: 0.4366 (tp) REVERT: 5O 223 ARG cc_start: 0.1481 (OUTLIER) cc_final: 0.0822 (mtt-85) REVERT: 5O 353 MET cc_start: 0.2566 (OUTLIER) cc_final: 0.1937 (mpp) REVERT: 5X 186 ARG cc_start: 0.7531 (tmm160) cc_final: 0.6955 (ptm-80) REVERT: 5X 337 GLU cc_start: 0.7012 (tp30) cc_final: 0.6564 (mt-10) REVERT: 5X 352 TRP cc_start: 0.4988 (t-100) cc_final: 0.4577 (t-100) REVERT: 5X 375 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: 5X 491 PHE cc_start: -0.1486 (OUTLIER) cc_final: -0.2818 (m-10) REVERT: 5b 14 ASP cc_start: 0.7224 (t0) cc_final: 0.7011 (t0) REVERT: 5b 36 LYS cc_start: 0.6849 (pttt) cc_final: 0.5867 (mmtt) REVERT: 5e 72 LYS cc_start: 0.5605 (mtmt) cc_final: 0.5099 (tttp) REVERT: 5f 11 LEU cc_start: 0.5133 (pt) cc_final: 0.4179 (mt) REVERT: 5g 20 LYS cc_start: 0.6503 (mtpp) cc_final: 0.6014 (mmpt) REVERT: 5g 47 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.4898 (tt0) REVERT: 62 54 MET cc_start: 0.2264 (mtt) cc_final: 0.1106 (ptm) REVERT: 64 15 MET cc_start: 0.1245 (mmm) cc_final: 0.0220 (mtp) REVERT: 64 36 MET cc_start: 0.1879 (tpp) cc_final: 0.0432 (mtm) REVERT: 65 81 MET cc_start: 0.2937 (mpp) cc_final: 0.2608 (ptt) REVERT: R 436 VAL cc_start: 0.5764 (t) cc_final: 0.5439 (m) REVERT: R 442 MET cc_start: 0.6976 (tpp) cc_final: 0.6506 (tpp) REVERT: R 465 ASP cc_start: 0.6831 (t70) cc_final: 0.6487 (t0) REVERT: S 718 ARG cc_start: 0.6648 (ptm-80) cc_final: 0.5774 (ptt90) REVERT: S 724 GLU cc_start: 0.7847 (pt0) cc_final: 0.7305 (pt0) REVERT: S 740 LYS cc_start: 0.5626 (OUTLIER) cc_final: 0.4576 (pttt) REVERT: S 746 ARG cc_start: 0.7214 (mtt-85) cc_final: 0.6971 (mtt-85) REVERT: U 101 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7128 (ptt-90) REVERT: U 178 ASN cc_start: 0.8195 (p0) cc_final: 0.7832 (p0) REVERT: U 270 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: U 394 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: U 402 LYS cc_start: 0.8117 (ptmt) cc_final: 0.7901 (pttp) outliers start: 347 outliers final: 157 residues processed: 1251 average time/residue: 1.5712 time to fit residues: 2713.4299 Evaluate side-chains 1130 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 926 time to evaluate : 7.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 30 THR Chi-restraints excluded: chain 41 residue 33 ASP Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 42 residue 56 VAL Chi-restraints excluded: chain 42 residue 66 VAL Chi-restraints excluded: chain 42 residue 99 MET Chi-restraints excluded: chain 42 residue 101 LEU Chi-restraints excluded: chain 42 residue 104 ASP Chi-restraints excluded: chain 42 residue 110 LEU Chi-restraints excluded: chain 4A residue 443 LYS Chi-restraints excluded: chain 4A residue 447 LYS Chi-restraints excluded: chain 4A residue 526 LYS Chi-restraints excluded: chain 4A residue 579 VAL Chi-restraints excluded: chain 4A residue 631 VAL Chi-restraints excluded: chain 4A residue 637 THR Chi-restraints excluded: chain 4B residue 382 THR Chi-restraints excluded: chain 4B residue 418 ASN Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4B residue 496 MET Chi-restraints excluded: chain 4C residue 157 GLN Chi-restraints excluded: chain 4C residue 172 SER Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 177 GLN Chi-restraints excluded: chain 4C residue 189 GLU Chi-restraints excluded: chain 4C residue 209 GLU Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 274 ILE Chi-restraints excluded: chain 4C residue 307 SER Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 45 THR Chi-restraints excluded: chain 4D residue 51 SER Chi-restraints excluded: chain 4D residue 53 PHE Chi-restraints excluded: chain 4D residue 85 SER Chi-restraints excluded: chain 4D residue 87 GLN Chi-restraints excluded: chain 4b residue 26 ILE Chi-restraints excluded: chain 4e residue 14 MET Chi-restraints excluded: chain 4g residue 48 MET Chi-restraints excluded: chain 4g residue 51 SER Chi-restraints excluded: chain 51 residue 10 LEU Chi-restraints excluded: chain 51 residue 28 THR Chi-restraints excluded: chain 51 residue 29 ILE Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 51 residue 59 SER Chi-restraints excluded: chain 52 residue 11 MET Chi-restraints excluded: chain 52 residue 31 VAL Chi-restraints excluded: chain 52 residue 66 VAL Chi-restraints excluded: chain 52 residue 111 ARG Chi-restraints excluded: chain 53 residue 20 CYS Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 38 ASN Chi-restraints excluded: chain 53 residue 66 SER Chi-restraints excluded: chain 53 residue 72 ILE Chi-restraints excluded: chain 5A residue 85 LYS Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 181 ASN Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 533 LYS Chi-restraints excluded: chain 5A residue 560 SER Chi-restraints excluded: chain 5A residue 647 LEU Chi-restraints excluded: chain 5A residue 697 MET Chi-restraints excluded: chain 5A residue 733 THR Chi-restraints excluded: chain 5A residue 804 GLU Chi-restraints excluded: chain 5A residue 1023 ASN Chi-restraints excluded: chain 5A residue 1194 CYS Chi-restraints excluded: chain 5A residue 1220 VAL Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1416 ILE Chi-restraints excluded: chain 5A residue 1450 GLN Chi-restraints excluded: chain 5A residue 1509 PHE Chi-restraints excluded: chain 5A residue 1513 MET Chi-restraints excluded: chain 5A residue 1606 ILE Chi-restraints excluded: chain 5A residue 1639 VAL Chi-restraints excluded: chain 5A residue 1776 ILE Chi-restraints excluded: chain 5A residue 1779 PHE Chi-restraints excluded: chain 5A residue 1786 TYR Chi-restraints excluded: chain 5A residue 1800 THR Chi-restraints excluded: chain 5A residue 1809 ILE Chi-restraints excluded: chain 5A residue 1873 GLU Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 1943 LEU Chi-restraints excluded: chain 5A residue 1966 HIS Chi-restraints excluded: chain 5A residue 2150 GLN Chi-restraints excluded: chain 5A residue 2171 GLU Chi-restraints excluded: chain 5A residue 2284 MET Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 312 PHE Chi-restraints excluded: chain 5B residue 314 THR Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 423 MET Chi-restraints excluded: chain 5B residue 557 LYS Chi-restraints excluded: chain 5B residue 654 THR Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 773 GLU Chi-restraints excluded: chain 5B residue 778 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 871 THR Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 995 ASN Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1344 ASP Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1400 ARG Chi-restraints excluded: chain 5B residue 1456 VAL Chi-restraints excluded: chain 5B residue 1507 SER Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1729 ASP Chi-restraints excluded: chain 5B residue 1807 GLU Chi-restraints excluded: chain 5B residue 1886 ASP Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1910 SER Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5B residue 2085 GLN Chi-restraints excluded: chain 5B residue 2086 GLN Chi-restraints excluded: chain 5B residue 2114 MET Chi-restraints excluded: chain 5B residue 2124 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 112 THR Chi-restraints excluded: chain 5C residue 147 ASP Chi-restraints excluded: chain 5C residue 291 MET Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 397 ASP Chi-restraints excluded: chain 5C residue 507 VAL Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 562 THR Chi-restraints excluded: chain 5C residue 566 THR Chi-restraints excluded: chain 5C residue 587 VAL Chi-restraints excluded: chain 5C residue 668 GLU Chi-restraints excluded: chain 5C residue 669 THR Chi-restraints excluded: chain 5C residue 705 VAL Chi-restraints excluded: chain 5C residue 707 ILE Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 783 LEU Chi-restraints excluded: chain 5C residue 856 HIS Chi-restraints excluded: chain 5C residue 884 GLU Chi-restraints excluded: chain 5D residue 5 LEU Chi-restraints excluded: chain 5D residue 16 GLN Chi-restraints excluded: chain 5D residue 37 THR Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 106 MET Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5D residue 138 THR Chi-restraints excluded: chain 5J residue 88 LEU Chi-restraints excluded: chain 5J residue 137 LYS Chi-restraints excluded: chain 5J residue 242 LYS Chi-restraints excluded: chain 5J residue 267 VAL Chi-restraints excluded: chain 5J residue 296 LEU Chi-restraints excluded: chain 5J residue 386 ILE Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 404 VAL Chi-restraints excluded: chain 5J residue 460 ILE Chi-restraints excluded: chain 5J residue 473 LEU Chi-restraints excluded: chain 5J residue 576 VAL Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5J residue 783 SER Chi-restraints excluded: chain 5J residue 930 LEU Chi-restraints excluded: chain 5O residue 69 VAL Chi-restraints excluded: chain 5O residue 154 VAL Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 219 VAL Chi-restraints excluded: chain 5O residue 223 ARG Chi-restraints excluded: chain 5O residue 241 LEU Chi-restraints excluded: chain 5O residue 353 MET Chi-restraints excluded: chain 5X residue 282 THR Chi-restraints excluded: chain 5X residue 375 GLU Chi-restraints excluded: chain 5X residue 491 PHE Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 66 VAL Chi-restraints excluded: chain 5b residue 81 THR Chi-restraints excluded: chain 5f residue 33 LEU Chi-restraints excluded: chain 5f residue 47 THR Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5f residue 75 VAL Chi-restraints excluded: chain 5g residue 31 LEU Chi-restraints excluded: chain 5g residue 47 GLU Chi-restraints excluded: chain 5g residue 56 ASN Chi-restraints excluded: chain 5g residue 73 LEU Chi-restraints excluded: chain 64 residue 56 MET Chi-restraints excluded: chain 64 residue 71 ILE Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain 65 residue 72 ILE Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 404 PHE Chi-restraints excluded: chain R residue 447 VAL Chi-restraints excluded: chain S residue 714 ASP Chi-restraints excluded: chain S residue 716 THR Chi-restraints excluded: chain S residue 740 LYS Chi-restraints excluded: chain U residue 101 ARG Chi-restraints excluded: chain U residue 129 SER Chi-restraints excluded: chain U residue 270 MET Chi-restraints excluded: chain U residue 346 THR Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 525 LYS Chi-restraints excluded: chain U residue 529 LEU Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain U residue 543 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 975 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 576 optimal weight: 8.9990 chunk 739 optimal weight: 4.9990 chunk 572 optimal weight: 10.0000 chunk 851 optimal weight: 9.9990 chunk 565 optimal weight: 0.9980 chunk 1008 optimal weight: 2.9990 chunk 630 optimal weight: 2.9990 chunk 614 optimal weight: 8.9990 chunk 465 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 42 49 ASN 42 62 HIS 4A 445 GLN 4A 508 GLN 4A 600 HIS ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 448 HIS 4C 108 ASN 4C 376 ASN 4D 27 GLN 4D 31 ASN 4D 34 GLN 4D 47 ASN 4b 76 ASN ** 4e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 834 HIS 5A1066 GLN 5A1241 HIS 5A1363 GLN ** 5A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A1784 ASN ** 5A2150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 771 ASN ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1591 HIS ** 5B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B2102 HIS ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 583 ASN ** 5D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 465 HIS ** 5J 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 825 GLN ** 5J 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5X 467 GLN ** 5b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5e 16 GLN ** 5e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 91629 Z= 0.363 Angle : 0.680 14.439 125157 Z= 0.341 Chirality : 0.046 0.292 14117 Planarity : 0.005 0.114 15038 Dihedral : 14.291 177.937 15520 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 4.02 % Allowed : 22.46 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.08), residues: 10226 helix: 0.18 (0.08), residues: 4050 sheet: -0.97 (0.12), residues: 1696 loop : -1.17 (0.09), residues: 4480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP5B1432 HIS 0.012 0.001 HIS4A 600 PHE 0.032 0.002 PHE5A1379 TYR 0.031 0.002 TYR5A 520 ARG 0.010 0.001 ARG5B 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 975 time to evaluate : 7.881 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: X 103 MET cc_start: 0.0655 (ppp) cc_final: -0.0153 (tpt) REVERT: X 104 MET cc_start: 0.3483 (mmt) cc_final: 0.1283 (tmm) REVERT: X 130 ASN cc_start: 0.6622 (t0) cc_final: 0.6008 (t0) REVERT: 41 46 THR cc_start: 0.6127 (OUTLIER) cc_final: 0.5688 (m) REVERT: 42 71 LYS cc_start: 0.5690 (tppt) cc_final: 0.4846 (tttt) REVERT: 42 110 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6404 (tm) REVERT: 4A 443 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7521 (tttp) REVERT: 4A 447 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7231 (mmtp) REVERT: 4A 497 GLU cc_start: 0.2745 (tp30) cc_final: 0.1976 (mp0) REVERT: 4B 245 MET cc_start: 0.5352 (tpp) cc_final: 0.4906 (ttp) REVERT: 4B 520 MET cc_start: 0.2346 (mmm) cc_final: 0.2111 (mmm) REVERT: 4B 522 GLU cc_start: 0.4597 (mm-30) cc_final: 0.4324 (mm-30) REVERT: 4C 93 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.4903 (tp) REVERT: 4C 102 GLU cc_start: 0.6191 (tm-30) cc_final: 0.5789 (pt0) REVERT: 4C 104 GLU cc_start: 0.6826 (pt0) cc_final: 0.5961 (tp30) REVERT: 4C 157 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.5223 (mp10) REVERT: 4C 173 THR cc_start: 0.6827 (OUTLIER) cc_final: 0.6579 (p) REVERT: 4C 177 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: 4C 189 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6190 (pt0) REVERT: 4C 361 LYS cc_start: 0.5440 (mttt) cc_final: 0.4828 (mmtm) REVERT: 4b 28 ILE cc_start: 0.5683 (mt) cc_final: 0.5304 (pp) REVERT: 4g 13 MET cc_start: 0.2499 (mmm) cc_final: 0.0547 (pp-130) REVERT: 4g 48 MET cc_start: 0.1328 (OUTLIER) cc_final: -0.0601 (tmm) REVERT: 51 10 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.5490 (mt) REVERT: 51 67 TYR cc_start: 0.5247 (p90) cc_final: 0.4579 (p90) REVERT: 52 111 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.5099 (ttp80) REVERT: 53 54 ARG cc_start: 0.5841 (ptm160) cc_final: 0.5393 (mtm110) REVERT: 5A 25 MET cc_start: 0.0745 (OUTLIER) cc_final: -0.0851 (mpt) REVERT: 5A 804 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: 5A 978 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: 5A 1009 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8053 (mtt) REVERT: 5A 1023 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8163 (p0) REVERT: 5A 1048 MET cc_start: 0.7924 (mmm) cc_final: 0.7681 (mmm) REVERT: 5A 1450 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: 5A 1474 MET cc_start: 0.8350 (tpp) cc_final: 0.8037 (tpp) REVERT: 5A 1513 MET cc_start: 0.4351 (OUTLIER) cc_final: 0.4076 (ppp) REVERT: 5A 1587 GLU cc_start: 0.7526 (tp30) cc_final: 0.7305 (tp30) REVERT: 5A 1599 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6538 (tp40) REVERT: 5A 1607 GLU cc_start: 0.7702 (tt0) cc_final: 0.7046 (tt0) REVERT: 5A 1776 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6214 (mp) REVERT: 5A 1786 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: 5A 1843 GLU cc_start: 0.7272 (pt0) cc_final: 0.6728 (pp20) REVERT: 5A 1873 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: 5A 2099 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8084 (tm-30) REVERT: 5A 2150 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: 5B 48 GLU cc_start: 0.6819 (pm20) cc_final: 0.6473 (mp0) REVERT: 5B 712 ILE cc_start: 0.8143 (mp) cc_final: 0.7895 (mp) REVERT: 5B 760 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5198 (tp30) REVERT: 5B 773 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6284 (mt-10) REVERT: 5B 1003 GLN cc_start: 0.7736 (mt0) cc_final: 0.7517 (mt0) REVERT: 5B 1207 ASP cc_start: 0.6727 (t0) cc_final: 0.6384 (t0) REVERT: 5B 1300 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6928 (mm-30) REVERT: 5B 1344 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6472 (m-30) REVERT: 5B 1483 ARG cc_start: 0.6502 (tmm-80) cc_final: 0.6301 (ttp80) REVERT: 5B 1687 MET cc_start: 0.8892 (mtt) cc_final: 0.8588 (mtt) REVERT: 5B 1705 MET cc_start: 0.8629 (mtt) cc_final: 0.8319 (mtp) REVERT: 5B 1791 GLN cc_start: 0.7004 (tp40) cc_final: 0.6588 (tp40) REVERT: 5B 1807 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: 5B 1834 MET cc_start: 0.7753 (mmm) cc_final: 0.7462 (mmt) REVERT: 5B 1953 MET cc_start: 0.5971 (ptm) cc_final: 0.5670 (ptp) REVERT: 5B 2085 GLN cc_start: 0.4263 (OUTLIER) cc_final: 0.2939 (mm-40) REVERT: 5B 2086 GLN cc_start: 0.2769 (OUTLIER) cc_final: 0.1848 (pm20) REVERT: 5C 422 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8326 (mttm) REVERT: 5C 623 GLU cc_start: 0.7581 (mp0) cc_final: 0.7238 (mm-30) REVERT: 5D 22 GLU cc_start: 0.7499 (mp0) cc_final: 0.7276 (mp0) REVERT: 5D 53 LYS cc_start: 0.7801 (ttpp) cc_final: 0.7417 (ttpp) REVERT: 5D 91 MET cc_start: 0.7743 (mtp) cc_final: 0.7516 (mtm) REVERT: 5D 92 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7110 (mp) REVERT: 5D 93 ASP cc_start: 0.8181 (t70) cc_final: 0.7901 (t70) REVERT: 5J 134 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6781 (mt-10) REVERT: 5J 137 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6884 (tttp) REVERT: 5J 139 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.6348 (pm20) REVERT: 5J 341 LYS cc_start: 0.7517 (mmtp) cc_final: 0.7268 (mmmm) REVERT: 5J 714 MET cc_start: 0.4751 (tmm) cc_final: 0.4467 (tmm) REVERT: 5O 146 ARG cc_start: 0.2138 (OUTLIER) cc_final: 0.1860 (pmt170) REVERT: 5O 223 ARG cc_start: 0.1574 (OUTLIER) cc_final: 0.0849 (mtt-85) REVERT: 5O 353 MET cc_start: 0.2892 (OUTLIER) cc_final: 0.1829 (mpp) REVERT: 5X 186 ARG cc_start: 0.7500 (tmm160) cc_final: 0.6918 (ptm-80) REVERT: 5X 337 GLU cc_start: 0.7001 (tp30) cc_final: 0.6515 (mt-10) REVERT: 5X 352 TRP cc_start: 0.5073 (t-100) cc_final: 0.4742 (t-100) REVERT: 5X 375 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6627 (tm-30) REVERT: 5b 36 LYS cc_start: 0.6887 (pttt) cc_final: 0.6051 (mptt) REVERT: 5b 65 ARG cc_start: 0.5282 (ttp-170) cc_final: 0.5078 (ttp-170) REVERT: 5e 54 MET cc_start: 0.2895 (ttm) cc_final: 0.2685 (tpp) REVERT: 5f 11 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4484 (mt) REVERT: 5g 20 LYS cc_start: 0.6453 (mtpp) cc_final: 0.5873 (mmpt) REVERT: 5g 47 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.4949 (tp30) REVERT: 62 54 MET cc_start: 0.2439 (mtt) cc_final: 0.1217 (ptm) REVERT: 64 15 MET cc_start: 0.1106 (mmm) cc_final: 0.0577 (mmm) REVERT: 65 81 MET cc_start: 0.3138 (mpp) cc_final: 0.2760 (ptt) REVERT: R 436 VAL cc_start: 0.6047 (t) cc_final: 0.5713 (m) REVERT: R 442 MET cc_start: 0.6909 (tpp) cc_final: 0.6536 (tpp) REVERT: R 443 ASN cc_start: 0.6513 (t0) cc_final: 0.4451 (p0) REVERT: R 465 ASP cc_start: 0.6847 (t70) cc_final: 0.6543 (t0) REVERT: S 740 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.4670 (pttt) REVERT: S 746 ARG cc_start: 0.7213 (mtt-85) cc_final: 0.6859 (mtt-85) REVERT: U 101 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7259 (ptt-90) REVERT: U 394 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: U 402 LYS cc_start: 0.8059 (ptmt) cc_final: 0.7857 (pttp) outliers start: 366 outliers final: 176 residues processed: 1229 average time/residue: 1.6031 time to fit residues: 2721.2020 Evaluate side-chains 1120 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 902 time to evaluate : 7.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 142 ASN Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 30 THR Chi-restraints excluded: chain 41 residue 33 ASP Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 42 residue 56 VAL Chi-restraints excluded: chain 42 residue 101 LEU Chi-restraints excluded: chain 42 residue 104 ASP Chi-restraints excluded: chain 42 residue 110 LEU Chi-restraints excluded: chain 4A residue 443 LYS Chi-restraints excluded: chain 4A residue 447 LYS Chi-restraints excluded: chain 4A residue 508 GLN Chi-restraints excluded: chain 4A residue 526 LYS Chi-restraints excluded: chain 4A residue 631 VAL Chi-restraints excluded: chain 4A residue 637 THR Chi-restraints excluded: chain 4B residue 382 THR Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4B residue 477 TRP Chi-restraints excluded: chain 4B residue 496 MET Chi-restraints excluded: chain 4C residue 62 GLU Chi-restraints excluded: chain 4C residue 93 ILE Chi-restraints excluded: chain 4C residue 157 GLN Chi-restraints excluded: chain 4C residue 172 SER Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 177 GLN Chi-restraints excluded: chain 4C residue 189 GLU Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 274 ILE Chi-restraints excluded: chain 4C residue 299 CYS Chi-restraints excluded: chain 4C residue 307 SER Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 45 THR Chi-restraints excluded: chain 4D residue 69 LEU Chi-restraints excluded: chain 4D residue 85 SER Chi-restraints excluded: chain 4D residue 121 GLN Chi-restraints excluded: chain 4b residue 26 ILE Chi-restraints excluded: chain 4e residue 14 MET Chi-restraints excluded: chain 4f residue 40 MET Chi-restraints excluded: chain 4f residue 63 LEU Chi-restraints excluded: chain 4g residue 48 MET Chi-restraints excluded: chain 4g residue 51 SER Chi-restraints excluded: chain 4g residue 61 VAL Chi-restraints excluded: chain 51 residue 10 LEU Chi-restraints excluded: chain 51 residue 28 THR Chi-restraints excluded: chain 51 residue 29 ILE Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 51 residue 59 SER Chi-restraints excluded: chain 52 residue 31 VAL Chi-restraints excluded: chain 52 residue 66 VAL Chi-restraints excluded: chain 52 residue 111 ARG Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 38 ASN Chi-restraints excluded: chain 53 residue 66 SER Chi-restraints excluded: chain 53 residue 72 ILE Chi-restraints excluded: chain 5A residue 25 MET Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 181 ASN Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 560 SER Chi-restraints excluded: chain 5A residue 647 LEU Chi-restraints excluded: chain 5A residue 733 THR Chi-restraints excluded: chain 5A residue 772 CYS Chi-restraints excluded: chain 5A residue 789 GLU Chi-restraints excluded: chain 5A residue 804 GLU Chi-restraints excluded: chain 5A residue 840 ILE Chi-restraints excluded: chain 5A residue 868 GLU Chi-restraints excluded: chain 5A residue 978 GLU Chi-restraints excluded: chain 5A residue 1009 MET Chi-restraints excluded: chain 5A residue 1023 ASN Chi-restraints excluded: chain 5A residue 1194 CYS Chi-restraints excluded: chain 5A residue 1220 VAL Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1416 ILE Chi-restraints excluded: chain 5A residue 1450 GLN Chi-restraints excluded: chain 5A residue 1497 THR Chi-restraints excluded: chain 5A residue 1509 PHE Chi-restraints excluded: chain 5A residue 1513 MET Chi-restraints excluded: chain 5A residue 1557 LEU Chi-restraints excluded: chain 5A residue 1639 VAL Chi-restraints excluded: chain 5A residue 1776 ILE Chi-restraints excluded: chain 5A residue 1779 PHE Chi-restraints excluded: chain 5A residue 1784 ASN Chi-restraints excluded: chain 5A residue 1786 TYR Chi-restraints excluded: chain 5A residue 1800 THR Chi-restraints excluded: chain 5A residue 1809 ILE Chi-restraints excluded: chain 5A residue 1873 GLU Chi-restraints excluded: chain 5A residue 1910 THR Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 1943 LEU Chi-restraints excluded: chain 5A residue 1981 VAL Chi-restraints excluded: chain 5A residue 2096 ASP Chi-restraints excluded: chain 5A residue 2150 GLN Chi-restraints excluded: chain 5B residue 109 THR Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 312 PHE Chi-restraints excluded: chain 5B residue 314 THR Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 557 LYS Chi-restraints excluded: chain 5B residue 654 THR Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 760 GLU Chi-restraints excluded: chain 5B residue 773 GLU Chi-restraints excluded: chain 5B residue 778 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 871 THR Chi-restraints excluded: chain 5B residue 976 THR Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1188 VAL Chi-restraints excluded: chain 5B residue 1309 VAL Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1344 ASP Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1400 ARG Chi-restraints excluded: chain 5B residue 1456 VAL Chi-restraints excluded: chain 5B residue 1507 SER Chi-restraints excluded: chain 5B residue 1509 THR Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1807 GLU Chi-restraints excluded: chain 5B residue 1871 LEU Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1910 SER Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5B residue 2076 LEU Chi-restraints excluded: chain 5B residue 2085 GLN Chi-restraints excluded: chain 5B residue 2086 GLN Chi-restraints excluded: chain 5B residue 2124 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 147 ASP Chi-restraints excluded: chain 5C residue 165 LEU Chi-restraints excluded: chain 5C residue 291 MET Chi-restraints excluded: chain 5C residue 308 CYS Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 397 ASP Chi-restraints excluded: chain 5C residue 422 LYS Chi-restraints excluded: chain 5C residue 507 VAL Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 562 THR Chi-restraints excluded: chain 5C residue 587 VAL Chi-restraints excluded: chain 5C residue 668 GLU Chi-restraints excluded: chain 5C residue 669 THR Chi-restraints excluded: chain 5C residue 705 VAL Chi-restraints excluded: chain 5C residue 707 ILE Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 783 LEU Chi-restraints excluded: chain 5C residue 856 HIS Chi-restraints excluded: chain 5C residue 870 THR Chi-restraints excluded: chain 5C residue 884 GLU Chi-restraints excluded: chain 5D residue 5 LEU Chi-restraints excluded: chain 5D residue 37 THR Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5D residue 138 THR Chi-restraints excluded: chain 5J residue 128 ILE Chi-restraints excluded: chain 5J residue 137 LYS Chi-restraints excluded: chain 5J residue 139 GLN Chi-restraints excluded: chain 5J residue 242 LYS Chi-restraints excluded: chain 5J residue 267 VAL Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 404 VAL Chi-restraints excluded: chain 5J residue 434 VAL Chi-restraints excluded: chain 5J residue 460 ILE Chi-restraints excluded: chain 5J residue 576 VAL Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5J residue 783 SER Chi-restraints excluded: chain 5J residue 797 ASN Chi-restraints excluded: chain 5J residue 930 LEU Chi-restraints excluded: chain 5O residue 69 VAL Chi-restraints excluded: chain 5O residue 146 ARG Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 219 VAL Chi-restraints excluded: chain 5O residue 223 ARG Chi-restraints excluded: chain 5O residue 241 LEU Chi-restraints excluded: chain 5O residue 276 ILE Chi-restraints excluded: chain 5O residue 353 MET Chi-restraints excluded: chain 5X residue 282 THR Chi-restraints excluded: chain 5X residue 284 ILE Chi-restraints excluded: chain 5X residue 375 GLU Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 66 VAL Chi-restraints excluded: chain 5b residue 81 THR Chi-restraints excluded: chain 5f residue 11 LEU Chi-restraints excluded: chain 5f residue 33 LEU Chi-restraints excluded: chain 5f residue 47 THR Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5f residue 75 VAL Chi-restraints excluded: chain 5g residue 31 LEU Chi-restraints excluded: chain 5g residue 46 VAL Chi-restraints excluded: chain 5g residue 47 GLU Chi-restraints excluded: chain 5g residue 73 LEU Chi-restraints excluded: chain 64 residue 56 MET Chi-restraints excluded: chain 64 residue 71 ILE Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain 65 residue 72 ILE Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 404 PHE Chi-restraints excluded: chain R residue 447 VAL Chi-restraints excluded: chain S residue 714 ASP Chi-restraints excluded: chain S residue 716 THR Chi-restraints excluded: chain S residue 740 LYS Chi-restraints excluded: chain U residue 101 ARG Chi-restraints excluded: chain U residue 129 SER Chi-restraints excluded: chain U residue 230 ILE Chi-restraints excluded: chain U residue 270 MET Chi-restraints excluded: chain U residue 324 SER Chi-restraints excluded: chain U residue 346 THR Chi-restraints excluded: chain U residue 353 MET Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain U residue 543 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 623 optimal weight: 30.0000 chunk 402 optimal weight: 0.8980 chunk 602 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 640 optimal weight: 2.9990 chunk 686 optimal weight: 0.7980 chunk 498 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 792 optimal weight: 0.0980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 42 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 42 62 HIS ** 4A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4A 600 HIS 4B 222 ASN ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4C 108 ASN 4D 27 GLN 4D 34 GLN ** 4e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A1188 ASN ** 5A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A2150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 259 HIS ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1591 HIS ** 5B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 402 HIS 5C 583 ASN 5C 837 GLN ** 5D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5b 37 HIS ** 5b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 166 ASN ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 91629 Z= 0.225 Angle : 0.633 18.671 125157 Z= 0.315 Chirality : 0.043 0.296 14117 Planarity : 0.004 0.105 15038 Dihedral : 14.201 174.731 15520 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 3.21 % Allowed : 23.61 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -0.81 (0.08), residues: 10226 helix: 0.34 (0.08), residues: 4063 sheet: -0.93 (0.12), residues: 1704 loop : -1.10 (0.09), residues: 4459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP4B 392 HIS 0.012 0.001 HIS4A 600 PHE 0.032 0.001 PHE4D 53 TYR 0.035 0.001 TYR5A 520 ARG 0.013 0.000 ARG5B 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 956 time to evaluate : 7.659 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: X 103 MET cc_start: 0.0627 (ppp) cc_final: -0.0151 (tpt) REVERT: X 104 MET cc_start: 0.3336 (mmt) cc_final: 0.1251 (tmm) REVERT: X 130 ASN cc_start: 0.6522 (t0) cc_final: 0.5924 (t0) REVERT: 41 46 THR cc_start: 0.6169 (OUTLIER) cc_final: 0.5743 (m) REVERT: 42 71 LYS cc_start: 0.5586 (tppt) cc_final: 0.4827 (tttt) REVERT: 43 82 MET cc_start: 0.2352 (tpp) cc_final: 0.1501 (mpt) REVERT: 4A 443 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7367 (tttp) REVERT: 4A 447 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7233 (mmtp) REVERT: 4A 497 GLU cc_start: 0.2418 (tp30) cc_final: 0.1227 (mp0) REVERT: 4A 526 LYS cc_start: 0.5385 (OUTLIER) cc_final: 0.4915 (mtmm) REVERT: 4B 347 TRP cc_start: 0.4413 (p90) cc_final: 0.4031 (p-90) REVERT: 4B 522 GLU cc_start: 0.4596 (mm-30) cc_final: 0.3472 (mm-30) REVERT: 4C 64 MET cc_start: 0.6350 (tmm) cc_final: 0.6027 (tpt) REVERT: 4C 102 GLU cc_start: 0.6128 (tm-30) cc_final: 0.5743 (pt0) REVERT: 4C 104 GLU cc_start: 0.6691 (pt0) cc_final: 0.5890 (tp30) REVERT: 4C 157 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.4842 (mp10) REVERT: 4C 173 THR cc_start: 0.6901 (OUTLIER) cc_final: 0.6638 (p) REVERT: 4C 177 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: 4C 189 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6255 (pt0) REVERT: 4C 361 LYS cc_start: 0.5416 (mttt) cc_final: 0.4802 (mmtm) REVERT: 4b 28 ILE cc_start: 0.5579 (mt) cc_final: 0.5194 (pp) REVERT: 4g 43 ASP cc_start: 0.5451 (m-30) cc_final: 0.5180 (t0) REVERT: 51 10 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.5461 (mt) REVERT: 52 111 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.4860 (ttp80) REVERT: 5A 25 MET cc_start: 0.0642 (OUTLIER) cc_final: -0.0834 (mpt) REVERT: 5A 170 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6959 (p0) REVERT: 5A 551 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7520 (mm) REVERT: 5A 804 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: 5A 861 ARG cc_start: 0.8154 (ptp-110) cc_final: 0.7862 (mtm180) REVERT: 5A 1048 MET cc_start: 0.7926 (mmm) cc_final: 0.7602 (mmm) REVERT: 5A 1354 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.4152 (mtm-85) REVERT: 5A 1450 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: 5A 1474 MET cc_start: 0.8314 (tpp) cc_final: 0.7818 (tpp) REVERT: 5A 1599 GLN cc_start: 0.6994 (tp-100) cc_final: 0.6517 (tp40) REVERT: 5A 1607 GLU cc_start: 0.7700 (tt0) cc_final: 0.7013 (tt0) REVERT: 5A 1776 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.6077 (mp) REVERT: 5A 1786 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: 5A 1873 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: 5A 2099 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7948 (tm-30) REVERT: 5A 2150 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: 5A 2265 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: 5B 48 GLU cc_start: 0.6733 (pm20) cc_final: 0.6412 (mp0) REVERT: 5B 712 ILE cc_start: 0.8149 (mp) cc_final: 0.7883 (mp) REVERT: 5B 773 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: 5B 1300 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6796 (mm-30) REVERT: 5B 1344 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6458 (m-30) REVERT: 5B 1483 ARG cc_start: 0.6479 (tmm-80) cc_final: 0.6242 (ttp80) REVERT: 5B 1687 MET cc_start: 0.8917 (mtt) cc_final: 0.8562 (mtt) REVERT: 5B 1705 MET cc_start: 0.8585 (mtt) cc_final: 0.8329 (mtp) REVERT: 5B 1807 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6561 (tt0) REVERT: 5B 1902 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5765 (mmm) REVERT: 5B 2085 GLN cc_start: 0.4272 (OUTLIER) cc_final: 0.2990 (mm-40) REVERT: 5B 2086 GLN cc_start: 0.2684 (OUTLIER) cc_final: 0.2166 (pm20) REVERT: 5B 2114 MET cc_start: 0.4132 (mpp) cc_final: 0.2359 (ttt) REVERT: 5C 366 GLN cc_start: 0.8077 (mt0) cc_final: 0.7864 (mt0) REVERT: 5C 407 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7777 (mt-10) REVERT: 5C 623 GLU cc_start: 0.7520 (mp0) cc_final: 0.7202 (mm-30) REVERT: 5C 668 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: 5D 16 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7390 (mm110) REVERT: 5D 22 GLU cc_start: 0.7558 (mp0) cc_final: 0.7328 (mp0) REVERT: 5D 39 MET cc_start: 0.7506 (mtm) cc_final: 0.7179 (mtp) REVERT: 5D 53 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7300 (ttpp) REVERT: 5D 91 MET cc_start: 0.7710 (mtp) cc_final: 0.7466 (mtm) REVERT: 5D 92 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7144 (mp) REVERT: 5D 93 ASP cc_start: 0.8062 (t70) cc_final: 0.7734 (t70) REVERT: 5J 137 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7027 (tttp) REVERT: 5J 341 LYS cc_start: 0.7448 (mmtp) cc_final: 0.7227 (mmmm) REVERT: 5J 714 MET cc_start: 0.4635 (tmm) cc_final: 0.4356 (tmm) REVERT: 5O 223 ARG cc_start: 0.1619 (OUTLIER) cc_final: 0.0941 (mtt-85) REVERT: 5O 353 MET cc_start: 0.2650 (OUTLIER) cc_final: 0.1875 (mpp) REVERT: 5X 186 ARG cc_start: 0.7489 (tmm160) cc_final: 0.6950 (ptm-80) REVERT: 5X 352 TRP cc_start: 0.5017 (t-100) cc_final: 0.4679 (t-100) REVERT: 5X 375 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6449 (tm-30) REVERT: 5X 557 MET cc_start: 0.1575 (pmm) cc_final: -0.1629 (ptp) REVERT: 5X 588 MET cc_start: 0.2793 (OUTLIER) cc_final: 0.2458 (mtm) REVERT: 5X 687 MET cc_start: 0.0751 (mtm) cc_final: 0.0431 (mmm) REVERT: 5b 36 LYS cc_start: 0.6885 (pttt) cc_final: 0.5900 (mmtt) REVERT: 5e 54 MET cc_start: 0.2885 (ttm) cc_final: 0.2514 (tpp) REVERT: 5f 11 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.4413 (mt) REVERT: 5g 47 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.5024 (tp30) REVERT: 62 54 MET cc_start: 0.2421 (mtt) cc_final: 0.1212 (ptm) REVERT: 62 89 GLU cc_start: 0.3389 (OUTLIER) cc_final: 0.3007 (mt-10) REVERT: 63 84 MET cc_start: 0.1933 (mpt) cc_final: 0.0868 (ptp) REVERT: 64 15 MET cc_start: 0.0893 (mmm) cc_final: 0.0549 (mmm) REVERT: 65 81 MET cc_start: 0.3272 (mpp) cc_final: 0.2945 (ptt) REVERT: R 436 VAL cc_start: 0.6081 (t) cc_final: 0.5749 (m) REVERT: R 442 MET cc_start: 0.6899 (tpp) cc_final: 0.6386 (tpp) REVERT: R 443 ASN cc_start: 0.6469 (t0) cc_final: 0.4463 (p0) REVERT: R 465 ASP cc_start: 0.6840 (t70) cc_final: 0.6529 (t0) REVERT: S 558 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6320 (mp0) REVERT: S 740 LYS cc_start: 0.5649 (OUTLIER) cc_final: 0.4633 (pttt) REVERT: S 746 ARG cc_start: 0.7184 (mtt-85) cc_final: 0.6940 (mtt-85) REVERT: U 101 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7173 (ptt-90) REVERT: U 169 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8559 (m) REVERT: U 178 ASN cc_start: 0.8263 (p0) cc_final: 0.7874 (p0) REVERT: U 270 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8271 (mmm) REVERT: U 394 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: U 397 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8485 (m) REVERT: U 402 LYS cc_start: 0.8081 (ptmt) cc_final: 0.7871 (pttp) REVERT: U 482 GLU cc_start: 0.6921 (pm20) cc_final: 0.6610 (pt0) outliers start: 292 outliers final: 150 residues processed: 1158 average time/residue: 1.5954 time to fit residues: 2569.6600 Evaluate side-chains 1087 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 893 time to evaluate : 7.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 30 THR Chi-restraints excluded: chain 41 residue 33 ASP Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 42 residue 56 VAL Chi-restraints excluded: chain 42 residue 99 MET Chi-restraints excluded: chain 42 residue 104 ASP Chi-restraints excluded: chain 4A residue 443 LYS Chi-restraints excluded: chain 4A residue 447 LYS Chi-restraints excluded: chain 4A residue 526 LYS Chi-restraints excluded: chain 4A residue 579 VAL Chi-restraints excluded: chain 4A residue 631 VAL Chi-restraints excluded: chain 4A residue 637 THR Chi-restraints excluded: chain 4B residue 222 ASN Chi-restraints excluded: chain 4B residue 382 THR Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4C residue 157 GLN Chi-restraints excluded: chain 4C residue 172 SER Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 177 GLN Chi-restraints excluded: chain 4C residue 189 GLU Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 274 ILE Chi-restraints excluded: chain 4C residue 299 CYS Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 85 SER Chi-restraints excluded: chain 4b residue 26 ILE Chi-restraints excluded: chain 4f residue 40 MET Chi-restraints excluded: chain 4g residue 51 SER Chi-restraints excluded: chain 4g residue 61 VAL Chi-restraints excluded: chain 51 residue 10 LEU Chi-restraints excluded: chain 51 residue 28 THR Chi-restraints excluded: chain 51 residue 29 ILE Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 51 residue 59 SER Chi-restraints excluded: chain 52 residue 31 VAL Chi-restraints excluded: chain 52 residue 66 VAL Chi-restraints excluded: chain 52 residue 111 ARG Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 38 ASN Chi-restraints excluded: chain 53 residue 72 ILE Chi-restraints excluded: chain 5A residue 25 MET Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 492 VAL Chi-restraints excluded: chain 5A residue 551 LEU Chi-restraints excluded: chain 5A residue 560 SER Chi-restraints excluded: chain 5A residue 647 LEU Chi-restraints excluded: chain 5A residue 733 THR Chi-restraints excluded: chain 5A residue 804 GLU Chi-restraints excluded: chain 5A residue 840 ILE Chi-restraints excluded: chain 5A residue 868 GLU Chi-restraints excluded: chain 5A residue 1163 ARG Chi-restraints excluded: chain 5A residue 1194 CYS Chi-restraints excluded: chain 5A residue 1220 VAL Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1354 ARG Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1416 ILE Chi-restraints excluded: chain 5A residue 1450 GLN Chi-restraints excluded: chain 5A residue 1509 PHE Chi-restraints excluded: chain 5A residue 1639 VAL Chi-restraints excluded: chain 5A residue 1776 ILE Chi-restraints excluded: chain 5A residue 1779 PHE Chi-restraints excluded: chain 5A residue 1786 TYR Chi-restraints excluded: chain 5A residue 1800 THR Chi-restraints excluded: chain 5A residue 1841 THR Chi-restraints excluded: chain 5A residue 1873 GLU Chi-restraints excluded: chain 5A residue 1910 THR Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 1943 LEU Chi-restraints excluded: chain 5A residue 1966 HIS Chi-restraints excluded: chain 5A residue 2150 GLN Chi-restraints excluded: chain 5A residue 2265 ASP Chi-restraints excluded: chain 5A residue 2284 MET Chi-restraints excluded: chain 5A residue 2297 GLN Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 312 PHE Chi-restraints excluded: chain 5B residue 314 THR Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 557 LYS Chi-restraints excluded: chain 5B residue 654 THR Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 773 GLU Chi-restraints excluded: chain 5B residue 778 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 871 THR Chi-restraints excluded: chain 5B residue 976 THR Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1344 ASP Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1400 ARG Chi-restraints excluded: chain 5B residue 1456 VAL Chi-restraints excluded: chain 5B residue 1469 VAL Chi-restraints excluded: chain 5B residue 1507 SER Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1807 GLU Chi-restraints excluded: chain 5B residue 1873 GLN Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1902 MET Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5B residue 2076 LEU Chi-restraints excluded: chain 5B residue 2085 GLN Chi-restraints excluded: chain 5B residue 2086 GLN Chi-restraints excluded: chain 5B residue 2124 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 112 THR Chi-restraints excluded: chain 5C residue 147 ASP Chi-restraints excluded: chain 5C residue 165 LEU Chi-restraints excluded: chain 5C residue 308 CYS Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 397 ASP Chi-restraints excluded: chain 5C residue 442 LYS Chi-restraints excluded: chain 5C residue 507 VAL Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 562 THR Chi-restraints excluded: chain 5C residue 566 THR Chi-restraints excluded: chain 5C residue 587 VAL Chi-restraints excluded: chain 5C residue 655 VAL Chi-restraints excluded: chain 5C residue 668 GLU Chi-restraints excluded: chain 5C residue 669 THR Chi-restraints excluded: chain 5C residue 705 VAL Chi-restraints excluded: chain 5C residue 707 ILE Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 783 LEU Chi-restraints excluded: chain 5C residue 870 THR Chi-restraints excluded: chain 5C residue 884 GLU Chi-restraints excluded: chain 5D residue 5 LEU Chi-restraints excluded: chain 5D residue 16 GLN Chi-restraints excluded: chain 5D residue 37 THR Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5D residue 138 THR Chi-restraints excluded: chain 5J residue 137 LYS Chi-restraints excluded: chain 5J residue 242 LYS Chi-restraints excluded: chain 5J residue 267 VAL Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 460 ILE Chi-restraints excluded: chain 5J residue 576 VAL Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5J residue 783 SER Chi-restraints excluded: chain 5J residue 797 ASN Chi-restraints excluded: chain 5J residue 930 LEU Chi-restraints excluded: chain 5O residue 69 VAL Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 219 VAL Chi-restraints excluded: chain 5O residue 223 ARG Chi-restraints excluded: chain 5O residue 241 LEU Chi-restraints excluded: chain 5O residue 353 MET Chi-restraints excluded: chain 5X residue 282 THR Chi-restraints excluded: chain 5X residue 375 GLU Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 522 VAL Chi-restraints excluded: chain 5X residue 588 MET Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 45 CYS Chi-restraints excluded: chain 5b residue 66 VAL Chi-restraints excluded: chain 5b residue 81 THR Chi-restraints excluded: chain 5f residue 11 LEU Chi-restraints excluded: chain 5f residue 33 LEU Chi-restraints excluded: chain 5f residue 47 THR Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5f residue 75 VAL Chi-restraints excluded: chain 5g residue 31 LEU Chi-restraints excluded: chain 5g residue 47 GLU Chi-restraints excluded: chain 5g residue 73 LEU Chi-restraints excluded: chain 62 residue 89 GLU Chi-restraints excluded: chain 64 residue 56 MET Chi-restraints excluded: chain 64 residue 71 ILE Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain 65 residue 72 ILE Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 404 PHE Chi-restraints excluded: chain R residue 447 VAL Chi-restraints excluded: chain S residue 714 ASP Chi-restraints excluded: chain S residue 716 THR Chi-restraints excluded: chain S residue 740 LYS Chi-restraints excluded: chain U residue 101 ARG Chi-restraints excluded: chain U residue 129 SER Chi-restraints excluded: chain U residue 169 THR Chi-restraints excluded: chain U residue 270 MET Chi-restraints excluded: chain U residue 324 SER Chi-restraints excluded: chain U residue 346 THR Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 529 LEU Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain U residue 543 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 917 optimal weight: 5.9990 chunk 965 optimal weight: 30.0000 chunk 881 optimal weight: 0.7980 chunk 939 optimal weight: 7.9990 chunk 565 optimal weight: 0.0000 chunk 409 optimal weight: 0.5980 chunk 737 optimal weight: 0.6980 chunk 288 optimal weight: 0.6980 chunk 848 optimal weight: 0.8980 chunk 888 optimal weight: 30.0000 chunk 936 optimal weight: 40.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 42 49 ASN 42 62 HIS 4A 600 HIS ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4C 108 ASN 4D 28 GLN 4D 34 GLN 4D 47 ASN 4D 115 GLN ** 4e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4f 58 HIS 5A1066 GLN 5A1241 HIS ** 5A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A1528 GLN 5A1784 ASN ** 5A2150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 771 ASN ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1591 HIS ** 5B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1863 HIS ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 402 HIS 5C 583 ASN 5C 837 GLN ** 5D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 695 GLN 5J 733 ASN ** 5J 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 166 ASN U 436 ASN U 461 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 91629 Z= 0.183 Angle : 0.618 18.446 125157 Z= 0.307 Chirality : 0.043 0.566 14117 Planarity : 0.004 0.102 15038 Dihedral : 14.101 174.159 15520 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 2.72 % Allowed : 24.30 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -0.64 (0.08), residues: 10226 helix: 0.51 (0.08), residues: 4058 sheet: -0.86 (0.12), residues: 1683 loop : -1.03 (0.09), residues: 4485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP5J 746 HIS 0.012 0.001 HIS4A 600 PHE 0.038 0.001 PHE5b 34 TYR 0.034 0.001 TYR5A 520 ARG 0.012 0.000 ARG5B 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 987 time to evaluate : 7.382 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: X 103 MET cc_start: 0.0571 (ppp) cc_final: -0.0182 (tpt) REVERT: X 104 MET cc_start: 0.3176 (mmt) cc_final: 0.1130 (tmm) REVERT: X 130 ASN cc_start: 0.6417 (t0) cc_final: 0.5848 (t0) REVERT: 41 30 THR cc_start: 0.4797 (OUTLIER) cc_final: 0.4179 (t) REVERT: 41 46 THR cc_start: 0.6229 (OUTLIER) cc_final: 0.5569 (p) REVERT: 42 71 LYS cc_start: 0.5574 (tppt) cc_final: 0.4867 (tttt) REVERT: 43 82 MET cc_start: 0.2111 (tpp) cc_final: 0.1397 (mpt) REVERT: 4A 447 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7294 (mmtp) REVERT: 4A 497 GLU cc_start: 0.2703 (tp30) cc_final: 0.1820 (mp0) REVERT: 4A 526 LYS cc_start: 0.5345 (OUTLIER) cc_final: 0.4884 (mtmm) REVERT: 4B 347 TRP cc_start: 0.4442 (p90) cc_final: 0.4089 (p-90) REVERT: 4B 522 GLU cc_start: 0.4508 (mm-30) cc_final: 0.3334 (mm-30) REVERT: 4C 64 MET cc_start: 0.6316 (tmm) cc_final: 0.5846 (tpt) REVERT: 4C 102 GLU cc_start: 0.6084 (tm-30) cc_final: 0.5735 (pt0) REVERT: 4C 104 GLU cc_start: 0.6546 (pt0) cc_final: 0.5911 (tp30) REVERT: 4C 173 THR cc_start: 0.6913 (OUTLIER) cc_final: 0.6640 (p) REVERT: 4C 177 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: 4C 189 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6312 (pt0) REVERT: 4C 361 LYS cc_start: 0.5442 (mttt) cc_final: 0.4954 (mmtm) REVERT: 4D 15 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5202 (m-30) REVERT: 4b 28 ILE cc_start: 0.5532 (mt) cc_final: 0.5158 (pp) REVERT: 4g 13 MET cc_start: 0.2109 (mmm) cc_final: 0.0544 (pp-130) REVERT: 4g 48 MET cc_start: 0.1043 (pmm) cc_final: -0.0981 (tmm) REVERT: 51 10 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.5426 (mt) REVERT: 52 111 ARG cc_start: 0.5453 (OUTLIER) cc_final: 0.4985 (ttp80) REVERT: 5A 25 MET cc_start: 0.0541 (OUTLIER) cc_final: -0.0805 (mpt) REVERT: 5A 170 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6783 (p0) REVERT: 5A 528 LYS cc_start: 0.6319 (ptmm) cc_final: 0.5947 (pttt) REVERT: 5A 551 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7500 (mm) REVERT: 5A 804 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: 5A 861 ARG cc_start: 0.8109 (ptp-110) cc_final: 0.7611 (mtm180) REVERT: 5A 1009 MET cc_start: 0.8341 (mtt) cc_final: 0.7020 (mtm) REVERT: 5A 1048 MET cc_start: 0.7902 (mmm) cc_final: 0.7575 (mmm) REVERT: 5A 1067 MET cc_start: 0.7571 (ptp) cc_final: 0.7350 (pmm) REVERT: 5A 1354 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.4157 (mtm-85) REVERT: 5A 1474 MET cc_start: 0.8223 (tpp) cc_final: 0.7724 (tpp) REVERT: 5A 1776 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.6063 (mp) REVERT: 5A 1873 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6795 (tt0) REVERT: 5A 1888 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6219 (tp30) REVERT: 5A 2099 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7938 (tm-30) REVERT: 5A 2150 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: 5B 48 GLU cc_start: 0.6835 (pm20) cc_final: 0.6493 (mp0) REVERT: 5B 712 ILE cc_start: 0.8128 (mp) cc_final: 0.7874 (mp) REVERT: 5B 748 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7275 (tm) REVERT: 5B 773 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6480 (mt-10) REVERT: 5B 1050 GLU cc_start: 0.7870 (mp0) cc_final: 0.7601 (pm20) REVERT: 5B 1300 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6765 (mm-30) REVERT: 5B 1344 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6427 (m-30) REVERT: 5B 1670 ASN cc_start: 0.7710 (t0) cc_final: 0.7457 (t0) REVERT: 5B 1687 MET cc_start: 0.8943 (mtt) cc_final: 0.8631 (mtt) REVERT: 5B 1705 MET cc_start: 0.8556 (mtt) cc_final: 0.8285 (mtp) REVERT: 5B 1791 GLN cc_start: 0.6868 (tp40) cc_final: 0.6237 (tp40) REVERT: 5B 1807 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6446 (tt0) REVERT: 5B 1834 MET cc_start: 0.7651 (mmm) cc_final: 0.7185 (mmt) REVERT: 5B 2085 GLN cc_start: 0.4252 (OUTLIER) cc_final: 0.3002 (mm-40) REVERT: 5B 2086 GLN cc_start: 0.2567 (OUTLIER) cc_final: 0.2121 (pm20) REVERT: 5B 2114 MET cc_start: 0.4698 (mpp) cc_final: 0.2978 (ttt) REVERT: 5C 366 GLN cc_start: 0.8009 (mt0) cc_final: 0.7807 (mt0) REVERT: 5C 407 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7767 (mt-10) REVERT: 5C 463 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7008 (mm-30) REVERT: 5C 623 GLU cc_start: 0.7516 (mp0) cc_final: 0.7176 (mm-30) REVERT: 5C 668 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7009 (pm20) REVERT: 5D 16 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.6329 (tm-30) REVERT: 5D 22 GLU cc_start: 0.7588 (mp0) cc_final: 0.7374 (mp0) REVERT: 5D 39 MET cc_start: 0.7509 (mtm) cc_final: 0.7099 (mtp) REVERT: 5D 53 LYS cc_start: 0.7639 (ttpp) cc_final: 0.7332 (ttpp) REVERT: 5D 91 MET cc_start: 0.7695 (mtp) cc_final: 0.7459 (mtm) REVERT: 5D 92 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7119 (mp) REVERT: 5D 93 ASP cc_start: 0.7928 (t70) cc_final: 0.7593 (t70) REVERT: 5J 341 LYS cc_start: 0.7365 (mmtp) cc_final: 0.7119 (mmmm) REVERT: 5J 505 GLN cc_start: 0.6292 (mp10) cc_final: 0.6088 (pm20) REVERT: 5J 583 PHE cc_start: 0.2045 (t80) cc_final: 0.1783 (t80) REVERT: 5J 695 GLN cc_start: 0.2579 (mm-40) cc_final: 0.2211 (mt0) REVERT: 5J 714 MET cc_start: 0.4683 (tmm) cc_final: 0.4424 (tmm) REVERT: 5J 930 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4743 (tm) REVERT: 5O 223 ARG cc_start: 0.1570 (OUTLIER) cc_final: 0.0902 (mtt-85) REVERT: 5O 353 MET cc_start: 0.2533 (OUTLIER) cc_final: 0.1671 (mpp) REVERT: 5X 186 ARG cc_start: 0.7488 (tmm160) cc_final: 0.7096 (ptm-80) REVERT: 5X 337 GLU cc_start: 0.6978 (tp30) cc_final: 0.6564 (pt0) REVERT: 5X 491 PHE cc_start: -0.1550 (OUTLIER) cc_final: -0.2866 (m-10) REVERT: 5X 557 MET cc_start: 0.1136 (pmm) cc_final: -0.2524 (mtp) REVERT: 5X 588 MET cc_start: 0.2779 (mtm) cc_final: 0.2448 (mtm) REVERT: 5b 36 LYS cc_start: 0.6844 (pttt) cc_final: 0.5945 (mmtt) REVERT: 5f 11 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4267 (mt) REVERT: 5g 31 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6078 (tp) REVERT: 5g 47 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5088 (tp30) REVERT: 62 54 MET cc_start: 0.2438 (mtt) cc_final: 0.1156 (ptm) REVERT: 64 15 MET cc_start: 0.0764 (mmm) cc_final: 0.0268 (mmm) REVERT: 64 71 ILE cc_start: 0.0110 (OUTLIER) cc_final: -0.0580 (mt) REVERT: 65 81 MET cc_start: 0.3097 (mpp) cc_final: 0.2864 (ptt) REVERT: R 436 VAL cc_start: 0.6192 (t) cc_final: 0.5866 (m) REVERT: R 442 MET cc_start: 0.6862 (tpp) cc_final: 0.6372 (tpp) REVERT: R 465 ASP cc_start: 0.6743 (t70) cc_final: 0.6453 (t0) REVERT: S 718 ARG cc_start: 0.6856 (ptm-80) cc_final: 0.5945 (ptt90) REVERT: S 724 GLU cc_start: 0.7875 (pt0) cc_final: 0.7612 (pt0) REVERT: S 740 LYS cc_start: 0.5738 (OUTLIER) cc_final: 0.4713 (pttt) REVERT: U 178 ASN cc_start: 0.8172 (p0) cc_final: 0.7828 (p0) REVERT: U 270 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8251 (mmm) REVERT: U 394 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: U 397 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8516 (m) REVERT: U 402 LYS cc_start: 0.8109 (ptmt) cc_final: 0.7888 (pttp) REVERT: U 482 GLU cc_start: 0.6882 (pm20) cc_final: 0.6597 (pt0) outliers start: 247 outliers final: 128 residues processed: 1155 average time/residue: 1.6536 time to fit residues: 2655.0361 Evaluate side-chains 1096 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 929 time to evaluate : 7.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 30 THR Chi-restraints excluded: chain 41 residue 33 ASP Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 42 residue 56 VAL Chi-restraints excluded: chain 42 residue 101 LEU Chi-restraints excluded: chain 42 residue 104 ASP Chi-restraints excluded: chain 4A residue 447 LYS Chi-restraints excluded: chain 4A residue 526 LYS Chi-restraints excluded: chain 4A residue 579 VAL Chi-restraints excluded: chain 4A residue 631 VAL Chi-restraints excluded: chain 4A residue 637 THR Chi-restraints excluded: chain 4B residue 382 THR Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4B residue 518 LEU Chi-restraints excluded: chain 4C residue 172 SER Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 177 GLN Chi-restraints excluded: chain 4C residue 189 GLU Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 274 ILE Chi-restraints excluded: chain 4C residue 299 CYS Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 53 PHE Chi-restraints excluded: chain 4D residue 85 SER Chi-restraints excluded: chain 4D residue 89 LEU Chi-restraints excluded: chain 4b residue 26 ILE Chi-restraints excluded: chain 4f residue 40 MET Chi-restraints excluded: chain 4g residue 51 SER Chi-restraints excluded: chain 4g residue 61 VAL Chi-restraints excluded: chain 51 residue 10 LEU Chi-restraints excluded: chain 51 residue 29 ILE Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 51 residue 59 SER Chi-restraints excluded: chain 52 residue 111 ARG Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 38 ASN Chi-restraints excluded: chain 53 residue 72 ILE Chi-restraints excluded: chain 5A residue 25 MET Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 492 VAL Chi-restraints excluded: chain 5A residue 551 LEU Chi-restraints excluded: chain 5A residue 647 LEU Chi-restraints excluded: chain 5A residue 804 GLU Chi-restraints excluded: chain 5A residue 840 ILE Chi-restraints excluded: chain 5A residue 868 GLU Chi-restraints excluded: chain 5A residue 1194 CYS Chi-restraints excluded: chain 5A residue 1220 VAL Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1354 ARG Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1416 ILE Chi-restraints excluded: chain 5A residue 1509 PHE Chi-restraints excluded: chain 5A residue 1776 ILE Chi-restraints excluded: chain 5A residue 1779 PHE Chi-restraints excluded: chain 5A residue 1841 THR Chi-restraints excluded: chain 5A residue 1873 GLU Chi-restraints excluded: chain 5A residue 1910 THR Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 1943 LEU Chi-restraints excluded: chain 5A residue 2150 GLN Chi-restraints excluded: chain 5A residue 2297 GLN Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 312 PHE Chi-restraints excluded: chain 5B residue 314 THR Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 557 LYS Chi-restraints excluded: chain 5B residue 606 THR Chi-restraints excluded: chain 5B residue 654 THR Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 773 GLU Chi-restraints excluded: chain 5B residue 778 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 871 THR Chi-restraints excluded: chain 5B residue 976 THR Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1344 ASP Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1456 VAL Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1807 GLU Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1910 SER Chi-restraints excluded: chain 5B residue 1930 LEU Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5B residue 2076 LEU Chi-restraints excluded: chain 5B residue 2085 GLN Chi-restraints excluded: chain 5B residue 2086 GLN Chi-restraints excluded: chain 5B residue 2124 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 112 THR Chi-restraints excluded: chain 5C residue 147 ASP Chi-restraints excluded: chain 5C residue 308 CYS Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 397 ASP Chi-restraints excluded: chain 5C residue 507 VAL Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 562 THR Chi-restraints excluded: chain 5C residue 566 THR Chi-restraints excluded: chain 5C residue 587 VAL Chi-restraints excluded: chain 5C residue 655 VAL Chi-restraints excluded: chain 5C residue 668 GLU Chi-restraints excluded: chain 5C residue 669 THR Chi-restraints excluded: chain 5C residue 705 VAL Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 870 THR Chi-restraints excluded: chain 5D residue 5 LEU Chi-restraints excluded: chain 5D residue 16 GLN Chi-restraints excluded: chain 5D residue 37 THR Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5D residue 138 THR Chi-restraints excluded: chain 5J residue 88 LEU Chi-restraints excluded: chain 5J residue 128 ILE Chi-restraints excluded: chain 5J residue 242 LYS Chi-restraints excluded: chain 5J residue 267 VAL Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 576 VAL Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5J residue 783 SER Chi-restraints excluded: chain 5J residue 797 ASN Chi-restraints excluded: chain 5J residue 930 LEU Chi-restraints excluded: chain 5O residue 69 VAL Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 219 VAL Chi-restraints excluded: chain 5O residue 223 ARG Chi-restraints excluded: chain 5O residue 241 LEU Chi-restraints excluded: chain 5O residue 353 MET Chi-restraints excluded: chain 5X residue 282 THR Chi-restraints excluded: chain 5X residue 491 PHE Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 522 VAL Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 66 VAL Chi-restraints excluded: chain 5b residue 81 THR Chi-restraints excluded: chain 5f residue 11 LEU Chi-restraints excluded: chain 5f residue 33 LEU Chi-restraints excluded: chain 5f residue 47 THR Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5f residue 75 VAL Chi-restraints excluded: chain 5g residue 31 LEU Chi-restraints excluded: chain 5g residue 47 GLU Chi-restraints excluded: chain 63 residue 52 MET Chi-restraints excluded: chain 64 residue 56 MET Chi-restraints excluded: chain 64 residue 71 ILE Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain 65 residue 72 ILE Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 404 PHE Chi-restraints excluded: chain R residue 447 VAL Chi-restraints excluded: chain S residue 645 CYS Chi-restraints excluded: chain S residue 716 THR Chi-restraints excluded: chain S residue 740 LYS Chi-restraints excluded: chain U residue 270 MET Chi-restraints excluded: chain U residue 324 SER Chi-restraints excluded: chain U residue 346 THR Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 535 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 616 optimal weight: 5.9990 chunk 993 optimal weight: 7.9990 chunk 606 optimal weight: 5.9990 chunk 471 optimal weight: 5.9990 chunk 690 optimal weight: 2.9990 chunk 1042 optimal weight: 2.9990 chunk 959 optimal weight: 6.9990 chunk 829 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 640 optimal weight: 3.9990 chunk 508 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 130 ASN 42 39 ASN 42 41 GLN 42 48 ASN 42 49 ASN 42 62 HIS 4A 600 HIS 4B 222 ASN ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 448 HIS 4C 108 ASN 4D 27 GLN 4D 28 GLN 4D 31 ASN 4D 34 GLN 4D 115 GLN ** 4e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 41 GLN 5A 429 ASN 5A 505 ASN 5A 584 HIS 5A 711 GLN 5A1066 GLN 5A1241 HIS ** 5A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A1599 GLN ** 5A1811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A1875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5A2150 GLN 5B 574 GLN 5B 618 HIS ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1322 GLN ** 5B1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1591 HIS 5B1863 HIS 5B2016 ASN ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 139 HIS 5C 548 ASN 5C 583 ASN ** 5C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5D 16 GLN ** 5D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5J 842 HIS 5J 887 GLN ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5O 188 GLN ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5e 83 ASN 65 78 ASN U 461 ASN ** U 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 91629 Z= 0.554 Angle : 0.793 17.619 125157 Z= 0.396 Chirality : 0.051 0.435 14117 Planarity : 0.006 0.068 15038 Dihedral : 14.344 179.151 15520 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 2.92 % Allowed : 24.73 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.08), residues: 10226 helix: 0.03 (0.08), residues: 4055 sheet: -0.97 (0.12), residues: 1691 loop : -1.17 (0.09), residues: 4480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP5B1432 HIS 0.022 0.002 HIS5J 865 PHE 0.069 0.003 PHE4D 53 TYR 0.037 0.003 TYR5A 453 ARG 0.010 0.001 ARG5B 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20452 Ramachandran restraints generated. 10226 Oldfield, 0 Emsley, 10226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 954 time to evaluate : 7.341 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: X 104 MET cc_start: 0.3622 (mmt) cc_final: 0.1893 (tmm) REVERT: X 130 ASN cc_start: 0.6325 (OUTLIER) cc_final: 0.5771 (t0) REVERT: 42 71 LYS cc_start: 0.5748 (tppt) cc_final: 0.4953 (tttt) REVERT: 43 82 MET cc_start: 0.2522 (tpp) cc_final: 0.1762 (mpt) REVERT: 4A 497 GLU cc_start: 0.2266 (tp30) cc_final: 0.1678 (mp0) REVERT: 4B 222 ASN cc_start: 0.4151 (OUTLIER) cc_final: 0.2706 (t0) REVERT: 4B 347 TRP cc_start: 0.4823 (OUTLIER) cc_final: 0.4363 (p-90) REVERT: 4B 520 MET cc_start: 0.2856 (mmm) cc_final: 0.2129 (mmm) REVERT: 4B 522 GLU cc_start: 0.4635 (mm-30) cc_final: 0.4008 (mm-30) REVERT: 4C 64 MET cc_start: 0.6694 (tmm) cc_final: 0.6113 (tpt) REVERT: 4C 102 GLU cc_start: 0.6174 (tm-30) cc_final: 0.5762 (pt0) REVERT: 4C 104 GLU cc_start: 0.6780 (pt0) cc_final: 0.6044 (tp30) REVERT: 4C 157 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.4985 (mp10) REVERT: 4C 173 THR cc_start: 0.6850 (OUTLIER) cc_final: 0.6614 (p) REVERT: 4C 177 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: 4C 189 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6351 (pt0) REVERT: 4C 361 LYS cc_start: 0.5441 (mttt) cc_final: 0.4845 (mmtm) REVERT: 4D 15 ASP cc_start: 0.6056 (OUTLIER) cc_final: 0.5162 (m-30) REVERT: 4g 13 MET cc_start: 0.2078 (mmm) cc_final: 0.0260 (pp-130) REVERT: 4g 48 MET cc_start: 0.1455 (pmm) cc_final: 0.0912 (pmm) REVERT: 51 10 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.5421 (mt) REVERT: 52 111 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5127 (ttp80) REVERT: 5A 25 MET cc_start: 0.0711 (OUTLIER) cc_final: -0.0667 (mpt) REVERT: 5A 170 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7201 (p0) REVERT: 5A 290 ASP cc_start: 0.7677 (t70) cc_final: 0.7466 (t0) REVERT: 5A 573 GLN cc_start: 0.7980 (mt0) cc_final: 0.7632 (mt0) REVERT: 5A 861 ARG cc_start: 0.8216 (ptp-110) cc_final: 0.7940 (ptp-110) REVERT: 5A 964 ASP cc_start: 0.7736 (p0) cc_final: 0.7471 (p0) REVERT: 5A 1354 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.4013 (mtm-85) REVERT: 5A 1420 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8603 (m-40) REVERT: 5A 1474 MET cc_start: 0.8411 (tpp) cc_final: 0.7926 (tpp) REVERT: 5A 1565 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7282 (mmtp) REVERT: 5A 1607 GLU cc_start: 0.7688 (tt0) cc_final: 0.7006 (tt0) REVERT: 5A 1776 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6212 (mp) REVERT: 5A 1843 GLU cc_start: 0.7229 (pt0) cc_final: 0.6741 (pp20) REVERT: 5A 1873 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: 5A 2099 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8061 (tm-30) REVERT: 5B 48 GLU cc_start: 0.7020 (pm20) cc_final: 0.6754 (mp0) REVERT: 5B 712 ILE cc_start: 0.8217 (mp) cc_final: 0.7931 (mp) REVERT: 5B 1003 GLN cc_start: 0.7804 (mt0) cc_final: 0.7570 (mt0) REVERT: 5B 1207 ASP cc_start: 0.7001 (t0) cc_final: 0.6671 (t0) REVERT: 5B 1300 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6953 (mm-30) REVERT: 5B 1318 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: 5B 1344 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: 5B 1367 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6969 (ttm) REVERT: 5B 1483 ARG cc_start: 0.6676 (tmm-80) cc_final: 0.6366 (ttp80) REVERT: 5B 1586 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6364 (ttt90) REVERT: 5B 1622 GLU cc_start: 0.6345 (pp20) cc_final: 0.6123 (pp20) REVERT: 5B 1687 MET cc_start: 0.8919 (mtt) cc_final: 0.8604 (mtt) REVERT: 5B 1791 GLN cc_start: 0.7030 (tp40) cc_final: 0.6616 (tp40) REVERT: 5B 1807 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: 5B 1834 MET cc_start: 0.7719 (mmm) cc_final: 0.7317 (mmt) REVERT: 5B 2085 GLN cc_start: 0.4294 (OUTLIER) cc_final: 0.2930 (mm-40) REVERT: 5B 2086 GLN cc_start: 0.2575 (OUTLIER) cc_final: 0.2083 (pm20) REVERT: 5B 2114 MET cc_start: 0.4681 (mpp) cc_final: 0.2817 (ttt) REVERT: 5C 623 GLU cc_start: 0.7558 (mp0) cc_final: 0.7172 (mm-30) REVERT: 5D 22 GLU cc_start: 0.7613 (mp0) cc_final: 0.7263 (mp0) REVERT: 5D 53 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7545 (ttpp) REVERT: 5D 91 MET cc_start: 0.7733 (mtp) cc_final: 0.7472 (mtm) REVERT: 5D 92 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7275 (mp) REVERT: 5D 93 ASP cc_start: 0.8327 (t70) cc_final: 0.8027 (t70) REVERT: 5J 137 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.6978 (tttp) REVERT: 5J 341 LYS cc_start: 0.7688 (mmtp) cc_final: 0.7434 (mmmm) REVERT: 5J 505 GLN cc_start: 0.6545 (mp10) cc_final: 0.6179 (pm20) REVERT: 5J 695 GLN cc_start: 0.2286 (mm-40) cc_final: 0.1952 (mt0) REVERT: 5J 724 MET cc_start: 0.4114 (ppp) cc_final: 0.3883 (ppp) REVERT: 5J 855 ARG cc_start: 0.5623 (mtm180) cc_final: 0.5404 (mtp85) REVERT: 5O 223 ARG cc_start: 0.1700 (OUTLIER) cc_final: 0.1024 (mtt-85) REVERT: 5X 186 ARG cc_start: 0.7565 (tmm160) cc_final: 0.7066 (ptm-80) REVERT: 5X 557 MET cc_start: 0.1490 (pmm) cc_final: -0.2291 (mtp) REVERT: 5X 588 MET cc_start: 0.2894 (OUTLIER) cc_final: 0.2403 (mtm) REVERT: 5b 36 LYS cc_start: 0.6883 (pttt) cc_final: 0.5882 (mmtt) REVERT: 5g 47 GLU cc_start: 0.5490 (OUTLIER) cc_final: 0.4796 (tp30) REVERT: 62 54 MET cc_start: 0.2747 (mtt) cc_final: 0.1464 (ptm) REVERT: 62 89 GLU cc_start: 0.3359 (OUTLIER) cc_final: 0.3032 (mt-10) REVERT: 64 15 MET cc_start: 0.0763 (mmm) cc_final: 0.0533 (mmm) REVERT: 64 71 ILE cc_start: -0.0106 (OUTLIER) cc_final: -0.0783 (mt) REVERT: 65 81 MET cc_start: 0.3414 (mpp) cc_final: 0.3070 (ptt) REVERT: R 442 MET cc_start: 0.6706 (tpp) cc_final: 0.6208 (tpp) REVERT: R 465 ASP cc_start: 0.6927 (t70) cc_final: 0.6580 (t0) REVERT: S 740 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.4747 (pttt) REVERT: U 270 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8315 (mmm) REVERT: U 394 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: U 402 LYS cc_start: 0.8076 (ptmt) cc_final: 0.7870 (pttp) REVERT: U 537 ILE cc_start: 0.8889 (tt) cc_final: 0.8653 (tt) outliers start: 266 outliers final: 161 residues processed: 1141 average time/residue: 1.5993 time to fit residues: 2517.7334 Evaluate side-chains 1096 residues out of total 9192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 902 time to evaluate : 7.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 130 ASN Chi-restraints excluded: chain 41 residue 16 THR Chi-restraints excluded: chain 41 residue 28 THR Chi-restraints excluded: chain 41 residue 30 THR Chi-restraints excluded: chain 41 residue 33 ASP Chi-restraints excluded: chain 41 residue 46 THR Chi-restraints excluded: chain 42 residue 101 LEU Chi-restraints excluded: chain 42 residue 110 LEU Chi-restraints excluded: chain 4A residue 395 ILE Chi-restraints excluded: chain 4A residue 447 LYS Chi-restraints excluded: chain 4A residue 526 LYS Chi-restraints excluded: chain 4A residue 579 VAL Chi-restraints excluded: chain 4A residue 631 VAL Chi-restraints excluded: chain 4A residue 637 THR Chi-restraints excluded: chain 4B residue 222 ASN Chi-restraints excluded: chain 4B residue 347 TRP Chi-restraints excluded: chain 4B residue 382 THR Chi-restraints excluded: chain 4B residue 453 THR Chi-restraints excluded: chain 4B residue 477 TRP Chi-restraints excluded: chain 4B residue 518 LEU Chi-restraints excluded: chain 4C residue 62 GLU Chi-restraints excluded: chain 4C residue 157 GLN Chi-restraints excluded: chain 4C residue 172 SER Chi-restraints excluded: chain 4C residue 173 THR Chi-restraints excluded: chain 4C residue 177 GLN Chi-restraints excluded: chain 4C residue 189 GLU Chi-restraints excluded: chain 4C residue 267 VAL Chi-restraints excluded: chain 4C residue 274 ILE Chi-restraints excluded: chain 4C residue 299 CYS Chi-restraints excluded: chain 4D residue 15 ASP Chi-restraints excluded: chain 4D residue 51 SER Chi-restraints excluded: chain 4D residue 53 PHE Chi-restraints excluded: chain 4D residue 85 SER Chi-restraints excluded: chain 4D residue 121 GLN Chi-restraints excluded: chain 4b residue 26 ILE Chi-restraints excluded: chain 4f residue 40 MET Chi-restraints excluded: chain 4g residue 51 SER Chi-restraints excluded: chain 4g residue 61 VAL Chi-restraints excluded: chain 51 residue 10 LEU Chi-restraints excluded: chain 51 residue 28 THR Chi-restraints excluded: chain 51 residue 29 ILE Chi-restraints excluded: chain 51 residue 46 THR Chi-restraints excluded: chain 51 residue 59 SER Chi-restraints excluded: chain 52 residue 66 VAL Chi-restraints excluded: chain 52 residue 111 ARG Chi-restraints excluded: chain 53 residue 22 THR Chi-restraints excluded: chain 53 residue 38 ASN Chi-restraints excluded: chain 53 residue 72 ILE Chi-restraints excluded: chain 5A residue 25 MET Chi-restraints excluded: chain 5A residue 97 HIS Chi-restraints excluded: chain 5A residue 170 ASP Chi-restraints excluded: chain 5A residue 181 ASN Chi-restraints excluded: chain 5A residue 327 VAL Chi-restraints excluded: chain 5A residue 334 THR Chi-restraints excluded: chain 5A residue 492 VAL Chi-restraints excluded: chain 5A residue 627 CYS Chi-restraints excluded: chain 5A residue 647 LEU Chi-restraints excluded: chain 5A residue 733 THR Chi-restraints excluded: chain 5A residue 804 GLU Chi-restraints excluded: chain 5A residue 840 ILE Chi-restraints excluded: chain 5A residue 868 GLU Chi-restraints excluded: chain 5A residue 1163 ARG Chi-restraints excluded: chain 5A residue 1194 CYS Chi-restraints excluded: chain 5A residue 1220 VAL Chi-restraints excluded: chain 5A residue 1315 VAL Chi-restraints excluded: chain 5A residue 1354 ARG Chi-restraints excluded: chain 5A residue 1365 ILE Chi-restraints excluded: chain 5A residue 1385 VAL Chi-restraints excluded: chain 5A residue 1416 ILE Chi-restraints excluded: chain 5A residue 1420 ASN Chi-restraints excluded: chain 5A residue 1557 LEU Chi-restraints excluded: chain 5A residue 1639 VAL Chi-restraints excluded: chain 5A residue 1776 ILE Chi-restraints excluded: chain 5A residue 1779 PHE Chi-restraints excluded: chain 5A residue 1800 THR Chi-restraints excluded: chain 5A residue 1809 ILE Chi-restraints excluded: chain 5A residue 1841 THR Chi-restraints excluded: chain 5A residue 1873 GLU Chi-restraints excluded: chain 5A residue 1910 THR Chi-restraints excluded: chain 5A residue 1939 ILE Chi-restraints excluded: chain 5A residue 1943 LEU Chi-restraints excluded: chain 5A residue 1981 VAL Chi-restraints excluded: chain 5A residue 2150 GLN Chi-restraints excluded: chain 5A residue 2297 GLN Chi-restraints excluded: chain 5B residue 272 LEU Chi-restraints excluded: chain 5B residue 312 PHE Chi-restraints excluded: chain 5B residue 314 THR Chi-restraints excluded: chain 5B residue 411 LEU Chi-restraints excluded: chain 5B residue 557 LYS Chi-restraints excluded: chain 5B residue 654 THR Chi-restraints excluded: chain 5B residue 748 LEU Chi-restraints excluded: chain 5B residue 778 LEU Chi-restraints excluded: chain 5B residue 837 GLU Chi-restraints excluded: chain 5B residue 871 THR Chi-restraints excluded: chain 5B residue 976 THR Chi-restraints excluded: chain 5B residue 992 TYR Chi-restraints excluded: chain 5B residue 1029 VAL Chi-restraints excluded: chain 5B residue 1318 GLU Chi-restraints excluded: chain 5B residue 1342 SER Chi-restraints excluded: chain 5B residue 1344 ASP Chi-restraints excluded: chain 5B residue 1367 MET Chi-restraints excluded: chain 5B residue 1380 THR Chi-restraints excluded: chain 5B residue 1456 VAL Chi-restraints excluded: chain 5B residue 1469 VAL Chi-restraints excluded: chain 5B residue 1509 THR Chi-restraints excluded: chain 5B residue 1518 VAL Chi-restraints excluded: chain 5B residue 1586 ARG Chi-restraints excluded: chain 5B residue 1807 GLU Chi-restraints excluded: chain 5B residue 1873 GLN Chi-restraints excluded: chain 5B residue 1889 VAL Chi-restraints excluded: chain 5B residue 1908 LEU Chi-restraints excluded: chain 5B residue 1910 SER Chi-restraints excluded: chain 5B residue 1930 LEU Chi-restraints excluded: chain 5B residue 2067 VAL Chi-restraints excluded: chain 5B residue 2076 LEU Chi-restraints excluded: chain 5B residue 2085 GLN Chi-restraints excluded: chain 5B residue 2086 GLN Chi-restraints excluded: chain 5B residue 2092 LEU Chi-restraints excluded: chain 5B residue 2124 VAL Chi-restraints excluded: chain 5C residue 105 MET Chi-restraints excluded: chain 5C residue 112 THR Chi-restraints excluded: chain 5C residue 147 ASP Chi-restraints excluded: chain 5C residue 308 CYS Chi-restraints excluded: chain 5C residue 334 ILE Chi-restraints excluded: chain 5C residue 357 THR Chi-restraints excluded: chain 5C residue 388 VAL Chi-restraints excluded: chain 5C residue 397 ASP Chi-restraints excluded: chain 5C residue 501 ILE Chi-restraints excluded: chain 5C residue 507 VAL Chi-restraints excluded: chain 5C residue 515 THR Chi-restraints excluded: chain 5C residue 562 THR Chi-restraints excluded: chain 5C residue 587 VAL Chi-restraints excluded: chain 5C residue 655 VAL Chi-restraints excluded: chain 5C residue 668 GLU Chi-restraints excluded: chain 5C residue 669 THR Chi-restraints excluded: chain 5C residue 705 VAL Chi-restraints excluded: chain 5C residue 707 ILE Chi-restraints excluded: chain 5C residue 735 PHE Chi-restraints excluded: chain 5C residue 870 THR Chi-restraints excluded: chain 5C residue 917 VAL Chi-restraints excluded: chain 5D residue 5 LEU Chi-restraints excluded: chain 5D residue 37 THR Chi-restraints excluded: chain 5D residue 47 SER Chi-restraints excluded: chain 5D residue 92 ILE Chi-restraints excluded: chain 5D residue 137 SER Chi-restraints excluded: chain 5J residue 128 ILE Chi-restraints excluded: chain 5J residue 137 LYS Chi-restraints excluded: chain 5J residue 242 LYS Chi-restraints excluded: chain 5J residue 267 VAL Chi-restraints excluded: chain 5J residue 403 SER Chi-restraints excluded: chain 5J residue 404 VAL Chi-restraints excluded: chain 5J residue 576 VAL Chi-restraints excluded: chain 5J residue 743 THR Chi-restraints excluded: chain 5J residue 783 SER Chi-restraints excluded: chain 5J residue 797 ASN Chi-restraints excluded: chain 5J residue 930 LEU Chi-restraints excluded: chain 5O residue 69 VAL Chi-restraints excluded: chain 5O residue 176 VAL Chi-restraints excluded: chain 5O residue 193 THR Chi-restraints excluded: chain 5O residue 219 VAL Chi-restraints excluded: chain 5O residue 223 ARG Chi-restraints excluded: chain 5O residue 241 LEU Chi-restraints excluded: chain 5X residue 282 THR Chi-restraints excluded: chain 5X residue 284 ILE Chi-restraints excluded: chain 5X residue 367 ASP Chi-restraints excluded: chain 5X residue 502 VAL Chi-restraints excluded: chain 5X residue 522 VAL Chi-restraints excluded: chain 5X residue 588 MET Chi-restraints excluded: chain 5X residue 737 VAL Chi-restraints excluded: chain 5b residue 81 THR Chi-restraints excluded: chain 5f residue 33 LEU Chi-restraints excluded: chain 5f residue 68 ASN Chi-restraints excluded: chain 5f residue 75 VAL Chi-restraints excluded: chain 5g residue 31 LEU Chi-restraints excluded: chain 5g residue 47 GLU Chi-restraints excluded: chain 62 residue 89 GLU Chi-restraints excluded: chain 63 residue 52 MET Chi-restraints excluded: chain 64 residue 56 MET Chi-restraints excluded: chain 64 residue 71 ILE Chi-restraints excluded: chain 65 residue 30 MET Chi-restraints excluded: chain 65 residue 72 ILE Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 404 PHE Chi-restraints excluded: chain R residue 447 VAL Chi-restraints excluded: chain S residue 645 CYS Chi-restraints excluded: chain S residue 714 ASP Chi-restraints excluded: chain S residue 716 THR Chi-restraints excluded: chain S residue 740 LYS Chi-restraints excluded: chain U residue 270 MET Chi-restraints excluded: chain U residue 324 SER Chi-restraints excluded: chain U residue 346 THR Chi-restraints excluded: chain U residue 394 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 543 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 659 optimal weight: 0.5980 chunk 883 optimal weight: 30.0000 chunk 254 optimal weight: 1.9990 chunk 765 optimal weight: 40.0000 chunk 122 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 chunk 831 optimal weight: 0.0470 chunk 347 optimal weight: 0.9980 chunk 853 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 42 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 42 62 HIS ** 4A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4A 600 HIS 4B 222 ASN ** 4B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 479 HIS 4C 108 ASN 4D 34 GLN ** 4D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 328 HIS 5A 561 HIS 5A 875 HIS ** 5A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A1599 GLN ** 5A1811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A1875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A2150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A2240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 618 HIS 5B 951 GLN ** 5B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B1591 HIS 5B1863 HIS ** 5C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 139 HIS 5C 402 HIS ** 5C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5C 583 ASN ** 5C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5D 16 GLN ** 5D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5J 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5X 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5b 37 HIS ** 5b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5e 83 ASN U 489 GLN ** U 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.210491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.177057 restraints weight = 189566.957| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.31 r_work: 0.3773 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 91629 Z= 0.464 Angle : 0.879 59.200 125157 Z= 0.453 Chirality : 0.048 0.767 14117 Planarity : 0.006 0.186 15038 Dihedral : 14.345 179.062 15520 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 2.63 % Allowed : 25.29 % Favored : 72.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.08), residues: 10226 helix: 0.01 (0.08), residues: 4055 sheet: -0.99 (0.12), residues: 1686 loop : -1.18 (0.09), residues: 4485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP4B 477 HIS 0.018 0.002 HIS5J 865 PHE 0.063 0.002 PHE S 559 TYR 0.035 0.002 TYR5A 453 ARG 0.009 0.001 ARG5J 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40337.15 seconds wall clock time: 699 minutes 28.31 seconds (41968.31 seconds total)